Os02g0477700 - Revision history

Xysj2017: /* Annotated Information */

2017-02-14T02:28:38Z

‎Annotated Information

Xysj2017: /* Phenotypic analysis */

2017-02-14T02:28:23Z

‎Phenotypic analysis

Xysj2017: /* Phenotypic analysis */

2017-02-14T02:28:13Z

‎Phenotypic analysis

Xysj2017: /* Phenotypic analysis */

2017-02-14T02:27:51Z

‎Phenotypic analysis

Xysj2017 at 02:27, 14 February 2017

2017-02-14T02:27:22Z

Xysj2017 at 02:24, 14 February 2017

2017-02-14T02:24:12Z

192.168.72.52 at 06:36, 14 May 2015

2015-05-14T06:36:30Z

Horatioguo: /* References */

2014-06-10T12:19:12Z

‎References

Horatioguo: /* Labs working on this gene */

2014-06-10T12:15:27Z

‎Labs working on this gene

Horatioguo: /* Evolution */

2014-06-10T12:13:53Z

‎Evolution

@@ Line 5: / Line 5: @@
 *'''''Os02g0477700''''' '''''<=>''''' '''''DWARF50''''','''''D50'''''
 ===Function===
 * '''''D50''''' encodes putative inositol polyphosphate 5-phosphatase (5PTase), which may be involved in phosphoinositide signalling required for many essential cellular functions, such as cytoskeleton organization, endocytosis and vesicular trafficking in eukaryotes.
 * The putative 5PTase, encoded by '''''D50''''', is essential for IM formation, including the direction of cell division, deposition of cell wall pectins and control of actin organization.
 ===Phenotypic analysis===
 * The d50 mutation induced abnormally oriented cell division, irregular deposition of cell wall pectins and thick actin bundles in the parenchyma cells of the IM, resulting in abnormally organized cell files of the internode parenchyma and dwarf phenotype.
 * 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, the researchers 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).

@@ Line 10: / Line 10: @@
 ===Phenotypic analysis===
 [[File:Figure1.JPG|right|thumb|527px|'''Figure 1.''' ''Phenotypes of rice d50 mutant, F71, in matured internodes.<ref name="ref1" />.'']]
 * The d50 mutation induced abnormally oriented cell division, irregular deposition of cell wall pectins and thick actin bundles in the parenchyma cells of the IM, resulting in abnormally organized cell files of the internode parenchyma and dwarf phenotype.
 * 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, the researchers 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).

@@ Line 9: / Line 9: @@
 ===Phenotypic analysis===
-[[File:Figure1.JPG|center|thumb|727px|'''Figure 1.''' ''Phenotypes of rice d50 mutant, F71, in matured internodes.<ref name="ref1" />.'']]
+[[File:Figure1.JPG|right|thumb|527px|'''Figure 1.''' ''Phenotypes of rice d50 mutant, F71, in matured internodes.<ref name="ref1" />.'']]
 <br>
 * The d50 mutation induced abnormally oriented cell division, irregular deposition of cell wall pectins and thick actin bundles in the parenchyma cells of the IM, resulting in abnormally organized cell files of the internode parenchyma and dwarf phenotype.

@@ Line 9: / Line 9: @@
 ===Phenotypic analysis===
 * The d50 mutation induced abnormally oriented cell division, irregular deposition of cell wall pectins and thick actin bundles in the parenchyma cells of the IM, resulting in abnormally organized cell files of the internode parenchyma and dwarf phenotype.
 * 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, the researchers 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.
 ==Labs working on this gene==

@@ Line 5: / Line 5: @@
 *'''''Os02g0477700''''' '''''<=>''''' '''''DWARF50''''','''''D50'''''
 ===Function===
-* D50 encodes putative inositol polyphosphate 5-phosphatase (5PTase), which may be involved in phosphoinositide signalling required for many essential cellular functions, such as cytoskeleton organization, endocytosis and vesicular trafficking in eukaryotes.
+* '''''D50''''' encodes putative inositol polyphosphate 5-phosphatase (5PTase), which may be involved in phosphoinositide signalling required for many essential cellular functions, such as cytoskeleton organization, endocytosis and vesicular trafficking in eukaryotes.
 * 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, the researchers 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.
+[[File:Figure1.JPG|center|thumb|727px|'''Figure 1.''' ''Phenotypes of rice d50 mutant, F71, in matured internodes.<ref name="ref1" />.'']]
 ==Labs working on this gene==

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+The rice '''''Os02g0477700''''' was reported as '''''DWARF50''''' in 2012 <ref name="ref1" /> by researchers from Japan.
 ==Annotated Information==
 ===Function===
-Please input function information here.
+* D50 encodes putative inositol polyphosphate 5-phosphatase (5PTase), which may be involved in phosphoinositide signalling required for many essential cellular functions, such as cytoskeleton organization, endocytosis and vesicular trafficking in eukaryotes.
-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.
+* 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, the researchers 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).
 [[File:Figure1.JPG‎]]
@@ Line 47: / Line 51: @@
 ==Labs working on this gene==
-Please input related labs here.
+* Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16
 Naka-cho, Koganei, Tokyo 184-8588, Japan,
-Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology,
+* Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan,
-Naka-cho, Koganei, Tokyo 184-8588, Japan, 2Graduate School of Agriculture, Tokyo University of Agriculture and
+* Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
-Technology, Fuchu, Tokyo 183-8509, Japan, 3Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka
+* Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601 and 5 College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
 ==References==
-Please input cited references here.
+<references>
+* <ref name="ref1">
-[1]DWARF50 (D50), a rice (Oryza sativa L.) gene encoding inositol polyphosphate 5-phosphatase, is required for proper development of intercalary meristempce.
+Sato-Izawa K, Nakaba S, Tamura K, Yamagishi Y, Nakano Y, Nishikubo N, Kawai S,
-[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.
+Kajita S, Ashikari M, Funada R, Katayama Y, Kitano H. DWARF50 (D50), a rice
-[3]Caffall K.H. & Mohnen D. (2009) The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydrate Research 344, 1879–1900.
+(Oryza sativa L.) gene encoding inositol polyphosphate 5-phosphatase, is required
 ==Structured Information==
       [[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 2]]

← Older revision		Revision as of 06:36, 14 May 2015
Line 63:		Line 63:

	==Structured Information==		==Structured Information==
−	~~{{JaponicaGene\|~~	+	[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 2]]
−	~~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]]

← Older revision		Revision as of 12:13, 10 June 2014
Line 34:		Line 34:

	You can also add sub-section(s) at will.		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==		==Labs working on this gene==