http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=GaojinRiceWiki - User contributions [en]2026-05-26T16:37:10ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176369Os03g02372502014-06-02T18:26:12Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture <ref name="Ashikari et al., 2005" /><ref name="Song et al., 2007" /><ref name="Xue et al., 2008" /><ref name="Huang et al., 2009" /><ref name="Jiao et al., 2010" /><ref name="Miura et al., 2010" />. Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades <ref name="Maeda, 1965" /><ref name="Kaufman et al., 1987" /><ref name="Abe et al.,1994a" />. In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="Yu et al., 2007" />. In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1<ref name="Yu et al., 2007" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<ref name="ref1" /><br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<ref name="Abe et al.,1994a">Abe K, Takahashi H, Suge H(1994a) Graviresponding sites in shoots of normal and‘lazy’ rice seedlings. Physiol Plant92:371–374</ref><br />
<ref name="Ashikari et al., 2005">Ashikari M, Sakakibara H, Lin SY,Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M(2005) Cytokinin oxidase regulates rice grain production. Science309:741–745</ref><br />
<ref name="Huang et al., 2009">Huang X,Qian Q,Liu Z,Sun H,He S,Luo D,Xia G,Chu C,Li J,Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice.Nat Genet41:494–497</ref><br />
<ref name="Jiao et al., 2010">Jiao Y,Wang Y,Xue D,Wang J,Yan M,Liu G,Dong G,Zeng D,Lu Z,Zhu X, et al(2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet42:541–544</ref><br />
<ref name="Kaufman et al., 1987">Kaufman PB, Brock TG, Song I, Rho YB, Ghosheh NS(1987) How cereal grass shoots perceive and respond to gravity. Am J Bot74:1446–1457</ref><br />
<ref name="Maeda, 1965">Maeda E(1965) Rate of lamina inclination in excised rice leaves. Physiol Plant18:813–827</ref><br />
<ref name="Miura et al., 2010">Miura K, Ikeda M, Matsubara A, SongX-J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M(2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet42:545–549</ref><br />
<ref name="Song et al., 2007">Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X(2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet39:623–630</ref><br />
<ref name="Xue et al., 2008">Xue W,Xing Y,Weng X,Zhao Y,Tang W,Wang L,Zhou H,Yu S,Xu C,Li X, et al(2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet40:761–767</ref><br />
<ref name="Yu et al., 2007">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X,et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176368Os03g02372502014-06-02T18:25:02Z<p>Gaojin: /* Structured Information */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture <ref name="Ashikari et al., 2005" /><ref name="Song et al., 2007" /><ref name="Xue et al., 2008" /><ref name="Huang et al., 2009" /><ref name="Jiao et al., 2010" /><ref name="Miura et al., 2010" />. Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades <ref name="Maeda, 1965" /><ref name="Kaufman et al., 1987" /><ref name="Abe et al.,1994a" />. In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="Yu et al., 2007" />. In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1<ref name="Yu et al., 2007" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<ref name="Abe et al.,1994a">Abe K, Takahashi H, Suge H(1994a) Graviresponding sites in shoots of normal and‘lazy’ rice seedlings. Physiol Plant92:371–374</ref><br />
<ref name="Ashikari et al., 2005">Ashikari M, Sakakibara H, Lin SY,Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M(2005) Cytokinin oxidase regulates rice grain production. Science309:741–745</ref><br />
<ref name="Huang et al., 2009">Huang X,Qian Q,Liu Z,Sun H,He S,Luo D,Xia G,Chu C,Li J,Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice.Nat Genet41:494–497</ref><br />
<ref name="Jiao et al., 2010">Jiao Y,Wang Y,Xue D,Wang J,Yan M,Liu G,Dong G,Zeng D,Lu Z,Zhu X, et al(2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet42:541–544</ref><br />
<ref name="Kaufman et al., 1987">Kaufman PB, Brock TG, Song I, Rho YB, Ghosheh NS(1987) How cereal grass shoots perceive and respond to gravity. Am J Bot74:1446–1457</ref><br />
<ref name="Maeda, 1965">Maeda E(1965) Rate of lamina inclination in excised rice leaves. Physiol Plant18:813–827</ref><br />
<ref name="Miura et al., 2010">Miura K, Ikeda M, Matsubara A, SongX-J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M(2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet42:545–549</ref><br />
<ref name="Song et al., 2007">Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X(2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet39:623–630</ref><br />
<ref name="Xue et al., 2008">Xue W,Xing Y,Weng X,Zhao Y,Tang W,Wang L,Zhou H,Yu S,Xu C,Li X, et al(2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet40:761–767</ref><br />
<ref name="Yu et al., 2007">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X,et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176367Os03g02372502014-06-02T18:24:16Z<p>Gaojin: /* References */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture <ref name="Ashikari et al., 2005" /><ref name="Song et al., 2007" /><ref name="Xue et al., 2008" /><ref name="Huang et al., 2009" /><ref name="Jiao et al., 2010" /><ref name="Miura et al., 2010" />. Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades <ref name="Maeda, 1965" /><ref name="Kaufman et al., 1987" /><ref name="Abe et al.,1994a" />. In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="Yu et al., 2007" />. In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1<ref name="Yu et al., 2007" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]<br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<ref name="Abe et al.,1994a">Abe K, Takahashi H, Suge H(1994a) Graviresponding sites in shoots of normal and‘lazy’ rice seedlings. Physiol Plant92:371–374</ref><br />
<ref name="Ashikari et al., 2005">Ashikari M, Sakakibara H, Lin SY,Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M(2005) Cytokinin oxidase regulates rice grain production. Science309:741–745</ref><br />
<ref name="Huang et al., 2009">Huang X,Qian Q,Liu Z,Sun H,He S,Luo D,Xia G,Chu C,Li J,Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice.Nat Genet41:494–497</ref><br />
<ref name="Jiao et al., 2010">Jiao Y,Wang Y,Xue D,Wang J,Yan M,Liu G,Dong G,Zeng D,Lu Z,Zhu X, et al(2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet42:541–544</ref><br />
<ref name="Kaufman et al., 1987">Kaufman PB, Brock TG, Song I, Rho YB, Ghosheh NS(1987) How cereal grass shoots perceive and respond to gravity. Am J Bot74:1446–1457</ref><br />
<ref name="Maeda, 1965">Maeda E(1965) Rate of lamina inclination in excised rice leaves. Physiol Plant18:813–827</ref><br />
<ref name="Miura et al., 2010">Miura K, Ikeda M, Matsubara A, SongX-J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M(2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet42:545–549</ref><br />
<ref name="Song et al., 2007">Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X(2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet39:623–630</ref><br />
<ref name="Xue et al., 2008">Xue W,Xing Y,Weng X,Zhao Y,Tang W,Wang L,Zhou H,Yu S,Xu C,Li X, et al(2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet40:761–767</ref><br />
<ref name="Yu et al., 2007">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X,et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176366Os03g02372502014-06-02T18:23:47Z<p>Gaojin: /* References */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture <ref name="Ashikari et al., 2005" /><ref name="Song et al., 2007" /><ref name="Xue et al., 2008" /><ref name="Huang et al., 2009" /><ref name="Jiao et al., 2010" /><ref name="Miura et al., 2010" />. Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades <ref name="Maeda, 1965" /><ref name="Kaufman et al., 1987" /><ref name="Abe et al.,1994a" />. In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="Yu et al., 2007" />. In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1<ref name="Yu et al., 2007" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]<br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<br />
<br />
<ref name="Abe et al.,1994a">Abe K, Takahashi H, Suge H(1994a) Graviresponding sites in shoots of normal and‘lazy’ rice seedlings. Physiol Plant92:371–374</ref><br />
<ref name="Ashikari et al., 2005">Ashikari M, Sakakibara H, Lin SY,Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M(2005) Cytokinin oxidase regulates rice grain production. Science309:741–745</ref><br />
<ref name="Huang et al., 2009">Huang X,Qian Q,Liu Z,Sun H,He S,Luo D,Xia G,Chu C,Li J,Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice.Nat Genet41:494–497</ref><br />
<ref name="Jiao et al., 2010">Jiao Y,Wang Y,Xue D,Wang J,Yan M,Liu G,Dong G,Zeng D,Lu Z,Zhu X, et al(2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet42:541–544</ref><br />
<ref name="Kaufman et al., 1987">Kaufman PB, Brock TG, Song I, Rho YB, Ghosheh NS(1987) How cereal grass shoots perceive and respond to gravity. Am J Bot74:1446–1457</ref><br />
<ref name="Maeda, 1965">Maeda E(1965) Rate of lamina inclination in excised rice leaves. Physiol Plant18:813–827</ref><br />
<ref name="Miura et al., 2010">Miura K, Ikeda M, Matsubara A, SongX-J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M(2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet42:545–549</ref><br />
<ref name="Song et al., 2007">Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X(2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet39:623–630</ref><br />
<ref name="Xue et al., 2008">Xue W,Xing Y,Weng X,Zhao Y,Tang W,Wang L,Zhou H,Yu S,Xu C,Li X, et al(2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet40:761–767</ref><br />
<ref name="Yu et al., 2007">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X,et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176365Os03g02372502014-06-02T18:23:21Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture <ref name="Ashikari et al., 2005" /><ref name="Song et al., 2007" /><ref name="Xue et al., 2008" /><ref name="Huang et al., 2009" /><ref name="Jiao et al., 2010" /><ref name="Miura et al., 2010" />. Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades <ref name="Maeda, 1965" /><ref name="Kaufman et al., 1987" /><ref name="Abe et al.,1994a" />. In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="Yu et al., 2007" />. In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1<ref name="Yu et al., 2007" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]<br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0237250&diff=176364Os03g02372502014-06-02T18:08:58Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Loose Plant Architecture1,the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana),regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint.<br />
LPA1 was also found to affect shoot gravitropism.<ref name="ref1" /><br />
LPA1 encodes a predicted 438-amino acid protein.Sequence analysis indicated that LPA1 is a typical Cys-2/His-2 zinc finger protein, belonging to the plant-specific IDD protein family,where it was also known as OsIDD14 <ref name="ref3" />. It is interesting that OsIDD12, OsIDD13, and OsIDD14/LPA1 are more similar to one another and divergent from the other 12 rice members, like AtIDD14,AtIDD15/SHOOT GRAVITROPISM5 (SGR5), and AtIDD16 among the 16 Arabidopsis (Arabidopsis<br />
thaliana) members <ref name="ref3" />, suggesting the specificity of the six proteins in the IDD protein family.LPA1 defines a novel subfamily of IDD proteins with distinct domains and motifs.<br />
<br />
=== Mutation ===<br />
[[File:F 1.jpg|right|thumb|200px|''Morphological comparison between the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 2.jpg|right|thumb|200px|''Gravitropism analysis of the wild type and ''lpa1'' (from reference <ref name="ref1" />).'']]<br />
Thelpa1 mutant was a naturally occurring mutant isolated from anindicavariety, Zhongxian3037. During both the vegetative and reproductive stages,''lpa1'' always exhibited loose plant architecture with larger tiller angle and leaf angle than those of the wild type (Fig.1, A and B).The tiller angle at heading date and found that the maximum angle was 17.3° inlpa1 but only 9.8° in the wild type (Fig. 1C). Careful observation showed that the large tiller angle of ''lpa1'' was caused by the more symmetrical growth of the tiller node compared with the wild type (Fig. 1D).The leaf angles: each angle was larger in ''lpa1'' than in the wild type, and this difference was more obvious in older leaves, where the maximum angle of the fourth leaf could reach up to 61.2° in ''lpa1'' but only 27.4° in the wild type (Fig. 1E). This difference was further confirmed by the dynamic change observed in the newly developing leaf (Fig. 1F). Detailed examination revealed that the large leaf angle of ''lpa1'' was caused by a more rapid elongation on the adaxial side of the lamina joint (Fig. 1, G and H).<br />
<br />
In rice, the lazy1 mutant exhibits a tiller-spreading phenotype resulting from reduced shoot gravitropism <ref name="ref2" />. To examine whether lpa1 was also involved in the same process, we analyzed the gravity response of young seedlings. The result revealed that both light- and dark-grown mutant seedlings had a reduced gravity response and could not grow upright eventually (Fig. 2, A–C). However,lpa1roots showed a normal gravity response (Fig. 2D). These results indicated thatLPA1is only involved in shoot gravitropism in rice.<br />
<br />
===Expression===<br />
[[File:F 3.jpg|right|thumb|200px|''Functional verification of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
[[File:F 4.jpg|right|thumb|200px|''Expression pattern of ''LPA1'' (from reference <ref name="ref1" />).'']]<br />
To investigate the effects of LOC_Os03g13400, an RNA interference (RNAi) vector and an overexpression (OE) vector driven by the cauliflower mosaic virus (CaMV) 35S promoter were constructed and transformed into Yandao8 (a wild-type japonicavariety with compact plant architecture). Most RNAi and OE transgenic plants showed loose and compact plant architectures with differing degrees, respectively, compared with Yandao8 (Fig. 3A), from which one typical RNAi plant and one typical OE plant were selected for detailed analysis.<br />
Following two generations of self-pollination, the RNAi and OE transgenic plants showed stable phenotypes. Detailed observation showed that both tiller angle and leaf angle increased in the RNAi plant but decreased in the OE plant (Fig. 3, B and C). Real-time PCR analysis showed that the expression level of LOC_Os03g13400 was down-regulated nearly 4-fold in the RNAi plant but up-regulated more than 20-fold in the OE plant (Fig. 3, D and E). Furthermore, the gravity response was also reduced in the RNAi seedlings (Fig. 3F). These results strongly confirmed that LOC_Os03g13400 is LPA1 and also showed that the transcription level of LPA1 is closely associated with rice plant architecture.<br />
Real-time PCR revealed thatLPA1 was highly expressed in the lamina joint and internodes, especially in young tissues. However, older tiller base also showed<br />
a high expression level equivalent to the young second internode (Fig. 4A). LPA1 was also moderately expressed in coleoptile, root, seedling, and panicle but was barely detectable in leaf blade and leaf sheath (Fig. 4A). The higher expression levels of LPA1 in the lamina joint and tiller node correspond well with the main phenotypes of the mutant.LPA1 was exceptionally abundant in leaf sheath pulvinus, about 35-fold higher than in the coleoptile, strongly suggesting an important role for LPA1 in leaf sheath pulvinus gravitropism (Fig. 4B). Additionally, the expression of LPA1 in dark-grown etiolated seedlings was 1.5-fold higher than it was in those grown in the light (Fig. 4C), indicating that light can inhibit the expression of LPA1.<br />
<br />
===Evolution===<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1andPROG1are not very suitable for rice breeding, while TAC1has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle <ref name="ref4" />.LPA1 showed an inclined tiller angle of 17.3°,similar to TAC1<ref name="ref4" />. Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore,LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
<br />
== Knowledge Extension ==<br />
In recent years, some genes that affect rice grain yield have been identified, shedding light on some of the molecular mechanisms underlying ideal plant architecture (Ashikari et al., 2005; Song et al., 2007; Xue et al., 2008; Huang et al., 2009; Jiao et al., 2010; Miura et al., 2010). Gravity is an important regulator of plant architecture. In grasses, because of the short-lived coleoptiles, the leaf sheath pulvini and lamina joints are the major gravity-responding organs, which control the growth orientations of seedlings, tillers, and leaf blades (Maeda, 1965; Kaufman et al., 1987; Abe et al.,1994a). In the study, LPA1 showed a specific expression pattern, and the high expression level in the leaf sheath pulvinus and lamina joint suggests that LPA1 mainly functions in the gravitropism of these tissues,corresponding to its limited effect on coleoptile gravitropism. This analysis demonstrated that LPA1 affects rice plant architecture by regulating shoot gravitropism in later developmental stages.<br />
There are several genes that control tiller angle in rice. LAZY1 and PROG1 lead to the prostrate growth of tillers, but the major QTL,TAC1, only slightly enlarges the tiller angle in indica rice. Because of their larger effects,LAZY1 and PROG1 are not very suitable for rice breeding, while TAC1 has been extensively utilized in rice plant architecture breeding owing to its smaller effect on tiller angle (Yu et al., 2007). In the study,LPA1showed an inclined tiller angle of 17.3°, similar to TAC1(Yu et al., 2007). Although the equivalent effect made too many difficulties in map-based cloning of LPA1, it revealed the potential utilization of LPA1 in rice plant architecture breeding. Moreover, the transgenic results further demonstrated that rice plant architecture was correlated with the endogenous expression level of LPA1.Therefore, LPA1 is a useful gene for plant architecture modification in rice breeding.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]<br />
<br />
==Labs working on this gene==<br />
State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Xinru Wu;Ding Tang;Ming Li;Kejian Wang;Zhukuan Cheng.Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice. Plant Physiology, 2013, 161(1): 317-329 </ref><br />
<ref name="ref2">Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J(2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410</ref><br />
<ref name="ref3">ColasantiJ,TremblayR,WongAYM,ConevaV,KozakiA,MableBK(2006) The maize INDETERMINATEIflowering time regulator defines a highly conserved zincfinger protein family in higher plants. BMC Genomics7:158</ref><br />
<ref name="ref4">Yu B, Lin Z, Li H, Li X, Li J, Wang Y, Zhang X, Zhu Z, Zhai W, Wang X, et al(2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898</ref><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os03g0237250|<br />
Description = Zinc finger, C2H2-type domain containing protein|<br />
Version = NM_001186408.1 GI:297721946 GeneID:9270511|<br />
Length = 837 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0237250, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:7289669..7290505|<br />
CDS = 7289669..7290246,7290328..7290505|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:7289669..7290505<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</cdnaseq>|<br />
AA = <aaseq>MALVKSHHQMLASSSTSSSSPSSQQQQPPPPASNSSSLAAAAAD QPSPAKRKRRPPGTPDPDAEVVALSPRTLLESDRYVCEICGQGFQREQNLQMHRRRHK VPWRLVKRPAAATAAEDGGAAGGGGGAGGGAGGGGARKRVFVCPEPSCLHHDPAHALG DLVGIKKHFRRKHGGRRQWVCARCAKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRYV HHPLSSSSNLRSVHGGRRRMHYYYYVRTLTIHD</aaseq>|<br />
DNA = <dnaseqindica>260..837#1..178#atggcactggtcaagagccaccaccaaatgttggcctcttcttccacctcgtcctcctcaccctcctcccagcagcagcagcctccaccgccggcgtcgaactcctccagcctcgccgccgccgccgccgaccagccctcccccgccaagcgcaagaggcgccctcccggcacgccaggtacgtatatacgtatgtgttggagacattgataccatcatgcatgcatggtgttcgatcatggagcccgtgtgtacgtagacccagatgcggaggtggtggcgctgtcgccgaggacgctgctggagtcggacaggtacgtgtgcgagatctgcgggcaggggttccagcgggagcagaacctgcagatgcaccggcgccggcacaaggtgccgtggcggctggtcaagcgccccgcggcggcgacggcggcggaggacggcggcgccgcgggtggcggcggcggcgccggcggcggcgcgggcggcggaggggcgcggaagcgcgtgttcgtgtgcccggagccgagctgcctccaccacgacccggcacacgcgctgggcgacctcgtcggcatcaagaagcacttccggcgcaagcacggcggccggcggcagtgggtgtgtgcccgctgcgccaagggctacgccgtccagtccgactacaaggcccacctcaagacctgcggcacccgcggccactcctgcgactgcggccgcgtcttctcccggtacgtacaccaccccctctcctcctcctcaaacctacgtagcgttcatggcggccggcgacgcatgcactactactactacgtacgaacgctaaccatccatgattag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186408.1 RefSeq:Os03g0237250]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=176359Os03g07065002014-06-02T17:57:43Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
<br />
== background ==<br />
Plant architecture is determined by the pattern of shoot branching <ref name="McSteen and Leyser 2005" />. In most higher plants, shoot branches develop from axillary buds in the axils of leaves. Not all of the axillary buds develop, and each is subjected to a decision to continue growth or to become dormant, depending on a complex interplay between environmental and endogenous cues. Plant hormones are major players in the control of axillary bud growth. It has been known for a long time that two hormones in particular, auxin and cytokinin, are involved in this control. Auxin, which is supplied from the apical bud, indirectly suppresses axillary bud outgrowth, while cytokinins directly induce branching. During the past two decades, genetic and physiological analyses in pea and Arabidopsis have predicted the involvement of an additional, novel hormone in the control of shoot branching (for reviews, see<ref name="Beveridge 2006" /><ref name="Ongaro and Leyser 2008" /> . Recently it was demonstrated that the novel hormone, which inhibits bud outgrowth, is the group of compounds called strigolactones (SLs) or their downstream metabolites <ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. <br />
Prior to the discovery of SLs as the branching hormone, more axillary growth1 (max1) to max4in Arabidopsis and five ramosus (rms) mutants in garden pea ( Pisum sativum) had been identifi ed as components of a novel graft-transmissible branching signal pathway <ref name="Strinberg et al. 2002" /><ref name="Sorefan et al. 2003" />.Consistent with results obtained from grafting experiments, max1 max3 and max4 were shown to be SL deficient, and their defects were rescued by the external application of an SL<ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. On the other hand, a mutant of the MAX2 gene, which encodes an F-box leucine-rich repeat (LRR)-containing protein, was not rescued by the SL <ref name="Strinberg et al. 2002" />. MAX1 encodes CYP711A1, a class III cytochrome P450 <ref name="Booker et al. 2005" />. MAX3 and MAX4 encode carotenoid cleavage dioxygenases (CCDs) <ref name="Sorefan et al. 2003" /><ref name="Booker et al. 2004" />. <br />
The SL pathway seems to be well conserved across species <ref name="Beveridge and Kyozuka 2010"/>. Molecular cloning showed that pea RMS1, RMS4and RMS5are orthologs of MAX4, MAX2 and MAX3, respectively <ref name="Sorefan et al. 2003" /><ref name="Foo et al. 2005" /><ref name="Jhonson et al. 2006" /><ref name="Beveridge et al. 2009" />. Analyses of branching mutants in rice indicated that the pathway is also conserved in monocot species. We reported on five tillering dwarf mutants of rice, dwarf3 (d3), d10, d14, d17 and d27<ref name="Ishikawa et al. 2005" />. The high tillering dwarf1 (htd1) mutant, which resembles the five d mutants, was also described <ref name="Zou et al. 2006" />. After the molecular cloning, it turned out that D3and D10are orthologs of MAX2/RMS4and MAX4/RMS1, respectively <ref name="Ishikawa et al. 2005" /><ref name="Arite et al. 2007" />, while HTD1 encodes an ortholog of MAX3/RMS5, and is the same locus as D17<ref name="Zou et al. 2006" /><ref name="Umehara et al. 2008" />. Meanwhile, D14and D27were shown to be novel genes that work in the SL pathway <ref name="Arite et al. 2009" /><ref name="Lin et al. 2009" />. D27 encodes an iron-containing protein and is likely to be involved in SL biosynthesis <ref name="Lin et al. 2009" />. The d14mutant, also reported as d88and htd2, is insensitive to exogenous SL application and contains elevated SL levels <ref name="Arite et al. 2009" /><ref name="Gao et al. 2009" /><ref name="Liu et al. 2009" />. Although its molecular function has not yet been determined, it is postulated that D14also works in SL signaling <ref name="Arite et al. 2009" />. <br />
The mechanisms controlling cross-talk between the hormones are beginning to be elucidated. Recently it was revealed that one role of auxin is to suppress cytokinin biosynthesis in the stem <ref name="Tanaka et al. 2006" /><ref name="Shimizu-Sato et al. 2009" />. When the auxin supply from the apical bud is blocked, expression of isopentenyltransferase ( IPT) genes, which encode a rate-limiting enzyme of cytokinin biosynthesis, is rapidly up-regulated, and this results in the rapid synthesis of cytokinins in the stem. This cytokinin is transported to axillary buds and induces bud outgrowth. In addition, the auxin-dependent up-regulation of SL biosynthesis genes has been observed in all plant species analyzed so far <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" />. Although actual changes in SL levels have not yet been observed, a likely scenario is that the apically derived auxin induces SL biosynthesis, and the SLs act as second messengers to inhibit axillary bud outgrowth. Furthermore, SL biosynthesis is controlled by feedback regulation <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" /> and, at least in Arabidopsis, this feedback regulation is mostly dependent on auxin signaling<ref name="Heyward et al. 2009" />. Together, these observations suggest that the growth of axillary buds is controlled by multiple independent and interacting pathways <ref name="Dun et al. 2009" />. <br />
Despite the remarkable progress in our understanding of the frameworks that control axillary bud outgrowth, little is known so far about how SLs act to control shoot branching. As a fi rst step towards understanding SL action at the molecular level, we report here that rice FINE CULM1 (FC1) partially works downstream of SLs to inhibit bud outgrowth. We propose that FC1serves as a hub gene where multiple signals are integrated to fi ne-tune the development of axillary buds. <br />
<br />
<br />
<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
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<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<br />
<br />
<ref name="Arite et al. 2007">Arite , T. , Iwata , H. , Ohshima , K. , Maekawa , M. , Nakajima , M. , Kojima , M. , et al . ( 2007 ) DWARF10, an RMS1/MAX4/DAD1ortholog, controls lateral bud outgrowth in rice . Plant J. 51 : 1019 – 1029 . </ref><br />
<ref name="Arite et al. 2009">Arite , T. , Umehara , M. , Ishikawa , S. , Hanada , A. , Maekawa , M. , et al . ( 2009 ) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers . Plant Cell Physiol. 5 0 : 1416 – 1424 . </ref><br />
<ref name="Beveridge 2006">Beveridge , C.A. ( 2006 ) Axillary bud outgrowth: sending a message . Curr. Opin. Plant Biol. 9 : 35 – 40 . </ref><br />
<ref name="Beveridge et al. 2009">Beveridge , C.A. , Dun , E.A. and Rameau , C. ( 2009 ) Pea has its tendril in branching discoveries spanning a century from auxin to strigolactones . Plant Physiol. 151 : 985 – 990 . </ref><br />
<ref name="Beveridge and Kyozuka 2010">Beveridge , C.A. and Kyozuka , J. ( 2010 ) New genes in the strigolactonerelated shoot branching pathway . Curr. Opin. Plant Biol. 13 : 34 – 39 . </ref><br />
<ref name="Booker et al. 2004">Booker , J. , Auldridge , M. , Wills , S. , McCarty , D. , Klee , H. and Leyser , O. ( 2004 ) MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling molecule . Curr. Biol. 1 4 : 1232 – 1238 . </ref><br />
<ref name="Booker et al. 2005">Booker , J. , Sieberer , T. , Wright , W. , Williamson , L. , Willett , B. , Stirnberg , P. , et al . ( 2005 ) MAX1encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoidderived branch-inhibiting hormone . Dev. Cell 8 : 443 – 449 .</ref><br />
<ref name="Dun et al. 2009">Dun E.A. , Hanan , J. and Beveridge , C. ( 2009 ) Computational modeling and molecular physiology experiments reveal new insight into shoot branching in pea . Plant Cell 21 : 3459 – 3472 . </ref><br />
<ref name="Foo et al. 2005">Foo , E. , Bullier , E. , Goussot , M. , Foucher , F. , Rameau , C. and Beveridge , C.A. ( 2005 ) The branching gene RAMOSUS1mediates interactions among two novel signals and auxin in pea . Plant Cell 17 : 464 – 474 . </ref><br />
<ref name="Gao et al. 2009">Gao , Z. , Qian , Q. , Liu , X. , Yan , M. , Feng , Q. and Dong , G. , ( 2009 ) Dwarf 88, a novel putative esterase gene affecting architecture of rice plant . Plant Mol. Biol. 71 : 265 – 276 . </ref><br />
<ref name="Gomez-Roldan et al. 2008">Gomez-Roldan , V. , Fermas , S. , Brewer , P.B. , Puech-Pagès , V. , Dun , E.A. , Pillot , J.P. , et al . ( 2008 ) Strigolactone inhibition of shoot branching . Nature 455 : 189 – 194 . </ref><br />
<ref name="Heyward et al. 2009">Heyward , A. , Stirnberg , P. , Beveridge , C. and Leyser , O. ( 2009 ) Interaction between auxin and strigolactone in shoot branching control . Plant Physiol. 151 : 400 – 412 .</ref><br />
<ref name="Ishikawa et al. 2005">Ishikawa , S. , Maekawa , M. , Arite , T. , Onishi , K. , Takamure , I. and Kyozuka , J. ( 2005 ) Suppression of tiller bud activity in tillering dwarf mutants of rice . Plant Cell Physiol. 46 : 79 – 86 . </ref><br />
<ref name="Jhonson et al. 2006">Jhonson , X. , Brcich , T. , Dun , E.A. , Goussot , M. , Haurogné , K. , Beveridge , C.A. , et al . ( 2006 ) Branching genes are conserved across species. Genes controlling a novel signal in pea are coregulated by other long-distance signals . Plant Physiol. 142 : 1014 – 1026 . </ref><br />
<ref name="Lin et al. 2009">Lin , H. , Wang , R. , Qian , Q. , Yan , M , Meng , X. , Fu , Z. , et al . ( 2009 ) DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth . Plant Cell 2 1 : 1512 – 1525 . </ref><br />
<ref name="Liu et al. 2009">Liu , W. , Wu , C. , Fu , Y. , Hu , G. , Si , H. , Li , Z. , et al . ( 2009 ) Identifi cation and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice . Planta 230 : 649 – 658 .</ref><br />
<ref name="McSteen and Leyser 2005">McSteen , P. and Leyser , O. ( 2005 ) Shoot branching . Annu. Rev. Plant Biol. 56 : 353 – 374 . </ref><br />
<ref name="Ongaro and Leyser 2008">Ongaro , V. and Leyser , O. ( 2008 ) Hormonal control of shoot branching . J. Exp. Bot. 59 : 67 – 74 .</ref><br />
<ref name="Shimizu-Sato et al. 2009">Shimizu-Sato , T. , Tanaka , M. and Mori , H. ( 2009 ) Auxin–cytokinin interactions in the control of shoot branching . Plant Mol. Biol. 6 9 : 429 – 435 . </ref><br />
<ref name="Sorefan et al. 2003">Sorefan , K. , Booker , J. , Haurogne , K. , Goussot , M. , Bainbridge , K. , Foo , E. , et al . ( 2003 ) MAX4and RMS1are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea . Genes Dev. 17 : 1469 – 1474 . </ref><br />
<ref name="Strinberg et al. 2002">Stirnberg , P. , van de Sande , K. and Leyser , H.M.O. ( 2002 ) MAX1 and MAX2control shoot lateral branching in Arabidopsis . Development 129 : 1131 – 1141 .</ref><br />
<ref name="Tanaka et al. 2006">Tanaka , M. , Takei , K. , Kojima , M. , Sakakibara , H. and Mori , H. ( 2006 ) Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance . Plant J. 45 : 1028 – 36 . </ref><br />
<ref name="Umehara et al. 2008">Umehara , M. , Hanada , A. , Yoshida , S. , Akiyama , K. , Arite , T. , Takeda-Kamiya , N. , et al . ( 2008 ) Inhibition of shoot branching by new terpenoid plant hormones . Nature 455 : 195 – 200 . </ref><br />
<ref name="Zou et al. 2006">Zou , J. , Zhang , S. , Zhang , W. , Li , G. , Chen , Z. , Zhai , W. , et al . ( 2006 ) The rice HIGH-TILLERING DWARF1encoding an ortholog of Arabidopsis MAX3is required for negative regulation of the outgrowth of axillary buds . Plant J. 48 : 687 – 698 . </ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=176357Os03g07065002014-06-02T17:54:36Z<p>Gaojin: /* background */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
<br />
== background ==<br />
Plant architecture is determined by the pattern of shoot branching <ref name="McSteen and Leyser 2005" />. In most higher plants, shoot branches develop from axillary buds in the axils of leaves. Not all of the axillary buds develop, and each is subjected to a decision to continue growth or to become dormant, depending on a complex interplay between environmental and endogenous cues. Plant hormones are major players in the control of axillary bud growth. It has been known for a long time that two hormones in particular, auxin and cytokinin, are involved in this control. Auxin, which is supplied from the apical bud, indirectly suppresses axillary bud outgrowth, while cytokinins directly induce branching. During the past two decades, genetic and physiological analyses in pea and Arabidopsis have predicted the involvement of an additional, novel hormone in the control of shoot branching (for reviews, see<ref name="Beveridge 2006" /><ref name="Ongaro and Leyser 2008" /> . Recently it was demonstrated that the novel hormone, which inhibits bud outgrowth, is the group of compounds called strigolactones (SLs) or their downstream metabolites <ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. <br />
Prior to the discovery of SLs as the branching hormone, more axillary growth1 (max1) to max4in Arabidopsis and five ramosus (rms) mutants in garden pea ( Pisum sativum) had been identifi ed as components of a novel graft-transmissible branching signal pathway <ref name="Strinberg et al. 2002" /><ref name="Sorefan et al. 2003" />.Consistent with results obtained from grafting experiments, max1 max3 and max4 were shown to be SL deficient, and their defects were rescued by the external application of an SL<ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. On the other hand, a mutant of the MAX2 gene, which encodes an F-box leucine-rich repeat (LRR)-containing protein, was not rescued by the SL <ref name="Strinberg et al. 2002" />. MAX1 encodes CYP711A1, a class III cytochrome P450 <ref name="Booker et al. 2005" />. MAX3 and MAX4 encode carotenoid cleavage dioxygenases (CCDs) <ref name="Sorefan et al. 2003" /><ref name="Booker et al. 2004" />. <br />
The SL pathway seems to be well conserved across species <ref name="Beveridge and Kyozuka 2010"/>. Molecular cloning showed that pea RMS1, RMS4and RMS5are orthologs of MAX4, MAX2 and MAX3, respectively <ref name="Sorefan et al. 2003" /><ref name="Foo et al. 2005" /><ref name="Jhonson et al. 2006" /><ref name="Beveridge et al. 2009" />. Analyses of branching mutants in rice indicated that the pathway is also conserved in monocot species. We reported on five tillering dwarf mutants of rice, dwarf3 (d3), d10, d14, d17 and d27<ref name="Ishikawa et al. 2005" />. The high tillering dwarf1 (htd1) mutant, which resembles the five d mutants, was also described <ref name="Zou et al. 2006" />. After the molecular cloning, it turned out that D3and D10are orthologs of MAX2/RMS4and MAX4/RMS1, respectively <ref name="Ishikawa et al. 2005" /><ref name="Arite et al. 2007" />, while HTD1 encodes an ortholog of MAX3/RMS5, and is the same locus as D17<ref name="Zou et al. 2006" /><ref name="Umehara et al. 2008" />. Meanwhile, D14and D27were shown to be novel genes that work in the SL pathway <ref name="Arite et al. 2009" /><ref name="Lin et al. 2009" />. D27 encodes an iron-containing protein and is likely to be involved in SL biosynthesis <ref name="Lin et al. 2009" />. The d14mutant, also reported as d88and htd2, is insensitive to exogenous SL application and contains elevated SL levels <ref name="Arite et al. 2009" /><ref name="Gao et al. 2009" /><ref name="Liu et al. 2009" />. Although its molecular function has not yet been determined, it is postulated that D14also works in SL signaling <ref name="Arite et al. 2009" />. <br />
The mechanisms controlling cross-talk between the hormones are beginning to be elucidated. Recently it was revealed that one role of auxin is to suppress cytokinin biosynthesis in the stem <ref name="Tanaka et al. 2006" /><ref name="Shimizu-Sato et al. 2009" />. When the auxin supply from the apical bud is blocked, expression of isopentenyltransferase ( IPT) genes, which encode a rate-limiting enzyme of cytokinin biosynthesis, is rapidly up-regulated, and this results in the rapid synthesis of cytokinins in the stem. This cytokinin is transported to axillary buds and induces bud outgrowth. In addition, the auxin-dependent up-regulation of SL biosynthesis genes has been observed in all plant species analyzed so far <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" />. Although actual changes in SL levels have not yet been observed, a likely scenario is that the apically derived auxin induces SL biosynthesis, and the SLs act as second messengers to inhibit axillary bud outgrowth. Furthermore, SL biosynthesis is controlled by feedback regulation <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" /> and, at least in Arabidopsis, this feedback regulation is mostly dependent on auxin signaling<ref name="Heyward et al. 2009" />. Together, these observations suggest that the growth of axillary buds is controlled by multiple independent and interacting pathways <ref name="Dun et al. 2009" />. <br />
Despite the remarkable progress in our understanding of the frameworks that control axillary bud outgrowth, little is known so far about how SLs act to control shoot branching. As a fi rst step towards understanding SL action at the molecular level, we report here that rice FINE CULM1 (FC1) partially works downstream of SLs to inhibit bud outgrowth. We propose that FC1serves as a hub gene where multiple signals are integrated to fi ne-tune the development of axillary buds. <br />
<br />
<br />
<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<br />
<ref name="Arite et al. 2007">Arite , T. , Iwata , H. , Ohshima , K. , Maekawa , M. , Nakajima , M. , Kojima , M. , et al . ( 2007 ) DWARF10, an RMS1/MAX4/DAD1ortholog, controls lateral bud outgrowth in rice . Plant J. 51 : 1019 – 1029 . </ref><br />
<ref name="Arite et al. 2009">Arite , T. , Umehara , M. , Ishikawa , S. , Hanada , A. , Maekawa , M. , et al . ( 2009 ) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers . Plant Cell Physiol. 5 0 : 1416 – 1424 . </ref><br />
<ref name="Beveridge 2006">Beveridge , C.A. ( 2006 ) Axillary bud outgrowth: sending a message . Curr. Opin. Plant Biol. 9 : 35 – 40 . </ref><br />
<ref name="Beveridge et al. 2009">Beveridge , C.A. , Dun , E.A. and Rameau , C. ( 2009 ) Pea has its tendril in branching discoveries spanning a century from auxin to strigolactones . Plant Physiol. 151 : 985 – 990 . </ref><br />
<ref name="Beveridge and Kyozuka 2010">Beveridge , C.A. and Kyozuka , J. ( 2010 ) New genes in the strigolactonerelated shoot branching pathway . Curr. Opin. Plant Biol. 13 : 34 – 39 . </ref><br />
<ref name="Booker et al. 2004">Booker , J. , Auldridge , M. , Wills , S. , McCarty , D. , Klee , H. and Leyser , O. ( 2004 ) MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling molecule . Curr. Biol. 1 4 : 1232 – 1238 . </ref><br />
<ref name="Booker et al. 2005">Booker , J. , Sieberer , T. , Wright , W. , Williamson , L. , Willett , B. , Stirnberg , P. , et al . ( 2005 ) MAX1encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoidderived branch-inhibiting hormone . Dev. Cell 8 : 443 – 449 .</ref><br />
<ref name="Dun et al. 2009">Dun E.A. , Hanan , J. and Beveridge , C. ( 2009 ) Computational modeling and molecular physiology experiments reveal new insight into shoot branching in pea . Plant Cell 21 : 3459 – 3472 . </ref><br />
<ref name="Foo et al. 2005">Foo , E. , Bullier , E. , Goussot , M. , Foucher , F. , Rameau , C. and Beveridge , C.A. ( 2005 ) The branching gene RAMOSUS1mediates interactions among two novel signals and auxin in pea . Plant Cell 17 : 464 – 474 . </ref><br />
<ref name="Gao et al. 2009">Gao , Z. , Qian , Q. , Liu , X. , Yan , M. , Feng , Q. and Dong , G. , ( 2009 ) Dwarf 88, a novel putative esterase gene affecting architecture of rice plant . Plant Mol. Biol. 71 : 265 – 276 . </ref><br />
<ref name="Gomez-Roldan et al. 2008">Gomez-Roldan , V. , Fermas , S. , Brewer , P.B. , Puech-Pagès , V. , Dun , E.A. , Pillot , J.P. , et al . ( 2008 ) Strigolactone inhibition of shoot branching . Nature 455 : 189 – 194 . </ref><br />
<ref name="Heyward et al. 2009">Heyward , A. , Stirnberg , P. , Beveridge , C. and Leyser , O. ( 2009 ) Interaction between auxin and strigolactone in shoot branching control . Plant Physiol. 151 : 400 – 412 .</ref><br />
<ref name="Ishikawa et al. 2005">Ishikawa , S. , Maekawa , M. , Arite , T. , Onishi , K. , Takamure , I. and Kyozuka , J. ( 2005 ) Suppression of tiller bud activity in tillering dwarf mutants of rice . Plant Cell Physiol. 46 : 79 – 86 . </ref><br />
<ref name="Jhonson et al. 2006">Jhonson , X. , Brcich , T. , Dun , E.A. , Goussot , M. , Haurogné , K. , Beveridge , C.A. , et al . ( 2006 ) Branching genes are conserved across species. Genes controlling a novel signal in pea are coregulated by other long-distance signals . Plant Physiol. 142 : 1014 – 1026 . </ref><br />
<ref name="Lin et al. 2009">Lin , H. , Wang , R. , Qian , Q. , Yan , M , Meng , X. , Fu , Z. , et al . ( 2009 ) DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth . Plant Cell 2 1 : 1512 – 1525 . </ref><br />
<ref name="Liu et al. 2009">Liu , W. , Wu , C. , Fu , Y. , Hu , G. , Si , H. , Li , Z. , et al . ( 2009 ) Identifi cation and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice . Planta 230 : 649 – 658 .</ref><br />
<ref name="McSteen and Leyser 2005">McSteen , P. and Leyser , O. ( 2005 ) Shoot branching . Annu. Rev. Plant Biol. 56 : 353 – 374 . </ref><br />
<ref name="Ongaro and Leyser 2008">Ongaro , V. and Leyser , O. ( 2008 ) Hormonal control of shoot branching . J. Exp. Bot. 59 : 67 – 74 .</ref><br />
<ref name="ref1">Shimizu-Sato , T. , Tanaka , M. and Mori , H. ( 2009 ) Auxin–cytokinin interactions in the control of shoot branching . Plant Mol. Biol. 6 9 : 429 – 435 . </ref><br />
<ref name="Sorefan et al. 2003">Sorefan , K. , Booker , J. , Haurogne , K. , Goussot , M. , Bainbridge , K. , Foo , E. , et al . ( 2003 ) MAX4and RMS1are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea . Genes Dev. 17 : 1469 – 1474 . </ref><br />
<ref name="Strinberg et al. 2002">Stirnberg , P. , van de Sande , K. and Leyser , H.M.O. ( 2002 ) MAX1 and MAX2control shoot lateral branching in Arabidopsis . Development 129 : 1131 – 1141 .</ref><br />
<ref name="ref1">Tanaka , M. , Takei , K. , Kojima , M. , Sakakibara , H. and Mori , H. ( 2006 ) Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance . Plant J. 45 : 1028 – 36 . </ref><br />
<ref name="Umehara et al. 2008">Umehara , M. , Hanada , A. , Yoshida , S. , Akiyama , K. , Arite , T. , Takeda-Kamiya , N. , et al . ( 2008 ) Inhibition of shoot branching by new terpenoid plant hormones . Nature 455 : 195 – 200 . </ref><br />
<ref name="Zou et al. 2006">Zou , J. , Zhang , S. , Zhang , W. , Li , G. , Chen , Z. , Zhai , W. , et al . ( 2006 ) The rice HIGH-TILLERING DWARF1encoding an ortholog of Arabidopsis MAX3is required for negative regulation of the outgrowth of axillary buds . Plant J. 48 : 687 – 698 . </ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=176356Os03g07065002014-06-02T17:50:04Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
<br />
== background ==<br />
Plant architecture is determined by the pattern of shoot branching <ref name="McSteen and Leyser 2005" />. In most higher plants, shoot branches develop from axillary buds in the axils of leaves. Not all of the axillary buds develop, and each is subjected to a decision to continue growth or to become dormant, depending on a complex interplay between environmental and endogenous cues. Plant hormones are major players in the control of axillary bud growth. It has been known for a long time that two hormones in particular, auxin and cytokinin, are involved in this control. Auxin, which is supplied from the apical bud, indirectly suppresses axillary bud outgrowth, while cytokinins directly induce branching. During the past two decades, genetic and physiological analyses in pea and Arabidopsis have predicted the involvement of an additional, novel hormone in the control of shoot branching (for reviews, see<ref name="Beveridge 2006" /><ref name="Ongaro and Leyser 2008" /> . Recently it was demonstrated that the novel hormone, which inhibits bud outgrowth, is the group of compounds called strigolactones (SLs) or their downstream metabolites <ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. <br />
Prior to the discovery of SLs as the branching hormone, more axillary growth1 (max1) to max4in Arabidopsis and five ramosus (rms) mutants in garden pea ( Pisum sativum) had been identifi ed as components of a novel graft-transmissible branching signal pathway <ref name="Strinberg et al. 2002" /><ref name="Sorefan et al. 2003" />.Consistent with results obtained from grafting experiments, max1 max3 and max4 were shown to be SL deficient, and their defects were rescued by the external application of an SL<ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. On the other hand, a mutant of the MAX2 gene, which encodes an F-box leucine-rich repeat (LRR)-containing protein, was not rescued by the SL <ref name="Stirnberg et al. 2002" />. MAX1 encodes CYP711A1, a class III cytochrome P450 <ref name="Booker et al. 2005" />. MAX3 and MAX4 encode carotenoid cleavage dioxygenases (CCDs) <ref name="Sorefan et al. 2003" /><ref name="Booker et al. 2004" />. <br />
The SL pathway seems to be well conserved across species <ref name="Beveridge and Kyozuka 2010"/>. Molecular cloning showed that pea RMS1, RMS4and RMS5are orthologs of MAX4, MAX2 and MAX3, respectively <ref name="Sorefan et al. 2003" /><ref name="Foo et al. 2005" /><ref name="Jhonson et al. 2006" /><ref name="Beveridge et al. 2009" />. Analyses of branching mutants in rice indicated that the pathway is also conserved in monocot species. We reported on five tillering dwarf mutants of rice, dwarf3 (d3), d10, d14, d17 and d27<ref name="Ishikawa et al. 2005" />. The high tillering dwarf1 (htd1) mutant, which resembles the five d mutants, was also described <ref name="Zou et al. 2006" />. After the molecular cloning, it turned out that D3and D10are orthologs of MAX2/RMS4and MAX4/RMS1, respectively <ref name="Ishikawa et al. 2005" /><ref name="Arite et al. 2007" />, while HTD1 encodes an ortholog of MAX3/RMS5, and is the same locus as D17<ref name="Zou et al. 2006" /><ref name="Umehara et al. 2008" />. Meanwhile, D14and D27were shown to be novel genes that work in the SL pathway <ref name="Arite et al. 2009" /><ref name="Lin et al. 2009" />. D27 encodes an iron-containing protein and is likely to be involved in SL biosynthesis <ref name="Lin et al. 2009" />. The d14mutant, also reported as d88and htd2, is insensitive to exogenous SL application and contains elevated SL levels <ref name="Arite et al. 2009" /><ref name="Gao et al. 2009" /><ref name="Liu et al. 2009" />. Although its molecular function has not yet been determined, it is postulated that D14also works in SL signaling <ref name="Arite et al. 2009" />. <br />
The mechanisms controlling cross-talk between the hormones are beginning to be elucidated. Recently it was revealed that one role of auxin is to suppress cytokinin biosynthesis in the stem <ref name="Tanaka et al. 2006" /><ref name="Shimizu-Sato et al. 2009" />. When the auxin supply from the apical bud is blocked, expression of isopentenyltransferase ( IPT) genes, which encode a rate-limiting enzyme of cytokinin biosynthesis, is rapidly up-regulated, and this results in the rapid synthesis of cytokinins in the stem. This cytokinin is transported to axillary buds and induces bud outgrowth. In addition, the auxin-dependent up-regulation of SL biosynthesis genes has been observed in all plant species analyzed so far <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" />. Although actual changes in SL levels have not yet been observed, a likely scenario is that the apically derived auxin induces SL biosynthesis, and the SLs act as second messengers to inhibit axillary bud outgrowth. Furthermore, SL biosynthesis is controlled by feedback regulation <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" /> and, at least in Arabidopsis, this feedback regulation is mostly dependent on auxin signaling<ref name="Heyward et al. 2009" />. Together, these observations suggest that the growth of axillary buds is controlled by multiple independent and interacting pathways <ref name="Dun et al. 2009" />. <br />
Despite the remarkable progress in our understanding of the frameworks that control axillary bud outgrowth, little is known so far about how SLs act to control shoot branching. As a fi rst step towards understanding SL action at the molecular level, we report here that rice FINE CULM1 (FC1) partially works downstream of SLs to inhibit bud outgrowth. We propose that FC1serves as a hub gene where multiple signals are integrated to fi ne-tune the development of axillary buds. <br />
<br />
<br />
<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<br />
<ref name="Arite et al. 2007">Arite , T. , Iwata , H. , Ohshima , K. , Maekawa , M. , Nakajima , M. , Kojima , M. , et al . ( 2007 ) DWARF10, an RMS1/MAX4/DAD1ortholog, controls lateral bud outgrowth in rice . Plant J. 51 : 1019 – 1029 . </ref><br />
<ref name="Arite et al. 2009">Arite , T. , Umehara , M. , Ishikawa , S. , Hanada , A. , Maekawa , M. , et al . ( 2009 ) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers . Plant Cell Physiol. 5 0 : 1416 – 1424 . </ref><br />
<ref name="Beveridge 2006">Beveridge , C.A. ( 2006 ) Axillary bud outgrowth: sending a message . Curr. Opin. Plant Biol. 9 : 35 – 40 . </ref><br />
<ref name="Beveridge et al. 2009">Beveridge , C.A. , Dun , E.A. and Rameau , C. ( 2009 ) Pea has its tendril in branching discoveries spanning a century from auxin to strigolactones . Plant Physiol. 151 : 985 – 990 . </ref><br />
<ref name="Beveridge and Kyozuka 2010">Beveridge , C.A. and Kyozuka , J. ( 2010 ) New genes in the strigolactonerelated shoot branching pathway . Curr. Opin. Plant Biol. 13 : 34 – 39 . </ref><br />
<ref name="Booker et al. 2004">Booker , J. , Auldridge , M. , Wills , S. , McCarty , D. , Klee , H. and Leyser , O. ( 2004 ) MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling molecule . Curr. Biol. 1 4 : 1232 – 1238 . </ref><br />
<ref name="Booker et al. 2005">Booker , J. , Sieberer , T. , Wright , W. , Williamson , L. , Willett , B. , Stirnberg , P. , et al . ( 2005 ) MAX1encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoidderived branch-inhibiting hormone . Dev. Cell 8 : 443 – 449 .</ref><br />
<ref name="Dun et al. 2009">Dun E.A. , Hanan , J. and Beveridge , C. ( 2009 ) Computational modeling and molecular physiology experiments reveal new insight into shoot branching in pea . Plant Cell 21 : 3459 – 3472 . </ref><br />
<ref name="Foo et al. 2005">Foo , E. , Bullier , E. , Goussot , M. , Foucher , F. , Rameau , C. and Beveridge , C.A. ( 2005 ) The branching gene RAMOSUS1mediates interactions among two novel signals and auxin in pea . Plant Cell 17 : 464 – 474 . </ref><br />
<ref name="Gao et al. 2009">Gao , Z. , Qian , Q. , Liu , X. , Yan , M. , Feng , Q. and Dong , G. , ( 2009 ) Dwarf 88, a novel putative esterase gene affecting architecture of rice plant . Plant Mol. Biol. 71 : 265 – 276 . </ref><br />
<ref name="Gomez-Roldan et al. 2008">Gomez-Roldan , V. , Fermas , S. , Brewer , P.B. , Puech-Pagès , V. , Dun , E.A. , Pillot , J.P. , et al . ( 2008 ) Strigolactone inhibition of shoot branching . Nature 455 : 189 – 194 . </ref><br />
<ref name="Heyward et al. 2009">Heyward , A. , Stirnberg , P. , Beveridge , C. and Leyser , O. ( 2009 ) Interaction between auxin and strigolactone in shoot branching control . Plant Physiol. 151 : 400 – 412 .</ref><br />
<ref name="Ishikawa et al. 2005">Ishikawa , S. , Maekawa , M. , Arite , T. , Onishi , K. , Takamure , I. and Kyozuka , J. ( 2005 ) Suppression of tiller bud activity in tillering dwarf mutants of rice . Plant Cell Physiol. 46 : 79 – 86 . </ref><br />
<ref name="Jhonson et al. 2006">Jhonson , X. , Brcich , T. , Dun , E.A. , Goussot , M. , Haurogné , K. , Beveridge , C.A. , et al . ( 2006 ) Branching genes are conserved across species. Genes controlling a novel signal in pea are coregulated by other long-distance signals . Plant Physiol. 142 : 1014 – 1026 . </ref><br />
<ref name="Lin et al. 2009">Lin , H. , Wang , R. , Qian , Q. , Yan , M , Meng , X. , Fu , Z. , et al . ( 2009 ) DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth . Plant Cell 2 1 : 1512 – 1525 . </ref><br />
<ref name="Liu et al. 2009">Liu , W. , Wu , C. , Fu , Y. , Hu , G. , Si , H. , Li , Z. , et al . ( 2009 ) Identifi cation and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice . Planta 230 : 649 – 658 .</ref><br />
<ref name="McSteen and Leyser 2005">McSteen , P. and Leyser , O. ( 2005 ) Shoot branching . Annu. Rev. Plant Biol. 56 : 353 – 374 . </ref><br />
<ref name="Ongaro and Leyser 2008">Ongaro , V. and Leyser , O. ( 2008 ) Hormonal control of shoot branching . J. Exp. Bot. 59 : 67 – 74 .</ref><br />
<ref name="ref1">Shimizu-Sato , T. , Tanaka , M. and Mori , H. ( 2009 ) Auxin–cytokinin interactions in the control of shoot branching . Plant Mol. Biol. 6 9 : 429 – 435 . </ref><br />
<ref name="Sorefan et al. 2003">Sorefan , K. , Booker , J. , Haurogne , K. , Goussot , M. , Bainbridge , K. , Foo , E. , et al . ( 2003 ) MAX4and RMS1are orthologous dioxygenase-like genes that regulate shoot branching in Arabidopsis and pea . Genes Dev. 17 : 1469 – 1474 . </ref><br />
<ref name="Strinberg et al. 2002">Stirnberg , P. , van de Sande , K. and Leyser , H.M.O. ( 2002 ) MAX1 and MAX2control shoot lateral branching in Arabidopsis . Development 129 : 1131 – 1141 .</ref><br />
<ref name="ref1">Tanaka , M. , Takei , K. , Kojima , M. , Sakakibara , H. and Mori , H. ( 2006 ) Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance . Plant J. 45 : 1028 – 36 . </ref><br />
<ref name="Umehara et al. 2008">Umehara , M. , Hanada , A. , Yoshida , S. , Akiyama , K. , Arite , T. , Takeda-Kamiya , N. , et al . ( 2008 ) Inhibition of shoot branching by new terpenoid plant hormones . Nature 455 : 195 – 200 . </ref><br />
<ref name="Zou et al. 2006">Zou , J. , Zhang , S. , Zhang , W. , Li , G. , Chen , Z. , Zhai , W. , et al . ( 2006 ) The rice HIGH-TILLERING DWARF1encoding an ortholog of Arabidopsis MAX3is required for negative regulation of the outgrowth of axillary buds . Plant J. 48 : 687 – 698 . </ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=176355Os03g07065002014-06-02T17:49:16Z<p>Gaojin: /* Annotated Information */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
<br />
== background ==<br />
Plant architecture is determined by the pattern of shoot branching <ref name="McSteen and Leyser 2005" />. In most higher plants, shoot branches develop from axillary buds in the axils of leaves. Not all of the axillary buds develop, and each is subjected to a decision to continue growth or to become dormant, depending on a complex interplay between environmental and endogenous cues. Plant hormones are major players in the control of axillary bud growth. It has been known for a long time that two hormones in particular, auxin and cytokinin, are involved in this control. Auxin, which is supplied from the apical bud, indirectly suppresses axillary bud outgrowth, while cytokinins directly induce branching. During the past two decades, genetic and physiological analyses in pea and Arabidopsis have predicted the involvement of an additional, novel hormone in the control of shoot branching (for reviews, see<ref name="Beveridge 2006" /><ref name="Ongaro and Leyser 2008" /> . Recently it was demonstrated that the novel hormone, which inhibits bud outgrowth, is the group of compounds called strigolactones (SLs) or their downstream metabolites <ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. <br />
Prior to the discovery of SLs as the branching hormone, more axillary growth1 (max1) to max4in Arabidopsis and five ramosus (rms) mutants in garden pea ( Pisum sativum) had been identifi ed as components of a novel graft-transmissible branching signal pathway <ref name="Strinberg et al. 2002" /><ref name="Sorefan et al. 2003" />.Consistent with results obtained from grafting experiments, max1 max3 and max4 were shown to be SL deficient, and their defects were rescued by the external application of an SL<ref name="Gomez-Roldan et al. 2008" /><ref name="Umehara et al. 2008" />. On the other hand, a mutant of the MAX2 gene, which encodes an F-box leucine-rich repeat (LRR)-containing protein, was not rescued by the SL <ref name="Stirnberg et al. 2002" />. MAX1 encodes CYP711A1, a class III cytochrome P450 <ref name="Booker et al. 2005" />. MAX3 and MAX4 encode carotenoid cleavage dioxygenases (CCDs) <ref name="Sorefan et al. 2003" /><ref name="Booker et al. 2004" />. <br />
The SL pathway seems to be well conserved across species <ref name="Beveridge and Kyozuka 2010"/>. Molecular cloning showed that pea RMS1, RMS4and RMS5are orthologs of MAX4, MAX2 and MAX3, respectively <ref name="Sorefan et al. 2003" /><ref name="Foo et al. 2005" /><ref name="Jhonson et al. 2006" /><ref name="Beveridge et al. 2009" />. Analyses of branching mutants in rice indicated that the pathway is also conserved in monocot species. We reported on five tillering dwarf mutants of rice, dwarf3 (d3), d10, d14, d17 and d27<ref name="Ishikawa et al. 2005" />. The high tillering dwarf1 (htd1) mutant, which resembles the five d mutants, was also described <ref name="Zou et al. 2006" />. After the molecular cloning, it turned out that D3and D10are orthologs of MAX2/RMS4and MAX4/RMS1, respectively <ref name="Ishikawa et al. 2005" /><ref name="Arite et al. 2007" />, while HTD1 encodes an ortholog of MAX3/RMS5, and is the same locus as D17<ref name="Zou et al. 2006" /><ref name="Umehara et al. 2008" />. Meanwhile, D14and D27were shown to be novel genes that work in the SL pathway <ref name="Arite et al. 2009" /><ref name="Lin et al. 2009" />. D27 encodes an iron-containing protein and is likely to be involved in SL biosynthesis <ref name="Lin et al. 2009" />. The d14mutant, also reported as d88and htd2, is insensitive to exogenous SL application and contains elevated SL levels <ref name="Arite et al. 2009" /><ref name="Gao et al. 2009" /><ref name="Liu et al. 2009" />. Although its molecular function has not yet been determined, it is postulated that D14also works in SL signaling <ref name="Arite et al. 2009" />. <br />
The mechanisms controlling cross-talk between the hormones are beginning to be elucidated. Recently it was revealed that one role of auxin is to suppress cytokinin biosynthesis in the stem <ref name="Tanaka et al. 2006" /><ref name="Shimizu-Sato et al. 2009" />. When the auxin supply from the apical bud is blocked, expression of isopentenyltransferase ( IPT) genes, which encode a rate-limiting enzyme of cytokinin biosynthesis, is rapidly up-regulated, and this results in the rapid synthesis of cytokinins in the stem. This cytokinin is transported to axillary buds and induces bud outgrowth. In addition, the auxin-dependent up-regulation of SL biosynthesis genes has been observed in all plant species analyzed so far <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" />. Although actual changes in SL levels have not yet been observed, a likely scenario is that the apically derived auxin induces SL biosynthesis, and the SLs act as second messengers to inhibit axillary bud outgrowth. Furthermore, SL biosynthesis is controlled by feedback regulation <ref name="Arite et al. 2007" /><ref name="Heyward et al. 2009" /> and, at least in Arabidopsis, this feedback regulation is mostly dependent on auxin signaling<ref name="Heyward et al. 2009" />. Together, these observations suggest that the growth of axillary buds is controlled by multiple independent and interacting pathways <ref name="Dun et al. 2009" />. <br />
Despite the remarkable progress in our understanding of the frameworks that control axillary bud outgrowth, little is known so far about how SLs act to control shoot branching. As a fi rst step towards understanding SL action at the molecular level, we report here that rice FINE CULM1 (FC1) partially works downstream of SLs to inhibit bud outgrowth. We propose that FC1serves as a hub gene where multiple signals are integrated to fi ne-tune the development of axillary buds. <br />
<br />
<br />
<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174500Os07g01297002014-05-30T06:08:21Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
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*1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
*2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
*3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
*4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
*5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
*6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
*7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
*8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
*9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
*10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
*11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
*12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
*13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
*14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<references><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174499Os07g01297002014-05-30T06:08:03Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
<br />
OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
<references><br />
*1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
*2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
*3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
*4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
*5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
*6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
*7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
*8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
*9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
*10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
*11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
*12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
*13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
*14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174498Os07g01297002014-05-30T06:07:38Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
<br />
OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
<br />
*1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
*2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
*3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
*4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
*5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
*6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
*7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
*8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
*9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
*10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
*11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
*12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
*13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
*14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174496Os07g01297002014-05-30T06:07:06Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
<br />
OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
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*1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
*2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
*3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
*4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
*5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
*6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
*7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
*8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
*9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
*10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
*11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
*12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
*13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
*14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174495Os07g01297002014-05-30T06:06:15Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
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*1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
*2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
*3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
*4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
*5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
*6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
*7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
*8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
*9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
*10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
*11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
*12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
*13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
*14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174494Os07g01297002014-05-30T06:04:26Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
<br />
1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174493Os07g01297002014-05-30T06:04:04Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
<references><br />
1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365<br />
2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238<br />
3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098<br />
4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364<br />
5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice mbryogenesis Plant Molecular Biology, 1999, 39(2): 257-271<br />
6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002<br />
7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664<br />
8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997<br />
9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174492Os07g01297002014-05-30T06:02:46Z<p>Gaojin: Undo revision 174491 by Gaojin (talk)</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
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OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Yukihiro Ito;Nori Kurata<br />
Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice<br />
Plant Science, 2008, 174(3): 357-365<br />
2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata<br />
KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice<br />
Genesis, 2001, 30(4): 231-238<br />
3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka<br />
Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15<br />
The Plant Cell, 2001, 13(9): 2085-2098<br />
4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka<br />
Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants<br />
Developmental Biology, 2000, 220(2): 358-364<br />
5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer<br />
Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis<br />
Plant Molecular Biology, 1999, 39(2): 257-271<br />
6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka<br />
Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants<br />
The EMBO Journal, 1999, 18(4): 992-1002<br />
7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka<br />
Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development<br />
The Plant Cell, 1999, 11(9): 1651-1664<br />
8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka<br />
Isolation and characterization of a rice homebox gene, OSH15<br />
Plant Molecular Biology, 1998, 38(6): 983-997<br />
9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.<br />
10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.<br />
11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. <br />
12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. <br />
13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. <br />
14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0129700&diff=174491Os07g01297002014-05-30T05:59:48Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
OSH15 cDNA 1566 bp, contains five exons and encoding a 355 amino acid composition of protein products.Mutant d6 - tankanshirasasa and d6-1 is due to part of the loss of the exon 4 and exon 5 ;Mutant d6 - ID6 is because of missing part of a total of about 700 bp of exon 1 and 5 'UTR and 1 part of introns .（Sato et al., 1999）<br />
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OSH15 encoding a protein containing homologous heterotypic structure domain.OSH15 might be responsible for decide the position of elongation internode of grassroots outside cells, control of small vascular bundle sheath, sclerenchyma and the growth of epidermal cells;OSH15 possible in two ways to control the morphology and differentiation of internodes cell: one is the OSH15 may adjust the intercalary meristem cell division rate of intercalary meristem and maintain the quarter life to influence the internode elongation;The second is OSH15 may as the development of dermal cells develop into thick wall switch (Sato et al., 1999)<br />
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KNOX homologous genes alien to maintaining culture cell in undifferentiated state is enough, on the stage of meristematic cells pending the formation and maintaining of has an important role.Reference OSH1 (Ito et al., 2001) <br />
<br />
OSH a gene expression can induce transgenic rice leaf sheath of ectopic bud, their ectopic expression interfere with leaf development and to promote leaf is in a state of undifferentiated, reference OsH43 (Sentoku et al., 2000)<br />
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===Expression===<br />
Please input expression information here.<br />
To identify model of crop rice involves genes during embryogenesis, the Japanese scholar built specific cDNA library at the stage of embryonic development after organ differentiation in the former .The author focuses on KNOX (corn knotted1 similar mutant) homologous alien genes which may function in the regulation of rice embryogenesis. In early zygote embryo library，researchers identified three types of KNOX genes, two of them are Oskn2 and OsKn3, while OsH1 OsKN1 was previously reported.In situ hybridization showed that in the early embryonic development, three KNOX genes in the shoot apex meristem SAM organogenesis of regional expression.Show three KNOX genes are involved in regulating the formation of SAM.But before someone reports OsH1 involved in maintaining function of SAM.Oskn3 may participate in the shape of organs positioning mode, its expression can be divided with SMA form the boundary of different embryonic organs.Oskn2 expression patterns showed that the gene in shield and the development of the ectoderm.Oskn2 and OsKn3 expressed in tobacco further support the KNOX is involved in cell fate determination.Just like Knotted1 OsH1 ectopic expression of Oskn3 transformant in nutrition growth phase has the most significant phenotypic effects, OsKn2 transformant at vegetative stage has a relatively small change but flowers form is more serious.KNOX transgenic tobacco produce similar phenotypes, suggesting that the function of the gene product overlap each other, but different target genes or the special factor to determine the cell type the KNOX genes more precise behavior (Postma - Haarsma, et al., 1999).<br />
Homologous alien genes in many eukaryotes have an important regulatory role in the plant and the decision of the body， including to the establishment of a cell or area. Japanese scholars separated and identified a piece of code is KNOTTED homologous protein cDNA sequence of alien box, named OsH15.In OsH15 cDNA of expression in the tomato, the tomato development certain parts of the disorder, phenotypic change obviously, so think OsH15 involved in plant growth.OSH15 do through the entire plant life cycle of the in situ hybridization and the analysis and comparison with OSH1, the authors found that in the early stages of embryogenesis, two genes into SAM in the future development at the same site expression mode, while in the later performance, OSH1 can increased expression in the SAM, and OSH15 expressed in SAM would stop, but still can be in some boundary ring of embryonic organ models that can be observed.This expression pattern in nutrition or reproductive stem end, or plant HuaFen in similar groups.In situ hybridization showed that OSH1 play an important role in stems form , the early embryogenesis, and taking part in the shoot apex meristem of the surrounding organs (Sato et al., 1998)<br />
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===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
Please input related labs here.<br />
1. Makoto Matsuoka <br />
Personal Home Page: http://www.bio.nagoya-u.ac.jp/gcoe/english/member/matsuoka.html<br />
2. KURATA, Nori Professor <br />
Personal Home Page: http://www.nig.ac.jp/section/kurata/kurata-e.html<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">1. Yukihiro Ito;Nori Kurata Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice Plant Science, 2008, 174(3): 357-365 </ref><br />
<ref name="ref2">2. Yukihiro Ito;Mitsugu Eiguchi;Nori Kurata KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice Genesis, 2001, 30(4): 231-238</ref><br />
<ref name="ref3">3. Hiroshi Nagasaki;Tomoaki Sakamoto;Yutaka Sato;Makoto Matsuoka Functional Analysis of the Conserved Domains of a Rice KNOX Homeodomain Protein, OSH15 The Plant Cell, 2001, 13(9): 2085-2098</ref><br />
<ref name="ref4">4. Naoki Sentoku;Yutaka Sato;Makoto Matsuoka Overexpression of Rice OSH Genes Induces Ectopic Shoots on Leaf Sheaths of Transgenic Rice Plants Developmental Biology, 2000, 220(2): 358-364</ref><br />
<ref name="ref5">5. A. Dorien Postma-Haarsma;Ira I.G.S. Verwoert;Oscar P. Stronk;Jan Koster;Gerda E.M. Lamers;J. Harry C. Hoge;Annemarie H. Meijer Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis Plant Molecular Biology, 1999, 39(2): 257-271</ref><br />
<ref name="ref6">6. Yutaka Sato;Naoki Sentoku;Yoshio Miura;Hirohiko Hirochika;Hidemi Kitano and Makoto Matsuoka Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants The EMBO Journal, 1999, 18(4): 992-1002</ref><br />
<ref name="ref7">7. Naoki Sentoku;Yutaka Sato;Nori Kurata;Yukihiro Ito;Hidemi Kitano;Makoto Matsuoka Regional Expression of the Rice KN1-Type Homeobox Gene Family during Embryo, Shoot, and Flower Development The Plant Cell, 1999, 11(9): 1651-1664</ref><br />
<ref name="ref8">8. Yutaka Sato;Naoki Sentoku;Yasuo Nagato;Makoto Matsuoka Isolation and characterization of a rice homebox gene, OSH15 Plant Molecular Biology, 1998, 38(6): 983-997</ref><br />
<ref name="ref9">9. Douglas, S. J., et al. (2002). "KNAT1 and ERECTA regulate inflorescence architecture in Arabidopsis." The Plant Cell Online 14(3): 547-558.</ref><br />
<ref name="ref10">10. Ha, C. M., et al. (2003). "The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis." Development 130(1): 161-172.</ref><br />
<ref name="ref11">11. Itoh, H., et al. (2004). "A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase." Plant molecular biology 54(4): 533-547. </ref><br />
<ref name="ref12">12. Komatsu, K., et al. (2003). "LAX and SPA: major regulators of shoot branching in rice." Proceedings of the National Academy of Sciences 100(20): 11765-11770. </ref><br />
<ref name="ref13">13. Ori, N., et al. (2000). "Mechanisms that control knox gene expression in the Arabidopsis shoot." Development 127(24): 5523-5532. </ref><br />
14. Sakamoto, T., et al. (2006). "Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice." Plant Physiology 142(1): 54-62.</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0129700|<br />
Description = OSH15 protein (Homeobox gene)|<br />
Version = NM_001065353.1 GI:115470438 GeneID:4342320|<br />
Length = 6062 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0129700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1598277..1604338|<br />
CDS = 1598405..1598743,1598853..1598963,1599113..1599269,1603366..1603619,1603762..1603968<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1598277..1604338<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccgatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtga</cdnaseq>|<br />
AA = <aaseq>MDQSFGNLGGGGGAGGSGKAAASSFLQLPLSTAAAATAYYGTPL ALHQAAAAAGPSQYHGHGHPHHGGGHHHSKHGGAGGGEISAAEAESIKAKIMAHPQYS ALLAAYLDCQKVGAPPEVLERLTATAAKLDARPPGRHDARDPELDQFMEAYCNMLAKY REELTRPIDEAMEFLKRVESQLDTIAGGAHGGGAGSARLLLADGKSECVGSSEDDMDP SGRENEPPEIDPRAEDKELKFQLLKKYSGYLSSLRQEFSKKKKKGKLPKEARQKLLHW WELHYKWPYPSETEKIALAESTGLDQKQINNWFINQRKRHWKPSEDMPFVMMEGFHPQ NAAALYMDGPFMADGMYRLGS</aaseq>|<br />
DNA = <dnaseqindica>129..467#577..687#837..993#5090..5343#5486..5692#ctcccctccctctcgccattggagctagacagctcgagctccaggaggaagaagagagagagcctagctgctagggtttccatcggatttggttttttattttctttttgtttcttgtgtgtgttttgatggatcagagctttgggaatcttggaggaggaggaggagcaggggggagcggcaaggcggcggcgtcgtcgttcctgcagctgccgctgtccacggcggcggcggccaccgcgtactacggcacgccgctcgccttgcaccaggcggcggccgcggctggcccgtcgcagtaccacggtcacggtcacccccaccacggcggcggccaccaccacagcaagcacggcggcgccggtggtggggagatctcggcggcggaggccgagtccatcaaggccaagatcatggcgcacccccagtactccgccctcctcgcagcctacctcgactgccagaaagtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccaggtcggagcgccgccggaggtgctggagaggctgaccgccacggcggcaaagctggacgcccgccctcccggccgccacgacgcgcgcgacccggagctcgaccagttcatggttcgttcgtccccccccaactccggcgaccagttcatatatcgttcatgatatattgacccgtccgtacgacgttgaatcgatcaatcaccgatgttggttgcattgatcgggttgattaatcggaatcgaatcaatcttcgacgcaggaggcgtactgcaacatgctggccaagtacagggaggagctgacgcggccgatcgacgaggccatggagttcctcaagagggtggagtcgcagctcgacaccatcgccggcggcgcccatggcggcggcgccggctcggcgcgcctcctcctcgccggtaaatcaaccaatcatccatccccctcctcctgctctcgcctgcggttttacttctatttacacacatgctccttctgcttcttctcttctgctgctgctgctgctgctgatgatgatgatctcgtcgtcggcggcgatggcggcggcggcggcggcggaggcttaccgcattaggaaatagtttgatccggataatggaggtggttgctttggatgattgccattgttagtatagctacccatccaaagccctgtggattagtaatttatttattggggttagtaacaagacgcctttgcagcagcatgcactaacaaaagtaattaaactaacaattagtagcggtctagtcgagtgattaatctaatcatgttggcaaccagggcactgtgagcaaccatgtctcaagcttctcctcctctcgtttcagcagcttcacctccattgtttattgcatccatccatccatccatggcagcagctagcacagcctagttgcaaaacacaacacatgctagcctttcaactcaaccatttcttttttcccctctttcttttggccatgaattgtctcttctctctttcttttcttactgctctactagatgacaagtgactagaagccttgtctttagggttccaaggcatgcagggcagaggagagaatcagcctgtctatagactaatagctagattgatggagattctgaatggtgattaagcccagtaaacaatggtttgaggaagagtattataactacatagagatgtatggcagtacaagcttggttaatcatctctctggttgctgctgattggatagcatgcatgcatctaccccggatcagtagtattattcttttcttgctctagtggaagtagagccatatgcattggaaattgttgtcatggggctagctaggtacccaatgttgcagcagcactgtacgaaccgtctttcttcttcgcacgtagcactgcagctgttcttgtaatggttttgggatgcagcacagattcatctgggcgttcgtgttttccggggggttgtactgtcgattgctgcagggcaggataatcaattaatatgatagagatctgatgaactgttgatagactactgttgaatgctttttattttctgtgcatatatatatgtatagaagtattggagaagagtgtctgattggtagatcaaactaggtcagttgcatttgattcatgatggaaattaagacagttgttggagcttgccagctgctactagtagttttcctttttttttcttgtgaaagattcaatttgattaagcagagatgcaactttattaggcaatattagtggaagtcccttaaatgaaaagttacagaaccatatattatcaaaggtttttatgaacaatatacaaatttattctatgatcattttttatattactaaatctatgttcgtcagatattgggaaagattcacccggcacttatgctgcaaatgtgaactcttctctattatctaaaacaaatgggagagattactagtttcttatctctgtgatgctcaaaacctcacatggtgattctgtattctctctatataagcctagcgcatctatgctgaattttcacaaataaatctcaactattgaaattaggccacttcaaaagatcttttgtcaatgagtttgctatatgttggtttacttctatgattgcttttttgataatgtatttcatctcatcctcgcgcatgcatgcccggttatttattgccagttatgtgttccatttgagatttaaagaaccagctaatatattattattgtttttcttgtttgttatggtatgacaactgtcctagcaaatccacatccacacatcgatctatatatcttaaccaatcagcaaggctctatttgtttgtatagatcagcatgttgtttatatcgcatcattggtattaaattgtaacagttgcctactatactggtgaaacttctgcctttaaaacaaatgacactagcttatacattaaacaaatatgattgtgcaaatgcatttactaattttttttatctaataaactgtgcttgtcacttgtcagtgtttaacaaactgtccatttttcagtcattcataagtgtcagtttccgcaccattagttttagtattatggtttcctactcttgccatgtatgcttaattagattcactttgctgaaacttggaaaattaccattaatgtgtccaaatccatggactggttttgattttataattttatcaaaactgtttgagaaatgtatttttcaaatgaattatcatgtttactcattccacaagttaattaacgtgtttctcctcaaaataagctaatgcgttttctataggcgccacaaataaaaagcaaagggttcattcacaaaattttgaaggttttttttagcaaataccaagtgccatgttattaaaagattaaaatcttgtcactgttaatgcattagtacatcaggaataattctttttctgcgtagaagcacaagggcaacattggtgtatttgtcatgccatttccttttttcatgttatttgtacctcatcttaaaaaaaaggagaaagtattacataggggactaatagcttatgtgaaagaccaccgactggtttataattaaacactggctcatttctttgaagctttttttttaaggatctggttttccctctagtagttctgagctgatgaaaagtttctatagcgggttactgagagaattacagtcattgtgctaccatgagaataaatacaataacagagtaacaaccatgagaatatgttcaagaactaatggattctaaaatttgaaaggcgcttaaaatgttttcttgacactattcatgatgagaattaaacggttaatcaagtaagacatgggacgataacaactactacctaatcctgtaaatctacagaatctccatgcttttcagttgctttttatgcacccacaatatagttttcagttgcatgttatcattggaggatgtagaatactcatgcatgcacaattttttataatatggggccacatatattatcttttattttcttgtatcacatcctgggtcagatcaacaactgtcactgtacagtttcctatgtatagatcaattattttgattgcccatctgaaattaagttatggtcatatgtatctttatttattttgaagttgatctccgaattattcaattacataggcccaagacaacgctttatgtgtgatatttttgtttctggttgtatggtagtaatttttgtttttttgcttttattttatccatttctttgttatatgctatattctgtaggacgcatggtcagcatgtgaccattctgtttagagcagagaaatgctctgtcaattctttatttctttccactaaatgattctttatctactgccataatatgtattcctttgaccattggaccaagttttttaggccaaagacctagcttttatataaagcaaaagaacataggtgataagagataggaccaagtttcagtcagtatcatttttttcgtcgaagcctgggactctacgtatacctagttcagtggtttctactatttggtttatcaaacactgttttaaaaccataatctgcacaccacaatctggtcaatatatctttcaactggctgatttggcacaaatcaaacctgacaaattaataaacctaaagcagtgctagttttatccttgtattgaatatccttgtcttttcacttgcatagttttttttaccgttttttatagtgttttcttctacgaaatcagtagggcaggatccttcttgaaatccatactctttactgtagctactctaccagtagtcaaatacacagtgtcaccctattcttgcattccaaaatggatagagttgtttacccacagctatgggcctttctgcgtctgttccattgctgaccaacatggtctagactgaagctcattccaacaatacaatagaaatctgatgaacaaaatgtagtatgatctcttacattaaccaccttttgtctgcagatggtaaatctgaatgtgttggttcttctgaggatgacatggacccaagtggccgcgaaaacgagccgcctgagatcgacccgcgcgctgaggataaggagctcaagtttcagcttctgaagaagtacagtggctacttgagcagcctaaggcaagaattttccaagaaaaagaagaaaggaaagctgcctaaggaggccaggcagaagctgcttcactggtgggagctgcactacaagtggccttacccctcagtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtaggagacggagaagattgcgcttgcggaatcgacaggactagatcagaagcagatcaacaactggttcatcaaccagaggaaacggcactggaagccatcggaggacatgccgttcgtcatgatggaaggttttcacccacagaatgctgctgcattgtacatggatggcccgttcatggcagatggaatgtaccgcctcggttcgtgaacctcgatctcgatcatcggcgtgtttgatgagagatccaatgccaagataaattgatcatggaatgtattcagcatgcgttgcaatgcatggacattgttatggaatttttggtttatttacctttcaccgtggattgacaaggtctcgatcatgttagtgttgatggcttatagttctccagtaatgttgttgtttttcctttcgatggcttgtaaaagtttaggtgtatcggaatttcgatcaacttgctcgtacgctggtaattaatttggtgatggtctatatgttgtatggttgtgcgtttcagattggtgttcaaagttgcctatctgaaacaattatatatatttatattgcttctcatttt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065353.1 RefSeq:Os07g0129700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174485Os01g01971002014-05-30T05:49:33Z<p>Gaojin: /* Expression */</p>
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<div>Please input one-sentence summary here.<br />
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==Annotated Information==<br />
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This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png|right|thumb|250px|]]<br />
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=== Mutantion ===<br />
[[File:Figure2.png|right|thumb|150px|]][[File:Figure3.png|right|thumb|150px|]]<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
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===Evolution===<br />
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We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
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*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
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==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaag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/>
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174484Os01g01971002014-05-30T05:49:03Z<p>Gaojin: /* Evolution */</p>
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<div>Please input one-sentence summary here.<br />
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==Annotated Information==<br />
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This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png]]<br />
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=== Mutantion ===<br />
[[File:Figure2.png|right|thumb|150px|]][[File:Figure3.png|right|thumb|150px|]]<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
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===Evolution===<br />
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We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
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=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
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*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
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==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaagagacagagatagtaccaaattctatttctataattttcttaaatacagtaaattatttcttctcgcgaggaggattacactgcgtaggaacactaggtcatttttcatgtgaaagaaaaaaatggaagctacgaggaagacaaataatttcggcgcgcggggcgaaaaagaagaagatcaaggaagatacccaaggtgggaggtcggtccagcctctattgcgaatagagcggggtgttgttccgcgcgtggggccacacgtgcgcgcacatgcggcgcatatccatcccttcccccccacacccacatgtgtgcatgcatgcggactacgccgctgtacgcgtgcgtggcttacggcgcccgctgctacagctacagcgcccgcacgtgtcagctaccacgccacgccctgcatgcccaccgccgctgcacctccccttgagacgtggtcgctgggcggtggtgggtctcacatgtcagtacgtctttcgtcaaaaaaaaaattcaactttaatttgtttttttcatggtctcacaaccatgtagcttaccaatgcaaacagactaatctaaaaaaaaaaaaataagcttagctataatgcacgcttcgattaagcaatgttacgatgcgtgtgcttagctcaggatagtgcctatattgacacgaaaatatactacatccatataaaaaaatataagcattttttactataaatttatatatttattcatatttatagctaaaaatacttatattttgggtcggagcgagtatcatattttgattaccagtcgtccatcagctatggagtctgtatagggctacgtcctacgttcgggaggtagaaaatatggtgatttattttatttttttgcggggaaatatggtgatttattaatatatgattaattaagtattagttaaaaacttaaagaataggttaatataaatttaaaaataatttttatataaaaaatcgtattgtttagtagtttagaaaatgtgccggatcgggttgagttgggaaaggaggcgggaagaagcgtggtgtagtaattggcgaagggggtaagaagggggagaccggagacatgggtgtgatggttaggcagccggaatgggctctctatcgactcgaacagttggatgagatgagacgagatgggtgacatgcgtgcgtgcatgcatactttgtgccttgtccggtccgtgactgaactgaatcccaggaacgcgaatataatactgtagcacgcacgcacgcacgcacgcatccagctgatctagccggccgagatgtgccactttgaccggtcgtcagacacgctgcatcaatgtaggagcacgtgccagggtatggtcgctgcatgcctgcctgcaaacaatactatactcctcccataaacaaatcaaactccaacaagagaatccgacttgctagaaaaacatcatatcactttaaacaatggagattggagagtccatcagtccaatgtgtttttctgtcttctttgaccatcttccaattccccattatgcttgtgctgacctctatctaattgatcctaagagaagcgttttgcaacatcttgtaaaaaagcaaatcacataatattactcgtgctttatgtagctaagctacattggatcaggatcctctgcagtcaaagtcacgtgactttgtcactgacattgtgggtccgataatcattgggtccacatgtcttacaaagacaatccggctacatcatcatgccagtttccgtaataaattgaccagtaatttagtactatggactttagaacctggcacatgcatagcacagattcatgcatgcgtgcactgcatctgcacgcatttgcattggttgcacaagcagctagctggcctacatataacatattactgtgttatgcgagcaactggccactgtccacatgaagccagtaaatcaactatcaacattgatagtagtaaagctcttgttcagagttgcaggcatataggtgctccctgcatggtttgctcaaacttaagatagatgatactacattctaaaaatgcaagtatttctggtatgtatctggacaagatggttaggactctagctataacatagaaaatgcttatattagaatacacttcattcgtctcaaaatataaggtattttgatcggatatcgatcccatccggttaaataccttaagtagggagtggcagtggcatcaccatcgatcatgtgttattgataaatgattatgattatgagatctcttatctacaatctctttctgaataatcgacctgctgatccatccattgcatgcatggttgttgcctgacaaggacattgaaatggactgctaattgctgccatggatgcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174483Os01g01971002014-05-30T05:48:16Z<p>Gaojin: /* Mutantion */</p>
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<div>Please input one-sentence summary here.<br />
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==Annotated Information==<br />
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This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png]]<br />
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=== Mutantion ===<br />
[[File:Figure2.png|right|thumb|150px|]][[File:Figure3.png|right|thumb|150px|]]<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
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===Evolution===<br />
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We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
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[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
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*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
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==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaagagacagagatagtaccaaattctatttctataattttcttaaatacagtaaattatttcttctcgcgaggaggattacactgcgtaggaacactaggtcatttttcatgtgaaagaaaaaaatggaagctacgaggaagacaaataatttcggcgcgcggggcgaaaaagaagaagatcaaggaagatacccaaggtgggaggtcggtccagcctctattgcgaatagagcggggtgttgttccgcgcgtggggccacacgtgcgcgcacatgcggcgcatatccatcccttcccccccacacccacatgtgtgcatgcatgcggactacgccgctgtacgcgtgcgtggcttacggcgcccgctgctacagctacagcgcccgcacgtgtcagctaccacgccacgccctgcatgcccaccgccgctgcacctccccttgagacgtggtcgctgggcggtggtgggtctcacatgtcagtacgtctttcgtcaaaaaaaaaattcaactttaatttgtttttttcatggtctcacaaccatgtagcttaccaatgcaaacagactaatctaaaaaaaaaaaaataagcttagctataatgcacgcttcgattaagcaatgttacgatgcgtgtgcttagctcaggatagtgcctatattgacacgaaaatatactacatccatataaaaaaatataagcattttttactataaatttatatatttattcatatttatagctaaaaatacttatattttgggtcggagcgagtatcatattttgattaccagtcgtccatcagctatggagtctgtatagggctacgtcctacgttcgggaggtagaaaatatggtgatttattttatttttttgcggggaaatatggtgatttattaatatatgattaattaagtattagttaaaaacttaaagaataggttaatataaatttaaaaataatttttatataaaaaatcgtattgtttagtagtttagaaaatgtgccggatcgggttgagttgggaaaggaggcgggaagaagcgtggtgtagtaattggcgaagggggtaagaagggggagaccggagacatgggtgtgatggttaggcagccggaatgggctctctatcgactcgaacagttggatgagatgagacgagatgggtgacatgcgtgcgtgcatgcatactttgtgccttgtccggtccgtgactgaactgaatcccaggaacgcgaatataatactgtagcacgcacgcacgcacgcacgcatccagctgatctagccggccgagatgtgccactttgaccggtcgtcagacacgctgcatcaatgtaggagcacgtgccagggtatggtcgctgcatgcctgcctgcaaacaatactatactcctcccataaacaaatcaaactccaacaagagaatccgacttgctagaaaaacatcatatcactttaaacaatggagattggagagtccatcagtccaatgtgtttttctgtcttctttgaccatcttccaattccccattatgcttgtgctgacctctatctaattgatcctaagagaagcgttttgcaacatcttgtaaaaaagcaaatcacataatattactcgtgctttatgtagctaagctacattggatcaggatcctctgcagtcaaagtcacgtgactttgtcactgacattgtgggtccgataatcattgggtccacatgtcttacaaagacaatccggctacatcatcatgccagtttccgtaataaattgaccagtaatttagtactatggactttagaacctggcacatgcatagcacagattcatgcatgcgtgcactgcatctgcacgcatttgcattggttgcacaagcagctagctggcctacatataacatattactgtgttatgcgagcaactggccactgtccacatgaagccagtaaatcaactatcaacattgatagtagtaaagctcttgttcagagttgcaggcatataggtgctccctgcatggtttgctcaaacttaagatagatgatactacattctaaaaatgcaagtatttctggtatgtatctggacaagatggttaggactctagctataacatagaaaatgcttatattagaatacacttcattcgtctcaaaatataaggtattttgatcggatatcgatcccatccggttaaataccttaagtagggagtggcagtggcatcaccatcgatcatgtgttattgataaatgattatgattatgagatctcttatctacaatctctttctgaataatcgacctgctgatccatccattgcatgcatggttgttgcctgacaaggacattgaaatggactgctaattgctgccatggatgcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174481Os01g01971002014-05-30T05:45:31Z<p>Gaojin: /* References */</p>
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<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
<br />
This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png]]<br />
<br />
=== Mutantion ===<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
[[File:Figure2.png]][[File:Figure3.png]]<br />
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===Evolution===<br />
<br />
We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
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*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
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==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaagagacagagatagtaccaaattctatttctataattttcttaaatacagtaaattatttcttctcgcgaggaggattacactgcgtaggaacactaggtcatttttcatgtgaaagaaaaaaatggaagctacgaggaagacaaataatttcggcgcgcggggcgaaaaagaagaagatcaaggaagatacccaaggtgggaggtcggtccagcctctattgcgaatagagcggggtgttgttccgcgcgtggggccacacgtgcgcgcacatgcggcgcatatccatcccttcccccccacacccacatgtgtgcatgcatgcggactacgccgctgtacgcgtgcgtggcttacggcgcccgctgctacagctacagcgcccgcacgtgtcagctaccacgccacgccctgcatgcccaccgccgctgcacctccccttgagacgtggtcgctgggcggtggtgggtctcacatgtcagtacgtctttcgtcaaaaaaaaaattcaactttaatttgtttttttcatggtctcacaaccatgtagcttaccaatgcaaacagactaatctaaaaaaaaaaaaataagcttagctataatgcacgcttcgattaagcaatgttacgatgcgtgtgcttagctcaggatagtgcctatattgacacgaaaatatactacatccatataaaaaaatataagcattttttactataaatttatatatttattcatatttatagctaaaaatacttatattttgggtcggagcgagtatcatattttgattaccagtcgtccatcagctatggagtctgtatagggctacgtcctacgttcgggaggtagaaaatatggtgatttattttatttttttgcggggaaatatggtgatttattaatatatgattaattaagtattagttaaaaacttaaagaataggttaatataaatttaaaaataatttttatataaaaaatcgtattgtttagtagtttagaaaatgtgccggatcgggttgagttgggaaaggaggcgggaagaagcgtggtgtagtaattggcgaagggggtaagaagggggagaccggagacatgggtgtgatggttaggcagccggaatgggctctctatcgactcgaacagttggatgagatgagacgagatgggtgacatgcgtgcgtgcatgcatactttgtgccttgtccggtccgtgactgaactgaatcccaggaacgcgaatataatactgtagcacgcacgcacgcacgcacgcatccagctgatctagccggccgagatgtgccactttgaccggtcgtcagacacgctgcatcaatgtaggagcacgtgccagggtatggtcgctgcatgcctgcctgcaaacaatactatactcctcccataaacaaatcaaactccaacaagagaatccgacttgctagaaaaacatcatatcactttaaacaatggagattggagagtccatcagtccaatgtgtttttctgtcttctttgaccatcttccaattccccattatgcttgtgctgacctctatctaattgatcctaagagaagcgttttgcaacatcttgtaaaaaagcaaatcacataatattactcgtgctttatgtagctaagctacattggatcaggatcctctgcagtcaaagtcacgtgactttgtcactgacattgtgggtccgataatcattgggtccacatgtcttacaaagacaatccggctacatcatcatgccagtttccgtaataaattgaccagtaatttagtactatggactttagaacctggcacatgcatagcacagattcatgcatgcgtgcactgcatctgcacgcatttgcattggttgcacaagcagctagctggcctacatataacatattactgtgttatgcgagcaactggccactgtccacatgaagccagtaaatcaactatcaacattgatagtagtaaagctcttgttcagagttgcaggcatataggtgctccctgcatggtttgctcaaacttaagatagatgatactacattctaaaaatgcaagtatttctggtatgtatctggacaagatggttaggactctagctataacatagaaaatgcttatattagaatacacttcattcgtctcaaaatataaggtattttgatcggatatcgatcccatccggttaaataccttaagtagggagtggcagtggcatcaccatcgatcatgtgttattgataaatgattatgattatgagatctcttatctacaatctctttctgaataatcgacctgctgatccatccattgcatgcatggttgttgcctgacaaggacattgaaatggactgctaattgctgccatggatgcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174480Os01g01971002014-05-30T05:45:09Z<p>Gaojin: /* Evolution */</p>
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<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
<br />
This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png]]<br />
<br />
=== Mutantion ===<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
[[File:Figure2.png]][[File:Figure3.png]]<br />
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===Evolution===<br />
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We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
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You can also add sub-section(s) at will.<br />
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==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
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*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
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==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaagagacagagatagtaccaaattctatttctataattttcttaaatacagtaaattatttcttctcgcgaggaggattacactgcgtaggaacactaggtcatttttcatgtgaaagaaaaaaatggaagctacgaggaagacaaataatttcggcgcgcggggcgaaaaagaagaagatcaaggaagatacccaaggtgggaggtcggtccagcctctattgcgaatagagcggggtgttgttccgcgcgtggggccacacgtgcgcgcacatgcggcgcatatccatcccttcccccccacacccacatgtgtgcatgcatgcggactacgccgctgtacgcgtgcgtggcttacggcgcccgctgctacagctacagcgcccgcacgtgtcagctaccacgccacgccctgcatgcccaccgccgctgcacctccccttgagacgtggtcgctgggcggtggtgggtctcacatgtcagtacgtctttcgtcaaaaaaaaaattcaactttaatttgtttttttcatggtctcacaaccatgtagcttaccaatgcaaacagactaatctaaaaaaaaaaaaataagcttagctataatgcacgcttcgattaagcaatgttacgatgcgtgtgcttagctcaggatagtgcctatattgacacgaaaatatactacatccatataaaaaaatataagcattttttactataaatttatatatttattcatatttatagctaaaaatacttatattttgggtcggagcgagtatcatattttgattaccagtcgtccatcagctatggagtctgtatagggctacgtcctacgttcgggaggtagaaaatatggtgatttattttatttttttgcggggaaatatggtgatttattaatatatgattaattaagtattagttaaaaacttaaagaataggttaatataaatttaaaaataatttttatataaaaaatcgtattgtttagtagtttagaaaatgtgccggatcgggttgagttgggaaaggaggcgggaagaagcgtggtgtagtaattggcgaagggggtaagaagggggagaccggagacatgggtgtgatggttaggcagccggaatgggctctctatcgactcgaacagttggatgagatgagacgagatgggtgacatgcgtgcgtgcatgcatactttgtgccttgtccggtccgtgactgaactgaatcccaggaacgcgaatataatactgtagcacgcacgcacgcacgcacgcatccagctgatctagccggccgagatgtgccactttgaccggtcgtcagacacgctgcatcaatgtaggagcacgtgccagggtatggtcgctgcatgcctgcctgcaaacaatactatactcctcccataaacaaatcaaactccaacaagagaatccgacttgctagaaaaacatcatatcactttaaacaatggagattggagagtccatcagtccaatgtgtttttctgtcttctttgaccatcttccaattccccattatgcttgtgctgacctctatctaattgatcctaagagaagcgttttgcaacatcttgtaaaaaagcaaatcacataatattactcgtgctttatgtagctaagctacattggatcaggatcctctgcagtcaaagtcacgtgactttgtcactgacattgtgggtccgataatcattgggtccacatgtcttacaaagacaatccggctacatcatcatgccagtttccgtaataaattgaccagtaatttagtactatggactttagaacctggcacatgcatagcacagattcatgcatgcgtgcactgcatctgcacgcatttgcattggttgcacaagcagctagctggcctacatataacatattactgtgttatgcgagcaactggccactgtccacatgaagccagtaaatcaactatcaacattgatagtagtaaagctcttgttcagagttgcaggcatataggtgctccctgcatggtttgctcaaacttaagatagatgatactacattctaaaaatgcaagtatttctggtatgtatctggacaagatggttaggactctagctataacatagaaaatgcttatattagaatacacttcattcgtctcaaaatataaggtattttgatcggatatcgatcccatccggttaaataccttaagtagggagtggcagtggcatcaccatcgatcatgtgttattgataaatgattatgattatgagatctcttatctacaatctctttctgaataatcgacctgctgatccatccattgcatgcatggttgttgcctgacaaggacattgaaatggactgctaattgctgccatggatgcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=174479Os01g01971002014-05-30T05:44:19Z<p>Gaojin: /* Labs working on this gene */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
<br />
This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
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===Expression===<br />
RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:6.png]]<br />
<br />
=== Mutantion ===<br />
''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
[[File:Figure2.png]][[File:Figure3.png]]<br />
<br />
===Evolution===<br />
You can also add sub-section(s) at will.<br />
We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
<br />
==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
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*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
<br />
*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
<br />
*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
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*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
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*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
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*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
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*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os01g0197100|<br />
Description = Similar to Cytochrome P450 90C1 (EC 1.14.-.-) (ROTUNDIFOLIA3)|<br />
Version = NM_001048832.1 GI:115435077 GeneID:4327329|<br />
Length = 7389 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0197100, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:5235623..5243011|<br />
CDS = 5235623..5235873,5235958..5236285,5236786..5236935,5237255..5237503,5238581..5238670<br>,5238781..5238966,5239477..5239598,5242915..5243011|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:5235623..5243011<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</cdnaseq>|<br />
AA = <aaseq>MVSAAAGWAAPAFAVAAVVIWVVLCSELLRRRRRGAGSGKGDAA AAARLPPGSFGWPVVGETLEFVSCAYSPRPEAFVDKRRKLHGSAVFRSHLFGSATVVT ADAEVSRFVLQSDARAFVPWYPRSLTELMGKSSILLINGALQRRVHGLVGAFFKSSHL KSQLTADMRRRLSPALSSFPDSSLLHVQHLAKSVVFEILVRGLIGLEAGEEMQQLKQQ FQEFIVGLMSLPIKLPGTRLYRSLQAKKKMARLIQRIIREKRARRAAASPPRDAIDVL IGDGSDELTDELISDNMIDLMIPAEDSVPVLITLAVKFLSECPLALHQLEEENIQLKR RKTDMGETLQWTDYMSLSFTQHVITETLRLGNIIGGIMRKAVRDVEVKGHLIPKGWCV FVYFRSVHLDDTLYDEPYKFNPWRWKEKDMSNGSFTPFGGGQRLCPGLDLARLEASIF LHHLVTSFRWVAEEDHIVNFPTVRLKRGMPIRVTAKEDDD</aaseq>|<br />
DNA = <dnaseqindica>1..251#336..663#1164..1313#1633..1881#2959..3048#3159..3344#3855..3976#7293..7389#atggtgtcggcggccgccggttgggcggcgccggcgtttgcggtcgccgccgtggttatttgggtggtgctgtgtagtgagctcctgcggaggcggcggcgtggtgcaggcagcggcaagggggacgcggcggcggcggcgcgcctcccgccggggagcttcgggtggccagtggtgggcgagacgctggagttcgtgtcgtgcgcctactcgccgcgccccgaggcgttcgtcgacaagcgccggaagctgtaagcctagccacctccgccgccgccgccgtcccgaggcgttcggctctgactgacgggcatgggtgtgcatgcatggtgcaggcacgggagcgcggtgttcaggtcgcacctgttcgggtcggcgacggtggtgacggcggacgcggaggtgagccggttcgtgctgcagagcgacgcgcgggcgttcgtgccgtggtacccgcggtcgctgacggagctgatgggcaagtcctccatcctcctcatcaacggcgcgctccagcgacgcgtccacggcctcgtcggcgccttcttcaagtcctcccacctcaagtcccagctcaccgccgacatgcgccgccgcctctcccccgccctctcctccttccccgactcctccctcctccacgtccagcacctcgccaagtcggtacgtcctccttcttctccctctccggcgagctcctcgacgagatagagtgggtggatgaattggaggaggagcagagtgggtgggcgtgggcgagcgccggcgtgcgtgcacacgtgcgcgcccgtgtcaccacatggaagtaacttacacaaggccgggaaagggaaggcccaaaaggagtgggcccaatcacacacactctctctctctctctctctctctctctctcatctcatattctgactctagagagagagagagtggctcacctccatgtgggccccaccccatcggagtagagttaccactaccagcagccgaaaatccacgttcctgttcgccaccagagcgtgtgtttgtgcactcgtaaatgtttattttttctctgcgtattcctctggaagagatgcaaatacagtcttgaacatttgtaatttttagagatgaggatggaacgaaatgtaattgcaagaaatggtgatgaaatgcaaatgcaggtggtgttcgaaatcctggtgaggggcctgatcgggctggaggcaggggaggagatgcagcagctgaagcagcaattccaggaatttattgtcggcctcatgtccctccccattaagctgcctggcactaggctctacagatcactccaggtactctctctctctctctctccctctcatctaagttctctttctctctctacctgtagtactccatgtaaacctgcactgcaccacacattgatctctactactctcttctgtcagccactctgtctctcctttatgtctgatgttgctcagccctactccatgcagcatcagcagcagcatgatcagtgtctcagctgccatcaccattaacctctcttaatatgttctctctgtttcacaatcttggattaaatgtatacaattgcactcgatccattgcacatttttgacacattattgtgtgtgtggtcatcaggccaagaagaagatggcgaggctgatacagaggatcatccgggagaagagggcaaggagggccgccgcctcgccgccgcgggacgccatcgacgtgctcatcggagacggcagcgatgagctcaccgacgagctcatctccgacaacatgatcgacctcatgatccccgccgaggactccgtcccggtgctcatcacgctcgccgtcaagttcctcagcgagtgccctctcgccctgcaccaactggaagtaagcctgtatacctgaaacctctcttacaacacagtaagctcttaattggatcaatacctgcatataattagatgctagagatgaatcctgaacagaaaagaaaaataaaaccataccctaggaagtaattaaggatcctctgttgctgggcatgggcagtcagcaaaaagggtccagaactgaaaagagttggattttctttcttttttgtctgaaaggaacatgatcaactattcattttgtcagagccatgtgttgtgcatgatatactactatcactattgtctactacacacaatggcagaggatctgtgtccccaaacaaaaactagatcataaaaagcctacgaataagggagagatacgtaggtgggcagaagggatcagcagcatataaagggttgtgccaaccttggtccatccctttcttgttggcatcttagagctatcattattatttgttatctaatgtgccatctgaaaagaaatactactactacttgtgtttggaccaatctttgcaagatgacgtgcgttgcatcattgtcaatgtcaggtcgggtacatacatatcattagaacagagtcgccttctcacaaaagaaaaggcttactatcatgatgtatcatctacttacatatcattagtttgtgctattatgcgttttttttttctaaccggctataaacgcatgtgcaaggaatagtttttttggttgaagtatggagggttttttatcaactggggaaaaaagaaggttacataatttggctatttattctatggagattagaaggcagcagtaatatttcctagctagcatgtcctattacaccagtagcattgtgtcatatgctagattccatttacatcactacagtgctaagaaattactcgcgtgtcgactgtgtttctgttttgatgccatgtgagcaataaactcattgaaacctctgcatgtctaccactgttagagaacatgcatatcgcggctgaagataaaatccaccgtcagtaattacttgttgtaacaatgatgaataataacaccaatcacattctaatgctaccaggaggagaacatacagctcaagaggcgaaaaaccgacatgggtgagaccttgcaatggacagactacatgtcattgtcattcacacaacatgtaagtatagttcattaacactgtaacataaatttctatagctcaaaatctactggccccgtgtggtttttttcccatgaccccatgcgatttggaaaattggagtgtaggtgataacagagacgctgcggttgggcaacatcatcggtgggatcatgcgcaaggcggtgcgcgacgtcgaggtgaaggggcacctcatccccaaggggtggtgcgtgtttgtgtacttccggtcagtccacctcgatgatacgctctacgatgagccctacaagttcaacccatggaggtggaaggtaagaaagagccccacatttggtagagatgttcatccaattgctacccctttaggcaacaccagcataataaggatttgatgagtgcggttttggtgggactcctaacatgtgggcttacttctatatcagtaatctcatgatggatttgacattgccttgtactaacacttagtattgcagaaaataacagagattccctcaaagttgcattagtgattgatatatacacctaggcagaagtcaattgaatctcccaaaataactggatttggtagttctttgaactggtaaattcagacaacataagcttaagctgtccaggaaaggaatacacaccctttttttccctctattgtgtactttgtgtaagctctgaaaatgatatgcaaataattaatctaggcaaatgatggtgctgtactactgttgaggcatcctatcattatgatttgatttgggaagtctaataatgtgctaattggtcaagaaatcaatcaatctcaacaggagaaggacatgagcaatggcagcttcactccttttggtggtgggcagaggctgtgcccaggcctggatctggccaggctggaagcttccatcttccttcaccacttggtcaccagcttcaggtatggatcaccacatctcaatcttggccattcttagtgcagccattgattccaactccttagctttgtttcatgatcacttggcaacaatagcttttttttctttctagataatggaatacaaactacaacttttgcataattttccatgatcgctcggcaccgatagcatttttttctagataaaagaataaaaatcacgacctctacatcatataatgaatggaataaaaatcacggcctttgcatcatataatgcacgcaaccgggcaccaatggcatgcatctcatgtagtcatgtccctatcatttggccatgccctcttcgcatgcacattcatgttcctagtaataactaatctctgtagaacaatagaagagcggaacagtagatgaattatgcgttgattgacagaataattgtgggggggtatatagatcgggtacgtacatgaggatttgaagatcaagccgaatctttccagagataaaaaaaaaagaaaaaaattatgtcagataataactggtcctaatacgtcactagggatagcatcacgaggctttctcccatgcttatacctcctctgttatcatcttccttgagggagtgatcttactgtgcttaaggaggtatctaaagcggtggtgaagccagcgacatcgtcgagcccggataactaatagtgttttgtagtgatcaatccatttttacacgcgtcaacggtgattggtagtggagacgccgacagcgaagcctagacggtcgttcgacctggagccgtctccacctctgatcgaaagatatagtatggtattttcgcctctcacactgggagatacaactttcggcctacaaaatcaacttctggttttaaatctaagatatagattatttctagattcaagcttagaaattgttttttttaagagacagagatagtaccaaattctatttctataattttcttaaatacagtaaattatttcttctcgcgaggaggattacactgcgtaggaacactaggtcatttttcatgtgaaagaaaaaaatggaagctacgaggaagacaaataatttcggcgcgcggggcgaaaaagaagaagatcaaggaagatacccaaggtgggaggtcggtccagcctctattgcgaatagagcggggtgttgttccgcgcgtggggccacacgtgcgcgcacatgcggcgcatatccatcccttcccccccacacccacatgtgtgcatgcatgcggactacgccgctgtacgcgtgcgtggcttacggcgcccgctgctacagctacagcgcccgcacgtgtcagctaccacgccacgccctgcatgcccaccgccgctgcacctccccttgagacgtggtcgctgggcggtggtgggtctcacatgtcagtacgtctttcgtcaaaaaaaaaattcaactttaatttgtttttttcatggtctcacaaccatgtagcttaccaatgcaaacagactaatctaaaaaaaaaaaaataagcttagctataatgcacgcttcgattaagcaatgttacgatgcgtgtgcttagctcaggatagtgcctatattgacacgaaaatatactacatccatataaaaaaatataagcattttttactataaatttatatatttattcatatttatagctaaaaatacttatattttgggtcggagcgagtatcatattttgattaccagtcgtccatcagctatggagtctgtatagggctacgtcctacgttcgggaggtagaaaatatggtgatttattttatttttttgcggggaaatatggtgatttattaatatatgattaattaagtattagttaaaaacttaaagaataggttaatataaatttaaaaataatttttatataaaaaatcgtattgtttagtagtttagaaaatgtgccggatcgggttgagttgggaaaggaggcgggaagaagcgtggtgtagtaattggcgaagggggtaagaagggggagaccggagacatgggtgtgatggttaggcagccggaatgggctctctatcgactcgaacagttggatgagatgagacgagatgggtgacatgcgtgcgtgcatgcatactttgtgccttgtccggtccgtgactgaactgaatcccaggaacgcgaatataatactgtagcacgcacgcacgcacgcacgcatccagctgatctagccggccgagatgtgccactttgaccggtcgtcagacacgctgcatcaatgtaggagcacgtgccagggtatggtcgctgcatgcctgcctgcaaacaatactatactcctcccataaacaaatcaaactccaacaagagaatccgacttgctagaaaaacatcatatcactttaaacaatggagattggagagtccatcagtccaatgtgtttttctgtcttctttgaccatcttccaattccccattatgcttgtgctgacctctatctaattgatcctaagagaagcgttttgcaacatcttgtaaaaaagcaaatcacataatattactcgtgctttatgtagctaagctacattggatcaggatcctctgcagtcaaagtcacgtgactttgtcactgacattgtgggtccgataatcattgggtccacatgtcttacaaagacaatccggctacatcatcatgccagtttccgtaataaattgaccagtaatttagtactatggactttagaacctggcacatgcatagcacagattcatgcatgcgtgcactgcatctgcacgcatttgcattggttgcacaagcagctagctggcctacatataacatattactgtgttatgcgagcaactggccactgtccacatgaagccagtaaatcaactatcaacattgatagtagtaaagctcttgttcagagttgcaggcatataggtgctccctgcatggtttgctcaaacttaagatagatgatactacattctaaaaatgcaagtatttctggtatgtatctggacaagatggttaggactctagctataacatagaaaatgcttatattagaatacacttcattcgtctcaaaatataaggtattttgatcggatatcgatcccatccggttaaataccttaagtagggagtggcagtggcatcaccatcgatcatgtgttattgataaatgattatgattatgagatctcttatctacaatctctttctgaataatcgacctgctgatccatccattgcatgcatggttgttgcctgacaaggacattgaaatggactgctaattgctgccatggatgcaggtgggtggcggaggaggaccacatcgtcaacttccccaccgtgcggctcaagcggggcatgcccatcagggtcaccgccaaggaggacgacgactag</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048832.1 RefSeq:Os01g0197100]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os06g0110000&diff=174470Os06g01100002014-05-30T05:30:31Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
In the case of the rice plant, more tillering equates to more grain-bearing branches, hence a higher grain yield.The '''D3''' gene plays an important role <br />
in the control of tiller bud dormancy to suppress bud activity, encoding an F-box leucine-trich-repeat protein orthologous to Arabidopsis '''MAX2/ORE9'''<ref name="ref1" />. Besides, the d3 protein is also involved in darkness-induced senescence or H2O2-induced cell death in the plant leaves<ref name="ref2" />.<br />
<br />
===Mutation===<br />
[[File:1.jpg|right|thumb|120px|Figure 1．Phenotype of tillering dwarf mutants 6 and 10 weeks after the germination.(from reference <ref name="ref1" />).'']]<br />
To identify genes involved in the control of rice tillering, Ishikawa et al. analyzed d3, d7, d10, d14, d27 tillering dwarf mutants exhibit reduction of plant stature and an increase in tiller numbers, in the mutants, axillary meristems are normally established but the suppression of tiller bud activity is weakened<ref name="ref1" />. All mutants exhibited a similar abnormal appearance from the early stage of development, we can the this phenomena from figure 1.Yan et al found that darkness-induced senescence or H2O2-induced cell death in the thisd leaf [as measured by chlorophyll degradation, membrane ion leakage and expression of senescence-associated genes(SAGs)] in a d3 rice mutant was dalayed compared to that in its reference line Shiokari<ref name="ref2" />, we can see the leaf senescence phenomenon from the figure 2.<br />
[[File:2.jpg|right|thumb|120px|Figure 2．Representative third leaves of 1-d-old light-grown Shiokari and Id3 seeding transferred to darkness for the indicated times.(from reference <ref name="ref2" />).'']]<br />
In addition,Yasuno et al.compare the phenotype of the d3rcn1 double mutant with each single mutant and parental rice cultivar‘‘Shiokari’’, The reduction in tillering by the rcn1 mutation was independent of the d3 genotype, and tillering number of d3rcn1 double mutant was between those of the d3 and rcn1 mutants. The phenotypes of the 4 genotypes at heading time are shown in Figure 3.These results demonstrated that the Rcn1 gene was not involved in the D3-associated pathway in tillering control<ref name="ref3" />.<br />
<br />
[[File:Figure3.jpg|right|thumb|150px|Figure 3.phenotype of Shiokari, a new rcn1 mutant S-97-61, d3 mutant of near-isogenic line ID3, and d3rcn1 double mutant(DM) at heading time. S-97-61 was recovered fromM2 progeny derived from gamma-ray–irradiated Shiokari in the present study. DM was developed from progeny of a cross betweenID3 and S-97-61 in the present study. Vertical bar represents20 cm.(from reference <ref name="ref3" />).'']]<br />
<br />
===Expression===<br />
Tissue specificity of D3 expression was examined by RT–PCR analysis (Fig. 4A, B),the expression of D3 mRNA is regulated posttranscriptionaly or that transcripts with different lengths of 3′-untranslated regions are generated<ref name="ref1" />.The effect of d3 mutation on D3 mRNA expression was also analyzed by RT–PCR (Fig. 4C),it is strongly suggested that the function of the D3 gene is hampered in the Id3 mutant<ref name="ref1" />.The mRNA levels of D3 is increased during cell death by qRT-PCR analyzed.These results suggest that D3 protein is involved in leaf senescence or cell death. <br />
<br />
[[File:4.jpg]] <br />
<br />
Figure 4．Analysis of D3 expression. (A) Exon/intron structure of the D3 gene predicted on the basis of the cDNA sequence (AK065478) and cDNA regions amplified in RT–PCR analysis. D3 comprises four exons and three introns, and the predicted protein-coding region,shown as an open square, is present in the first exon. a–h represent the cDNA regions amplified in the RT–PCR analysis. A closed triangle represents the putative transposon insertion region in Id3. (B) Tissue specificity of D3 expression was examined by RT–PCR analysis using two sets of primers that amplify the b and d regions. L, leaves; R, roots; VM, vegetative meristems; RM, reproductive meristems. (C) Expression of D3 in the Id3 mutant. RNA samples isolated from young leaves were used for the RT–PCR analysis. S, wild-type Shiokari; Id3, Id3 mutant <ref name="ref1" />.<br />
<br />
===Evolution===<br />
The D3 gene sequenced and cloned by Ishikawa et al.A database search with the predicted D3 amino acid sequence indicated the presence of an N-terminal F-box and an LRR in the middle, suggesting that D3 is a member of the Fbox LRR family of proteins that function as a component of the ubiquitin E3 ligase complex(Figure5)<ref name="ref1" />.The D3 gene showed the highest sequence similarity to MAX2/ORE9 of Arabidopsis.The insertion of a putative transposon at the 154th amino acid of the predicted D3 protein caused an alteration of the amino acid sequence and generated a stop codon<ref name="ref2" />.<br />
[[File:5.jpg|right|thumb|150px|Figure 5 ]]<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
(1) Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
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(2)CREST, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan<br />
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(3) Research Institute for Bioresources, Okayama University,2-20-1Chuo, Kurashiki, Okayama, 710-0046 Japan<br />
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(4) Faculty of Agriculture, Hokkaido University, Sapporo, 060 Japan<br />
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(5) Department of Crop Science Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-5 Inada-cho,Obihiro, Hokkaido, 080-8555 Japan<br />
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(6) Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589 Japan<br />
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==References==<br />
<references><br />
<ref name="ref1"> Ishikawa S, Maekawa M, Arite T, Onishi K, Takamure I,Kyozuka J. Suppression of tiller bud activity in tillering dwarf mutants of rice[J]. Plant and Cell Physiology, 2005, 46(1): 79-86.</ref><br />
<br />
<ref name="ref2"> Yan H, Saika H, Maekawa M, Takamure I, Tsutsumi N,Kyozuka J, Nakazono M. Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death[J]. Genes & genetic systems, 2007, 82(4): 361-366.</ref><br />
<br />
<ref name="ref3"> Yasuno N, Yasui Y, Takamure I, Kato K. Genetic interaction between 2 tillering genes, reduced culm number 1 (rcn1) and tillering dwarf gene d3, in rice [J]. Journal of heredity, 2007, 98(2): 169-172.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os06g0110000|<br />
Description = Similar to DWARF3 (Fragment)|<br />
Version = NM_001063114.1 GI:115465959 GeneID:4339885|<br />
Length = 5774 bp|<br />
Definition = Oryza sativa Japonica Group Os06g0110000, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|<br />
AP = Chromosome 6:579671..585444|<br />
CDS = 579736..580004,582676..583426,583535..583624,584130..584208,584387..584493<br>,584619..584740,585003..585105|<br />
GCID = <gbrowseImage1><br />
name=NC_008399:579671..585444<br />
source=RiceChromosome06<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008399:579671..585444<br />
source=RiceChromosome06<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgatggagggcatgggcatggcggcggcgtgggcggcgggggacctgtgggtgctggcggcggcggtggtggccggcgtggtgctggtcgacgcggtggtgcggagggcgcacgactgggttcgcgtggcggcgctgggggcggagaggaggtcgaggttgccgccgggggagatggggtggccgatggtgggcagcatgtgggcgttcctccgcgccttcaagtccggcaaccccgacgccttcatcgcctccttcatccgacggtttgggcggacaggggtgtacaggacgttcatgttcagcagcccgacgatcctggcggtgacgccggaggcgtgcaagcaggtgctcatggacgacgagggcttcgtcaccggctggcccaaggccaccgtcaccctcatcggccccaaatccttcgtcaacatgtcctacgacgaccaccgccgcatccgcaagctcaccgccgcccccatcaacggcttcgacgccctcaccacctacctctccttcatcgaccagaccgtcgtcgcctccctccgccgctggtcctcgccggagtccggccaggtcgagttcctcaccgagctcaggcgcatgaccttcaagatcatcgtccagatcttcatgagcggcgccgacgacgccaccatggaggccctggagcggagctacaccgacctcaactacggcatgcgcgccatggccatcaacctccccggcttcgcctactaccgcgcgctcagggctcgccggaagctcgtgtccgtgctgcagggtgtgctcgacggccggagggccgccgccgccaagggcttcaaacgctccggggccatggacatgatggaccgcctcatcgaggccgaggacgaacgcggccgccgcctcgccgacgacgagatcgtcgacgtcctcatcatgtacctcaacgccggccacgagtcctccggccacatcaccatgtgggccaccgtcttcctccaggagaaccccgacatcttcgcaagagcaaaggctgagcaagaggagatcatgagaagcattccagcaacgcagaacggattaaccctcagggacttcaagaagatgcacttcctctcacaggttgtcgacgagacacttcgctgcgtcaacatctccttcgtgtccttccgtcaggccacaagagacatctttgtgaacggttatcttatccccaaggggtggaaggttcagctgtggtacagaagtgtgcacatggatgaccaagtttatcctgaccccaaaatgttcaacccttcaagatgggagggaccccctccgaaagccggaacattccttccatttggactgggagcaagactgtgccctggaaatgatcttgcaaagctggagatctctgtcttcctccatcattttctcctgggttacaagctgaagagggcaaatccaaagtgcagggtgagatatctgcctcatccccggcctgtggacaactgcttggcgacgatcaccaaagtttccgatgaacactaa</cdnaseq>|<br />
AA = <aaseq>MVMEGMGMAAAWAAGDLWVLAAAVVAGVVLVDAVVRRAHDWVRV AALGAERRSRLPPGEMGWPMVGSMWAFLRAFKSGNPDAFIASFIRRFGRTGVYRTFMF SSPTILAVTPEACKQVLMDDEGFVTGWPKATVTLIGPKSFVNMSYDDHRRIRKLTAAP INGFDALTTYLSFIDQTVVASLRRWSSPESGQVEFLTELRRMTFKIIVQIFMSGADDA TMEALERSYTDLNYGMRAMAINLPGFAYYRALRARRKLVSVLQGVLDGRRAAAAKGFK RSGAMDMMDRLIEAEDERGRRLADDEIVDVLIMYLNAGHESSGHITMWATVFLQENPD IFARAKAEQEEIMRSIPATQNGLTLRDFKKMHFLSQVVDETLRCVNISFVSFRQATRD IFVNGYLIPKGWKVQLWYRSVHMDDQVYPDPKMFNPSRWEGPPPKAGTFLPFGLGARL CPGNDLAKLEISVFLHHFLLGYKLKRANPKCRVRYLPHPRPVDNCLATITKVSDEH</aaseq>|<br />
DNA = <dnaseqindica>66..334#3006..3756#3865..3954#4460..4538#4717..4823#4949..5070#5333..5435#actcgtctctgcgtgcgtttcgttccttcgttgcgttgcgttggttcatcgatagatcgttctcgatggtgatggagggcatgggcatggcggcggcgtgggcggcgggggacctgtgggtgctggcggcggcggtggtggccggcgtggtgctggtcgacgcggtggtgcggagggcgcacgactgggttcgcgtggcggcgctgggggcggagaggaggtcgaggttgccgccgggggagatggggtggccgatggtgggcagcatgtgggcgttcctccgcgccttcaagtccggcaaccccgacgccttcatcgcctccttcatccgacggtcagtactaacatactcccctcctcctgccacgtgtcactggtggggtccacaccaatgctgacttgtgggccccaccggtgatcgatccttctttttttttttttgctctctttttcatcatatatgcacgtatacatgcataaagaaagaagtgatcttaattattcattcatctcaagaaattaaagaatgagaacacacacatctgcagagtgatcttttgatgcaagtgtgatctttgaatctctttgatcgccgcaacttggatcgaatcccacatatataaacgcagaatttcaattggtggtgtgcgtgagagagagatttggttgggtttggtttggtttggctgaccctggaaatgaaacccatcgagatgttgttatgatcgggaatttaggggttgttcagattaatgatattttaattggtaaagttgttaaaaatgtatatctatttagttttttttataaaactttggtaaatatataagaaatcctgtcaaaacttggtaatattgtcaaattgtaaaaattttgacaatgccaaaatttggtaatgtttgttttagttataatctgaacagccccttaatatggatccatactccatttgatttcaataagattgtggatggatggacggatcatggatgggttgctttttaatttatgtaaacatcaaaagatgctccccttttgaatggtactactgctagtatgatatagcgttgttgcaatgcatgatccatctatcagaccctagcatcaaggcatggtacttctttttctttttcttttcttttctttttgcactaggatgctcttcttctaccttttcatcatcatacctgatatgctgccctgccctggcctgttgtcaaaacccataccgatgtgtttttctcgcagcaataaaaatatattatgccttttattttatttatttttcacctttatgaacttgcatgcatatcttcatatccttcaaaacggtcctgttaaatattcatgttgatatgtctgaatcattgaccaaacacactcctgaaaagaaatcactagctaataagtatagctattactcctagaaaaccccatcctgttgtaaaaacagcaaaccatgggatatttgatggctttatgccatgtactattctgctgagtgatgtctaagcatttttggctcagattaggaattgtcggcacagctttatttgtacaagaattgacagcaattgatgctaatgtggtaggctcacgagaattcacagccagataaacgtacgagctagttttagccagtcattaggttgctgacaccgaaatgaaaattttgtggcacccactgtccatcatcagatttccaccactccagatatgcaacaacatattccaattttgccgaacaaagtttcaggacaaaaatctctttcggtgctttgctaaatagttaatacactgcttgctgatctcttgttgcatatatttactgttaagacaaattcggtgggcataactaggcatgcattagcttttgtttaatctgctatatatgccatgggaatcaatatcatatagctaggtgaaaacaaagcacccagtgctttccaaattagtatatgtgcgcttcaccctgattgtcgtttagtcaaacgtaatctcccacactcggattgatttggtgtccttttattgcttgtcttatgcactgattatcttaatcgctgttaaaaagatggttacacgtgttgttcatagattaatgccttctgttctgaaagatgcaacaatgtgttgcctttttgtcaagaaagataacacaaatgaggcacaagtagaaagattgttgcaagatcagttcttcagatttgcataggaaaaatgtttgtcatgtctgtaccattgtctgcatcacagcaaaatgacttttgtctcttcattcacttatctcagtatatttcttctgcatatatactagagtactagtttcagtaacaaagaactcatctgttaaaaaaaatcacttctttttgtgtgtgtgtgttcaagttgctctaatttatggcaactgaaacaagagactgatatcactggaacatcagcagcttaattcagaagttataacaaataaagttgtaatagtacattcatagcgaatgaagtgatggaatgaaacagaaatgctattaatcacaatcaaatcggaactaaaaatatgcaaacttatggtgatttggaagcatgggaatgcaaagaatggcaggtttgctctaatttctgacaactgaaacaagagttgacactgaaaacaagatcactgatcgttgtgatcacaaagtagtactccctccgtttcaaaatatttgacactgttgactttttagcatatgtttgaccgttcgtcttattcaaaaacttttgtgagatatgtaaaattatatgtccacataaaaatatatttaacaatgaatcaaatgataggaaaagaattaataattacttaaattttttaaataagacgaacggtcaaacatgtgtaaaaagtcaacgacgtcaaatatttcgaaacggagggagtagcaaatattgtagcacattgatagtaatcaaaagagaaacaaaaagaagaatgggaatttgatggtaagcatggaagaatggcacaggtttgggcggacaggggtgtacaggacgttcatgttcagcagcccgacgatcctggcggtgacgccggaggcgtgcaagcaggtgctcatggacgacgagggcttcgtcaccggctggcccaaggccaccgtcaccctcatcggccccaaatccttcgtcaacatgtcctacgacgaccaccgccgcatccgcaagctcaccgccgcccccatcaacggcttcgacgccctcaccacctacctctccttcatcgaccagaccgtcgtcgcctccctccgccgctggtcctcgccggagtccggccaggtcgagttcctcaccgagctcaggcgcatgaccttcaagatcatcgtccagatcttcatgagcggcgccgacgacgccaccatggaggccctggagcggagctacaccgacctcaactacggcatgcgcgccatggccatcaacctccccggcttcgcctactaccgcgcgctcagggctcgccggaagctcgtgtccgtgctgcagggtgtgctcgacggccggagggccgccgccgccaagggcttcaaacgctccggggccatggacatgatggaccgcctcatcgaggccgaggacgaacgcggccgccgcctcgccgacgacgagatcgtcgacgtcctcatcatgtacctcaacgccggccacgagtcctccggccacatcaccatgtgggccaccgtcttcctccaggagaaccccgacatcttcgcaagagcaaaggtcactcctcactctgcttctttttttttcctgtcactccaaatttggtttcaatcatctgaacttttgcattatttgaaattttgcatgatttgattttgagttcaggctgagcaagaggagatcatgagaagcattccagcaacgcagaacggattaaccctcagggacttcaagaagatgcacttcctctcacaggtataatataataatatatatagggaaactctattcatttcttaaagcgatatctccttgtttttttatgaaatttaaaaagtcattaacttttttaaaaaaattagtatgatatatcaacatatgatatgttacttcataaacatacatattcaaattcaacttatacaagtagaaacaaaaataacaaatttgatggatagaacgcgtaattcattgtcaaatttgttatttttgtttcgaattgtatatgtcgaattttaacttgcatgtttgtaaaaagatatatcatatattcatctaccttgacaaagttttttaaattttttgataacttttttgaacgccatgcacaaaacgagaggatgtccactcgagggacaaaaatccacttccatatatgcaaatgatttttaacacagtggaatatactactgctccagccgaattaccacagtaattactgcataactaatttgcacgctaatgatgatgaaatctgaaggttgtcgacgagacacttcgctgcgtcaacatctccttcgtgtccttccgtcaggccacaagagacatctttgtgaacggtgcgttttcacatagctgaaaatccatcccttaaagacatatcagaatcatcatcatctgaattctgattgatgttgttgtttctctagtgaaccacatcgactgattactactagtgcttgaaatgaaatgaaaatgaatgaatgaatgttatactaaccaagaagaacccagcaggttatcttatccccaaggggtggaaggttcagctgtggtacagaagtgtgcacatggatgaccaagtttatcctgaccccaaaatgttcaacccttcaagatgggaggtaaattaaattcaatccattcttctgcagtttttgtttcttcatcaaactagattaagctccatcgattctctgcctttttcagtgtgtttcaatggtcgatgtaattttttttgttctttcagggaccccctccgaaagccggaacattccttccatttggactgggagcaagactgtgccctggaaatgatcttgcaaagctggagatctctgtcttcctccatcattttctcctgggttacaagtaaacctcctctcaacatatttatgacaaaaaaaactactgttaactgaacatgattaattgtgaacagataaaagactaactgctgcacctctcttcttcttttcagtctttatttcttctactcttttcatttcattatcagtttacttgtagcttccaggatcaaaactgaaagttatgcctttcagaataccaactccaaaaaggataaaattgctttgttcaaagttcaaaactgaaagttgtctgctgtgtgcaggctgaagagggcaaatccaaagtgcagggtgagatatctgcctcatccccggcctgtggacaactgcttggcgacgatcaccaaagtttccgatgaacactaaaagttcagggattctttagctggaaccgaaaacagccaggctaggctacttgttcctctgggacaagtaaataaacatgattataaagtatatcacgtactctggaagaaaaaaaagagagagaagtgatgtgtattcgtcttgatatgctcgctttggtttcgcattgttcttgtttgtcctagcttaggacaaagattaaagtaaagcagttcgagttatactaacaagcttcctgaatatgggaaacacgcaagcattccccttcttttctatctatccacctcactgaatttggattgttctttatcagttaataaagatggcacgaaaagttgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063114.1 RefSeq:Os06g0110000]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 6]]<br />
[[Category:Chromosome 6]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os06g0110000&diff=174468Os06g01100002014-05-30T05:30:07Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
In the case of the rice plant, more tillering equates to more grain-bearing branches, hence a higher grain yield.The '''D3''' gene plays an important role <br />
in the control of tiller bud dormancy to suppress bud activity, encoding an F-box leucine-trich-repeat protein orthologous to Arabidopsis '''MAX2/ORE9'''<ref name="ref1" />. Besides, the d3 protein is also involved in darkness-induced senescence or H2O2-induced cell death in the plant leaves<ref name="ref2" />.<br />
<br />
===Mutation===<br />
[[File:1.jpg|right|thumb|120px|Figure 1．Phenotype of tillering dwarf mutants 6 and 10 weeks after the germination.(from reference <ref name="ref1" />).'']]<br />
To identify genes involved in the control of rice tillering, Ishikawa et al. analyzed d3, d7, d10, d14, d27 tillering dwarf mutants exhibit reduction of plant stature and an increase in tiller numbers, in the mutants, axillary meristems are normally established but the suppression of tiller bud activity is weakened<ref name="ref1" />. All mutants exhibited a similar abnormal appearance from the early stage of development, we can the this phenomena from figure 1.Yan et al found that darkness-induced senescence or H2O2-induced cell death in the thisd leaf [as measured by chlorophyll degradation, membrane ion leakage and expression of senescence-associated genes(SAGs)] in a d3 rice mutant was dalayed compared to that in its reference line Shiokari<ref name="ref2" />, we can see the leaf senescence phenomenon from the figure 2.<br />
[[File:2.jpg|right|thumb|120px|Figure 2．Representative third leaves of 1-d-old light-grown Shiokari and Id3 seeding transferred to darkness for the indicated times.(from reference <ref name="ref2" />).'']]<br />
In addition,Yasuno et al.compare the phenotype of the d3rcn1 double mutant with each single mutant and parental rice cultivar‘‘Shiokari’’, The reduction in tillering by the rcn1 mutation was independent of the d3 genotype, and tillering number of d3rcn1 double mutant was between those of the d3 and rcn1 mutants. The phenotypes of the 4 genotypes at heading time are shown in Figure 3.These results demonstrated that the Rcn1 gene was not involved in the D3-associated pathway in tillering control<ref name="ref3" />.<br />
<br />
[[File:Figure3.jpg|right|thumb|150px|Figure 3.phenotype of Shiokari, a new rcn1 mutant S-97-61, d3 mutant of near-isogenic line ID3, and d3rcn1 double mutant(DM) at heading time. S-97-61 was recovered fromM2 progeny derived from gamma-ray–irradiated Shiokari in the present study. DM was developed from progeny of a cross betweenID3 and S-97-61 in the present study. Vertical bar represents20 cm.(from reference <ref name="ref3" />).'']]<br />
<br />
===Expression===<br />
Tissue specificity of D3 expression was examined by RT–PCR analysis (Fig. 4A, B),the expression of D3 mRNA is regulated posttranscriptionaly or that transcripts with different lengths of 3′-untranslated regions are generated<ref name="ref1" />.The effect of d3 mutation on D3 mRNA expression was also analyzed by RT–PCR (Fig. 4C),it is strongly suggested that the function of the D3 gene is hampered in the Id3 mutant<ref name="ref1" />.The mRNA levels of D3 is increased during cell death by qRT-PCR analyzed.These results suggest that D3 protein is involved in leaf senescence or cell death. <br />
<br />
[[File:4.jpg]] <br />
<br />
Figure 4．Analysis of D3 expression. (A) Exon/intron structure of the D3 gene predicted on the basis of the cDNA sequence (AK065478) and cDNA regions amplified in RT–PCR analysis. D3 comprises four exons and three introns, and the predicted protein-coding region,shown as an open square, is present in the first exon. a–h represent the cDNA regions amplified in the RT–PCR analysis. A closed triangle represents the putative transposon insertion region in Id3. (B) Tissue specificity of D3 expression was examined by RT–PCR analysis using two sets of primers that amplify the b and d regions. L, leaves; R, roots; VM, vegetative meristems; RM, reproductive meristems. (C) Expression of D3 in the Id3 mutant. RNA samples isolated from young leaves were used for the RT–PCR analysis. S, wild-type Shiokari; Id3, Id3 mutant <ref name="ref1" />.<br />
<br />
===Evolution===<br />
The D3 gene sequenced and cloned by Ishikawa et al.A database search with the predicted D3 amino acid sequence indicated the presence of an N-terminal F-box and an LRR in the middle, suggesting that D3 is a member of the Fbox LRR family of proteins that function as a component of the ubiquitin E3 ligase complex(Figure5)<ref name="ref1" />.The D3 gene showed the highest sequence similarity to MAX2/ORE9 of Arabidopsis.The insertion of a putative transposon at the 154th amino acid of the predicted D3 protein caused an alteration of the amino acid sequence and generated a stop codon<ref name="ref2" />.<br />
[[File:5.jpg|right|thumb|150px|Figure 5 ]]<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
(1) Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
<br />
(2)CREST, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan<br />
<br />
(3) Research Institute for Bioresources, Okayama University,2-20-1Chuo, Kurashiki, Okayama, 710-0046 Japan<br />
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(4) Faculty of Agriculture, Hokkaido University, Sapporo, 060 Japan<br />
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(5) Department of Crop Science Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-5 Inada-cho,Obihiro, Hokkaido, 080-8555 Japan<br />
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(6) Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589 Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Ishikawa S, Maekawa M, Arite T, Onishi K, Takamure I,Kyozuka J. Suppression of tiller bud activity in tillering dwarf mutants of rice[J]. Plant and Cell Physiology, 2005, 46(1): 79-86.</ref><br />
<br />
<ref name="ref2"> Yan H, Saika H, Maekawa M, Takamure I, Tsutsumi N,Kyozuka J, Nakazono M. Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death[J]. Genes & genetic systems, 2007, 82(4): 361-366.</ref><br />
<br />
<ref name="ref3"> Yasuno N, Yasui Y, Takamure I, Kato K. Genetic interaction between 2 tillering genes, reduced culm number 1 (rcn1) and tillering dwarf gene d3, in rice [J]. Journal of heredity, 2007, 98(2): 169-172.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os06g0110000|<br />
Description = Similar to DWARF3 (Fragment)|<br />
Version = NM_001063114.1 GI:115465959 GeneID:4339885|<br />
Length = 5774 bp|<br />
Definition = Oryza sativa Japonica Group Os06g0110000, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|<br />
AP = Chromosome 6:579671..585444|<br />
CDS = 579736..580004,582676..583426,583535..583624,584130..584208,584387..584493<br>,584619..584740,585003..585105|<br />
GCID = <gbrowseImage1><br />
name=NC_008399:579671..585444<br />
source=RiceChromosome06<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008399:579671..585444<br />
source=RiceChromosome06<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggtgatggagggcatgggcatggcggcggcgtgggcggcgggggacctgtgggtgctggcggcggcggtggtggccggcgtggtgctggtcgacgcggtggtgcggagggcgcacgactgggttcgcgtggcggcgctgggggcggagaggaggtcgaggttgccgccgggggagatggggtggccgatggtgggcagcatgtgggcgttcctccgcgccttcaagtccggcaaccccgacgccttcatcgcctccttcatccgacggtttgggcggacaggggtgtacaggacgttcatgttcagcagcccgacgatcctggcggtgacgccggaggcgtgcaagcaggtgctcatggacgacgagggcttcgtcaccggctggcccaaggccaccgtcaccctcatcggccccaaatccttcgtcaacatgtcctacgacgaccaccgccgcatccgcaagctcaccgccgcccccatcaacggcttcgacgccctcaccacctacctctccttcatcgaccagaccgtcgtcgcctccctccgccgctggtcctcgccggagtccggccaggtcgagttcctcaccgagctcaggcgcatgaccttcaagatcatcgtccagatcttcatgagcggcgccgacgacgccaccatggaggccctggagcggagctacaccgacctcaactacggcatgcgcgccatggccatcaacctccccggcttcgcctactaccgcgcgctcagggctcgccggaagctcgtgtccgtgctgcagggtgtgctcgacggccggagggccgccgccgccaagggcttcaaacgctccggggccatggacatgatggaccgcctcatcgaggccgaggacgaacgcggccgccgcctcgccgacgacgagatcgtcgacgtcctcatcatgtacctcaacgccggccacgagtcctccggccacatcaccatgtgggccaccgtcttcctccaggagaaccccgacatcttcgcaagagcaaaggctgagcaagaggagatcatgagaagcattccagcaacgcagaacggattaaccctcagggacttcaagaagatgcacttcctctcacaggttgtcgacgagacacttcgctgcgtcaacatctccttcgtgtccttccgtcaggccacaagagacatctttgtgaacggttatcttatccccaaggggtggaaggttcagctgtggtacagaagtgtgcacatggatgaccaagtttatcctgaccccaaaatgttcaacccttcaagatgggagggaccccctccgaaagccggaacattccttccatttggactgggagcaagactgtgccctggaaatgatcttgcaaagctggagatctctgtcttcctccatcattttctcctgggttacaagctgaagagggcaaatccaaagtgcagggtgagatatctgcctcatccccggcctgtggacaactgcttggcgacgatcaccaaagtttccgatgaacactaa</cdnaseq>|<br />
AA = <aaseq>MVMEGMGMAAAWAAGDLWVLAAAVVAGVVLVDAVVRRAHDWVRV AALGAERRSRLPPGEMGWPMVGSMWAFLRAFKSGNPDAFIASFIRRFGRTGVYRTFMF SSPTILAVTPEACKQVLMDDEGFVTGWPKATVTLIGPKSFVNMSYDDHRRIRKLTAAP INGFDALTTYLSFIDQTVVASLRRWSSPESGQVEFLTELRRMTFKIIVQIFMSGADDA TMEALERSYTDLNYGMRAMAINLPGFAYYRALRARRKLVSVLQGVLDGRRAAAAKGFK RSGAMDMMDRLIEAEDERGRRLADDEIVDVLIMYLNAGHESSGHITMWATVFLQENPD IFARAKAEQEEIMRSIPATQNGLTLRDFKKMHFLSQVVDETLRCVNISFVSFRQATRD IFVNGYLIPKGWKVQLWYRSVHMDDQVYPDPKMFNPSRWEGPPPKAGTFLPFGLGARL CPGNDLAKLEISVFLHHFLLGYKLKRANPKCRVRYLPHPRPVDNCLATITKVSDEH</aaseq>|<br />
DNA = <dnaseqindica>66..334#3006..3756#3865..3954#4460..4538#4717..4823#4949..5070#5333..5435#actcgtctctgcgtgcgtttcgttccttcgttgcgttgcgttggttcatcgatagatcgttctcgatggtgatggagggcatgggcatggcggcggcgtgggcggcgggggacctgtgggtgctggcggcggcggtggtggccggcgtggtgctggtcgacgcggtggtgcggagggcgcacgactgggttcgcgtggcggcgctgggggcggagaggaggtcgaggttgccgccgggggagatggggtggccgatggtgggcagcatgtgggcgttcctccgcgccttcaagtccggcaaccccgacgccttcatcgcctccttcatccgacggtcagtactaacatactcccctcctcctgccacgtgtcactggtggggtccacaccaatgctgacttgtgggccccaccggtgatcgatccttctttttttttttttgctctctttttcatcatatatgcacgtatacatgcataaagaaagaagtgatcttaattattcattcatctcaagaaattaaagaatgagaacacacacatctgcagagtgatcttttgatgcaagtgtgatctttgaatctctttgatcgccgcaacttggatcgaatcccacatatataaacgcagaatttcaattggtggtgtgcgtgagagagagatttggttgggtttggtttggtttggctgaccctggaaatgaaacccatcgagatgttgttatgatcgggaatttaggggttgttcagattaatgatattttaattggtaaagttgttaaaaatgtatatctatttagttttttttataaaactttggtaaatatataagaaatcctgtcaaaacttggtaatattgtcaaattgtaaaaattttgacaatgccaaaatttggtaatgtttgttttagttataatctgaacagccccttaatatggatccatactccatttgatttcaataagattgtggatggatggacggatcatggatgggttgctttttaatttatgtaaacatcaaaagatgctccccttttgaatggtactactgctagtatgatatagcgttgttgcaatgcatgatccatctatcagaccctagcatcaaggcatggtacttctttttctttttcttttcttttctttttgcactaggatgctcttcttctaccttttcatcatcatacctgatatgctgccctgccctggcctgttgtcaaaacccataccgatgtgtttttctcgcagcaataaaaatatattatgccttttattttatttatttttcacctttatgaacttgcatgcatatcttcatatccttcaaaacggtcctgttaaatattcatgttgatatgtctgaatcattgaccaaacacactcctgaaaagaaatcactagctaataagtatagctattactcctagaaaaccccatcctgttgtaaaaacagcaaaccatgggatatttgatggctttatgccatgtactattctgctgagtgatgtctaagcatttttggctcagattaggaattgtcggcacagctttatttgtacaagaattgacagcaattgatgctaatgtggtaggctcacgagaattcacagccagataaacgtacgagctagttttagccagtcattaggttgctgacaccgaaatgaaaattttgtggcacccactgtccatcatcagatttccaccactccagatatgcaacaacatattccaattttgccgaacaaagtttcaggacaaaaatctctttcggtgctttgctaaatagttaatacactgcttgctgatctcttgttgcatatatttactgttaagacaaattcggtgggcataactaggcatgcattagcttttgtttaatctgctatatatgccatgggaatcaatatcatatagctaggtgaaaacaaagcacccagtgctttccaaattagtatatgtgcgcttcaccctgattgtcgtttagtcaaacgtaatctcccacactcggattgatttggtgtccttttattgcttgtcttatgcactgattatcttaatcgctgttaaaaagatggttacacgtgttgttcatagattaatgccttctgttctgaaagatgcaacaatgtgttgcctttttgtcaagaaagataacacaaatgaggcacaagtagaaagattgttgcaagatcagttcttcagatttgcataggaaaaatgtttgtcatgtctgtaccattgtctgcatcacagcaaaatgacttttgtctcttcattcacttatctcagtatatttcttctgcatatatactagagtactagtttcagtaacaaagaactcatctgttaaaaaaaatcacttctttttgtgtgtgtgtgttcaagttgctctaatttatggcaactgaaacaagagactgatatcactggaacatcagcagcttaattcagaagttataacaaataaagttgtaatagtacattcatagcgaatgaagtgatggaatgaaacagaaatgctattaatcacaatcaaatcggaactaaaaatatgcaaacttatggtgatttggaagcatgggaatgcaaagaatggcaggtttgctctaatttctgacaactgaaacaagagttgacactgaaaacaagatcactgatcgttgtgatcacaaagtagtactccctccgtttcaaaatatttgacactgttgactttttagcatatgtttgaccgttcgtcttattcaaaaacttttgtgagatatgtaaaattatatgtccacataaaaatatatttaacaatgaatcaaatgataggaaaagaattaataattacttaaattttttaaataagacgaacggtcaaacatgtgtaaaaagtcaacgacgtcaaatatttcgaaacggagggagtagcaaatattgtagcacattgatagtaatcaaaagagaaacaaaaagaagaatgggaatttgatggtaagcatggaagaatggcacaggtttgggcggacaggggtgtacaggacgttcatgttcagcagcccgacgatcctggcggtgacgccggaggcgtgcaagcaggtgctcatggacgacgagggcttcgtcaccggctggcccaaggccaccgtcaccctcatcggccccaaatccttcgtcaacatgtcctacgacgaccaccgccgcatccgcaagctcaccgccgcccccatcaacggcttcgacgccctcaccacctacctctccttcatcgaccagaccgtcgtcgcctccctccgccgctggtcctcgccggagtccggccaggtcgagttcctcaccgagctcaggcgcatgaccttcaagatcatcgtccagatcttcatgagcggcgccgacgacgccaccatggaggccctggagcggagctacaccgacctcaactacggcatgcgcgccatggccatcaacctccccggcttcgcctactaccgcgcgctcagggctcgccggaagctcgtgtccgtgctgcagggtgtgctcgacggccggagggccgccgccgccaagggcttcaaacgctccggggccatggacatgatggaccgcctcatcgaggccgaggacgaacgcggccgccgcctcgccgacgacgagatcgtcgacgtcctcatcatgtacctcaacgccggccacgagtcctccggccacatcaccatgtgggccaccgtcttcctccaggagaaccccgacatcttcgcaagagcaaaggtcactcctcactctgcttctttttttttcctgtcactccaaatttggtttcaatcatctgaacttttgcattatttgaaattttgcatgatttgattttgagttcaggctgagcaagaggagatcatgagaagcattccagcaacgcagaacggattaaccctcagggacttcaagaagatgcacttcctctcacaggtataatataataatatatatagggaaactctattcatttcttaaagcgatatctccttgtttttttatgaaatttaaaaagtcattaacttttttaaaaaaattagtatgatatatcaacatatgatatgttacttcataaacatacatattcaaattcaacttatacaagtagaaacaaaaataacaaatttgatggatagaacgcgtaattcattgtcaaatttgttatttttgtttcgaattgtatatgtcgaattttaacttgcatgtttgtaaaaagatatatcatatattcatctaccttgacaaagttttttaaattttttgataacttttttgaacgccatgcacaaaacgagaggatgtccactcgagggacaaaaatccacttccatatatgcaaatgatttttaacacagtggaatatactactgctccagccgaattaccacagtaattactgcataactaatttgcacgctaatgatgatgaaatctgaaggttgtcgacgagacacttcgctgcgtcaacatctccttcgtgtccttccgtcaggccacaagagacatctttgtgaacggtgcgttttcacatagctgaaaatccatcccttaaagacatatcagaatcatcatcatctgaattctgattgatgttgttgtttctctagtgaaccacatcgactgattactactagtgcttgaaatgaaatgaaaatgaatgaatgaatgttatactaaccaagaagaacccagcaggttatcttatccccaaggggtggaaggttcagctgtggtacagaagtgtgcacatggatgaccaagtttatcctgaccccaaaatgttcaacccttcaagatgggaggtaaattaaattcaatccattcttctgcagtttttgtttcttcatcaaactagattaagctccatcgattctctgcctttttcagtgtgtttcaatggtcgatgtaattttttttgttctttcagggaccccctccgaaagccggaacattccttccatttggactgggagcaagactgtgccctggaaatgatcttgcaaagctggagatctctgtcttcctccatcattttctcctgggttacaagtaaacctcctctcaacatatttatgacaaaaaaaactactgttaactgaacatgattaattgtgaacagataaaagactaactgctgcacctctcttcttcttttcagtctttatttcttctactcttttcatttcattatcagtttacttgtagcttccaggatcaaaactgaaagttatgcctttcagaataccaactccaaaaaggataaaattgctttgttcaaagttcaaaactgaaagttgtctgctgtgtgcaggctgaagagggcaaatccaaagtgcagggtgagatatctgcctcatccccggcctgtggacaactgcttggcgacgatcaccaaagtttccgatgaacactaaaagttcagggattctttagctggaaccgaaaacagccaggctaggctacttgttcctctgggacaagtaaataaacatgattataaagtatatcacgtactctggaagaaaaaaaagagagagaagtgatgtgtattcgtcttgatatgctcgctttggtttcgcattgttcttgtttgtcctagcttaggacaaagattaaagtaaagcagttcgagttatactaacaagcttcctgaatatgggaaacacgcaagcattccccttcttttctatctatccacctcactgaatttggattgttctttatcagttaataaagatggcacgaaaagttgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063114.1 RefSeq:Os06g0110000]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 6]]<br />
[[Category:Chromosome 6]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0746400&diff=174467Os01g07464002014-05-30T05:26:07Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
D10transcription might be a critical step in the regulation of the branching inhibitor pathway.<br />
==Annotated Information==<br />
===Function===<br />
D10,carotenoid cleavage dioxygenase 8（OsCCD8）controls lateral bud outgrowth of rice, and then ultimate control of rice tillers. OsCCD8 is an important enzyme of biosynthesis Strigolactones process.It´s involved in the biosynthesis of Strigolactones / Strigolactones derivative SL.And D10 may play an important role in auxin regulation of SL.D10 may plays an important role in regulate Strigolactones and its derivatives by auxin , but may reduce the transport ability of auxin and promote the synthesis of cytokinin by reducing the auxin levels at the same time.<br />
<br />
===Expression===<br />
[[File:Fig 1.jpg|right|thumb|250px|''Localization ofD10expression (from reference <ref name="ref3" />).'']]<br />
[[File:Fig 2.jpg|right|thumb|150px|''Analysis of feedback regulation of D10 and other branching genes (from reference <ref name="ref3" />).'']]<br />
<br />
D10 is a carotenoid cleavage dioxygenase, mainly expressed in vascular cells of various organs, and induced by exogenous auxin.D10 expression predominantly occurs in vascular cells in most organs. Real-time polymerase chain reaction analysis revealed that accumulation of D10 mRNA is induced by exogenous auxin.<br />
In addition, the expression of D10 up-regulated in 6 mutated branches,including d3,d10,d14,d17,d27,htdi.But MAX2 and MAX3 rice homologous gene D3 and HTD1 have no expression change in these mutants.<br />
These finding may indicate that D10's transcription may be key factor of regulating branches inhibition pathway. <ref name="ref3" /><br />
<br />
Tissue specificity of the expression of D10 and other rice branching genes was examined by reverse transcription polymerase chain reaction (RT-PCR) analysis (Figure 1a). Low levels of D10mRNA were detected in all tissues examined, except for the root tip. Expression in lateral buds and shoot apices was slightly higher than in panicles, leaves and roots. In contrast,D10likewas expressed predominantly in the panicle. As previously reported, D3andHTD1were expressed in all tissues <ref name="ref5" />.<br />
Tissue-specific distribution of D10 mRNA was further examined using the D10 promoter GUS(D10:GUS) chimeric gene (Figure 1b–h). Despite differences in the overall intensity of GUS activity, all nine transgenic lines showed a common pattern of GUS distribution. As shown in Figure 1b, GUS staining was detected in vascular cells in roots, nodes, internodes and the inflorescence. GUS expression was hardly observed in leaves . A relatively high level of GUS expression was observed in roots (Figure 1c,d). Consistent with the results obtained from RTPCR analysis, root tips did not show GUS activity. Analysis with a longitudinal section of the root indicated that the GUS activity was localized in the parenchyma cells in the root stele (Figure 1e,f). In the stem, GUS activity was localized in xylem parenchyma cells (Figure 1g,h).<br />
As shown in Figure 2, levels of D10transcripts were substantially increased in all five dmutants, whereas no such effect was observed infc1. Interestingly,D10like,D3andHTD1expression was unaltered indandfc1mutants, indicating that the level ofD10mRNA accumulation might be a critical step in the regulation of the synthesis of the branching inhibitor.<br />
<br />
{| class='wikitable' style="text-align:center"<br />
|-<br />
! | Primer<br />
! | Forward primer<br />
! | Reverse primer<br />
|-<br />
| rowspan="1"|Gene amplication<br />
| | 5'-CACCAGCACACATGCAAGAACGTC-3' <br />
| | 5-CTGCAGCATAGCGGGAGAC-3'<br />
|-<br />
| rowspan="1"|RT-PCR<br />
| | 5'-GGTAGCAACGAGAGGCAGTT-3'<br />
| | 5'-TCGACCTTGGTGAGCGTGTT-3' <br />
|}<br />
<br />
===Evolution===<br />
D10 orthologs have been isolated from four species: rice, pea, Arabidopsis and petunia. Feedback upregulation has been observed in three of them: pea RMS1 <ref name="ref1" />, petunia DAD1 <ref name="ref2" /> and rice D10. Although details of molecular mechanisms underlying the feedback control of D10, RMS1 and DAD1 remain to be unraveled, and although the extent of the upregulation varies widely between the three genes, the conservation of the feedback effect indicates that the adjustment of the branching inhibitor level by D10 plays a significant role in the control of shoot branching.<br />
D10 is a rice ortholog of MAX4/RMS1/DAD1 that encodes a carotenoid cleavage dioxygenase 8 and is supposed to be involved in the synthesis of an unidentified inhibitor of shoot branching.encoding a member of the 9-cis epoxycarotenoid dioxygenase family ,is responsible for the synthesis of a novel carotenoid-derived signal molecule that controls shoot branching in rice.<br />
<br />
=== Knowledge Extension ===<br />
Although molecular cloning has not yet been performed, the three genes D14,D17 and D27 are likely to function in the same pathway asD3andD10, because a feedback regulation of D10expression was observed in d14, d17 and d27 mutants as ind3, d10andhtd1. So far, mutants of four MAX loci in Arabidopsis, four peaRMSgenes (RMS1,RMS3, RMS4andRMS5) and one petunia gene,DAD1, which show similar enhanced-branching phenotypes, have been characterized at the molecular level.Although the rice mutant corresponding to max1has not yet been identified, the mapped positions ofD14,D17andD27suggest that none of them corresponds to MAX1.<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
* The State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences<br />
* College of Biological Sciences and Biotechnology, Beijing Forestry University<br />
* Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo<br />
*RIKEN Plant Science Center, Japan<br />
* Research Institute for Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Foo, E., Bullier, E., Goussot, M., Foucher, F., Rameau, C. and Beveridge, C.A.(2005) The branching gene RAMOUSUS1mediate interactions among two novel signals and auxin in pea.Plant Cell, 17, 464–474.</ref><br />
<ref name="ref2">Snowden, K.C., Simkin, A.J., Janssen, B.J., Templeton, K.R., Loucas, H.M., Simons, J.L., Karunairetnam, S., Gleave, A.P., Clark, D.G. and Klee, H.J.(2005) The decreased apical dominance1/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8gene affects branch production and plays a role in leaf senescence, root growth, and flower development.Plant Cell,17,746–759.</ref><br />
<ref name="ref3">Tomotsugu Arite;Hirotaka Iwata;Kenji Ohshima;Masahiko Maekawa;Masatoshi Nakajima;Mikiko Kojima;Hitoshi Sakakibara and Junko Kyozuka<br />
DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice.The Plant Journal, 2007, 51(6): 1019-1029.</ref><br />
<ref name="ref5">Ishikawa, S., Maekawa, M., Arite, T., Ohnishi, K., Takamure, I. and Kyozuka, J.(2005) Suppression of tiller bud activity in tillering dwarf mutants of rice.Plant Cell Physiol.46, 79–86.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
==Structured Information ==<br />
<br />
{{JaponicaGene|<br />
GeneName = Os01g0746400|<br />
Description = Carotenoid oxygenase family protein|<br />
Version = NM_001050764.2 GI:297597605 GeneID:4326177|<br />
Length = 3109 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0746400, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:32981304..32984412|<br />
CDS = 32981304..32981461,32981562..32981854,32981954..32982147,32982254..32982997,32984092..32984412<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:32981304..32984412<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:32981304..32984412<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgtctcccgctatgctgcaggcgtcgtcgctgtgcgtatccgcggcgctgtcaggcgccgcgagccggccgggccgcctggccagccaggggcaccagggcaagcgggccgtggcgcagcctctcgcggctagcgccgtgacggaggcagcgccgcccgcgccggtcgtcgcgccgccggcccgccccgtcgacgccccgcggcgccgtggcggacgtggcggcggcggaggcggcggcgagctcgtggcgtggaagagtgtacggcaggagaggtgggagggtgcgctcgaggtggacggagagctgcctctctggctggatggcacgtacctgaggaacggcccgggactatggaacctcggcgactacggcttccggcacctgttcgacggctacgcgacgctggtgcgcgtctcgttccgcggcggccgcgccgtgggcgcgcaccggcagatcgagtcggaggcgtacaaggcggcgcgcgcgcacggcaaggtgtgctaccgcgagttctcggaggtgcccaagccggacaacttcctgtcctacgtcggccagctggcgaccctcttctcgggctcgtcgctcaccgacaactccaacaccggcgtcgtcatgctcggcgacggccgcgtgctctgcctcacggagaccatcaagggctccatccaggtcgacccggacacgctcgacacggtcggcaagttccagtacacggacaagctgggcgggctgatccactcggcgcacccgatcgtgaccgacaccgagttctggacgctgatccccgacctgatccggcccggctacgtggtggcgaggatggacgccggtagcaacgagaggcagttcgtcggcagggtggactgccgcggcgggccggcgccagggtgggtgcactcgttccccgtcaccgagcactacgtcgtcgtgccggagatgccgctccgctactgcgccaagaacctcctccgcgccgagcccacgccgctgtacaagttcgagtggcacctcgagtccggcagctacatgcacgtcatgtgcaaggccagcggcaagattgtggcgagcgtggaggtgccgccgttcgtgacgttccacttcatcaacgcgtacgaggagacggacgaggaggggcgcgtgacggcgatcatcgccgactgctgcgagcacaacgccaacaccgccatcctcgacaagctccgcctccacaacctccgctcctccagcggccaggacgtcctccccgacgccagggtggggcggttcaggatccccctggacgggagccagttcggcgagctggagacggcgctggacccggaggagcacgggcggggcatggacatgtgcagcatcaacccggcgcacgtcggcagggagtaccggtacgcctacgcctgcggcgcccgccggccgtgcaacttccccaacacgctcaccaaggtcgacctggtggagaggacggccaagaactggcacgaggagggctccgtgccgtccgagcccttcttcgtgccacgccccggcgccaccgaggaagacgacggcgtggcgatatcgatggtgagcgccaaggacgggtcgggctatgcgctggtgctggacggcaagacgttcgaggaggtcgcgcgggccaagttcccgtacgggctgccctacggcttgcactgctgctgggtgcccaggaaaaggaacagcaagtaa</cdnaseq>|<br />
AA = <aaseq>MSPAMLQASSLCVSAALSGAASRPGRLASQGHQGKRAVAQPLAA SAVTEAAPPAPVVAPPARPVDAPRRRGGRGGGGGGGELVAWKSVRQERWEGALEVDGE LPLWLDGTYLRNGPGLWNLGDYGFRHLFDGYATLVRVSFRGGRAVGAHRQIESEAYKA ARAHGKVCYREFSEVPKPDNFLSYVGQLATLFSGSSLTDNSNTGVVMLGDGRVLCLTE TIKGSIQVDPDTLDTVGKFQYTDKLGGLIHSAHPIVTDTEFWTLIPDLIRPGYVVARM DAGSNERQFVGRVDCRGGPAPGWVHSFPVTEHYVVVPEMPLRYCAKNLLRAEPTPLYK FEWHLESGSYMHVMCKASGKIVASVEVPPFVTFHFINAYEETDEEGRVTAIIADCCEH NANTAILDKLRLHNLRSSSGQDVLPDARVGRFRIPLDGSQFGELETALDPEEHGRGMD MCSINPAHVGREYRYAYACGARRPCNFPNTLTKVDLVERTAKNWHEEGSVPSEPFFVP RPGATEEDDGVAISMVSAKDGSGYALVLDGKTFEEVARAKFPYGLPYGLHCCWVPRKR NSK</aaseq>|<br />
DNA = <dnaseqindica>2952..3109#2559..2851#2266..2459#1416..2159#1..321#atgtctcccgctatgctgcaggcgtcgtcgctgtgcgtatccgcggcgctgtcaggcgccgcgagccggccgggccgcctggccagccaggggcaccagggcaagcgggccgtggcgcagcctctcgcggctagcgccgtgacggaggcagcgccgcccgcgccggtcgtcgcgccgccggcccgccccgtcgacgccccgcggcgccgtggcggacgtggcggcggcggaggcggcggcgagctcgtggcgtggaagagtgtacggcaggagaggtgggagggtgcgctcgaggtggacggagagctgcctctctggctggtgggttaagcctcctactgattgcaaatctccctaaatatgacttgatttggcttttgccttctctccaccctaattaagtattcatgaacacaccataacctcagcattttataagatctgccggtggtcaagctaaggctagccgtgcatttttcattcaagaatgcgaatcttttctgttattttgattcaaaggtttcccagtactccatatcgctttcttgagatcatctataaactaaagatccttttgaacatcttagtaaaaaagcatgcacaacatcttcccacacattgagaaatacgaaaggcactttctggaccacatcactgtgcaacaaatcctttataattaacctaaccattttcatcttgtagcatctccttgattagtgcaggctaaccgctgacctagagcacatatatgcatatagccccagaagggtcctaaaaaggtaccagctttggccacgtacctagcatatttttaccagcagtatctaacacgccagggtatattacttgccgactgtcatttttaatttccactgtgccagcagttgctgaagcactcacccaaatcttcagtaatttgatcgacaaagaggagggcgacactaacttaccctatgctggcctagcgaaaaggagatggcatcttggcactcacgatgcttgcggggaacacaacatatatacccagattctctgctcacccctagcttcgatcggcgacaacaatggcatcactgtcttgtggttgcagttttgttgcaccccgcaactctctgaaaacaaaagtcaaaaaccttggtctcccctaactccaagtgatcttatcactgttcttgccaattttgatagtgacttgatttgaggaattaatacaggtgtacatgtagtataatattgttgtaactttgtagttacactcactaagctatggataatacaatcgtttcagctaattaaaaatgcaatcttctgaggtaagctcgtggatagattaatttgtcggtcgttaattagaggtggacggatttgtcgacgtgctgcaaatgattgatcggatcgatgcatacttgctgcaggatggcacgtacctgaggaacggcccgggactatggaacctcggcgactacggcttccggcacctgttcgacggctacgcgacgctggtgcgcgtctcgttccgcggcggccgcgccgtgggcgcgcaccggcagatcgagtcggaggcgtacaaggcggcgcgcgcgcacggcaaggtgtgctaccgcgagttctcggaggtgcccaagccggacaacttcctgtcctacgtcggccagctggcgaccctcttctcgggctcgtcgctcaccgacaactccaacaccggcgtcgtcatgctcggcgacggccgcgtgctctgcctcacggagaccatcaagggctccatccaggtcgacccggacacgctcgacacggtcggcaagttccagtacacggacaagctgggcgggctgatccactcggcgcacccgatcgtgaccgacaccgagttctggacgctgatccccgacctgatccggcccggctacgtggtggcgaggatggacgccggtagcaacgagaggcagttcgtcggcagggtggactgccgcggcgggccggcgccagggtgggtgcactcgttccccgtcaccgagcactacgtcgtcgtgccggagatgccgctccgctactgcgccaagaacctcctccgcgccgagcccacgccgctgtacaagttcgagtggcacctcgagtccggcagctacatgcacgtcatgtgcaaggccagcggcaagattgtaagccatcatcaatcgctgccgcccgtagtgcgttcccgttttgcctatttaattggttgggtgatctaatgatgatatttgtcgggacgatggccaaccgaaggtggcgagcgtggaggtgccgccgttcgtgacgttccacttcatcaacgcgtacgaggagacggacgaggaggggcgcgtgacggcgatcatcgccgactgctgcgagcacaacgccaacaccgccatcctcgacaagctccgcctccacaacctccgctcctccagcggccaggacgtcctccccgacgccaggtacgtacacacacgagccacacgacgacgtcccgccgtcaatttgctacgctacgcatgcacgtatgcacgatggatgacggggaacaccatgtgtagggtggggcggttcaggatccccctggacgggagccagttcggcgagctggagacggcgctggacccggaggagcacgggcggggcatggacatgtgcagcatcaacccggcgcacgtcggcagggagtaccggtacgcctacgcctgcggcgcccgccggccgtgcaacttccccaacacgctcaccaaggtcgacctggtggagaggacggccaagaactggcacgaggagggctccgtgccgtccgagcccttcttcgtgccacgccccggcgccaccgaggaagacgacggttagtgtcaccatctctcctcgttggctgcgtatacgtacgtcttggctttgcctcgtttcgtttgtaataacttgaccaactctgttattgatggcaggcgtggcgatatcgatggtgagcgccaaggacgggtcgggctatgcgctggtgctggacggcaagacgttcgaggaggtcgcgcgggccaagttcccgtacgggctgccctacggcttgcactgctgctgggtgcccaggaaaaggaacagcaagtaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001050764.2 RefSeq:Os01g0746400]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0746400&diff=174466Os01g07464002014-05-30T05:25:39Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
D10transcription might be a critical step in the regulation of the branching inhibitor pathway.<br />
==Annotated Information==<br />
===Function===<br />
D10,carotenoid cleavage dioxygenase 8（OsCCD8）controls lateral bud outgrowth of rice, and then ultimate control of rice tillers. OsCCD8 is an important enzyme of biosynthesis Strigolactones process.It´s involved in the biosynthesis of Strigolactones / Strigolactones derivative SL.And D10 may play an important role in auxin regulation of SL.D10 may plays an important role in regulate Strigolactones and its derivatives by auxin , but may reduce the transport ability of auxin and promote the synthesis of cytokinin by reducing the auxin levels at the same time.<br />
<br />
===Expression===<br />
[[File:Fig 1.jpg|right|thumb|250px|''Localization ofD10expression (from reference <ref name="ref3" />).'']]<br />
[[File:Fig 2.jpg|right|thumb|150px|''Analysis of feedback regulation of D10 and other branching genes (from reference <ref name="ref3" />).'']]<br />
<br />
D10 is a carotenoid cleavage dioxygenase, mainly expressed in vascular cells of various organs, and induced by exogenous auxin.D10 expression predominantly occurs in vascular cells in most organs. Real-time polymerase chain reaction analysis revealed that accumulation of D10 mRNA is induced by exogenous auxin.<br />
In addition, the expression of D10 up-regulated in 6 mutated branches,including d3,d10,d14,d17,d27,htdi.But MAX2 and MAX3 rice homologous gene D3 and HTD1 have no expression change in these mutants.<br />
These finding may indicate that D10's transcription may be key factor of regulating branches inhibition pathway. <ref name="ref3" /><br />
<br />
Tissue specificity of the expression of D10 and other rice branching genes was examined by reverse transcription polymerase chain reaction (RT-PCR) analysis (Figure 1a). Low levels of D10mRNA were detected in all tissues examined, except for the root tip. Expression in lateral buds and shoot apices was slightly higher than in panicles, leaves and roots. In contrast,D10likewas expressed predominantly in the panicle. As previously reported, D3andHTD1were expressed in all tissues <ref name="ref5" />.<br />
Tissue-specific distribution of D10 mRNA was further examined using the D10 promoter GUS(D10:GUS) chimeric gene (Figure 1b–h). Despite differences in the overall intensity of GUS activity, all nine transgenic lines showed a common pattern of GUS distribution. As shown in Figure 1b, GUS staining was detected in vascular cells in roots, nodes, internodes and the inflorescence. GUS expression was hardly observed in leaves . A relatively high level of GUS expression was observed in roots (Figure 1c,d). Consistent with the results obtained from RTPCR analysis, root tips did not show GUS activity. Analysis with a longitudinal section of the root indicated that the GUS activity was localized in the parenchyma cells in the root stele (Figure 1e,f). In the stem, GUS activity was localized in xylem parenchyma cells (Figure 1g,h).<br />
As shown in Figure 2, levels of D10transcripts were substantially increased in all five dmutants, whereas no such effect was observed infc1. Interestingly,D10like,D3andHTD1expression was unaltered indandfc1mutants, indicating that the level ofD10mRNA accumulation might be a critical step in the regulation of the synthesis of the branching inhibitor.<br />
<br />
{| class='wikitable' style="text-align:center"<br />
|-<br />
! | Primer<br />
! | Forward primer<br />
! | Reverse primer<br />
|-<br />
| rowspan="1"|Gene amplication<br />
| | 5'-CACCAGCACACATGCAAGAACGTC-3' <br />
| | 5-CTGCAGCATAGCGGGAGAC-3'<br />
|-<br />
| rowspan="1"|RT-PCR<br />
| | 5'-GGTAGCAACGAGAGGCAGTT-3'<br />
| | 5'-TCGACCTTGGTGAGCGTGTT-3' <br />
|}<br />
<br />
===Evolution===<br />
D10 orthologs have been isolated from four species: rice, pea, Arabidopsis and petunia. Feedback upregulation has been observed in three of them: pea RMS1 <ref name="ref1" />, petunia DAD1 <ref name="ref2" /> and rice D10. Although details of molecular mechanisms underlying the feedback control of D10, RMS1 and DAD1 remain to be unraveled, and although the extent of the upregulation varies widely between the three genes, the conservation of the feedback effect indicates that the adjustment of the branching inhibitor level by D10 plays a significant role in the control of shoot branching.<br />
D10 is a rice ortholog of MAX4/RMS1/DAD1 that encodes a carotenoid cleavage dioxygenase 8 and is supposed to be involved in the synthesis of an unidentified inhibitor of shoot branching.encoding a member of the 9-cis epoxycarotenoid dioxygenase family ,is responsible for the synthesis of a novel carotenoid-derived signal molecule that controls shoot branching in rice.<br />
<br />
=== Knowledge Extension ===<br />
Although molecular cloning has not yet been performed, the three genes D14,D17 and D27 are likely to function in the same pathway asD3andD10, because a feedback regulation of D10expression was observed in d14, d17 and d27 mutants as ind3, d10andhtd1. So far, mutants of four MAX loci in Arabidopsis, four peaRMSgenes (RMS1,RMS3, RMS4andRMS5) and one petunia gene,DAD1, which show similar enhanced-branching phenotypes, have been characterized at the molecular level.Although the rice mutant corresponding to max1has not yet been identified, the mapped positions ofD14,D17andD27suggest that none of them corresponds to MAX1.<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
* The State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences<br />
* College of Biological Sciences and Biotechnology, Beijing Forestry University<br />
* Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo<br />
*RIKEN Plant Science Center, Japan<br />
* Research Institute for Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Foo, E., Bullier, E., Goussot, M., Foucher, F., Rameau, C. and Beveridge, C.A.(2005) The branching gene RAMOUSUS1mediate interactions among two novel signals and auxin in pea.Plant Cell, 17, 464–474.</ref><br />
<ref name="ref2">Snowden, K.C., Simkin, A.J., Janssen, B.J., Templeton, K.R., Loucas, H.M., Simons, J.L., Karunairetnam, S., Gleave, A.P., Clark, D.G. and Klee, H.J.(2005) The decreased apical dominance1/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8gene affects branch production and plays a role in leaf senescence, root growth, and flower development.Plant Cell,17,746–759.</ref><br />
<ref name="ref3">Tomotsugu Arite;Hirotaka Iwata;Kenji Ohshima;Masahiko Maekawa;Masatoshi Nakajima;Mikiko Kojima;Hitoshi Sakakibara and Junko Kyozuka<br />
DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice.The Plant Journal, 2007, 51(6): 1019-1029.</ref><br />
<ref name="ref5">Ishikawa, S., Maekawa, M., Arite, T., Ohnishi, K., Takamure, I. and Kyozuka, J.(2005) Suppression of tiller bud activity in tillering dwarf mutants of rice.Plant Cell Physiol.46, 79–86.</ref><br />
</references><br />
<br />
==Structured Information ==<br />
<br />
{{JaponicaGene|<br />
GeneName = Os01g0746400|<br />
Description = Carotenoid oxygenase family protein|<br />
Version = NM_001050764.2 GI:297597605 GeneID:4326177|<br />
Length = 3109 bp|<br />
Definition = Oryza sativa Japonica Group Os01g0746400, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|<br />
AP = Chromosome 1:32981304..32984412|<br />
CDS = 32981304..32981461,32981562..32981854,32981954..32982147,32982254..32982997,32984092..32984412<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008394:32981304..32984412<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008394:32981304..32984412<br />
source=RiceChromosome01<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgtctcccgctatgctgcaggcgtcgtcgctgtgcgtatccgcggcgctgtcaggcgccgcgagccggccgggccgcctggccagccaggggcaccagggcaagcgggccgtggcgcagcctctcgcggctagcgccgtgacggaggcagcgccgcccgcgccggtcgtcgcgccgccggcccgccccgtcgacgccccgcggcgccgtggcggacgtggcggcggcggaggcggcggcgagctcgtggcgtggaagagtgtacggcaggagaggtgggagggtgcgctcgaggtggacggagagctgcctctctggctggatggcacgtacctgaggaacggcccgggactatggaacctcggcgactacggcttccggcacctgttcgacggctacgcgacgctggtgcgcgtctcgttccgcggcggccgcgccgtgggcgcgcaccggcagatcgagtcggaggcgtacaaggcggcgcgcgcgcacggcaaggtgtgctaccgcgagttctcggaggtgcccaagccggacaacttcctgtcctacgtcggccagctggcgaccctcttctcgggctcgtcgctcaccgacaactccaacaccggcgtcgtcatgctcggcgacggccgcgtgctctgcctcacggagaccatcaagggctccatccaggtcgacccggacacgctcgacacggtcggcaagttccagtacacggacaagctgggcgggctgatccactcggcgcacccgatcgtgaccgacaccgagttctggacgctgatccccgacctgatccggcccggctacgtggtggcgaggatggacgccggtagcaacgagaggcagttcgtcggcagggtggactgccgcggcgggccggcgccagggtgggtgcactcgttccccgtcaccgagcactacgtcgtcgtgccggagatgccgctccgctactgcgccaagaacctcctccgcgccgagcccacgccgctgtacaagttcgagtggcacctcgagtccggcagctacatgcacgtcatgtgcaaggccagcggcaagattgtggcgagcgtggaggtgccgccgttcgtgacgttccacttcatcaacgcgtacgaggagacggacgaggaggggcgcgtgacggcgatcatcgccgactgctgcgagcacaacgccaacaccgccatcctcgacaagctccgcctccacaacctccgctcctccagcggccaggacgtcctccccgacgccagggtggggcggttcaggatccccctggacgggagccagttcggcgagctggagacggcgctggacccggaggagcacgggcggggcatggacatgtgcagcatcaacccggcgcacgtcggcagggagtaccggtacgcctacgcctgcggcgcccgccggccgtgcaacttccccaacacgctcaccaaggtcgacctggtggagaggacggccaagaactggcacgaggagggctccgtgccgtccgagcccttcttcgtgccacgccccggcgccaccgaggaagacgacggcgtggcgatatcgatggtgagcgccaaggacgggtcgggctatgcgctggtgctggacggcaagacgttcgaggaggtcgcgcgggccaagttcccgtacgggctgccctacggcttgcactgctgctgggtgcccaggaaaaggaacagcaagtaa</cdnaseq>|<br />
AA = <aaseq>MSPAMLQASSLCVSAALSGAASRPGRLASQGHQGKRAVAQPLAA SAVTEAAPPAPVVAPPARPVDAPRRRGGRGGGGGGGELVAWKSVRQERWEGALEVDGE LPLWLDGTYLRNGPGLWNLGDYGFRHLFDGYATLVRVSFRGGRAVGAHRQIESEAYKA ARAHGKVCYREFSEVPKPDNFLSYVGQLATLFSGSSLTDNSNTGVVMLGDGRVLCLTE TIKGSIQVDPDTLDTVGKFQYTDKLGGLIHSAHPIVTDTEFWTLIPDLIRPGYVVARM DAGSNERQFVGRVDCRGGPAPGWVHSFPVTEHYVVVPEMPLRYCAKNLLRAEPTPLYK FEWHLESGSYMHVMCKASGKIVASVEVPPFVTFHFINAYEETDEEGRVTAIIADCCEH NANTAILDKLRLHNLRSSSGQDVLPDARVGRFRIPLDGSQFGELETALDPEEHGRGMD MCSINPAHVGREYRYAYACGARRPCNFPNTLTKVDLVERTAKNWHEEGSVPSEPFFVP RPGATEEDDGVAISMVSAKDGSGYALVLDGKTFEEVARAKFPYGLPYGLHCCWVPRKR NSK</aaseq>|<br />
DNA = <dnaseqindica>2952..3109#2559..2851#2266..2459#1416..2159#1..321#atgtctcccgctatgctgcaggcgtcgtcgctgtgcgtatccgcggcgctgtcaggcgccgcgagccggccgggccgcctggccagccaggggcaccagggcaagcgggccgtggcgcagcctctcgcggctagcgccgtgacggaggcagcgccgcccgcgccggtcgtcgcgccgccggcccgccccgtcgacgccccgcggcgccgtggcggacgtggcggcggcggaggcggcggcgagctcgtggcgtggaagagtgtacggcaggagaggtgggagggtgcgctcgaggtggacggagagctgcctctctggctggtgggttaagcctcctactgattgcaaatctccctaaatatgacttgatttggcttttgccttctctccaccctaattaagtattcatgaacacaccataacctcagcattttataagatctgccggtggtcaagctaaggctagccgtgcatttttcattcaagaatgcgaatcttttctgttattttgattcaaaggtttcccagtactccatatcgctttcttgagatcatctataaactaaagatccttttgaacatcttagtaaaaaagcatgcacaacatcttcccacacattgagaaatacgaaaggcactttctggaccacatcactgtgcaacaaatcctttataattaacctaaccattttcatcttgtagcatctccttgattagtgcaggctaaccgctgacctagagcacatatatgcatatagccccagaagggtcctaaaaaggtaccagctttggccacgtacctagcatatttttaccagcagtatctaacacgccagggtatattacttgccgactgtcatttttaatttccactgtgccagcagttgctgaagcactcacccaaatcttcagtaatttgatcgacaaagaggagggcgacactaacttaccctatgctggcctagcgaaaaggagatggcatcttggcactcacgatgcttgcggggaacacaacatatatacccagattctctgctcacccctagcttcgatcggcgacaacaatggcatcactgtcttgtggttgcagttttgttgcaccccgcaactctctgaaaacaaaagtcaaaaaccttggtctcccctaactccaagtgatcttatcactgttcttgccaattttgatagtgacttgatttgaggaattaatacaggtgtacatgtagtataatattgttgtaactttgtagttacactcactaagctatggataatacaatcgtttcagctaattaaaaatgcaatcttctgaggtaagctcgtggatagattaatttgtcggtcgttaattagaggtggacggatttgtcgacgtgctgcaaatgattgatcggatcgatgcatacttgctgcaggatggcacgtacctgaggaacggcccgggactatggaacctcggcgactacggcttccggcacctgttcgacggctacgcgacgctggtgcgcgtctcgttccgcggcggccgcgccgtgggcgcgcaccggcagatcgagtcggaggcgtacaaggcggcgcgcgcgcacggcaaggtgtgctaccgcgagttctcggaggtgcccaagccggacaacttcctgtcctacgtcggccagctggcgaccctcttctcgggctcgtcgctcaccgacaactccaacaccggcgtcgtcatgctcggcgacggccgcgtgctctgcctcacggagaccatcaagggctccatccaggtcgacccggacacgctcgacacggtcggcaagttccagtacacggacaagctgggcgggctgatccactcggcgcacccgatcgtgaccgacaccgagttctggacgctgatccccgacctgatccggcccggctacgtggtggcgaggatggacgccggtagcaacgagaggcagttcgtcggcagggtggactgccgcggcgggccggcgccagggtgggtgcactcgttccccgtcaccgagcactacgtcgtcgtgccggagatgccgctccgctactgcgccaagaacctcctccgcgccgagcccacgccgctgtacaagttcgagtggcacctcgagtccggcagctacatgcacgtcatgtgcaaggccagcggcaagattgtaagccatcatcaatcgctgccgcccgtagtgcgttcccgttttgcctatttaattggttgggtgatctaatgatgatatttgtcgggacgatggccaaccgaaggtggcgagcgtggaggtgccgccgttcgtgacgttccacttcatcaacgcgtacgaggagacggacgaggaggggcgcgtgacggcgatcatcgccgactgctgcgagcacaacgccaacaccgccatcctcgacaagctccgcctccacaacctccgctcctccagcggccaggacgtcctccccgacgccaggtacgtacacacacgagccacacgacgacgtcccgccgtcaatttgctacgctacgcatgcacgtatgcacgatggatgacggggaacaccatgtgtagggtggggcggttcaggatccccctggacgggagccagttcggcgagctggagacggcgctggacccggaggagcacgggcggggcatggacatgtgcagcatcaacccggcgcacgtcggcagggagtaccggtacgcctacgcctgcggcgcccgccggccgtgcaacttccccaacacgctcaccaaggtcgacctggtggagaggacggccaagaactggcacgaggagggctccgtgccgtccgagcccttcttcgtgccacgccccggcgccaccgaggaagacgacggttagtgtcaccatctctcctcgttggctgcgtatacgtacgtcttggctttgcctcgtttcgtttgtaataacttgaccaactctgttattgatggcaggcgtggcgatatcgatggtgagcgccaaggacgggtcgggctatgcgctggtgctggacggcaagacgttcgaggaggtcgcgcgggccaagttcccgtacgggctgccctacggcttgcactgctgctgggtgcccaggaaaaggaacagcaagtaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001050764.2 RefSeq:Os01g0746400]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174463Os03g02032002014-05-30T05:23:13Z<p>Gaojin: /* Annotated Information */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
HTD2gene could negatively regulate tiller bud outgrowth by the strigolactone pathway<br />
HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
[[File:Real-time PCR analysis of HTD2transcript levels in different issures.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
[[File:Phylogenetic tree of HTD2 and its homologous proteins.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The strigolactone signal regulates bud outgrowth by controlling auxin transport capacity in the stem in Arabidopsis .In max mutants, there is an increase in<br />
auxin transport capacity. The elevated capacity of auxin transport causes bud outgrowth,since increased expression of PIN auxin eZux carrier was observed in maxmutants and the pin1mutation suppressed the max phenotype. In htd2 mutant, the biosynthesis of strigolactone is likely to be arrested as a result of the htd2 mutation. The absence of strigolactone could result in increased auxin transport, further promoting bud outgrowth in the htd2 mutant.<br />
Four high tillering and dwarf genes, including D10,HTD1, D3and TB1, have been cloned in rice .Their orthologous genes have similar functions in Arabidopsis, pea and petunia .These findings indicate that monocot and eudicot plants share a conserved mechanism controlling shoot branching. In the present study, we identified a new high tillering and dwarf gene HTD2, which encodes an esterase/lipase/thioesterase. Although orthologous genes for HTD2 widely exist in other plants (Fig.Phylogenetic tree of HTD2 and its homologous proteins), none has been characterized so far. Characterization of the HTD2gene and study on its interaction with other tillering-related genes will be helpful to further understand the regulation mechanism of outgrowth of tiller buds in plants.<ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174462Os03g02032002014-05-30T05:22:48Z<p>Gaojin: /* Annotated Information */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
HTD2gene could negatively regulate tiller bud outgrowth by the strigolactone pathway<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
[[File:Real-time PCR analysis of HTD2transcript levels in different issures.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
[[File:Phylogenetic tree of HTD2 and its homologous proteins.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The strigolactone signal regulates bud outgrowth by controlling auxin transport capacity in the stem in Arabidopsis .In max mutants, there is an increase in<br />
auxin transport capacity. The elevated capacity of auxin transport causes bud outgrowth,since increased expression of PIN auxin eZux carrier was observed in maxmutants and the pin1mutation suppressed the max phenotype. In htd2 mutant, the biosynthesis of strigolactone is likely to be arrested as a result of the htd2 mutation. The absence of strigolactone could result in increased auxin transport, further promoting bud outgrowth in the htd2 mutant.<br />
Four high tillering and dwarf genes, including D10,HTD1, D3and TB1, have been cloned in rice .Their orthologous genes have similar functions in Arabidopsis, pea and petunia .These findings indicate that monocot and eudicot plants share a conserved mechanism controlling shoot branching. In the present study, we identified a new high tillering and dwarf gene HTD2, which encodes an esterase/lipase/thioesterase. Although orthologous genes for HTD2 widely exist in other plants (Fig.Phylogenetic tree of HTD2 and its homologous proteins), none has been characterized so far. Characterization of the HTD2gene and study on its interaction with other tillering-related genes will be helpful to further understand the regulation mechanism of outgrowth of tiller buds in plants.<ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174460Os03g02032002014-05-30T05:21:31Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
[[File:Real-time PCR analysis of HTD2transcript levels in different issures.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
[[File:Phylogenetic tree of HTD2 and its homologous proteins.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The strigolactone signal regulates bud outgrowth by controlling auxin transport capacity in the stem in Arabidopsis .In max mutants, there is an increase in<br />
auxin transport capacity. The elevated capacity of auxin transport causes bud outgrowth,since increased expression of PIN auxin eZux carrier was observed in maxmutants and the pin1mutation suppressed the max phenotype. In htd2 mutant, the biosynthesis of strigolactone is likely to be arrested as a result of the htd2 mutation. The absence of strigolactone could result in increased auxin transport, further promoting bud outgrowth in the htd2 mutant.<br />
Four high tillering and dwarf genes, including D10,HTD1, D3and TB1, have been cloned in rice .Their orthologous genes have similar functions in Arabidopsis, pea and petunia .These findings indicate that monocot and eudicot plants share a conserved mechanism controlling shoot branching. In the present study, we identified a new high tillering and dwarf gene HTD2, which encodes an esterase/lipase/thioesterase. Although orthologous genes for HTD2 widely exist in other plants (Fig.Phylogenetic tree of HTD2 and its homologous proteins), none has been characterized so far. Characterization of the HTD2gene and study on its interaction with other tillering-related genes will be helpful to further understand the regulation mechanism of outgrowth of tiller buds in plants.<ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Phylogenetic_tree_of_HTD2_and_its_homologous_proteins.png&diff=174459File:Phylogenetic tree of HTD2 and its homologous proteins.png2014-05-30T05:20:48Z<p>Gaojin: </p>
<hr />
<div></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174456Os03g02032002014-05-30T05:19:55Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
[[File:Real-time PCR analysis of HTD2transcript levels in different issures.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
<br />
The strigolactone signal regulates bud outgrowth by controlling auxin transport capacity in the stem in Arabidopsis .In max mutants, there is an increase in<br />
auxin transport capacity. The elevated capacity of auxin transport causes bud outgrowth,since increased expression of PIN auxin eZux carrier was observed in maxmutants and the pin1mutation suppressed the max phenotype. In htd2 mutant, the biosynthesis of strigolactone is likely to be arrested as a result of the htd2 mutation. The absence of strigolactone could result in increased auxin transport, further promoting bud outgrowth in the htd2 mutant.<br />
Four high tillering and dwarf genes, including D10,HTD1, D3and TB1, have been cloned in rice .Their orthologous genes have similar functions in Arabidopsis, pea and petunia .These findings indicate that monocot and eudicot plants share a conserved mechanism controlling shoot branching. In the present study, we identified a new high tillering and dwarf gene HTD2, which encodes an esterase/lipase/thioesterase. Although orthologous genes for HTD2 widely exist in other plants (Fig.Phylogenetic tree of HTD2 and its homologous proteins), none has been characterized so far. Characterization of the HTD2gene and study on its interaction with other tillering-related genes will be helpful to further understand the regulation mechanism of outgrowth of tiller buds in plants.<ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174455Os03g02032002014-05-30T05:14:39Z<p>Gaojin: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
[[File:Real-time PCR analysis of HTD2transcript levels in different issures.png|right|thumb|150px|''Semidwarf VS. normaltype rice plants at ripening (from reference <ref name="ref3" />).'']]<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Real-time_PCR_analysis_of_HTD2transcript_levels_in_different_issures.png&diff=174454File:Real-time PCR analysis of HTD2transcript levels in different issures.png2014-05-30T05:13:22Z<p>Gaojin: </p>
<hr />
<div></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174453Os03g02032002014-05-30T05:08:56Z<p>Gaojin: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inflorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2 in different tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174452Os03g02032002014-05-30T05:07:50Z<p>Gaojin: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
Leaves, inXorescences, internodes, nodes, roots and lateral buds (about 2 cm in length) were excised from 100-day-old wild-type plants. The mRNA expression of HTD2in diVerent tissues was analyzed by real-time PCR (Fig.6). The results showed that the highest expression levels were observed in leaves, followed by internodes, nodes, roots,lateral buds and inXorescences. The HTD2 expression levels in leaves were signiWcantly higher than that in other tissues <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174450Os03g02032002014-05-30T05:06:07Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174449Os03g02032002014-05-30T05:04:51Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174448Os03g02032002014-05-30T05:04:21Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174447Os03g02032002014-05-30T05:03:19Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174445Os03g02032002014-05-30T05:02:13Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<ref name="ref5">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174437Os03g02032002014-05-30T04:49:54Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=174436Os03g07065002014-05-30T04:49:25Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
<br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174435Os03g02032002014-05-30T04:48:32Z<p>Gaojin: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<references></div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=174431Os03g07065002014-05-30T04:46:50Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=174430Os03g07065002014-05-30T04:45:42Z<p>Gaojin: /* Knowledge Extension */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
In this study, we have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow us to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification ofD53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, our work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like a/b-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0706500&diff=174427Os03g07065002014-05-30T04:40:27Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
The OsTB1 gene, also known as FC1, encodes a protein which is a member of TCP gene family.The protein play a negative role in regulating tillering of rice.<br />
==Annotated Information==<br />
===Function===<br />
[[File:The_locus_of_OsTB1.png|right|thumb|150px|''The structure of the chromosomal region encompassing the OsTB1 gene(from reference <ref name="ref4" />).'']]<br />
[[File:OsTB1.png |right|thumb|150px|''Model of the OsMADS57-and OsTB1-mediated network for control of tillering(from reference <ref name="NATURE rice-1" />).'']]<br />
<br />
The rice ''TB1'' gene ''(OsTB1)'' was first identified based on its sequence similarity with maize ''TEOSINTE BRANCHED 1 (TB1)'' which is involved in lateral branching in maize. Both genes encode putative transcription factors carrying a basic helix-loop-helix type of DNA-binding motif, named the TCP domain<ref name="ref4" />. The deduced amino acid sequence of the ''OsTB1'' ORF comprises 388 amino acid residues that is a member of the TCP family of transcription factors<ref name="ref3" />. Note that the in-frame stop codon was found two codons upstream of the deduced first methionine, suggesting that the methionine is used as an initiation codon. The DNA fragment also contains 1261-and 1198-bp 5 'and 3'-non-coding regions, respectively. The OsTB1 protein contains three significant sequence motifs, the SP, TCP and R domains. The R domain contains basic amino acid residues and is conserved in subpopulations of the TCP family. The SP domain contains a number of serine and proline residues, and is found in a limited number of members whose primary structures entirely match that of ''TB1''. Although the precise molecular functions of these domains except for the TCP domain remain unknown, the close resemblance of the primary structures of ''OsTB1'' and maize ''TB1'' together with the entire sequences strongly suggests that the biological function of ''OsTB1'' is similar to that of maize ''TB1''. A series of genetic and reverse-genetic analyses thus conducted indicated that ''OsTB1'' is a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="NATURE rice-1" /><ref name="ref3" />.<br />
<br />
The OsMADS57 protein negatively regulates the expression of ''D14'' functioning in strigolactone(SL) signalling to control tillering. This negative regulation by ''OsMADS57'' is suppressed by interaction with ''OsTB1'', leading to the balanced expression of ''D14'' for tillering<ref name="NATURE rice-1" />.<br />
<br />
===Expression===<br />
[[File:Overexpression and the control.png|right|thumb|150px|''Gross morphology of a rice plant overproducing OsTB1(a) and a control one with an empty vector (from reference <ref name="ref4" />).'']]<br />
<br />
The expression of ''OsTB1'' was detected in vegetative apical meristems, young roots and tillers of rice, and it seemed that there was weak expression in developed spikelets, but no expression in young leaves. The expression of ''OsTB1''in tillers was stronger than in other tissues<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
The total number of tillers is significantly reduced by the overexpression of ''OsTB1'', but increased in an ''fc1'' mutant containing a loss-of-function mutation of OsTB1. This strongly suggests that ''OsTB1'' functions as a negative regulator for lateral branching in rice<ref name="ref4" /><ref name="ref3" />.An fc1 mutant strain, M56, exhibited a bushy morphology as to enhanced lateral branching. Quantitative analysis showed that the fc1 mutant generated a threefold higher number of tillers than the wild-type strain did.Sequencing analysis of the PCR amplified OsTB1 ORF from the fc1 genome revealed one nucleotide deletion in OsTB1. The C-base at the 327th nucleotide in the ORF was deleted in the fc1 mutant, resulting in a frame shift of the ORF generating a stop codon just downstream of the mutation<ref name="ref4" />.<br />
<br />
===Evolution===<br />
The OsTB1 shows 70%, 41%, 32% and 31% similarity with TB1, CYC, PCF1 and PCF2, respectively. The conserved TCP region of OsTB1 has 93%, 80%,49% and 46% similarity with TB1, CYC,PCF1 and PCF2,respectively. Moreover , the R conserved regions among TB1,CYC, OsTB1 are nearly identical<ref name="水稻OsTB1基因的结构及其表达分析-2" />.<br />
<br />
<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
<br />
==Labs working on this gene==<br />
*National Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Chinese Academy of Sciences, China<br />
*The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo 113-8657 ,Japan<br />
*Bioscience Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
<ref name="水稻OsTB1基因的结构及其表达分析-2">Hu W, Zhang S, Zhao Z, Sun C, Zhao Y, Luo D. The Analysis of the Structure and Expression of OsTBl Gene in rice[J]. Journal of plant physiology and molecular biology 2002; 29(6): 507-14.</ref><br />
<ref name="ref3">Minakuchi K, Kameoka H, Yasuno N, et al. FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice[J]. Plant and cell physiology 2010; 51(7): 1127-35.</ref><br />
<ref name="ref4">Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant Journal 2003; 33(3): 513-20</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
</references><br />
==Structured Information== <br />
{{JaponicaGene|<br />
GeneName = Os03g0706500|<br />
Description = TCP transcription factor family protein|<br />
Version = NM_001057563.1 GI:115454854 GeneID:4333856|<br />
Length = 1935 bp|<br />
Definition = Oryza sativa Japonica Group Os03g0706500, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|<br />
AP = Chromosome 3:29188933..29190867|<br />
CDS = 29189438..29190604|<br />
GCID = <gbrowseImage1><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008396:29188933..29190867<br />
source=RiceChromosome03<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctga</cdnaseq>|<br />
AA = <aaseq>MLPFFDSPSPMDIPLYQQLQLTPPSPKPDHHHHHHSTFFYYHHH PPPSPSFPSFPSPAAATIASPSPAMHPFMDLELEPHGQQLAAAEEDGAGGQGVDAGVP FGVDGAAAAAAARKDRHSKISTAGGMRDRRMRLSLDVARKFFALQDMLGFDKASKTVQ WLLNMSKAAIREIMSDDASSVCEEDGSSSLSVDGKQQQHSNPADRGGGAGDHKGAAHG HSDGKKPAKPRRAAANPKPPRRLANAHPVPDKESRAKARERARERTKEKNRMRWVTLA SAISVEAATAAAAAGEDKSPTSPSNNLNHSSSTNLVSTELEDGSSSTRHNGVGVSGGR MQEISAASEASDVIMAFANGGAYGDSGSYYLQQQHQQDQWELGGVVYANSRHYC</aaseq>|<br />
DNA = <dnaseqindica>506..1672#aagatggcaacaccctgatctctagcttagctgcagaggggagaggaacctcacatccaaactcctagctacaacttgtactagcatcctaagcaaccaagcacaaccaaagcaagcaagcacgaacaattctttcttcctctctacctctagctgctgcctgcctcctaatcctcctacccaccactccacatgagcccatgctgtgtgcctgtgtctgtgtgtgtgttctactcctaccatgagagaagagaccaagcatcaaccaagctagctagctcgtcctctcctcgatctctacttctctctcccacacaagctgagcgcccaggtaggctgcctgctaggtctcgtgcatggccggacacatctgatcatagcccactacggcactattccccccttccgcctcgcacgctgagaggtggccggagagggagggaggccagcgagcagcagtagcagcagcaacgcggctaggagtaaggagtcccatcagtaaagcatgcttcctttcttcgattccccaagccccatggacataccgctttaccaacagcttcagctcacccctccctctccaaagcccgaccaccaccaccaccaccattccaccttcttctactaccaccaccacccacctccctccccttccttcccctccttcccctcccccgccgccgccacgatcgcctcgccgtcgccggccatgcaccccttcatggacttggagttggagccgcatgggcagcagctggcggcggcggaggaggacggggcaggcgggcaaggcgtcgacgccggggtgcccttcggcgtcgacggagcggcggcggccgcggcggcgaggaaggaccggcacagcaagataagcaccgccggcgggatgagggaccggcggatgcggctgtccctcgacgtcgcccgcaagttcttcgcgctccaggacatgctcggcttcgacaaggccagcaagacggtgcaatggctcctcaacatgtccaaggccgccatccgggagatcatgagcgacgacgcctcctccgtctgcgaggaggacggctccagcagcctctccgtcgacggcaagcagcagcagcacagcaacccggcggatcggggcggcggcgccggggaccacaagggcgccgctcacggccacagcgacgggaagaagccggccaagccgagaagggcagcggccaacccgaagccaccgcggcggctggccaatgcgcaccccgtccccgacaaggagtcgcgcgccaaggcgagggagcgggcgcgggagcggaccaaggagaagaaccggatgcggtgggtcaccctcgcctcggcaatcagcgtcgaggcggccaccgcggcggcggccgcgggggaggacaagtcgccgacgagccccagcaacaacctgaaccactcatcgtccaccaatcttgtgagcaccgaattggaggacggctcctcgtcaacgcgccacaacggcgtcggcgtcagcggcggccggatgcaagaaatctcggcggctagcgaggcgagcgacgtgatcatggcgttcgccaacggcggcgcgtacggcgacagcggcagctactacctgcagcagcagcatcagcaggatcagtgggagctcggcggcgtcgtctacgccaattcgcggcactactgctgatgtgatcatccatccacacacgaacgaacgaacgaacggtacggcactaagatcgaactcctgcagctacataattatcctttgcttctcaagagtaataattcttgacgtgttaattaatccgggtgtgtattaattccctctttattattttttctcgcgtttatccggagttgactgtggtgaagacgaactttggtttggtcatcgcatggtgtgcattgcatatatagctagcactatcgtctgatcgatgattcatc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057563.1 RefSeq:Os03g0706500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Gaojinhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0203200&diff=174424Os03g02032002014-05-30T04:38:06Z<p>Gaojin: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The function of Dwarf 88 was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development <ref name="ref1" />.<br />
<br />
We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form <ref name="ref2" />. The d14 mutant exhibits increased shoot branching with reduced plant height like the previously characterized strigolactone-defi cient and -insensitive mutants d10 and d3 , respectively <ref name="ref2" />.<br />
<br />
The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway <ref name="ref3" />. which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not aVect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud <ref name="ref3" />.<br />
<br />
===Expression===<br />
The gene Dwarf 88 was expressed in most rice organs, with especially high levels in the vascular tissues <ref name="ref1" />. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant <ref name="ref1" />.<br />
<br />
The d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2 ′ - epi -5-deoxystrigol<br />
than the wild type. Positional cloning revealed that D14 encodes a protein of the α / β -fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones <ref name="ref2" />.<br />
<br />
HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a signiWcantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway <ref name="ref3" />.<br />
<br />
===Evolution===<br />
we identiWed a rice mutant htd2 from one of the 15,000 transgenic rice lines <ref name="ref3" />.<br />
<br />
==Labs working on this gene==<br />
*National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233 Shanghai, China<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006 Hangzhou, China<br />
*Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836 Japan<br />
*RIKEN Plant Science Center, Tsurumi, Yokohama, 230-0045 Japan<br />
*Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan<br />
*Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, 310006 Hangzhou, Zhejiang, China<br />
*Biotechnology Research Center, China Three Gorges University, 443002 Yichang, Hubei, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Gao Z, Qian Q, Liu X, et al. Dwarf 88, a novel putative esterase gene affecting architecture of rice plant[J]. Plant molecular biology, 2009, 71(3): 265-276.</ref><br />
<ref name="ref2">Arite T, Umehara M, Ishikawa S, et al. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers[J]. Plant and cell physiology, 2009, 50(8): 1416-1424.</ref><br />
<ref name="ref3">Liu W, Wu C, Fu Y, et al. Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice[J]. Planta, 2009, 230(4): 649-658.</ref><br />
<references></div>Gaojin