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Os02g0477700

2014-06-10T12:19:12Z

Horatioguo: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

Dwarfing of F71 mutant plants typically appears at the reproductive growth stage (Fig. 1a). In order to understand the cell morphology of the dwarf phenotype of F71, we observed matured tissue in the third internodes. Longitudinal sections showed that all wild-type parenchyma cells were fully elongated and arranged in fine cell files along with the internode elongation axis (Fig. 1b), while most F71 parenchyma cells had irregular shapes and sizes, consequently exhibiting abnormally organized cell files (Fig. 1c). Cross-sections showed that F71 had normal vascular bundles and cortical fibres similar to wild type, but their parenchyma cells were unequal in size (Fig. 1d, e) and had thickened cell walls (Fig. 1d, e; insets). These abnormal parenchyma cells in F71 were strongly stained by the Mäule reaction (Fig. 1f, g), which detects guaiacyl and syringyl groups of the cell wall phenolic components. These results are consistent with the results reported by Nishikubo et al. (2000). Nishikubo et al. also reported that parenchyma cells in F71 ectopically deposit polysaccharide-linked hydroxycinnamoyl esters in their cell walls. Thus, the d50 mutation in F71 appears to induce abnormally shaped and sized cells and ectopic deposition of cell wall components specifically in the parenchyma of elongated internodes. In other organs such as roots and leaves, abnormally shaped cells were not observed.

[[File:Figure1.JPG‎]]

Genetic analysis of d50 gene using F71

To identify the d50 gene, linkage analysis was performed using F2 populations derived from a cross between the F71 (japonica cv.) and Kasalath (indica cv.).We selected 188 F2 individuals showing the same phenotype of F71 and used them for linkage analysis with 131 restriction fragment length polymorphism (RFLP) markers. All analysed F2 dwarf plants showed japonica patterns at each RFLP marker (R1989, C196 and R1736), indicating that the d50 gene was located on the long arm of chromosome 2. In order to determine its exact location, we designed CAPS markers (Supporting Information Table S1) around the three RFLP markers based on the DNA sequences available from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). Linkage analysis using 2053 mapping plants showed that the d50 locus is positioned within a broad region with a genetic distance of 2.2 cM between E61832S and R1736 (Fig. 2a);none of the CAPS markers between E61832S and R1736 showed any evidence of recombination. Therefore, it was difficult to further map the d50 with F2 progenies from a cross between F71 and Kasalath.

===Expression===
Please input expression information here.

Positional cloning of d50 gene with DMT9 mutant allele

D50 locus has been known to be allelic with d12 (Murai et al. 1990), d32 (Sato et al. 2002) and DMT9 (originally
isolated from our research), which were derived from spontaneous mutation, g-ray irradiation and chemical mutagenesis with N-methyl-N-nitrosourea, respectively.These allelic mutants exhibit dwarf and abnormal internode parenchyma phenotypes similar to that of F71 (Supporting Information Fig. S1). To isolate the d50 gene, linkage analysis was performed using the F2 progenies collected from a cross between DMT9 and Kasalath. Linkage analysis using 990 mapping plants with CAPS markers between E61832S and R1736 progressively narrowed the d50 locus to a 43-kbp region (Fig. 2a). Within the 43-kbp region, six putative genes were identified. Sequence analysis of six putative genes in the DMT9 and its parent cultivar, Taichung 65, indicated a G-to-A mutation within one of the six putative genes. Sequence analysis of the products obtained from RT-PCR and RACE-PCR revealed that the candidate gene spans 3243 bp from the start to stop codon and encodes a 1080-aa peptide containing 11 exons and 10 introns (Fig. 2b). In the DMT9,G-to-A mutation at nucleotide 1023 results in theTGG codon (tryptophan) to a premature stop codon (Fig. 2b).

[[File:Figure 2.JPG]]

Expression pattern of D50 gene

To investigate the expression pattern of the D50 gene, we performed semiquantitative RT-PCR in various organs.
Strong D50 gene expression was detected in young third internodes and other organs, such as the seedling, root, leaf blade, leaf sheath and young flower (Fig. 6a), indicating that the D50 gene is expressed ubiquitously in various rice organs.We next used the GUS reporter gene to confirm the expression pattern of D50. In the 10 transgenic plants with a promoter–reporter construct, strong GUS expression was observed in the IM (Fig. 6b), young leaves (Fig. 6b, d) and root apex (Fig. 6c, e).The GUS activity was weak in elongating cells from leaves and roots and diminished in elongated cells (Fig. 6b, c). These results indicate that D50 is strongly expressed in young tissues. The effect of the d50 mutation was observed only in the internode parenchyma and not in other organs such as the root and leaves, suggesting that D50 or hydrolysis of a unique D50 substrate is essential for the accurate formation of the internodes, and other 5PTases in rice may redundantly function in other organs.

[[File:Figure 6.JPG]]

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

d50 induces abnormal organization of actin network

We found the organization of actin in F71 to be disturbed, with thick actin bundles even in the normally shaped cells in the IM parenchyma, because of the defect of the d50 gene (Fig. 9). In agreement with this finding, mutations of FRA3 also have been shown to cause a thick actin formation in interfascicular fibre cells (Zhong et al. 2004). Thick actin cables appeared to be caused by bundling, which is reminiscent of F-actin bundling caused by the actin drug latrunculin B (Mathur et al. 2003).
One study showed that in yeast and animals, PtdIns(4,5)P2 regulates actin polymerization by modulating actin regulatory proteins, such as cofilin, profilin, and capping proteins CapZ and gelsolin (Takenawa & Itoh 2001). In plants, PtdIns(4,5)P2 has also been shown to bind profilin (Kovar et al. 2001). Because PtdIns(4,5)P2 is a candidate substrate of D50, it is possible that the mutation of d50 directly affects actin organization.
Abnormal thick actin bundles in F71 were accompanied with irregular deposits of pectins in the cell wall and
abnormally oriented cell division in the IM (Figs 7–9). Baluška et al. (2001) have reported that epolymerization of actin filaments by latrunculin B induces a distorted cell division plane in maize roots, which is similar to the abnormally oriented cell division in F71. In addition, depolymerization of actin inhibits active endocytic internalization of cell wall pectins in meristematic maize root cells (Baluška
et al. 2002). The importance of actin cytoskeleton has also been implicated in tip growing cells in which active
endocytosis and exocytosis occur (Šamaj et al. 2004; Geisler et al. 2008). Therefore, the defect of the d50 gene
in F71 most likely induces abnormal actin network organization in the parenchyma cells of the IM. Subsequently,
there is a disruption in endocytic internalization of cell surface materials including pectins and/or balanced membrane trafficking between endocytosis and exocytosis, which may result in abnormal orientation of cell division and irregular deposition of pectins. To understand the detailed molecular mechanisms of phosphoinositide signalling during IM development, the nature of D50, such as its substrate specificity, ocalization and interacting proteins, should be investigated.

==Labs working on this gene==
Please input related labs here.

Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology,
Naka-cho, Koganei, Tokyo 184-8588, Japan, 2Graduate School of Agriculture, Tokyo University of Agriculture and
Technology, Fuchu, Tokyo 183-8509, Japan, 3Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka
833-0041, Japan, 4Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601 and 5College of Bioresource
Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan

==References==
Please input cited references here.

[1]DWARF50 (D50), a rice (Oryza sativa L.) gene encoding inositol polyphosphate 5-phosphatase, is required for proper development of intercalary meristempce.
[2]Baluška F., Jasik J., Edelmann H.G., Salajová T. & Volkmann D.(2001) Latrunculin B-induced plant dwarfism: plant cell elongation is F-actin dependent. Developmental Biology 231, 113–124.
[3]Caffall K.H. & Mohnen D. (2009) The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydrate Research 344, 1879–1900.

==Structured Information==
{{JaponicaGene|
GeneName = Os02g0477700|
Description = Similar to Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 protein)|
Version = NM_001053379.1 GI:115446128 GeneID:4329359|
Length = 4131 bp|
Definition = Oryza sativa Japonica Group Os02g0477700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|
AP = Chromosome 2:17139056..17143186|
CDS = 17142042..17142192,17142278..17142399,17142943..17143185|
GCID = <gbrowseImage1>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>tctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatgggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatga</cdnaseq>|
AA = <aaseq>SPGPIDNIMRSTLIEAEPLYKQFEYMKVLVGSWNVGQEKASYES LRAWLKLPTPEVGLVVVGLQEVDMGAGFLAMSAAKETVGLEGSPNGDWWLDAIGQQLK GYSFERVGSRQMAGLLICVWVRTHLKQFIGDIDNAAVACGLGRAIGNKVLLLSYCPTL SWRKMSLKCCL</aaseq>|
DNA = <dnaseqindica>995..1145#788..909#2..244#atctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagtaagtcaagtttaagttctagtttttttaattaaagttatttgaacacatgtttttgttatttacttgcacttagtcatctgctactattatacagaccaaatcctagtaacactgaacaagagtgttgttagacatcttgctcttgttgattttttttgttgaataatcattatcattatgtataagatacctcgttgtacaaatgtacaatgttatcttgaccacaaaaaaatacgcttgtttgacaggctgtacctcttttctctatcagtatgattagagttaagctattttttgccacagttttattaaatgtctacaatacaacactgattggcacaggatccatgtgccatccttgcaatgagtggcagcatatggatgaaactcaatgacacaatgatttaaccttgtcttgcactcttgctaaagatcgttctgccgttagacttcccaagaatattaataaagtataacatgaaactggcatggtttttgctacttctaatcctgatacttttgtacgtccacttgctttaggttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatggtaatctgttcaggacttattttatcctgcagcttcatctgccttttgtttgtgtataaattattcagtttcttctttttctcagggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatgaggcatttgacttatcaaacatatcatgacaaattttgttttgatctaagcatttcatgctttagccatcatatttattggagatgtgttcatattctggaacatttgagttaagggggggaatacctttgctggccactatatgccaaaactccctttcatgtttaagcacaatgctgattagttcattctagagaaaggtagcaaggaggataagatataccatataggcatacagtatataataaaaaggaatatatgctatatgatggaaatgtagtgtgacagcaagtgctatttgatttgttttctttcatgcattcacatgttgaacattgtttgtttacttgtttaaaatgaacatcttggaagttctgaaagttcaagttgttaacgatgcactaagcaaaaagattattcacatttgtccccatattcatttggtagcagttgttgtgcaaaaccaataaatcattgttaccaagatgatatctggtggtttgtgcatacaattaatgaatgagaggtgtgcaatactgatcagaaaatgaaaaaaaaaagacaaattttaaaacacattatgggcctaaaatgtaaccacccactagttctgttatttttctgggggagtacagatattacttcaaaaggactgtattctgtcttatctgctgctttgttcatgtatgcctatattagggagcagtgggattgaggatgagaatacatgataggagtatttgctttgtaaattgccattttgctgctcatatggaagctgtgagtcgacggaatgaagattttgaccatgtctttagaacaatgacctttgccaccccttcgagtggaataatgacaacatcaggtgtttgttcaaccttttcccattatttttcagtattttccaatgggcattcaagtcaaatgacctgtaaatttgttgtgatattacaatcagcaatgagcaaatcttatacactgttacttgttttggtggtcttgcagtttctagttctactggccagcttcttcgaggagcaaatgtatggtgtattaatgttggttcattacattttctcggtggatagggagtagattctcatcttgatatactaagttgttcctattataatttacagggatcaagaatgcctgagttgtcagacacggacatgattgtctttcttggtgacttcaattaccgcctttatgatatttcctatgatgatgcaatgggcttagtttcccggagatgctttgactggctaaaaaataatgaccaactgcgagcagaaatgagatctgggagagtcttccagggactacgtgaaggggatttcaagtttccccctacatacaaatttgagaaacatacagcaggcttatcaggtatcttactttgttttttattcgtggaatcccaaagtacatataaagatcatcacctttatttgtcatatagggtatgatagcagtgagaagaggcgcattcctgcctggtgtgacagaatcctatatcgtgatagccgagttagttcagggaatgagtgttccttggattgtcctgtggtttcttcaatatcactgtaagttatttgttgtgcatgtttttttttaacccgaaaaagcttaaaatatgtcaataccttgttattatgttttccaggtatgactcttgcatggaagcaacagatagtgatcacaaacctataaaatctgtgttcaatttggatattgcttatgttgacaaacagacaatgaggcagaaatatgtggagctaatgagctcaaataataaagtggtgcatttgcttcaggaacttgaagcattccctggagtaaatataaataattctaacatcatcttgcaagatcggaatccatctgttgtgaaattgcaaaacagaacagaagtcatcgcttgttttgagatcattggacaagcaccaaatttgtccagcacacatttctctgcttttcctgcatggctaaaggtgagtcaatgctttgtctgactccttttactgtatttttattaaaataatctaatactagcaacgtacaaaaactttgcacgaccgaatttctcatgttttacatgggcacaactgcagagtagtagaaatattagtctcttcagtatcaagagttatgacaaaagagagcatatggtttcagttatactccctccgtttcaggttataagacgttttgactttggtcaaagtcaaactacttcaaatttgattaagtttatagacaaatatagtaatatttataatactaaattagtttattaaatcaataattgaatatatttttataataaatttgtcttgggttgaaaatgttattattgttttctacaaacttagtcaaacttgaagtaatttgactttgaccaaagtcaaaaacatcttataacctgaaacggaggtagtagtagattgacgcgttggcattagtaaaggcagactccagaatttgttattacttgttttgcttgttttattcttcaccattattaattcactgttgtgagcttaatgttttgaaaactgtgggcatatattcaatataggtctctccagcagtcggcataatatctccgggacagacggtagaggtcactttgcagcacagagacctgcatagccaacaaaactataatggaacttcattggatattttgcctggtggagctacccaacaaaaggcagcaactgtttttgcgaaaataactggagtatattcaacagttgcaaaatattacgaaatacatgtacaacaccagaactgcaggagcacattgccatcgagaggttataacttaggtgaccggtttttttaattttgagtttggtatcaggaatttaggaaatgtatgttgtatcaaatgttctttttgagtgaagtcacaaaatcaaggctttctactaccctcaacatgtgtattttcaagagaggaaaattgtaaacagtgtagc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001053379.1 RefSeq:Os02g0477700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

Os02g0477700

2014-06-10T12:15:27Z

Horatioguo: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

Dwarfing of F71 mutant plants typically appears at the reproductive growth stage (Fig. 1a). In order to understand the cell morphology of the dwarf phenotype of F71, we observed matured tissue in the third internodes. Longitudinal sections showed that all wild-type parenchyma cells were fully elongated and arranged in fine cell files along with the internode elongation axis (Fig. 1b), while most F71 parenchyma cells had irregular shapes and sizes, consequently exhibiting abnormally organized cell files (Fig. 1c). Cross-sections showed that F71 had normal vascular bundles and cortical fibres similar to wild type, but their parenchyma cells were unequal in size (Fig. 1d, e) and had thickened cell walls (Fig. 1d, e; insets). These abnormal parenchyma cells in F71 were strongly stained by the Mäule reaction (Fig. 1f, g), which detects guaiacyl and syringyl groups of the cell wall phenolic components. These results are consistent with the results reported by Nishikubo et al. (2000). Nishikubo et al. also reported that parenchyma cells in F71 ectopically deposit polysaccharide-linked hydroxycinnamoyl esters in their cell walls. Thus, the d50 mutation in F71 appears to induce abnormally shaped and sized cells and ectopic deposition of cell wall components specifically in the parenchyma of elongated internodes. In other organs such as roots and leaves, abnormally shaped cells were not observed.

[[File:Figure1.JPG‎]]

Genetic analysis of d50 gene using F71

To identify the d50 gene, linkage analysis was performed using F2 populations derived from a cross between the F71 (japonica cv.) and Kasalath (indica cv.).We selected 188 F2 individuals showing the same phenotype of F71 and used them for linkage analysis with 131 restriction fragment length polymorphism (RFLP) markers. All analysed F2 dwarf plants showed japonica patterns at each RFLP marker (R1989, C196 and R1736), indicating that the d50 gene was located on the long arm of chromosome 2. In order to determine its exact location, we designed CAPS markers (Supporting Information Table S1) around the three RFLP markers based on the DNA sequences available from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). Linkage analysis using 2053 mapping plants showed that the d50 locus is positioned within a broad region with a genetic distance of 2.2 cM between E61832S and R1736 (Fig. 2a);none of the CAPS markers between E61832S and R1736 showed any evidence of recombination. Therefore, it was difficult to further map the d50 with F2 progenies from a cross between F71 and Kasalath.

===Expression===
Please input expression information here.

Positional cloning of d50 gene with DMT9 mutant allele

D50 locus has been known to be allelic with d12 (Murai et al. 1990), d32 (Sato et al. 2002) and DMT9 (originally
isolated from our research), which were derived from spontaneous mutation, g-ray irradiation and chemical mutagenesis with N-methyl-N-nitrosourea, respectively.These allelic mutants exhibit dwarf and abnormal internode parenchyma phenotypes similar to that of F71 (Supporting Information Fig. S1). To isolate the d50 gene, linkage analysis was performed using the F2 progenies collected from a cross between DMT9 and Kasalath. Linkage analysis using 990 mapping plants with CAPS markers between E61832S and R1736 progressively narrowed the d50 locus to a 43-kbp region (Fig. 2a). Within the 43-kbp region, six putative genes were identified. Sequence analysis of six putative genes in the DMT9 and its parent cultivar, Taichung 65, indicated a G-to-A mutation within one of the six putative genes. Sequence analysis of the products obtained from RT-PCR and RACE-PCR revealed that the candidate gene spans 3243 bp from the start to stop codon and encodes a 1080-aa peptide containing 11 exons and 10 introns (Fig. 2b). In the DMT9,G-to-A mutation at nucleotide 1023 results in theTGG codon (tryptophan) to a premature stop codon (Fig. 2b).

[[File:Figure 2.JPG]]

Expression pattern of D50 gene

To investigate the expression pattern of the D50 gene, we performed semiquantitative RT-PCR in various organs.
Strong D50 gene expression was detected in young third internodes and other organs, such as the seedling, root, leaf blade, leaf sheath and young flower (Fig. 6a), indicating that the D50 gene is expressed ubiquitously in various rice organs.We next used the GUS reporter gene to confirm the expression pattern of D50. In the 10 transgenic plants with a promoter–reporter construct, strong GUS expression was observed in the IM (Fig. 6b), young leaves (Fig. 6b, d) and root apex (Fig. 6c, e).The GUS activity was weak in elongating cells from leaves and roots and diminished in elongated cells (Fig. 6b, c). These results indicate that D50 is strongly expressed in young tissues. The effect of the d50 mutation was observed only in the internode parenchyma and not in other organs such as the root and leaves, suggesting that D50 or hydrolysis of a unique D50 substrate is essential for the accurate formation of the internodes, and other 5PTases in rice may redundantly function in other organs.

[[File:Figure 6.JPG]]

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

d50 induces abnormal organization of actin network

We found the organization of actin in F71 to be disturbed, with thick actin bundles even in the normally shaped cells in the IM parenchyma, because of the defect of the d50 gene (Fig. 9). In agreement with this finding, mutations of FRA3 also have been shown to cause a thick actin formation in interfascicular fibre cells (Zhong et al. 2004). Thick actin cables appeared to be caused by bundling, which is reminiscent of F-actin bundling caused by the actin drug latrunculin B (Mathur et al. 2003).
One study showed that in yeast and animals, PtdIns(4,5)P2 regulates actin polymerization by modulating actin regulatory proteins, such as cofilin, profilin, and capping proteins CapZ and gelsolin (Takenawa & Itoh 2001). In plants, PtdIns(4,5)P2 has also been shown to bind profilin (Kovar et al. 2001). Because PtdIns(4,5)P2 is a candidate substrate of D50, it is possible that the mutation of d50 directly affects actin organization.
Abnormal thick actin bundles in F71 were accompanied with irregular deposits of pectins in the cell wall and
abnormally oriented cell division in the IM (Figs 7–9). Baluška et al. (2001) have reported that epolymerization of actin filaments by latrunculin B induces a distorted cell division plane in maize roots, which is similar to the abnormally oriented cell division in F71. In addition, depolymerization of actin inhibits active endocytic internalization of cell wall pectins in meristematic maize root cells (Baluška
et al. 2002). The importance of actin cytoskeleton has also been implicated in tip growing cells in which active
endocytosis and exocytosis occur (Šamaj et al. 2004; Geisler et al. 2008). Therefore, the defect of the d50 gene
in F71 most likely induces abnormal actin network organization in the parenchyma cells of the IM. Subsequently,
there is a disruption in endocytic internalization of cell surface materials including pectins and/or balanced membrane trafficking between endocytosis and exocytosis, which may result in abnormal orientation of cell division and irregular deposition of pectins. To understand the detailed molecular mechanisms of phosphoinositide signalling during IM development, the nature of D50, such as its substrate specificity, ocalization and interacting proteins, should be investigated.

==Labs working on this gene==
Please input related labs here.

Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology,
Naka-cho, Koganei, Tokyo 184-8588, Japan, 2Graduate School of Agriculture, Tokyo University of Agriculture and
Technology, Fuchu, Tokyo 183-8509, Japan, 3Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka
833-0041, Japan, 4Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601 and 5College of Bioresource
Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os02g0477700|
Description = Similar to Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 protein)|
Version = NM_001053379.1 GI:115446128 GeneID:4329359|
Length = 4131 bp|
Definition = Oryza sativa Japonica Group Os02g0477700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|
AP = Chromosome 2:17139056..17143186|
CDS = 17142042..17142192,17142278..17142399,17142943..17143185|
GCID = <gbrowseImage1>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>tctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatgggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatga</cdnaseq>|
AA = <aaseq>SPGPIDNIMRSTLIEAEPLYKQFEYMKVLVGSWNVGQEKASYES LRAWLKLPTPEVGLVVVGLQEVDMGAGFLAMSAAKETVGLEGSPNGDWWLDAIGQQLK GYSFERVGSRQMAGLLICVWVRTHLKQFIGDIDNAAVACGLGRAIGNKVLLLSYCPTL SWRKMSLKCCL</aaseq>|
DNA = <dnaseqindica>995..1145#788..909#2..244#atctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagtaagtcaagtttaagttctagtttttttaattaaagttatttgaacacatgtttttgttatttacttgcacttagtcatctgctactattatacagaccaaatcctagtaacactgaacaagagtgttgttagacatcttgctcttgttgattttttttgttgaataatcattatcattatgtataagatacctcgttgtacaaatgtacaatgttatcttgaccacaaaaaaatacgcttgtttgacaggctgtacctcttttctctatcagtatgattagagttaagctattttttgccacagttttattaaatgtctacaatacaacactgattggcacaggatccatgtgccatccttgcaatgagtggcagcatatggatgaaactcaatgacacaatgatttaaccttgtcttgcactcttgctaaagatcgttctgccgttagacttcccaagaatattaataaagtataacatgaaactggcatggtttttgctacttctaatcctgatacttttgtacgtccacttgctttaggttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatggtaatctgttcaggacttattttatcctgcagcttcatctgccttttgtttgtgtataaattattcagtttcttctttttctcagggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatgaggcatttgacttatcaaacatatcatgacaaattttgttttgatctaagcatttcatgctttagccatcatatttattggagatgtgttcatattctggaacatttgagttaagggggggaatacctttgctggccactatatgccaaaactccctttcatgtttaagcacaatgctgattagttcattctagagaaaggtagcaaggaggataagatataccatataggcatacagtatataataaaaaggaatatatgctatatgatggaaatgtagtgtgacagcaagtgctatttgatttgttttctttcatgcattcacatgttgaacattgtttgtttacttgtttaaaatgaacatcttggaagttctgaaagttcaagttgttaacgatgcactaagcaaaaagattattcacatttgtccccatattcatttggtagcagttgttgtgcaaaaccaataaatcattgttaccaagatgatatctggtggtttgtgcatacaattaatgaatgagaggtgtgcaatactgatcagaaaatgaaaaaaaaaagacaaattttaaaacacattatgggcctaaaatgtaaccacccactagttctgttatttttctgggggagtacagatattacttcaaaaggactgtattctgtcttatctgctgctttgttcatgtatgcctatattagggagcagtgggattgaggatgagaatacatgataggagtatttgctttgtaaattgccattttgctgctcatatggaagctgtgagtcgacggaatgaagattttgaccatgtctttagaacaatgacctttgccaccccttcgagtggaataatgacaacatcaggtgtttgttcaaccttttcccattatttttcagtattttccaatgggcattcaagtcaaatgacctgtaaatttgttgtgatattacaatcagcaatgagcaaatcttatacactgttacttgttttggtggtcttgcagtttctagttctactggccagcttcttcgaggagcaaatgtatggtgtattaatgttggttcattacattttctcggtggatagggagtagattctcatcttgatatactaagttgttcctattataatttacagggatcaagaatgcctgagttgtcagacacggacatgattgtctttcttggtgacttcaattaccgcctttatgatatttcctatgatgatgcaatgggcttagtttcccggagatgctttgactggctaaaaaataatgaccaactgcgagcagaaatgagatctgggagagtcttccagggactacgtgaaggggatttcaagtttccccctacatacaaatttgagaaacatacagcaggcttatcaggtatcttactttgttttttattcgtggaatcccaaagtacatataaagatcatcacctttatttgtcatatagggtatgatagcagtgagaagaggcgcattcctgcctggtgtgacagaatcctatatcgtgatagccgagttagttcagggaatgagtgttccttggattgtcctgtggtttcttcaatatcactgtaagttatttgttgtgcatgtttttttttaacccgaaaaagcttaaaatatgtcaataccttgttattatgttttccaggtatgactcttgcatggaagcaacagatagtgatcacaaacctataaaatctgtgttcaatttggatattgcttatgttgacaaacagacaatgaggcagaaatatgtggagctaatgagctcaaataataaagtggtgcatttgcttcaggaacttgaagcattccctggagtaaatataaataattctaacatcatcttgcaagatcggaatccatctgttgtgaaattgcaaaacagaacagaagtcatcgcttgttttgagatcattggacaagcaccaaatttgtccagcacacatttctctgcttttcctgcatggctaaaggtgagtcaatgctttgtctgactccttttactgtatttttattaaaataatctaatactagcaacgtacaaaaactttgcacgaccgaatttctcatgttttacatgggcacaactgcagagtagtagaaatattagtctcttcagtatcaagagttatgacaaaagagagcatatggtttcagttatactccctccgtttcaggttataagacgttttgactttggtcaaagtcaaactacttcaaatttgattaagtttatagacaaatatagtaatatttataatactaaattagtttattaaatcaataattgaatatatttttataataaatttgtcttgggttgaaaatgttattattgttttctacaaacttagtcaaacttgaagtaatttgactttgaccaaagtcaaaaacatcttataacctgaaacggaggtagtagtagattgacgcgttggcattagtaaaggcagactccagaatttgttattacttgttttgcttgttttattcttcaccattattaattcactgttgtgagcttaatgttttgaaaactgtgggcatatattcaatataggtctctccagcagtcggcataatatctccgggacagacggtagaggtcactttgcagcacagagacctgcatagccaacaaaactataatggaacttcattggatattttgcctggtggagctacccaacaaaaggcagcaactgtttttgcgaaaataactggagtatattcaacagttgcaaaatattacgaaatacatgtacaacaccagaactgcaggagcacattgccatcgagaggttataacttaggtgaccggtttttttaattttgagtttggtatcaggaatttaggaaatgtatgttgtatcaaatgttctttttgagtgaagtcacaaaatcaaggctttctactaccctcaacatgtgtattttcaagagaggaaaattgtaaacagtgtagc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001053379.1 RefSeq:Os02g0477700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

Os02g0477700

2014-06-10T12:13:53Z

Horatioguo: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

Dwarfing of F71 mutant plants typically appears at the reproductive growth stage (Fig. 1a). In order to understand the cell morphology of the dwarf phenotype of F71, we observed matured tissue in the third internodes. Longitudinal sections showed that all wild-type parenchyma cells were fully elongated and arranged in fine cell files along with the internode elongation axis (Fig. 1b), while most F71 parenchyma cells had irregular shapes and sizes, consequently exhibiting abnormally organized cell files (Fig. 1c). Cross-sections showed that F71 had normal vascular bundles and cortical fibres similar to wild type, but their parenchyma cells were unequal in size (Fig. 1d, e) and had thickened cell walls (Fig. 1d, e; insets). These abnormal parenchyma cells in F71 were strongly stained by the Mäule reaction (Fig. 1f, g), which detects guaiacyl and syringyl groups of the cell wall phenolic components. These results are consistent with the results reported by Nishikubo et al. (2000). Nishikubo et al. also reported that parenchyma cells in F71 ectopically deposit polysaccharide-linked hydroxycinnamoyl esters in their cell walls. Thus, the d50 mutation in F71 appears to induce abnormally shaped and sized cells and ectopic deposition of cell wall components specifically in the parenchyma of elongated internodes. In other organs such as roots and leaves, abnormally shaped cells were not observed.

[[File:Figure1.JPG‎]]

Genetic analysis of d50 gene using F71

To identify the d50 gene, linkage analysis was performed using F2 populations derived from a cross between the F71 (japonica cv.) and Kasalath (indica cv.).We selected 188 F2 individuals showing the same phenotype of F71 and used them for linkage analysis with 131 restriction fragment length polymorphism (RFLP) markers. All analysed F2 dwarf plants showed japonica patterns at each RFLP marker (R1989, C196 and R1736), indicating that the d50 gene was located on the long arm of chromosome 2. In order to determine its exact location, we designed CAPS markers (Supporting Information Table S1) around the three RFLP markers based on the DNA sequences available from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). Linkage analysis using 2053 mapping plants showed that the d50 locus is positioned within a broad region with a genetic distance of 2.2 cM between E61832S and R1736 (Fig. 2a);none of the CAPS markers between E61832S and R1736 showed any evidence of recombination. Therefore, it was difficult to further map the d50 with F2 progenies from a cross between F71 and Kasalath.

===Expression===
Please input expression information here.

Positional cloning of d50 gene with DMT9 mutant allele

D50 locus has been known to be allelic with d12 (Murai et al. 1990), d32 (Sato et al. 2002) and DMT9 (originally
isolated from our research), which were derived from spontaneous mutation, g-ray irradiation and chemical mutagenesis with N-methyl-N-nitrosourea, respectively.These allelic mutants exhibit dwarf and abnormal internode parenchyma phenotypes similar to that of F71 (Supporting Information Fig. S1). To isolate the d50 gene, linkage analysis was performed using the F2 progenies collected from a cross between DMT9 and Kasalath. Linkage analysis using 990 mapping plants with CAPS markers between E61832S and R1736 progressively narrowed the d50 locus to a 43-kbp region (Fig. 2a). Within the 43-kbp region, six putative genes were identified. Sequence analysis of six putative genes in the DMT9 and its parent cultivar, Taichung 65, indicated a G-to-A mutation within one of the six putative genes. Sequence analysis of the products obtained from RT-PCR and RACE-PCR revealed that the candidate gene spans 3243 bp from the start to stop codon and encodes a 1080-aa peptide containing 11 exons and 10 introns (Fig. 2b). In the DMT9,G-to-A mutation at nucleotide 1023 results in theTGG codon (tryptophan) to a premature stop codon (Fig. 2b).

[[File:Figure 2.JPG]]

Expression pattern of D50 gene

To investigate the expression pattern of the D50 gene, we performed semiquantitative RT-PCR in various organs.
Strong D50 gene expression was detected in young third internodes and other organs, such as the seedling, root, leaf blade, leaf sheath and young flower (Fig. 6a), indicating that the D50 gene is expressed ubiquitously in various rice organs.We next used the GUS reporter gene to confirm the expression pattern of D50. In the 10 transgenic plants with a promoter–reporter construct, strong GUS expression was observed in the IM (Fig. 6b), young leaves (Fig. 6b, d) and root apex (Fig. 6c, e).The GUS activity was weak in elongating cells from leaves and roots and diminished in elongated cells (Fig. 6b, c). These results indicate that D50 is strongly expressed in young tissues. The effect of the d50 mutation was observed only in the internode parenchyma and not in other organs such as the root and leaves, suggesting that D50 or hydrolysis of a unique D50 substrate is essential for the accurate formation of the internodes, and other 5PTases in rice may redundantly function in other organs.

[[File:Figure 6.JPG]]

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

d50 induces abnormal organization of actin network

We found the organization of actin in F71 to be disturbed, with thick actin bundles even in the normally shaped cells in the IM parenchyma, because of the defect of the d50 gene (Fig. 9). In agreement with this finding, mutations of FRA3 also have been shown to cause a thick actin formation in interfascicular fibre cells (Zhong et al. 2004). Thick actin cables appeared to be caused by bundling, which is reminiscent of F-actin bundling caused by the actin drug latrunculin B (Mathur et al. 2003).
One study showed that in yeast and animals, PtdIns(4,5)P2 regulates actin polymerization by modulating actin regulatory proteins, such as cofilin, profilin, and capping proteins CapZ and gelsolin (Takenawa & Itoh 2001). In plants, PtdIns(4,5)P2 has also been shown to bind profilin (Kovar et al. 2001). Because PtdIns(4,5)P2 is a candidate substrate of D50, it is possible that the mutation of d50 directly affects actin organization.
Abnormal thick actin bundles in F71 were accompanied with irregular deposits of pectins in the cell wall and
abnormally oriented cell division in the IM (Figs 7–9). Baluška et al. (2001) have reported that epolymerization of actin filaments by latrunculin B induces a distorted cell division plane in maize roots, which is similar to the abnormally oriented cell division in F71. In addition, depolymerization of actin inhibits active endocytic internalization of cell wall pectins in meristematic maize root cells (Baluška
et al. 2002). The importance of actin cytoskeleton has also been implicated in tip growing cells in which active
endocytosis and exocytosis occur (Šamaj et al. 2004; Geisler et al. 2008). Therefore, the defect of the d50 gene
in F71 most likely induces abnormal actin network organization in the parenchyma cells of the IM. Subsequently,
there is a disruption in endocytic internalization of cell surface materials including pectins and/or balanced membrane trafficking between endocytosis and exocytosis, which may result in abnormal orientation of cell division and irregular deposition of pectins. To understand the detailed molecular mechanisms of phosphoinositide signalling during IM development, the nature of D50, such as its substrate specificity, ocalization and interacting proteins, should be investigated.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os02g0477700|
Description = Similar to Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 protein)|
Version = NM_001053379.1 GI:115446128 GeneID:4329359|
Length = 4131 bp|
Definition = Oryza sativa Japonica Group Os02g0477700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|
AP = Chromosome 2:17139056..17143186|
CDS = 17142042..17142192,17142278..17142399,17142943..17143185|
GCID = <gbrowseImage1>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>tctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatgggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatga</cdnaseq>|
AA = <aaseq>SPGPIDNIMRSTLIEAEPLYKQFEYMKVLVGSWNVGQEKASYES LRAWLKLPTPEVGLVVVGLQEVDMGAGFLAMSAAKETVGLEGSPNGDWWLDAIGQQLK GYSFERVGSRQMAGLLICVWVRTHLKQFIGDIDNAAVACGLGRAIGNKVLLLSYCPTL SWRKMSLKCCL</aaseq>|
DNA = <dnaseqindica>995..1145#788..909#2..244#atctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagtaagtcaagtttaagttctagtttttttaattaaagttatttgaacacatgtttttgttatttacttgcacttagtcatctgctactattatacagaccaaatcctagtaacactgaacaagagtgttgttagacatcttgctcttgttgattttttttgttgaataatcattatcattatgtataagatacctcgttgtacaaatgtacaatgttatcttgaccacaaaaaaatacgcttgtttgacaggctgtacctcttttctctatcagtatgattagagttaagctattttttgccacagttttattaaatgtctacaatacaacactgattggcacaggatccatgtgccatccttgcaatgagtggcagcatatggatgaaactcaatgacacaatgatttaaccttgtcttgcactcttgctaaagatcgttctgccgttagacttcccaagaatattaataaagtataacatgaaactggcatggtttttgctacttctaatcctgatacttttgtacgtccacttgctttaggttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatggtaatctgttcaggacttattttatcctgcagcttcatctgccttttgtttgtgtataaattattcagtttcttctttttctcagggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatgaggcatttgacttatcaaacatatcatgacaaattttgttttgatctaagcatttcatgctttagccatcatatttattggagatgtgttcatattctggaacatttgagttaagggggggaatacctttgctggccactatatgccaaaactccctttcatgtttaagcacaatgctgattagttcattctagagaaaggtagcaaggaggataagatataccatataggcatacagtatataataaaaaggaatatatgctatatgatggaaatgtagtgtgacagcaagtgctatttgatttgttttctttcatgcattcacatgttgaacattgtttgtttacttgtttaaaatgaacatcttggaagttctgaaagttcaagttgttaacgatgcactaagcaaaaagattattcacatttgtccccatattcatttggtagcagttgttgtgcaaaaccaataaatcattgttaccaagatgatatctggtggtttgtgcatacaattaatgaatgagaggtgtgcaatactgatcagaaaatgaaaaaaaaaagacaaattttaaaacacattatgggcctaaaatgtaaccacccactagttctgttatttttctgggggagtacagatattacttcaaaaggactgtattctgtcttatctgctgctttgttcatgtatgcctatattagggagcagtgggattgaggatgagaatacatgataggagtatttgctttgtaaattgccattttgctgctcatatggaagctgtgagtcgacggaatgaagattttgaccatgtctttagaacaatgacctttgccaccccttcgagtggaataatgacaacatcaggtgtttgttcaaccttttcccattatttttcagtattttccaatgggcattcaagtcaaatgacctgtaaatttgttgtgatattacaatcagcaatgagcaaatcttatacactgttacttgttttggtggtcttgcagtttctagttctactggccagcttcttcgaggagcaaatgtatggtgtattaatgttggttcattacattttctcggtggatagggagtagattctcatcttgatatactaagttgttcctattataatttacagggatcaagaatgcctgagttgtcagacacggacatgattgtctttcttggtgacttcaattaccgcctttatgatatttcctatgatgatgcaatgggcttagtttcccggagatgctttgactggctaaaaaataatgaccaactgcgagcagaaatgagatctgggagagtcttccagggactacgtgaaggggatttcaagtttccccctacatacaaatttgagaaacatacagcaggcttatcaggtatcttactttgttttttattcgtggaatcccaaagtacatataaagatcatcacctttatttgtcatatagggtatgatagcagtgagaagaggcgcattcctgcctggtgtgacagaatcctatatcgtgatagccgagttagttcagggaatgagtgttccttggattgtcctgtggtttcttcaatatcactgtaagttatttgttgtgcatgtttttttttaacccgaaaaagcttaaaatatgtcaataccttgttattatgttttccaggtatgactcttgcatggaagcaacagatagtgatcacaaacctataaaatctgtgttcaatttggatattgcttatgttgacaaacagacaatgaggcagaaatatgtggagctaatgagctcaaataataaagtggtgcatttgcttcaggaacttgaagcattccctggagtaaatataaataattctaacatcatcttgcaagatcggaatccatctgttgtgaaattgcaaaacagaacagaagtcatcgcttgttttgagatcattggacaagcaccaaatttgtccagcacacatttctctgcttttcctgcatggctaaaggtgagtcaatgctttgtctgactccttttactgtatttttattaaaataatctaatactagcaacgtacaaaaactttgcacgaccgaatttctcatgttttacatgggcacaactgcagagtagtagaaatattagtctcttcagtatcaagagttatgacaaaagagagcatatggtttcagttatactccctccgtttcaggttataagacgttttgactttggtcaaagtcaaactacttcaaatttgattaagtttatagacaaatatagtaatatttataatactaaattagtttattaaatcaataattgaatatatttttataataaatttgtcttgggttgaaaatgttattattgttttctacaaacttagtcaaacttgaagtaatttgactttgaccaaagtcaaaaacatcttataacctgaaacggaggtagtagtagattgacgcgttggcattagtaaaggcagactccagaatttgttattacttgttttgcttgttttattcttcaccattattaattcactgttgtgagcttaatgttttgaaaactgtgggcatatattcaatataggtctctccagcagtcggcataatatctccgggacagacggtagaggtcactttgcagcacagagacctgcatagccaacaaaactataatggaacttcattggatattttgcctggtggagctacccaacaaaaggcagcaactgtttttgcgaaaataactggagtatattcaacagttgcaaaatattacgaaatacatgtacaacaccagaactgcaggagcacattgccatcgagaggttataacttaggtgaccggtttttttaattttgagtttggtatcaggaatttaggaaatgtatgttgtatcaaatgttctttttgagtgaagtcacaaaatcaaggctttctactaccctcaacatgtgtattttcaagagaggaaaattgtaaacagtgtagc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001053379.1 RefSeq:Os02g0477700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

Os02g0477700

2014-06-10T12:09:13Z

Horatioguo: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

Dwarfing of F71 mutant plants typically appears at the reproductive growth stage (Fig. 1a). In order to understand the cell morphology of the dwarf phenotype of F71, we observed matured tissue in the third internodes. Longitudinal sections showed that all wild-type parenchyma cells were fully elongated and arranged in fine cell files along with the internode elongation axis (Fig. 1b), while most F71 parenchyma cells had irregular shapes and sizes, consequently exhibiting abnormally organized cell files (Fig. 1c). Cross-sections showed that F71 had normal vascular bundles and cortical fibres similar to wild type, but their parenchyma cells were unequal in size (Fig. 1d, e) and had thickened cell walls (Fig. 1d, e; insets). These abnormal parenchyma cells in F71 were strongly stained by the Mäule reaction (Fig. 1f, g), which detects guaiacyl and syringyl groups of the cell wall phenolic components. These results are consistent with the results reported by Nishikubo et al. (2000). Nishikubo et al. also reported that parenchyma cells in F71 ectopically deposit polysaccharide-linked hydroxycinnamoyl esters in their cell walls. Thus, the d50 mutation in F71 appears to induce abnormally shaped and sized cells and ectopic deposition of cell wall components specifically in the parenchyma of elongated internodes. In other organs such as roots and leaves, abnormally shaped cells were not observed.

[[File:Figure1.JPG‎]]

Genetic analysis of d50 gene using F71

To identify the d50 gene, linkage analysis was performed using F2 populations derived from a cross between the F71 (japonica cv.) and Kasalath (indica cv.).We selected 188 F2 individuals showing the same phenotype of F71 and used them for linkage analysis with 131 restriction fragment length polymorphism (RFLP) markers. All analysed F2 dwarf plants showed japonica patterns at each RFLP marker (R1989, C196 and R1736), indicating that the d50 gene was located on the long arm of chromosome 2. In order to determine its exact location, we designed CAPS markers (Supporting Information Table S1) around the three RFLP markers based on the DNA sequences available from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). Linkage analysis using 2053 mapping plants showed that the d50 locus is positioned within a broad region with a genetic distance of 2.2 cM between E61832S and R1736 (Fig. 2a);none of the CAPS markers between E61832S and R1736 showed any evidence of recombination. Therefore, it was difficult to further map the d50 with F2 progenies from a cross between F71 and Kasalath.

===Expression===
Please input expression information here.

Positional cloning of d50 gene with DMT9 mutant allele

D50 locus has been known to be allelic with d12 (Murai et al. 1990), d32 (Sato et al. 2002) and DMT9 (originally
isolated from our research), which were derived from spontaneous mutation, g-ray irradiation and chemical mutagenesis with N-methyl-N-nitrosourea, respectively.These allelic mutants exhibit dwarf and abnormal internode parenchyma phenotypes similar to that of F71 (Supporting Information Fig. S1). To isolate the d50 gene, linkage analysis was performed using the F2 progenies collected from a cross between DMT9 and Kasalath. Linkage analysis using 990 mapping plants with CAPS markers between E61832S and R1736 progressively narrowed the d50 locus to a 43-kbp region (Fig. 2a). Within the 43-kbp region, six putative genes were identified. Sequence analysis of six putative genes in the DMT9 and its parent cultivar, Taichung 65, indicated a G-to-A mutation within one of the six putative genes. Sequence analysis of the products obtained from RT-PCR and RACE-PCR revealed that the candidate gene spans 3243 bp from the start to stop codon and encodes a 1080-aa peptide containing 11 exons and 10 introns (Fig. 2b). In the DMT9,G-to-A mutation at nucleotide 1023 results in theTGG codon (tryptophan) to a premature stop codon (Fig. 2b).

[[File:Figure 2.JPG]]

Expression pattern of D50 gene

To investigate the expression pattern of the D50 gene, we performed semiquantitative RT-PCR in various organs.
Strong D50 gene expression was detected in young third internodes and other organs, such as the seedling, root, leaf blade, leaf sheath and young flower (Fig. 6a), indicating that the D50 gene is expressed ubiquitously in various rice organs.We next used the GUS reporter gene to confirm the expression pattern of D50. In the 10 transgenic plants with a promoter–reporter construct, strong GUS expression was observed in the IM (Fig. 6b), young leaves (Fig. 6b, d) and root apex (Fig. 6c, e).The GUS activity was weak in elongating cells from leaves and roots and diminished in elongated cells (Fig. 6b, c). These results indicate that D50 is strongly expressed in young tissues. The effect of the d50 mutation was observed only in the internode parenchyma and not in other organs such as the root and leaves, suggesting that D50 or hydrolysis of a unique D50 substrate is essential for the accurate formation of the internodes, and other 5PTases in rice may redundantly function in other organs.

[[File:Figure 6.JPG]]

===Evolution===
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==Labs working on this gene==
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==References==
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==Structured Information==
{{JaponicaGene|
GeneName = Os02g0477700|
Description = Similar to Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 protein)|
Version = NM_001053379.1 GI:115446128 GeneID:4329359|
Length = 4131 bp|
Definition = Oryza sativa Japonica Group Os02g0477700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|
AP = Chromosome 2:17139056..17143186|
CDS = 17142042..17142192,17142278..17142399,17142943..17143185|
GCID = <gbrowseImage1>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008395:17139056..17143186
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>tctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatgggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatga</cdnaseq>|
AA = <aaseq>SPGPIDNIMRSTLIEAEPLYKQFEYMKVLVGSWNVGQEKASYES LRAWLKLPTPEVGLVVVGLQEVDMGAGFLAMSAAKETVGLEGSPNGDWWLDAIGQQLK GYSFERVGSRQMAGLLICVWVRTHLKQFIGDIDNAAVACGLGRAIGNKVLLLSYCPTL SWRKMSLKCCL</aaseq>|
DNA = <dnaseqindica>995..1145#788..909#2..244#atctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagtaagtcaagtttaagttctagtttttttaattaaagttatttgaacacatgtttttgttatttacttgcacttagtcatctgctactattatacagaccaaatcctagtaacactgaacaagagtgttgttagacatcttgctcttgttgattttttttgttgaataatcattatcattatgtataagatacctcgttgtacaaatgtacaatgttatcttgaccacaaaaaaatacgcttgtttgacaggctgtacctcttttctctatcagtatgattagagttaagctattttttgccacagttttattaaatgtctacaatacaacactgattggcacaggatccatgtgccatccttgcaatgagtggcagcatatggatgaaactcaatgacacaatgatttaaccttgtcttgcactcttgctaaagatcgttctgccgttagacttcccaagaatattaataaagtataacatgaaactggcatggtttttgctacttctaatcctgatacttttgtacgtccacttgctttaggttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatggtaatctgttcaggacttattttatcctgcagcttcatctgccttttgtttgtgtataaattattcagtttcttctttttctcagggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatgaggcatttgacttatcaaacatatcatgacaaattttgttttgatctaagcatttcatgctttagccatcatatttattggagatgtgttcatattctggaacatttgagttaagggggggaatacctttgctggccactatatgccaaaactccctttcatgtttaagcacaatgctgattagttcattctagagaaaggtagcaaggaggataagatataccatataggcatacagtatataataaaaaggaatatatgctatatgatggaaatgtagtgtgacagcaagtgctatttgatttgttttctttcatgcattcacatgttgaacattgtttgtttacttgtttaaaatgaacatcttggaagttctgaaagttcaagttgttaacgatgcactaagcaaaaagattattcacatttgtccccatattcatttggtagcagttgttgtgcaaaaccaataaatcattgttaccaagatgatatctggtggtttgtgcatacaattaatgaatgagaggtgtgcaatactgatcagaaaatgaaaaaaaaaagacaaattttaaaacacattatgggcctaaaatgtaaccacccactagttctgttatttttctgggggagtacagatattacttcaaaaggactgtattctgtcttatctgctgctttgttcatgtatgcctatattagggagcagtgggattgaggatgagaatacatgataggagtatttgctttgtaaattgccattttgctgctcatatggaagctgtgagtcgacggaatgaagattttgaccatgtctttagaacaatgacctttgccaccccttcgagtggaataatgacaacatcaggtgtttgttcaaccttttcccattatttttcagtattttccaatgggcattcaagtcaaatgacctgtaaatttgttgtgatattacaatcagcaatgagcaaatcttatacactgttacttgttttggtggtcttgcagtttctagttctactggccagcttcttcgaggagcaaatgtatggtgtattaatgttggttcattacattttctcggtggatagggagtagattctcatcttgatatactaagttgttcctattataatttacagggatcaagaatgcctgagttgtcagacacggacatgattgtctttcttggtgacttcaattaccgcctttatgatatttcctatgatgatgcaatgggcttagtttcccggagatgctttgactggctaaaaaataatgaccaactgcgagcagaaatgagatctgggagagtcttccagggactacgtgaaggggatttcaagtttccccctacatacaaatttgagaaacatacagcaggcttatcaggtatcttactttgttttttattcgtggaatcccaaagtacatataaagatcatcacctttatttgtcatatagggtatgatagcagtgagaagaggcgcattcctgcctggtgtgacagaatcctatatcgtgatagccgagttagttcagggaatgagtgttccttggattgtcctgtggtttcttcaatatcactgtaagttatttgttgtgcatgtttttttttaacccgaaaaagcttaaaatatgtcaataccttgttattatgttttccaggtatgactcttgcatggaagcaacagatagtgatcacaaacctataaaatctgtgttcaatttggatattgcttatgttgacaaacagacaatgaggcagaaatatgtggagctaatgagctcaaataataaagtggtgcatttgcttcaggaacttgaagcattccctggagtaaatataaataattctaacatcatcttgcaagatcggaatccatctgttgtgaaattgcaaaacagaacagaagtcatcgcttgttttgagatcattggacaagcaccaaatttgtccagcacacatttctctgcttttcctgcatggctaaaggtgagtcaatgctttgtctgactccttttactgtatttttattaaaataatctaatactagcaacgtacaaaaactttgcacgaccgaatttctcatgttttacatgggcacaactgcagagtagtagaaatattagtctcttcagtatcaagagttatgacaaaagagagcatatggtttcagttatactccctccgtttcaggttataagacgttttgactttggtcaaagtcaaactacttcaaatttgattaagtttatagacaaatatagtaatatttataatactaaattagtttattaaatcaataattgaatatatttttataataaatttgtcttgggttgaaaatgttattattgttttctacaaacttagtcaaacttgaagtaatttgactttgaccaaagtcaaaaacatcttataacctgaaacggaggtagtagtagattgacgcgttggcattagtaaaggcagactccagaatttgttattacttgttttgcttgttttattcttcaccattattaattcactgttgtgagcttaatgttttgaaaactgtgggcatatattcaatataggtctctccagcagtcggcataatatctccgggacagacggtagaggtcactttgcagcacagagacctgcatagccaacaaaactataatggaacttcattggatattttgcctggtggagctacccaacaaaaggcagcaactgtttttgcgaaaataactggagtatattcaacagttgcaaaatattacgaaatacatgtacaacaccagaactgcaggagcacattgccatcgagaggttataacttaggtgaccggtttttttaattttgagtttggtatcaggaatttaggaaatgtatgttgtatcaaatgttctttttgagtgaagtcacaaaatcaaggctttctactaccctcaacatgtgtattttcaagagaggaaaattgtaaacagtgtagc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001053379.1 RefSeq:Os02g0477700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

File:Figure 6.JPG

2014-06-10T12:08:48Z

Horatioguo: Expression pattern of D50 in various organs. (a) Gene expression analysis by semiquantitative RT-PCR of D50 from various organs. The expression level of an ubiquitin gene was used as an internal control. (b–e) Expression analysis of D50 using the GUS re

Expression pattern of D50 in various organs.
(a) Gene expression analysis by semiquantitative RT-PCR of
D50 from various organs. The expression level of an ubiquitin
gene was used as an internal control. (b–e) Expression analysis
of D50 using the GUS reporter gene shows D50 expression in
young tissue such as developing leaves (b, d), root apex
(c, e), and IM (b). Bars: 500 mm (b, c), and 100 mm (d, e).

Os02g0477700

2014-06-10T12:04:32Z

Horatioguo: /* Expression */

File:Figure 2.JPG

2014-06-10T12:03:50Z

Horatioguo: Map-based cloning of d50 gene. (a) Fine mapping of d50 locus. The d50 was located in the 43-kb region between CD5 and RB2. The number indicates recombinants identified from F2 mapping plants. Predicted gene-coding regions are indicated by gray arrows, and

Map-based cloning of d50 gene. (a) Fine mapping of d50 locus. The d50 was located in the 43-kb region between CD5 and
RB2. The number indicates recombinants identified from F2 mapping plants. Predicted gene-coding regions are indicated by gray arrows,
and the D50 gene is indicated by a black arrow. (b) Schema of D50 gene. The D50 gene contains 11 exons (boxes) separated by 10 introns
(lines). Predicted protein-coding regions are indicated by black boxes, the 5-phosphatase domain by blue boxes, and the WD repeats by
red boxes. Mutation points of each F71 mutant allele are shown. (c) Complementation of F71 phenotypes by D50 gene. F71 plants
introduced D50 cDNA under the 2-kbp promoter region exhibit normal plant height (left), whereas F71 plants introduced the empty
vector maintain a dwarf phenotype (right). (d) Cross-sections of transgenic F71 internodes stained by the Mäule reaction. Transgenic F71
plants containing the D50 gene (left) have normal parenchyma cells, whereas plants containing the empty vector (right) exhibit strong
staining of the Mäule reaction. (e) DNA gel blot analysis of d12 mutant (m) and its parent cultivar,Yukara (W), using two probes within
D50-coding region. The d12 exhibits no signal, indicating the D50-coding region is completely lost from the d12 genome. Bars: 10 cm (c)and 100 mm (d).

Os02g0477700

2014-06-10T11:57:39Z

Horatioguo: /* Function */

Os02g0477700

2014-06-10T11:54:02Z

Horatioguo: /* Function */

Os02g0477700

2014-06-10T11:53:03Z

Horatioguo: /* Function */

Os02g0477700

2014-06-10T11:50:15Z

Horatioguo: /* Function */

Os02g0477700

2014-06-10T08:23:30Z

Horatioguo: /* Function */

File:Figure1.JPG

2014-06-10T08:20:29Z

Horatioguo: Phenotypes of rice d50 mutant, F71, in matured internodes. (a)Wild type (left) and F71 (right) plants showing dwarf phenotype in F71 at the reproductive stage. (b, c) Longitudinal sections of elongated third internodes in wild-type Fujiminori (b) and F71

Phenotypes of rice d50 mutant, F71, in matured internodes. (a)Wild type (left) and F71 (right) plants showing dwarf phenotype in F71 at the reproductive stage. (b, c) Longitudinal sections of elongated third internodes in wild-type Fujiminori (b) and F71 (c), showing disordered parenchyma cell files in F71. (d, e) Transverse sections of wild type (d) and F71 (e) elongated third internodes. Higher magnification of parenchyma cell walls (circled areas) are presented in the insets. (f, g) Mäule reaction of wild-type (f) and F71 (g) showing strong staining in the parenchyma in F71. CF, cortical fibre; LVB, large vascular bundle; Pa, fundamental parenchyma; SVB, small vascular bundle. Bars: 20 cm (a); 200 mm (b, c); and 100 mm (d–g).