RiceWiki - User contributions [en]

Os01g0757200

2017-08-24T05:56:46Z

Xysj1980: /* Annotated Information */

'''Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs).'''
 
==Annotated Information==
[[File:1-f5aa.png |right |thumb |300px |''''''Figure 5. Severely Dwarfed and Semidwarfed Rice Mutants Obtained by T-DNA Activation Tagging.(A) The severe dwarf mutant GA2ox3ACT (M77777).'''''']]
===Function===
The members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination.
 
The severe dwarf mutant M77777, designated as GA2ox3ACT,carries a T-DNA insertion at a position 587 bp upstream of the translation start codon of GA2ox3 (Figure 5A). Accumulation of GA2ox3 mRNA was significantly enhanced in the heterozygous mutant. The GA2ox3ACT mutant did not produce seeds and was therefore maintained and propagated vegetatively.
 

===Expression===
Genes GA2ox3 was differentially expressed in leaves, and its expression was also temporally regulated (Figure 3B).
GA2ox3 accumulation of its mRNAs in leaves was detected prior to the transition from vegetative to reproductive growth phases.Since expression of most GA2oxs terminated after the active tillering stage, the pattern of tiller growth throughout the rice life cycle was examined. Tiller number increased from 30 to 50 DAI (active tillering), remained constant until 75 DAI, and then increased again until 90 DAI (late tillering)when the experiment was terminated (Figure 3C). Expression of each group of GA2oxs paralleled the active and late tillering stages (cf. Figures 3B with 3C). Germination was observed from 1 DAI and reached almost 100% at 2 DAI (Figure 4A). The accumulation of most GA2ox mRNAs was detectable starting from 0 to 1 DAI and maintained at similar levels afterward, except that of GA2ox5 and GA2ox9 was moderately reduced at 2 DAI (Figure 4B).
 

===Evolution===

==Labs working on this gene==
* Institute of Molecular Biology, National Chung-Hsing University, Taichung 402, Taiwan, Republic of China
* Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Department of Energy Plant Research Laboratory and Department of Plant Biology, Michigan State University,East Lansing, Michigan 48824-1312
 

==References==
Please input cited references here.

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0757200

2017-08-24T05:56:31Z

Xysj1980:

Os01g0757200

2017-08-24T05:56:02Z

Xysj1980: /* Annotated Information */

'''Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs).'''
 
==Annotated Information==
===Function===
The members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination.
 
The severe dwarf mutant M77777, designated as GA2ox3ACT,carries a T-DNA insertion at a position 587 bp upstream of the translation start codon of GA2ox3 (Figure 5A). Accumulation of GA2ox3 mRNA was significantly enhanced in the heterozygous mutant. The GA2ox3ACT mutant did not produce seeds and was therefore maintained and propagated vegetatively.
 
[[File:1-f5aa.png |right |thumb |300px |''''''Figure 5. Severely Dwarfed and Semidwarfed Rice Mutants Obtained by T-DNA Activation Tagging.(A) The severe dwarf mutant GA2ox3ACT (M77777).'''''']]

===Expression===
Genes GA2ox3 was differentially expressed in leaves, and its expression was also temporally regulated (Figure 3B).
GA2ox3 accumulation of its mRNAs in leaves was detected prior to the transition from vegetative to reproductive growth phases.Since expression of most GA2oxs terminated after the active tillering stage, the pattern of tiller growth throughout the rice life cycle was examined. Tiller number increased from 30 to 50 DAI (active tillering), remained constant until 75 DAI, and then increased again until 90 DAI (late tillering)when the experiment was terminated (Figure 3C). Expression of each group of GA2oxs paralleled the active and late tillering stages (cf. Figures 3B with 3C). Germination was observed from 1 DAI and reached almost 100% at 2 DAI (Figure 4A). The accumulation of most GA2ox mRNAs was detectable starting from 0 to 1 DAI and maintained at similar levels afterward, except that of GA2ox5 and GA2ox9 was moderately reduced at 2 DAI (Figure 4B).
[[File:1-f3b.png |left |thumb |10000px |''''''Figure 3. Differential Expression of Two Groups of GA2oxs Regulates Flower and Tiller Development.(B) Temporal expression patterns of GA2oxs in rice. The last fully expanded leaves were collected from rice plants at different developmental stages. Total RNA was isolated and analyzed by RT-PCR using GA2ox and GA3ox2 gene-specific primers (see Supplemental Table 4 online). The 18S rRNA gene (rRNA) was used as a control.'''''']]
[[File:1-f4b.png |center |thumb |10000px |''''''Figure 4. C20 GA2oxs Could Be Responsible for Regulating Seed Germination.(B) Expression patterns of GA2oxs in rice seedlings between 0 and ;5 DAI. Total RNA was isolated from embryos at each time point and
analyzed by RT-PCR. The 18S rRNA gene (rRNA) was used as a control.'''''']]
 

===Evolution===

==Labs working on this gene==
* Institute of Molecular Biology, National Chung-Hsing University, Taichung 402, Taiwan, Republic of China
* Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Department of Energy Plant Research Laboratory and Department of Plant Biology, Michigan State University,East Lansing, Michigan 48824-1312
 

==References==
Please input cited references here.

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0757200

2017-08-24T05:55:30Z

Xysj1980: /* Function */

'''Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs).'''
 
==Annotated Information==
===Function===
The members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination.
 
The severe dwarf mutant M77777, designated as GA2ox3ACT,carries a T-DNA insertion at a position 587 bp upstream of the translation start codon of GA2ox3 (Figure 5A). Accumulation of GA2ox3 mRNA was significantly enhanced in the heterozygous mutant. The GA2ox3ACT mutant did not produce seeds and was therefore maintained and propagated vegetatively.
 
[[File:1-f5aa.png |right |thumb |300px |''''''Figure 5. Severely Dwarfed and Semidwarfed Rice Mutants Obtained by T-DNA Activation Tagging.(A) The severe dwarf mutant GA2ox3ACT (M77777).'''''']]

===Expression===
Genes GA2ox3 was differentially expressed in leaves, and its expression was also temporally regulated (Figure 3B).
GA2ox3 accumulation of its mRNAs in leaves was detected prior to the transition from vegetative to reproductive growth phases.Since expression of most GA2oxs terminated after the active tillering stage, the pattern of tiller growth throughout the rice life cycle was examined. Tiller number increased from 30 to 50 DAI (active tillering), remained constant until 75 DAI, and then increased again until 90 DAI (late tillering)when the experiment was terminated (Figure 3C). Expression of each group of GA2oxs paralleled the active and late tillering stages (cf. Figures 3B with 3C). Germination was observed from 1 DAI and reached almost 100% at 2 DAI (Figure 4A). The accumulation of most GA2ox mRNAs was detectable starting from 0 to 1 DAI and maintained at similar levels afterward, except that of GA2ox5 and GA2ox9 was moderately reduced at 2 DAI (Figure 4B).
[[File:1-f3b.png |left |thumb |10000px |''''''Figure 3. Differential Expression of Two Groups of GA2oxs Regulates Flower and Tiller Development.(B) Temporal expression patterns of GA2oxs in rice. The last fully expanded leaves were collected from rice plants at different developmental stages. Total RNA was isolated and analyzed by RT-PCR using GA2ox and GA3ox2 gene-specific primers (see Supplemental Table 4 online). The 18S rRNA gene (rRNA) was used as a control.'''''']]
[[File:1-f4b.png |center |thumb |10000px |''''''Figure 4. C20 GA2oxs Could Be Responsible for Regulating Seed Germination.(B) Expression patterns of GA2oxs in rice seedlings between 0 and ;5 DAI. Total RNA was isolated from embryos at each time point and
analyzed by RT-PCR. The 18S rRNA gene (rRNA) was used as a control.'''''']]
 
[[File:1-f3c.png |left |thumb |10000px |''''''Figure 3. Differential Expression of Two Groups of GA2oxs Regulates Flower and Tiller Development.(C) Tiller development during the life cycle of rice. A total of eight plants were used for counting tiller number, and error bars indicate the SE of the mean at each time point.'''''']]
[[File:1-f4a.png |center |thumb |10000px |''''''Figure 4. C20 GA2oxs Could Be Responsible for Regulating Seed Germination.(A) Germination rate of rice seeds reached 100% at 2 DAI.'''''']]
 
 
 
 
 
 
 
 

===Evolution===
[[File:1-f1.png |center |thumb |10000px |''''''Figure 2. Phylogenetic Tree Based on the Comparison of Plant GA2oxs.Amino acid sequences of 29 GA2oxs from nine plant species (see Supplemental Table 3 online). Plant species: At, Arabidopsis thaliana;Cm, Cucurbita maxima; Ls, Lactuca sativa; Nt, Nicotiana sylvestris; Pc,Phaseolus coccineus; PaPt, Populus alba 3 P. tremuloides; Ps, Pisum sativum; So, Spinacia oleracea. The scale value of 0.1 indicates 0.1 amino acid substitutions per site'''''']]

==Labs working on this gene==
* Institute of Molecular Biology, National Chung-Hsing University, Taichung 402, Taiwan, Republic of China
* Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
* Department of Energy Plant Research Laboratory and Department of Plant Biology, Michigan State University,East Lansing, Michigan 48824-1312
 

==References==
Please input cited references here.

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0233500

2017-03-28T08:44:52Z

Xysj1980:

The rice '''''Os01g0233500''''' was reported as '''''Orysa;CycA1;1''''' in 2006 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Function===
* Cyclins, the known activators for activity of CDKs, play crucial roles for cell cycle progression in eukaryotes.<ref name="ref1" /><ref name="ref2" />
* In plants, cyclin binding not only activates CDKs by inducing a configuration alteration at the catalytic sites, but also contributes to the subcellular localization and substrate specificity of the complex as well as regulation of protein stability.<ref name="ref1" /><ref name="ref2" />

===Evolution===
* Phylogenetic analysis indicated that both Arabidopsis and rice shared eight types of cyclins, A-, B-, D-, H-, L-, SDS-, T- and P-type, whereas C- and J18-type cyclins were specific to Arabidopsis, and F-type cyclins, lacking clear homologues in Arabidopsis, were unique to rice.<ref name="ref1" />

===Knowledge extension===
* Similar to animals and yeasts, cell proliferation in plants is mainly controlled by a family of cyclin-dependent kinases (CDKs). The activity of CDKs is directly regulated by binding and activation of cyclins as well as other mechanisms that consist of protein phosphorylation/ dephosphorylation by specific kinases/phosphatases, proteolysis, CDK inhibitor protein (CKI) binding, etc.
* Cyclins were initially discovered in marine inverte-brates as proteins that accumulated at specific time points of the cell cycle and were subsequently degraded quickly.<ref name="ref1" />

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

==Labs working on this gene==
* Rice Functional Genomics, Joint Laboratory of Temasek Life Sciences Laboratory of Singapore and Institute of Genetics and Developmental Biology
* Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, 100101 Beijing, China
* Rice Functional Genomics Group, Temasek Life Science Laboratory, 1 Research Link, The National University of Singapore, 117604 Singapore, Singapore

==References==
<references>
* <ref name="ref1">
La H, Li J, Ji Z, Cheng Y, Li X, Jiang S, Venkatesh PN, Ramachandran S.
Genome-wide analysis of cyclin family in rice (Oryza Sativa L.). Mol Genet
Genomics. 2006 Apr;275(4):374-86. Epub 2006 Jan 25. PubMed PMID: 16435118.
</ref>
* <ref name="ref2">
Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, DePamphilis CW, Ma H.
Genome-wide analysis of the cyclin family in Arabidopsis and comparative
phylogenetic analysis of plant cyclin-like proteins. Plant Physiol. 2004
Jun;135(2):1084-99. PubMed PMID: 15208425; PubMed Central PMCID: PMC514142.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0233500

2017-03-28T08:44:09Z

Xysj1980:

The rice '''''Os01g0233500''''' was reported as '''''Orysa;CycA1;1''''' in 2006 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Function===
* Cyclins, the known activators for activity of CDKs, play crucial roles for cell cycle progression in eukaryotes.
* In plants, cyclin binding not only activates CDKs by inducing a configuration alteration at the catalytic sites, but also contributes to the subcellular localization and substrate specificity of the complex as well as regulation of protein stability.

===Evolution===
* Phylogenetic analysis indicated that both Arabidopsis and rice shared eight types of cyclins, A-, B-, D-, H-, L-, SDS-, T- and P-type, whereas C- and J18-type cyclins were specific to Arabidopsis, and F-type cyclins, lacking clear homologues in Arabidopsis, were unique to rice.

===Knowledge extension===
* Similar to animals and yeasts, cell proliferation in plants is mainly controlled by a family of cyclin-dependent kinases (CDKs). The activity of CDKs is directly regulated by binding and activation of cyclins as well as other mechanisms that consist of protein phosphorylation/ dephosphorylation by specific kinases/phosphatases, proteolysis, CDK inhibitor protein (CKI) binding, etc.
* Cyclins were initially discovered in marine inverte-brates as proteins that accumulated at specific time points of the cell cycle and were subsequently degraded quickly.

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

==Labs working on this gene==
* Rice Functional Genomics, Joint Laboratory of Temasek Life Sciences Laboratory of Singapore and Institute of Genetics and Developmental Biology
* Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, 100101 Beijing, China
* Rice Functional Genomics Group, Temasek Life Science Laboratory, 1 Research Link, The National University of Singapore, 117604 Singapore, Singapore

==References==
<references>
* <ref name="ref1">
La H, Li J, Ji Z, Cheng Y, Li X, Jiang S, Venkatesh PN, Ramachandran S.
Genome-wide analysis of cyclin family in rice (Oryza Sativa L.). Mol Genet
Genomics. 2006 Apr;275(4):374-86. Epub 2006 Jan 25. PubMed PMID: 16435118.
</ref>
* <ref name="ref2">
Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, DePamphilis CW, Ma H.
Genome-wide analysis of the cyclin family in Arabidopsis and comparative
phylogenetic analysis of plant cyclin-like proteins. Plant Physiol. 2004
Jun;135(2):1084-99. PubMed PMID: 15208425; PubMed Central PMCID: PMC514142.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0513100

2017-03-28T08:02:25Z

Xysj1980:

The rice '''''Os01g0513100''''' was reported as '''''OsPP2C03''''' in 2008 <ref name="ref1" /> by researchers from China.
==Annotated Information==
===Gene Symbol===
*'''''Os01g0513100''''' '''''<=>''''' '''''OsPP2C03'''''
===Function===
* The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes.<ref name="ref1" />
* Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis.<ref name="ref1" /> <ref name="ref2" />
===Expression===
* The expression analyses from the researchers provide evidences that PP2C genes in different subfamilies might play different functional roles in distinct signaling pathways.<ref name="ref1" />
===Knowledge extension===
* The reversible phosphorylation of proteins is a fundamental mechanism by which living organisms modulate cellular processes including cell cycle events, growth factor responses, hormone and environmental stimuli responses, metabolic control, and developmental processes.<ref name="ref1" />
You can also add sub-section(s) at will.
==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
* Biology Department, Millersville University of Pennsylvania, 288 Roddy Hall, 50 E Frederick St, PO Box 1002, Millersville PA, 17551-0302, USA
* Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, PR China
* Institutes of Biomedical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, PR China
* Centre for Forest Biology & Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada
==References==
<references>
* <ref name="ref1">
Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S, Zheng C, Zhong Y.
Genome-wide and expression analysis of protein phosphatase 2C in rice and
Arabidopsis. BMC Genomics. 2008 Nov 20;9:550. doi: 10.1186/1471-2164-9-550.
PubMed PMID: 19021904; PubMed Central PMCID: PMC2612031.
</ref>
* <ref name="ref2">
Umezawa T, Sugiyama N, Mizoguchi M, Hayashi S, Myouga F, Yamaguchi-Shinozaki
K, Ishihama Y, Hirayama T, Shinozaki K. Type 2C protein phosphatases directly
regulate abscisic acid-activated protein kinases in Arabidopsis. Proc Natl Acad
Sci U S A. 2009 Oct 13;106(41):17588-93. doi: 10.1073/pnas.0907095106. Epub 2009
Sep 29. PubMed PMID: 19805022; PubMed Central PMCID: PMC2754379.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0164600

2017-03-28T07:58:18Z

Xysj1980:

The rice '''''Os01g0164600''''' was reported as '''''OsPP2C01''''' in 2008 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os01g0164600''''' '''''<=>''''' '''''OsPP2C01'''''

===Function===
* The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes.<ref name="ref1" />
* Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis.<ref name="ref1" /> <ref name="ref2" />

===Expression===
* The expression analyses from the researchers provide evidences that PP2C genes in different subfamilies might play different functional roles in distinct signaling pathways.<ref name="ref1" />

===Knowledge extension===
* The reversible phosphorylation of proteins is a fundamental mechanism by which living organisms modulate cellular processes including cell cycle events, growth factor responses, hormone and environmental stimuli responses, metabolic control, and developmental processes.<ref name="ref1" />

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

==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
* Biology Department, Millersville University of Pennsylvania, 288 Roddy Hall, 50 E Frederick St, PO Box 1002, Millersville PA, 17551-0302, USA
* Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, PR China
* Institutes of Biomedical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, PR China
* Centre for Forest Biology & Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada

==References==
<references>
* <ref name="ref1">
Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S, Zheng C, Zhong Y.
Genome-wide and expression analysis of protein phosphatase 2C in rice and
Arabidopsis. BMC Genomics. 2008 Nov 20;9:550. doi: 10.1186/1471-2164-9-550.
PubMed PMID: 19021904; PubMed Central PMCID: PMC2612031.
</ref>
* <ref name="ref2">
Umezawa T, Sugiyama N, Mizoguchi M, Hayashi S, Myouga F, Yamaguchi-Shinozaki
K, Ishihama Y, Hirayama T, Shinozaki K. Type 2C protein phosphatases directly
regulate abscisic acid-activated protein kinases in Arabidopsis. Proc Natl Acad
Sci U S A. 2009 Oct 13;106(41):17588-93. doi: 10.1073/pnas.0907095106. Epub 2009
Sep 29. PubMed PMID: 19805022; PubMed Central PMCID: PMC2754379.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0164600

2017-03-28T07:57:51Z

Xysj1980:

The rice '''''Os01g0164600''''' was reported as '''''OsPP2C01''''' in 2008 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os01g0164600''''' '''''<=>''''' '''''OsPP2C01'''''

===Function===
* The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes.
* Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis.

===Expression===
* The expression analyses from the researchers provide evidences that PP2C genes in different subfamilies might play different functional roles in distinct signaling pathways.

===Knowledge extension===
* The reversible phosphorylation of proteins is a fundamental mechanism by which living organisms modulate cellular processes including cell cycle events, growth factor responses, hormone and environmental stimuli responses, metabolic control, and developmental processes.

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

==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
* Biology Department, Millersville University of Pennsylvania, 288 Roddy Hall, 50 E Frederick St, PO Box 1002, Millersville PA, 17551-0302, USA
* Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, PR China
* Institutes of Biomedical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, PR China
* Centre for Forest Biology & Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada

==References==
<references>
* <ref name="ref1">
Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S, Zheng C, Zhong Y.
Genome-wide and expression analysis of protein phosphatase 2C in rice and
Arabidopsis. BMC Genomics. 2008 Nov 20;9:550. doi: 10.1186/1471-2164-9-550.
PubMed PMID: 19021904; PubMed Central PMCID: PMC2612031.
</ref>
* <ref name="ref2">
Umezawa T, Sugiyama N, Mizoguchi M, Hayashi S, Myouga F, Yamaguchi-Shinozaki
K, Ishihama Y, Hirayama T, Shinozaki K. Type 2C protein phosphatases directly
regulate abscisic acid-activated protein kinases in Arabidopsis. Proc Natl Acad
Sci U S A. 2009 Oct 13;106(41):17588-93. doi: 10.1073/pnas.0907095106. Epub 2009
Sep 29. PubMed PMID: 19805022; PubMed Central PMCID: PMC2754379.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0252200

2017-03-27T16:16:47Z

Xysj1980:

The rice '''''Os01g0252200''''' was reported as '''''OsC3H3''''' in 2012 <ref name="ref1" /> by researchers from China.
==Annotated Information==
===Gene Symbol===
*'''''Os01g0252200''''' '''''<=>''''' '''''OsC3H3'''''
===Function===
* Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. <ref name="ref1" /> <ref name="ref2" />
* CCCH-type zinc finger proteins have essential functions in various developmental processes in plants.
* CCCH family genes have been known to play important roles in RNA processing as RNA-binding proteins.
* CCCH-type zinc finger proteins are RNA-binding proteins by virtue of the ability of their defining motif to directly bind to RNA, whereas most of the other zinc finger families are confirmed as DNA-binding or protein-binding proteins.
===Expression===
* The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could
have an effective role in stress tolerance.
===Evolution===
* A typical CCCH protein usually contains 1–6 CCCH-type zinc finger motifs.
* Based on the different numbers of amino acid spacers between cysteines and histidines in the CCCH motif, a consensus sequence for these was defined as C-X 4–15 -C-X 4–6 -C-X 3 -H (X represents any amino acid) based on the whole-genome analysis of rice and Arabidopsis CCCH proteins <ref name="ref1" /> <ref name="ref2" />
You can also add sub-section(s) at will.
==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, P.R. China
==References==
<references>
* <ref name="ref1">
Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C. Genome-wide analysis of CCCH zinc
finger family in Arabidopsis and rice. BMC Genomics. 2008 Jan 27;9:44. doi:
10.1186/1471-2164-9-44. PubMed PMID: 18221561; PubMed Central PMCID: PMC2267713.
</ref>
* <ref name="ref2">
Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B. CCCH-type
zinc finger family in maize: genome-wide identification, classification and
expression profiling under abscisic acid and drought treatments. PLoS One.
2012;7(7):e40120. doi: 10.1371/journal.pone.0040120. PubMed PMID: 22792223;
PubMed Central PMCID: PMC3391233.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0174600

2017-03-27T16:04:58Z

Xysj1980: /* Evolution */

The rice '''''Os01g0174600''''' was reported as '''''OsC3H1''''' in 2012 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os01g0174600''''' '''''<=>''''' '''''OsC3H1'''''

===Function===
* Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. <ref name="ref1" /> <ref name="ref2" />
* CCCH-type zinc finger proteins have essential functions in various developmental processes in plants.
* CCCH family genes have been known to play important roles in RNA processing as RNA-binding proteins.
* CCCH-type zinc finger proteins are RNA-binding proteins by virtue of the ability of their defining motif to directly bind to RNA, whereas most of the other zinc finger families are confirmed as DNA-binding or protein-binding proteins.

===Expression===
* The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could
have an effective role in stress tolerance.

===Evolution===
* A typical CCCH protein usually contains 1–6 CCCH-type zinc finger motifs.
* Based on the different numbers of amino acid spacers between cysteines and histidines in the CCCH motif, a consensus sequence for these was defined as C-X 4–15 -C-X 4–6 -C-X 3 -H (X represents any amino acid) based on the whole-genome analysis of rice and Arabidopsis CCCH proteins <ref name="ref1" /> <ref name="ref2" />

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

==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, P.R. China

==References==
<references>
* <ref name="ref1">
Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C. Genome-wide analysis of CCCH zinc
finger family in Arabidopsis and rice. BMC Genomics. 2008 Jan 27;9:44. doi:
10.1186/1471-2164-9-44. PubMed PMID: 18221561; PubMed Central PMCID: PMC2267713.
</ref>
* <ref name="ref2">
Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B. CCCH-type
zinc finger family in maize: genome-wide identification, classification and
expression profiling under abscisic acid and drought treatments. PLoS One.
2012;7(7):e40120. doi: 10.1371/journal.pone.0040120. PubMed PMID: 22792223;
PubMed Central PMCID: PMC3391233.
</ref>

</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0174600

2017-03-27T16:04:35Z

Xysj1980:

The rice '''''Os01g0174600''''' was reported as '''''OsC3H1''''' in 2012 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os01g0174600''''' '''''<=>''''' '''''OsC3H1'''''

===Function===
* Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. <ref name="ref1" /> <ref name="ref2" />
* CCCH-type zinc finger proteins have essential functions in various developmental processes in plants.
* CCCH family genes have been known to play important roles in RNA processing as RNA-binding proteins.
* CCCH-type zinc finger proteins are RNA-binding proteins by virtue of the ability of their defining motif to directly bind to RNA, whereas most of the other zinc finger families are confirmed as DNA-binding or protein-binding proteins.

===Expression===
* The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could
have an effective role in stress tolerance.

===Evolution===
* A typical CCCH protein usually contains 1–6 CCCH-type zinc finger motifs.
* Based on the different numbers of amino acid spacers between cysteines and histidines in the CCCH motif, a consensus sequence for these was defined as C-X 4–15 -C-X 4–6 -C-X 3 -H (X represents any amino acid) based on the whole-genome analysis of rice and Arabidopsis CCCH proteins
<ref name="ref1" /> <ref name="ref2" />
You can also add sub-section(s) at will.

==Labs working on this gene==
* State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, P.R. China

==References==
<references>
* <ref name="ref1">
Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C. Genome-wide analysis of CCCH zinc
finger family in Arabidopsis and rice. BMC Genomics. 2008 Jan 27;9:44. doi:
10.1186/1471-2164-9-44. PubMed PMID: 18221561; PubMed Central PMCID: PMC2267713.
</ref>
* <ref name="ref2">
Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B. CCCH-type
zinc finger family in maize: genome-wide identification, classification and
expression profiling under abscisic acid and drought treatments. PLoS One.
2012;7(7):e40120. doi: 10.1371/journal.pone.0040120. PubMed PMID: 22792223;
PubMed Central PMCID: PMC3391233.
</ref>

</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0859300

2017-03-27T12:08:03Z

Xysj1980: /* Mutation */

As a bZIP transcription factor,''OsABI5'' could regulate the adaptive stress response and plant fertility of rice<ref name="ref1"/><ref name="ref2"/>.
==Annotated Information==
===Function===
''OsABI5'' could prevent growth in a stressed environment. It plays a important role during plant development, especially in the regulation of plant fertility. It is associated with the ABA signaling pathway and stress tolerance. ''OsABI5'' is possibly involved in the formation of microspores and the regulation of plant fertility<ref name="ref1"/>.
Two ''OsABI5'' splicing variants were identified, designated ''OsABI5-1'', and ''OsABI5-2'' and their different expression patterns in tissues were analyzed. ''OsABI5'' variants may have overlapping and distinct functions to fine tune gene expression in ABA signaling as transcription factors together with ''OsVP1''
<ref name="ref2"/>.

'''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0003677 GO:0003677], [http://amigo.geneontology.org/amigo/term/0005634 GO:0005634], [http://amigo.geneontology.org/amigo/term/GO:0043565 GO:0043565], [http://amigo.geneontology.org/amigo/term/GO:0046983 GO:0046983]

===Mutation===
''OsABI5-1'' and ''OsABI5-2'' 
*Sequence analysis showed that the two ''OsABI5'' cDNAs are transcribed from the same initiation site and have a different exon. Exon skip was presented in the splicing variants. Amino acid analysis showed that the encoded peptides shared the identical bZIP domain, and the additional 10 amino acids of ''OsABI5-2'' presented behind the leucine zipper at the C-terminal. Southern blot analysis indicated that the ''OsABI5'' gene presented only one copy in the rice genome, which provide further support that ''OsABI5-1'' and ''OsABI5-2'' are different splicing variants of the ''OsABI5'' gene<ref name="ref2" />.
*Differential transactivation activity in ''OsABI5-1'' and ''OsABI5-2'':
''OsABI5-1'' and ''OsABI5-2'' had obvious transactivation capacity.By quantitative b-galactosidase assays using ONPG as a substrate, the ''OsABI5-1'' fusion construct showed a nearly twofold higher activity level than the ''OsABI5-2'' fusion construct, suggesting that deletion of additional protein sequences elevated the transactivation activity, and the additional 10 amino acids behind the bZIP domain of ''OsABI5-2'' can affect the activity strength<ref name="ref2" />.
*DNA binding activity of ''OsABI5-1'' and ''OsABI5-2'' to the cis-acting G-box element in yeast:
* ''OsABI5-2'' can function as a transacting factor for the G-box element and the additional 10 amino acids of ''OsABI5-2'' are necessary for the binding specificity to the G-box. The binding activity of O''sABI5-1'' to the G-box element is disrupted by deleting the 10 amino acids<ref name="ref2" />.
*Interaction between ''OsABI5-1'' and ''OsABI5-2'':
''OsABI5-1'' and ''OsABI5-2'' could interact directly in vitro, and that ''OsABI5-2'' could interact with itself. In Arabidopsis, hetero and homo-dimerization among homologs of the ''ABI5'' family have already been documented. Whether ''OsABI5-1'' and ''OsABI5-2'' could form heterodimers remains to be confirmed<ref name="ref2" />.

===Expression===
[[File: OsABI5 ExpressionPattern1.png|right|thumb|300px|'''Figure 1.''' ''RT-PCR analysis of OsABI5 expression patterns under ABA and stress conditions(from reference <ref name="ref1"/>).'']]
[[File: OsABI5 variants Expression2.png|right|thumb|300px|'''Figure 2.''' ''Expression patterns of OsABI5 variants in different tissues by RT-PCR. (from reference <ref name="ref2"/>).'']]
*RT-PCR: ''OsABI5'' was induced within 1 h after ABA and high-salt treatment, and the mRNA level continuously increased up to 24 h. Cold treatment initially suppressed ''OsABI5'' expression within 5 h, and then induced it to reach its maximum at 24 h. When plants were subjected to dehydration stress, ''OsABI5'' expression was suppressed within 24 h(figure 1) <ref name="ref1"/>.
*Semi-quantitative RT-PCR showed that the expression of ''OsABI5'' was suppressed to different degrees and the decreased fertility rate of rice was correlated with the expression of ''OsABI5''<ref name="ref1"/>.
*Over-expression of ''OsABI5'' in rice conferred high sensitivity to salt stress. Repression of ''OsABI5'' promoted stress tolerance and resulted in low fertility of rice<ref name="ref1"/>.
*RT-PCR showed that the ''OsABI5-2'' transcript was constitutively detected in root, leaf, and young panicle. The expression abundance of ''OsABI5-1'' was different in various tissues, with an expression in the leaf as high as ''OsABI5-2'', and a low expression in the root and panicle (Figure 2). Expression of ''OsABI5-1'' or ''OsABI5-2'' can rescue ABA insensitivity of ''abi5-1'' and confer ABA hypersensitivity to WT transgenic plants in Arabidopsis<ref name="ref2"/>.

===Subcellular localization===
The OsABI5::GFP fusion protein was targeted to the nuclei of the cells, which suggested that OsABI5 was a nuclear protein and functioned as a transcription factor to regulate expression of down-stream genes<ref name="ref1" />.

===Evolution===
*homology gene:
**It shares high amino acid sequence homology with Arabidopsis ''AtABI5''and barley ''HvABI5'' within five regions. Amino acids homology analysis showed that the OsABI5-encoded peptide contains a typical basic leucine zipper domain. The deduced amino acid sequence of ''OsABI5'' contains conserved regions similar to other ''ABI5'' or ''ABI5-like'' genes in other species. The Arabidopsis ''AtABI5'' gene is involved in seed dormancy, maturation and stress responses. <ref name="ref1"/><ref name="ref3"/>.
**''OsABI5'' displayed high homology with the Arabidopsis ''AtABI5'' gene, suggesting similar functions in the adaptive stress response and the ABA signaling pathway. ''OsABI5'' may have overlapping and distinct functions with ''AtABI5'' during plant development<ref name="ref3"/>.The ''ABI5'' gene (ABA insensitive 5) of Arabidopsis encodes a basic leucine zipper factor required for ABA response in the seed and vegetative tissues. <ref name="ref4"/>

===Knowledge Extension===
*Abscisic Acid (ABA) is an important phytohormone involved in abiotic stress resistance in plants. A group of bZIP transcription factors play important roles in the ABA signaling pathway in ''Arabidopsis''. ''OsABI5''(''Os01g0859300'') is a member of bZIP transcription factors,which also named ''OsbZIP10''(''Os01g0859300''). Most of these ''OsbZIPs'' were significantly induced by ABA, ACC and abiotic stresses<ref name="ref5"/>.
*All of the bZIPs could be classified into three subgroups. Each subgroup contains both rice and Arabidopsis bZIPs, indicating that the divergence of these subgroups predated the divergence of dicots and monocots. It also indicated that the protein sequences of these bZIPs were well conserved between dicots and monocots<ref name="ref5"/>.
*Co-transformation experiments with ABI5 cDNA constructs resulted in specific transactivation of the ABA-inducible wheat Em, Arabidopsis AtEm6, bean-Phaseolin, and barley HVA1 and HVA22 promoters<ref name="ref4"/>.

==Labs working on this gene==
Key Laboratory of Molecular and Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, P.O. Box 2707, South 1-3, Zhongguancun, Beijing 100080, P.R. China

==References==
<references>
* <ref name="ref1">
Zou M, Guan Y, Ren H, et al. A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance[J]. Plant molecular biology, 2008, 66(6): 675-683.
</ref>
* <ref name="ref2">
Zou M, Guan Y, Ren H, et al. Characterization of alternative splicing products of bZIP transcription factors OsABI5[J]. Biochemical and biophysical research communications, 2007, 360(2): 307-313.
</ref>
* <ref name="ref3">
Brocard I M, Lynch T J, Finkelstein R R. Regulation and role of the Arabidopsis abscisic acid-insensitive 5 gene in abscisic acid, sugar, and stress response[J]. Plant Physiology, 2002, 129(4): 1533-1543.
</ref>
* <ref name="ref4">
Gampala S S L, Finkelstein R R, Sun S S M, et al. ABI5 interacts with abscisic acid signaling effectors in rice protoplasts[J]. Journal of Biological Chemistry, 2002, 277(3): 1689-1694.</ref>
</ref>
* <ref name="ref5">
Lu G, Gao C, Zheng X, et al. Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice[J]. Planta, 2009, 229(3): 605-615.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0805600

2017-03-27T11:56:23Z

Xysj1980:

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Function1.png|right|thumb|250px|"Fig. 1 The suppression of Orysa;CycB1;1 produces aberrant rice seeds. a Mature seeds of wild type (WT), Pubi::GUS (CK), Pubi::CycB1;1OE (OE) and Pubi::CycB1;1RNAi transgenic (TL3 and TL4) rice. TL transgenic line. Arrows indicate the embryos; b CK and TL4-II seeds at diVerent development stages; c statistical analysis of the 1,000 kernel weights of WT, CK, OE, TL4-I and TL4-II seeds; d expression analysis of Orysa;CycB1;1 in TL4-I and TL4-II seedlings; e RT-PCR analysis of Orysa;CycB1;1 in Pubi::CycB1;1RNAi and Pubi::CycB1;1OE transgenic rice plants. Bar 2.6 mm (a), 3.0 mm (b)"]]
The cell cycle is an important process during seed development in plants and its progression is driven by a number of core regulators such as the cyclins. Currently, however, little is known regarding the role of the cyclins in embryo and endosperm development in cereals. In current study, we show that the knockdown of Orysa;CycB1;1 in rice results in the production of abnormal seeds, which at maturity contain only an enlarged embryo. It was further found that a delayed and abnormal cellularization occurred in the endosperm in these knockdown seeds which eventually became abortive. Moreover, the observed development of the enlarged embryo was also morphologically abnormal and found to be caused by an enlarged cell size rather than an increased cell number. Expression analysis showed that Orysa;CycB1;1 transcripts were localized in the endosperm and embryo. Genome-wide transcriptional profiling further indicated that a large number of genes are responsible for the phenotype of the enlarged embryo. The results of the knockdown of Orysa;CycB1;1 via an endosperm or an embryo-specific promoter also suggest that the enlarged embryo may be correlated to the abortive endosperm. The results suggest that Orysa;CycB1;1 expression is critical for endosperm formation via the regulation of mitotic division, and that the endosperm plays an important role in maintenance of embryo development in rice.(Fig.1)<ref name="ref1"></ref>

===Expression===
B-type cyclins play key roles in the mitotic cell cycle and endoreduplication. Our previous study showed that knockdown of Orysa;CycB1;1 resulted in abnormal seeds and low seed production. To investigate the functions of Btype cyclins in plant reproductive growth, the research analyzed the ploidy of the abnormal Pubi::CycB1;1RNAi embryo. The results showed that the abnormal Pubi::CycB1;1RNAi embryo was triploid. The triploid seedlings had larger reproductive organs than those of control plants, and were abortive. Semi-quantitative RT-PCR and in situ hybridization analyses showed that Orysa;CycB1;1 transcripts were localized in cells of anthers and ovaries. This indicated that Orysa;CycB1;1 is critical for reproductive growth and might be involved in gametogenesis in rice. The results of this study increase our understanding of the functions of B-type cyclins in rice reproductive growth.[[File:Expression1.png|right|thumb|250px|"Fig. 2. Aberrant rice seeds produced by Pubi::CycB1;1RNAi transgenic plants. "]][[File:Expression2.png|right|thumb|250px|"Fig. 3. Expression of Orysa;CycB1;1 in rice plants."]](Fig.2;Fig.3)<ref name="ref2"></ref>

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

==Labs working on this gene==
*Rice Functional Genomics, Joint Laboratory of Temasek Life Sciences Laboratory of Singapore
*Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences,Beijing, China
*Rice Functional Genomics Group, Temasek Life Science Laboratory, 1 Research Link, The National University of Singapore, Singapore
*Institut de Biotechnologie des Plantes, UMR 8618, Universit´e Paris-Sud, Bâtiment 630, 91405 Orsay Cedex, France
*Department of Plant Genetics(VIB), Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
*Institute of Biotechnology, Tennis Court Road, CB2 1QT Cambridge, UK

==References==
<references>
<ref name="ref1">Jing Guo , Fang Wang , Jian Song , Wei Sun and Xian Sheng Zhang.The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice.Planta (2010) 231:293–303.</ref>
<ref name="ref2">Jing Guo, Fang Wang and Xian Sheng Zhang.Knockdown Expression of the B-type Cyclin Gene Orysa;CycB1;1 Leads to Triploid Rice.J. Plant Biol. (2014) 57:43-47.</ref>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0805600

2017-03-27T11:55:19Z

Xysj1980:

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Function1.png|right|thumb|250px|"Fig. 1 The suppression of Orysa;CycB1;1 produces aberrant rice seeds. a Mature seeds of wild type (WT), Pubi::GUS (CK), Pubi::CycB1;1OE (OE) and Pubi::CycB1;1RNAi transgenic (TL3 and TL4) rice. TL transgenic line. Arrows indicate the embryos; b CK and TL4-II seeds at diVerent development stages; c statistical analysis of the 1,000 kernel weights of WT, CK, OE, TL4-I and TL4-II seeds; d expression analysis of Orysa;CycB1;1 in TL4-I and TL4-II seedlings; e RT-PCR analysis of Orysa;CycB1;1 in Pubi::CycB1;1RNAi and Pubi::CycB1;1OE transgenic rice plants. Bar 2.6 mm (a), 3.0 mm (b)"]]
The cell cycle is an important process during seed development in plants and its progression is driven by a number of core regulators such as the cyclins. Currently, however, little is known regarding the role of the cyclins in embryo and endosperm development in cereals. In current study, we show that the knockdown of Orysa;CycB1;1 in rice results in the production of abnormal seeds, which at maturity contain only an enlarged embryo. It was further found that a delayed and abnormal cellularization occurred in the endosperm in these knockdown seeds which eventually became abortive. Moreover, the observed development of the enlarged embryo was also morphologically abnormal and found to be caused by an enlarged cell size rather than an increased cell number. Expression analysis showed that Orysa;CycB1;1 transcripts were localized in the endosperm and embryo. Genome-wide transcriptional profiling further indicated that a large number of genes are responsible for the phenotype of the enlarged embryo. The results of the knockdown of Orysa;CycB1;1 via an endosperm or an embryo-specific promoter also suggest that the enlarged embryo may be correlated to the abortive endosperm. The results suggest that Orysa;CycB1;1 expression is critical for endosperm formation via the regulation of mitotic division, and that the endosperm plays an important role in maintenance of embryo development in rice.(Fig.1)<ref name="ref1"></ref>

===Expression===
B-type cyclins play key roles in the mitotic cell cycle and endoreduplication. Our previous study showed that knockdown of Orysa;CycB1;1 resulted in abnormal seeds and low seed production. To investigate the functions of Btype cyclins in plant reproductive growth, the research analyzed the ploidy of the abnormal Pubi::CycB1;1RNAi embryo. The results showed that the abnormal Pubi::CycB1;1RNAi embryo was triploid. The triploid seedlings had larger reproductive organs than those of control plants, and were abortive. Semi-quantitative RT-PCR and in situ hybridization analyses showed that Orysa;CycB1;1 transcripts were localized in cells of anthers and ovaries. This indicated that Orysa;CycB1;1 is critical for reproductive growth and might be involved in gametogenesis in rice. The results of this study increase our understanding of the functions of B-type cyclins in rice reproductive growth.[[File:Expression1.png|right|thumb|250px|"Fig. 2. Aberrant rice seeds produced by Pubi::CycB1;1RNAi transgenic plants. (A) Mature seeds of wild-type (CK), and Pubi::CycB1;1RNAi type I and type II. (B) Histological analysis of CK seeds. (C) Seeds of Pubi::CycB1;1RNAi triploid plant at 15 DAP were filled with liquid and lacked an embryo and endosperm. (D and E) Flow cytometry analysis of CK (D) and type II embryos (E) at 15 DAP. Bars: 2.6 mm in A-C."]][[File:Expression2.png|right|thumb|250px|"Fig. 3. Expression of Orysa;CycB1;1 in rice plants. (A) Semiquantitative RT-PCR analysis of Orysa;CycB1;1 expression in rice tissues. (B-D) Expression of PCycB1;1::GUS in rice floret (B), anther (C), and ovary (D) as indicated. E and F Localization of Orysa;CycB1;1 transcripts in young floret (E) and ovary (F) as revealed by in situ hybridization. (G) The negative controls using a Orysa;CycB1;1 sense probe. Bars: 1 mm in B–D, and 250 μm in E, F, and G."]](Fig.2;Fig.3)<ref name="ref2"></ref>

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

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

==Labs working on this gene==
*Rice Functional Genomics, Joint Laboratory of Temasek Life Sciences Laboratory of Singapore
*Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences,Beijing, China
*Rice Functional Genomics Group, Temasek Life Science Laboratory, 1 Research Link, The National University of Singapore, Singapore
*Institut de Biotechnologie des Plantes, UMR 8618, Universit´e Paris-Sud, Bâtiment 630, 91405 Orsay Cedex, France
*Department of Plant Genetics(VIB), Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
*Institute of Biotechnology, Tennis Court Road, CB2 1QT Cambridge, UK

==References==
<references>
<ref name="ref1">Jing Guo , Fang Wang , Jian Song , Wei Sun and Xian Sheng Zhang.The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice.Planta (2010) 231:293–303.</ref>
<ref name="ref2">Jing Guo, Fang Wang and Xian Sheng Zhang.Knockdown Expression of the B-type Cyclin Gene Orysa;CycB1;1 Leads to Triploid Rice.J. Plant Biol. (2014) 57:43-47.</ref>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os04g0622600

2017-03-27T11:53:06Z

Xysj1980: /* Structured Information */

Xa-1 is one of bacterial blight resistance genes in rice. Although at least 38 resistance genes have been identified, Xa-1 is specific to ''X. oryzae pv. Oryzae''. Xa-1 can be considered as a dominant resistance gene<ref name="ref1" />.
==Annotated Information==
===Function===
The Xa1 gene in rice confers resistance to Japanese race 1 of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial blight (BB). We isolated the Xa1 gene by a map-based cloning strategy. The deduced amino acid sequence of the Xa1 gene product contains nucleotide binding sites (NBS) and a new type of leucine-rich repeats (LRR); thus, Xa1 is a member of the NBS-LRR class of plant disease-resistance genes, but quite different from Xa21, another BB-resistance gene isolated from rice. <ref name="ref2" /><ref name="ref3" />
Xa1 Is a Single-Copy Gene. Southern hybridization analysis was carried out by using the genomic DNAs from resistance line IR-BB1 and susceptible isogenic line IR24. The NBS region of Xa1 hybridized to a single band of DNA from IR-BB1 and IR24, suggesting that Xa1 is a single-copy gene and IR24 also has a sequence homologous to Xa1 at the same locus.<ref name="ref2" /><ref name="ref3" />

===Expression===
Xa1 gene expression was induced on inoculation with a bacterial pathogen and wound, unlike other isolated resistance genes in plants, which show constitutive expression. The induced expression may be involved in enhancement of resistance against the pathogen.<ref name="ref2" />[[File:rice4.jpg‎|right|thumb|250px|]]
So far, there is no report of induced expressed R gene. Interestingly, Xa1 mRNA was detected from rice leaves at 5
days after cutting with water and inoculation of both the compatible and incompatible strains of Xoo, but was not detected in intact leaves. These findings suggested that the Xa1 gene expression may be induced by stimulus of wounding involved in pathogen infection, and accumulation of Xa1 gene product may lead to high efficiency of interaction with avr gene product. This interaction may activate the signal transductions involved in Xa1-madiated BB resistance. Thus, it is likely that Xa1 plays an important role in pathogen recognition, which is supported by the analysis of race-specific resistance of the Xa1 transformants. Which factors regulate the expression of Xa1 remains an interesting question.<ref name="ref2" />

===Evolution===
[[File:rice3.jpg‎|right|thumb|150px|]][[File:rice2.jpg‎|right|thumb|150px|]]
Map-based cloning methods have been applied for isolation of Xa-1, one of the bacterial blight resistance genes in rice.Xa-1 was previously mapped on chromosome 4 using molecular markers. For positional cloning of Xa-1, a high-resolution genetic map was made for theXa-1 region using an F2population of 402 plants and additional molecular markers. Three restriction fragment length polymorphism (RFLP) markers, XNpb235, XNpb264 andC600 were found to be linked tightly to Xa-1, with no recombinants, and U08750 was mapped 1.5 cM from Xa-1. The screening of a yeast artificial chromosome (YAC) library using theseXa-1-linked RFLP markers resulted in the identification of ten contiguous YAC clones. Among these, one YAC clone, designated Y5212, with an insert of 340 kb, hybridized with all three tightly linked markers. This YAC was confirmed to possess the Xa-1 allele by mapping the Xa-1 gene between both end clones of this YAC (Y5212R and Y5212L).<ref name="ref1" />

Based on the deduced amino acid sequence, the Xa1 gene is a class 1 resistance gene; a cytoplasmic receptor-like protein with NBS and LRR domains. Thus, the structure is quite different from the first cloned rice resistance gene, Xa21 (16), which is a class 4 gene. The most intriguing finding is that the expression of Xa1, unlike any previously studied resistance genes, is induced by pathogen infection and wound.<ref name="ref2" />

===Structure===
*The composite nucleotide sequence of the Xa1 cDNA encoded a 5,406-bp ORF that was flanked by 59 and 39 untranslated regions of 112 and 392 bp, respectively. The nucleotide sequence of the 13.5-kb EcoRI-BamHI genomic fragment was also determined and compared with that of the cDNA sequence. The Xa1 gene was composed of four exons separated by three introns.<ref name="ref2" />[[File:rice1.jpg|right|thumb|250px|]]
*The C-terminal half of Xa1 gene is composed of LRR, the common motif of the several classes of resistance genes.
*XA1 protein contains 22 potential N-linked glycosylation sites. Six of these sites are at amino acid position 36 of each LRR repeat. These structural characteristics suggest that the Xa1 product interacts with other proteins in a defense reaction–signal transduction pathway<ref name="ref2" />.

==Labs working on this gene==
*Department of Agriculture, Kyushu University, 6-10-1, Hakozaki, Higashiku, Fukuoka 812, Japan
*Rice Genome Research Program, National Institute of Agrobiological ResourcesySociety for Techno-innovation of Agriculture, Forestry and Fisheries, Kannondai, Tsukuba, Ibaraki 305, Japan
*National Institute of Agrobiological Resources, 1-2-1, Kannondai, Tsukuba, Ibaraki 305, Japan
*Plant Breeding Laboratory, Department of Agriculture, Kyushu University, Hakozaki, Higashiku, Fukuoka 812-81, Japan

==References==
<references>
* <ref name="ref1">
Yoshimura S, Umehara Y, Kurata N, et al. Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice[J]. Theoretical and Applied Genetics, 1996, 93(1-2): 117-122.
</ref>
* <ref name="ref2">
oshimura S, Yamanouchi U, Katayose Y, et al. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation[J]. Proceedings of the National Academy of Sciences, 1998, 95(4): 1663-1668.
</ref>
* <ref name="ref3">
Sasaki T. The rice genome project in Japan[J]. Proceedings of the National Academy of Sciences, 1998, 95(5): 2027-2028.
</ref>
</references>

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0622600

2017-03-27T11:52:44Z

Xysj1980: /* Structure */

Xa-1 is one of bacterial blight resistance genes in rice. Although at least 38 resistance genes have been identified, Xa-1 is specific to ''X. oryzae pv. Oryzae''. Xa-1 can be considered as a dominant resistance gene<ref name="ref1" />.
==Annotated Information==
===Function===
The Xa1 gene in rice confers resistance to Japanese race 1 of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial blight (BB). We isolated the Xa1 gene by a map-based cloning strategy. The deduced amino acid sequence of the Xa1 gene product contains nucleotide binding sites (NBS) and a new type of leucine-rich repeats (LRR); thus, Xa1 is a member of the NBS-LRR class of plant disease-resistance genes, but quite different from Xa21, another BB-resistance gene isolated from rice. <ref name="ref2" /><ref name="ref3" />
Xa1 Is a Single-Copy Gene. Southern hybridization analysis was carried out by using the genomic DNAs from resistance line IR-BB1 and susceptible isogenic line IR24. The NBS region of Xa1 hybridized to a single band of DNA from IR-BB1 and IR24, suggesting that Xa1 is a single-copy gene and IR24 also has a sequence homologous to Xa1 at the same locus.<ref name="ref2" /><ref name="ref3" />

===Expression===
Xa1 gene expression was induced on inoculation with a bacterial pathogen and wound, unlike other isolated resistance genes in plants, which show constitutive expression. The induced expression may be involved in enhancement of resistance against the pathogen.<ref name="ref2" />[[File:rice4.jpg‎|right|thumb|250px|]]
So far, there is no report of induced expressed R gene. Interestingly, Xa1 mRNA was detected from rice leaves at 5
days after cutting with water and inoculation of both the compatible and incompatible strains of Xoo, but was not detected in intact leaves. These findings suggested that the Xa1 gene expression may be induced by stimulus of wounding involved in pathogen infection, and accumulation of Xa1 gene product may lead to high efficiency of interaction with avr gene product. This interaction may activate the signal transductions involved in Xa1-madiated BB resistance. Thus, it is likely that Xa1 plays an important role in pathogen recognition, which is supported by the analysis of race-specific resistance of the Xa1 transformants. Which factors regulate the expression of Xa1 remains an interesting question.<ref name="ref2" />

===Evolution===
[[File:rice3.jpg‎|right|thumb|150px|]][[File:rice2.jpg‎|right|thumb|150px|]]
Map-based cloning methods have been applied for isolation of Xa-1, one of the bacterial blight resistance genes in rice.Xa-1 was previously mapped on chromosome 4 using molecular markers. For positional cloning of Xa-1, a high-resolution genetic map was made for theXa-1 region using an F2population of 402 plants and additional molecular markers. Three restriction fragment length polymorphism (RFLP) markers, XNpb235, XNpb264 andC600 were found to be linked tightly to Xa-1, with no recombinants, and U08750 was mapped 1.5 cM from Xa-1. The screening of a yeast artificial chromosome (YAC) library using theseXa-1-linked RFLP markers resulted in the identification of ten contiguous YAC clones. Among these, one YAC clone, designated Y5212, with an insert of 340 kb, hybridized with all three tightly linked markers. This YAC was confirmed to possess the Xa-1 allele by mapping the Xa-1 gene between both end clones of this YAC (Y5212R and Y5212L).<ref name="ref1" />

Based on the deduced amino acid sequence, the Xa1 gene is a class 1 resistance gene; a cytoplasmic receptor-like protein with NBS and LRR domains. Thus, the structure is quite different from the first cloned rice resistance gene, Xa21 (16), which is a class 4 gene. The most intriguing finding is that the expression of Xa1, unlike any previously studied resistance genes, is induced by pathogen infection and wound.<ref name="ref2" />

===Structure===
*The composite nucleotide sequence of the Xa1 cDNA encoded a 5,406-bp ORF that was flanked by 59 and 39 untranslated regions of 112 and 392 bp, respectively. The nucleotide sequence of the 13.5-kb EcoRI-BamHI genomic fragment was also determined and compared with that of the cDNA sequence. The Xa1 gene was composed of four exons separated by three introns.<ref name="ref2" />[[File:rice1.jpg|right|thumb|250px|]]
*The C-terminal half of Xa1 gene is composed of LRR, the common motif of the several classes of resistance genes.
*XA1 protein contains 22 potential N-linked glycosylation sites. Six of these sites are at amino acid position 36 of each LRR repeat. These structural characteristics suggest that the Xa1 product interacts with other proteins in a defense reaction–signal transduction pathway<ref name="ref2" />.

==Labs working on this gene==
*Department of Agriculture, Kyushu University, 6-10-1, Hakozaki, Higashiku, Fukuoka 812, Japan
*Rice Genome Research Program, National Institute of Agrobiological ResourcesySociety for Techno-innovation of Agriculture, Forestry and Fisheries, Kannondai, Tsukuba, Ibaraki 305, Japan
*National Institute of Agrobiological Resources, 1-2-1, Kannondai, Tsukuba, Ibaraki 305, Japan
*Plant Breeding Laboratory, Department of Agriculture, Kyushu University, Hakozaki, Higashiku, Fukuoka 812-81, Japan

==References==
<references>
* <ref name="ref1">
Yoshimura S, Umehara Y, Kurata N, et al. Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice[J]. Theoretical and Applied Genetics, 1996, 93(1-2): 117-122.
</ref>
* <ref name="ref2">
oshimura S, Yamanouchi U, Katayose Y, et al. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation[J]. Proceedings of the National Academy of Sciences, 1998, 95(4): 1663-1668.
</ref>
* <ref name="ref3">
Sasaki T. The rice genome project in Japan[J]. Proceedings of the National Academy of Sciences, 1998, 95(5): 2027-2028.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0622600

2017-03-27T11:52:32Z

Xysj1980:

Xa-1 is one of bacterial blight resistance genes in rice. Although at least 38 resistance genes have been identified, Xa-1 is specific to ''X. oryzae pv. Oryzae''. Xa-1 can be considered as a dominant resistance gene<ref name="ref1" />.
==Annotated Information==
===Function===
The Xa1 gene in rice confers resistance to Japanese race 1 of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial blight (BB). We isolated the Xa1 gene by a map-based cloning strategy. The deduced amino acid sequence of the Xa1 gene product contains nucleotide binding sites (NBS) and a new type of leucine-rich repeats (LRR); thus, Xa1 is a member of the NBS-LRR class of plant disease-resistance genes, but quite different from Xa21, another BB-resistance gene isolated from rice. <ref name="ref2" /><ref name="ref3" />
Xa1 Is a Single-Copy Gene. Southern hybridization analysis was carried out by using the genomic DNAs from resistance line IR-BB1 and susceptible isogenic line IR24. The NBS region of Xa1 hybridized to a single band of DNA from IR-BB1 and IR24, suggesting that Xa1 is a single-copy gene and IR24 also has a sequence homologous to Xa1 at the same locus.<ref name="ref2" /><ref name="ref3" />

===Expression===
Xa1 gene expression was induced on inoculation with a bacterial pathogen and wound, unlike other isolated resistance genes in plants, which show constitutive expression. The induced expression may be involved in enhancement of resistance against the pathogen.<ref name="ref2" />[[File:rice4.jpg‎|right|thumb|250px|]]
So far, there is no report of induced expressed R gene. Interestingly, Xa1 mRNA was detected from rice leaves at 5
days after cutting with water and inoculation of both the compatible and incompatible strains of Xoo, but was not detected in intact leaves. These findings suggested that the Xa1 gene expression may be induced by stimulus of wounding involved in pathogen infection, and accumulation of Xa1 gene product may lead to high efficiency of interaction with avr gene product. This interaction may activate the signal transductions involved in Xa1-madiated BB resistance. Thus, it is likely that Xa1 plays an important role in pathogen recognition, which is supported by the analysis of race-specific resistance of the Xa1 transformants. Which factors regulate the expression of Xa1 remains an interesting question.<ref name="ref2" />

===Evolution===
[[File:rice3.jpg‎|right|thumb|150px|]][[File:rice2.jpg‎|right|thumb|150px|]]
Map-based cloning methods have been applied for isolation of Xa-1, one of the bacterial blight resistance genes in rice.Xa-1 was previously mapped on chromosome 4 using molecular markers. For positional cloning of Xa-1, a high-resolution genetic map was made for theXa-1 region using an F2population of 402 plants and additional molecular markers. Three restriction fragment length polymorphism (RFLP) markers, XNpb235, XNpb264 andC600 were found to be linked tightly to Xa-1, with no recombinants, and U08750 was mapped 1.5 cM from Xa-1. The screening of a yeast artificial chromosome (YAC) library using theseXa-1-linked RFLP markers resulted in the identification of ten contiguous YAC clones. Among these, one YAC clone, designated Y5212, with an insert of 340 kb, hybridized with all three tightly linked markers. This YAC was confirmed to possess the Xa-1 allele by mapping the Xa-1 gene between both end clones of this YAC (Y5212R and Y5212L).<ref name="ref1" />

Based on the deduced amino acid sequence, the Xa1 gene is a class 1 resistance gene; a cytoplasmic receptor-like protein with NBS and LRR domains. Thus, the structure is quite different from the first cloned rice resistance gene, Xa21 (16), which is a class 4 gene. The most intriguing finding is that the expression of Xa1, unlike any previously studied resistance genes, is induced by pathogen infection and wound.<ref name="ref2" />

===Structure===
*The composite nucleotide sequence of the Xa1 cDNA encoded a 5,406-bp ORF that was flanked by 59 and 39 untranslated regions of 112 and 392 bp, respectively. The nucleotide sequence of the 13.5-kb EcoRI-BamHI genomic fragment was also determined and compared with that of the cDNA sequence. The Xa1 gene was composed of four exons separated by three introns.<ref name="ref2" />[[File:rice1.jpg|right|thumb|250px|]]
*The C-terminal half of Xa1 gene is composed of LRR, the common motif of the several classes of resistance genes.
*XA1 protein contains 22 potential N-linked glycosylation sites. Six of these sites are at amino acid position 36 of each LRR repeat. These structural characteristics suggest that the Xa1 product interacts with other proteins in a defense reaction–signal transduction pathway<ref name="ref2" />.

Identification of the Xa1 Candidate cDNA Clone by High-Resolution Mapping and Sequence Analysis.We isolated a 340-kb YAC clone, Y5212, that spans the Xa1 locus (Fig. 1A) (27). To identify expressed sequences in the region of Y5212, a cDNA library of IR-BB1 (Xa1yXa1) was constructed with vector lambda gt10 and screened with Y5212clone DNA. Thirty-three positive clones were obtained; they were classified into 21 classes based on their 39 sequences.<ref name="ref2" />

==Labs working on this gene==
*Department of Agriculture, Kyushu University, 6-10-1, Hakozaki, Higashiku, Fukuoka 812, Japan
*Rice Genome Research Program, National Institute of Agrobiological ResourcesySociety for Techno-innovation of Agriculture, Forestry and Fisheries, Kannondai, Tsukuba, Ibaraki 305, Japan
*National Institute of Agrobiological Resources, 1-2-1, Kannondai, Tsukuba, Ibaraki 305, Japan
*Plant Breeding Laboratory, Department of Agriculture, Kyushu University, Hakozaki, Higashiku, Fukuoka 812-81, Japan

==References==
<references>
* <ref name="ref1">
Yoshimura S, Umehara Y, Kurata N, et al. Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice[J]. Theoretical and Applied Genetics, 1996, 93(1-2): 117-122.
</ref>
* <ref name="ref2">
oshimura S, Yamanouchi U, Katayose Y, et al. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation[J]. Proceedings of the National Academy of Sciences, 1998, 95(4): 1663-1668.
</ref>
* <ref name="ref3">
Sasaki T. The rice genome project in Japan[J]. Proceedings of the National Academy of Sciences, 1998, 95(5): 2027-2028.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os09g0106700

2017-03-27T11:47:30Z

Xysj1980:

The rice '''''Os09g0106700''''' was reported as '''''PutAKT1''''' in 2009 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Function===
* ''PutAKT1'' is involved in mediating K+ uptake (i) both in low- and in high-afﬁnity K+ uptake range, and (ii)in ''P. tenuiﬂora'' , even under saltstress condition.The notion that ''AKT1''-type channels are the main K+ uptake pathway into the plant root was based on their dominant expression in the roots and studies of ''AKT1''-disrupted mutants.
*''PutAKT1'' not only increases tissue K+ accumulation, but also decreases Na+<ref name="ref 1"/>.

===Expression===
*The AKT1 is preferentially expressed in peripheral root cell layers and root hairs.
*Expression of ''PutAKT1'' increased the K+ content under normal K+ -starvation,and NaCl-stress conditions.
*The expression of ''PutAKT1'' was induced by K+-starvation stress in the roots and was not downregulated by the presence of excess Na+.Over-expressing ''PutAKT1'' showed enhanced salt tolerance compared to wild-type plants as shown by their shoot phenotype and dry weight.
* Expression of ''PutAKT1'' also showed a decrease in Na+ accumulation both in the shoot and in the root.
====Expression in experiment====
Subjected to NaCl and K+-starvation stresses for 24 h, ''PutAKT1'' was predominantly expressed in the roots under all conditions tested (about two-fold higher than in the shoots). To gain further insight into ionic stress regulation of PutAKT1 expression in roots, ''PutAKT1'' expression was monitored over a 24-h period.
*In rice, the expression
level of ''PutAKT1'' is down-regulated by excessive external NaCl. Under K+-starvation stress, ''PutAKT1'' was dramatically induced at 24 h of stress.

===Evolution===
*''PutAKT1'' belongs to the ''AKT1''-subfamily in the Shaker K+ channel family. ''PutAKT1'' was localized in the plasma membrane and it was preferentially expressed in the roots.there are three ''AKT1''-type K+ channel genes in Arabidopsis and two in rice.Genomic Southern-hybridizations using DIGlabeled PutAKT1 were performed with probes from the coding region of the PutAKT1. The result revealed a number of PutAKT1 hybridizing bands, suggesting that ''PutAKT''1 belongs to a small gene family.

==Labs working on this gene==
* Asian Natural Environmental Science Center (ANESC),The University of Tokyo, 1-1-1 Midori-Cho, Nishitokyo,Tokyo 188-0002, Japan
* Department of Agronomy and Horticulture,Bogor Agricultural University (IPB), Jl. Meranti, Kampus IPB, Darmaga Bogor 16680, Indonesia S. Liu
* Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China

==References==
<references>
* <ref name="ref1">
Ardie SW, Liu S, Takano T. Expression of the AKT1-type K(+) channel gene from
Puccinellia tenuiflora, PutAKT1, enhances salt tolerance in Arabidopsis. Plant
Cell Rep. 2010 Aug;29(8):865-74. doi: 10.1007/s00299-010-0872-2. PubMed PMID:
20532513.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os11g0591800

2017-03-27T11:46:35Z

Xysj1980:

The rice '''''Os11g0591800''''' was reported as '''''OsPR4d''''' in 2010 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os11g0591800''''' '''<=>''' '''''OsPR4d,PR4d'''''

===Function===
* '''''PR4''''' proteins constitute a pathogenesis-related (PR) protein family with a conserved BARWIN domain.
* The rice PR4 genes are also involved in abiotic stress responses and tolerance in addition to their responsiveness to pathogen attacks.

===Phenotypic analysis===
* Transgenic rice with overexpression of '''''OsPR4a''''' showed enhanced tolerance to drought at both seedling and reproductive stages..

===Expression===
* OsPR4 genes showed diverse temporal–spatial expression patterns, and their expressions are responsive to Magnaporthe grisea infection. Interestingly, the OsPR4 genes are also responsive to abiotic stresses.
* Their expression levels were strongly induced by at least one of the stress treatments including drought, salt, cold, wounding, heat shock, and ultraviolet.
* The transcript levels of OsPR4 genes were also induced by some phytohormones such as abscisic acid and jasmonic acid.
 
[[File:232-Os11g0592200.png|center|thumb|727px|'''Figure 4. (SnapShot)''' ''Expression level of OsPR4 genes in various tissues or organs. (A) Expression levels examined by quantitative real-time RT-PCR.<ref name="ref1" />.'']]

===Evolution===
* The PR4 genes are located in tandem on chromosome 11 and constitute a gene cluster with high sequence similarity to each other.
* The OsPR4 proteins have high sequence similarity to reported PR4 proteins from monocotyledonous species and are predicted to be class II PR4 proteins.
* Distinct diversification of plant PR4 proteins exists between monocotyledonous and dicotyledonous plants.

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

==Labs working on this gene==
* National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
* College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
==References==
<references>
* <ref name="ref1">
Wang N, Xiao B, Xiong L. Identification of a cluster of PR4-like genes
involved in stress responses in rice. J Plant Physiol. 2011 Dec
15;168(18):2212-24. doi: 10.1016/j.jplph.2011.07.013. PubMed PMID: 21955397.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 11]]

Os07g0459200

2017-03-27T11:39:22Z

Xysj1980: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
''OsABC1-10'' is located in chromosome 7 which contains 7 extrons, and encodes a protein of 623 amino acids.
===Function===
Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />. Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.
There are 15 non-redundant ABC1genes distributed on all rice chromosomes randomly except chromosomes 3, 8, 10, and 12 in rice, and were named from OsABC1-1 to OsABC1-15 according to their chromosomal location (table 1). However, there are 17 members of ABC1 family in ''Arabidopsis''. All of these genes contain introns and the number of intron varies greatly, and intron gain was an important event accompanying the recent evolution of the rice ABC1 family <ref name="ref4" />.
[[File:abc1-table.jpg|middle|thumb|530px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />. The XaXasX2QV segment that functions as a nucleotide-binding motif for protein kinases is highly conserved in ABC1 domain as well as lysine residue in N-terminal that as a binding site for chemical groups. In addition, other conserved amino acid valine and aspartate acid in the middle of the domain and glutamate acid in the C-terminal. It is also suggested that there are 10 putative motifs in rice ABC1 proteins.
The real-time PCR results show that 14 genes express mainly in leaves. The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

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

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os11g0591800

2017-03-27T11:38:55Z

Xysj1980: /* Annotated Information */

The rice '''''Os11g0591800''''' was reported as '''''OsPR4d''''' in 2009 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os11g0591800''''' '''<=>''' '''''OsPR4d,PR4d'''''

===Function===
* '''''PR4''''' proteins constitute a pathogenesis-related (PR) protein family with a conserved BARWIN domain.
* The rice PR4 genes are also involved in abiotic stress responses and tolerance in addition to their responsiveness to pathogen attacks.

===Phenotypic analysis===
* Transgenic rice with overexpression of '''''OsPR4a''''' showed enhanced tolerance to drought at both seedling and reproductive stages..

===Expression===
* OsPR4 genes showed diverse temporal–spatial expression patterns, and their expressions are responsive to Magnaporthe grisea infection. Interestingly, the OsPR4 genes are also responsive to abiotic stresses.
* Their expression levels were strongly induced by at least one of the stress treatments including drought, salt, cold, wounding, heat shock, and ultraviolet.
* The transcript levels of OsPR4 genes were also induced by some phytohormones such as abscisic acid and jasmonic acid.
 
[[File:232-Os11g0592200.png|center|thumb|727px|'''Figure 4. (SnapShot)''' ''Expression level of OsPR4 genes in various tissues or organs. (A) Expression levels examined by quantitative real-time RT-PCR.<ref name="ref1" />.'']]

===Evolution===
* The PR4 genes are located in tandem on chromosome 11 and constitute a gene cluster with high sequence similarity to each other.
* The OsPR4 proteins have high sequence similarity to reported PR4 proteins from monocotyledonous species and are predicted to be class II PR4 proteins.
* Distinct diversification of plant PR4 proteins exists between monocotyledonous and dicotyledonous plants.

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

==Labs working on this gene==
* National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
* College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
==References==
<references>
* <ref name="ref1">
Wang N, Xiao B, Xiong L. Identification of a cluster of PR4-like genes
involved in stress responses in rice. J Plant Physiol. 2011 Dec
15;168(18):2212-24. doi: 10.1016/j.jplph.2011.07.013. PubMed PMID: 21955397.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 11]]

Os09g0567800

2017-03-27T11:36:42Z

Xysj1980:

Please input one-sentence summary here.

==Annotated Information==
===Function===
This gene encodes an lipolytic enzyme(lipase) involved in the degradation of fat,which will form fatty acids, glycerol and monoglyceride or diacylglycerol.<ref name="ref1" />lipolytic enzyme perform essential roles in the digestion, transport and processing of dietary lipids (e.g. triglycerides, fats, oils) in most, if not all, living organisms.Most lipases act at a specific position on the glycerol backbone of lipid substrate (A1, A2 or A3)(small intestine).
Lipases are involved in diverse biological processes ranging from routine metabolism of dietary triglycerides to cell signaling<ref name="ref2" /> and inflammation.<ref name="ref3" />Thus, some lipase activities are confined to specific compartments within cells while others work in extracellular spaces.Other lipase enzymes, such as pancreatic lipases, are secreted into extracellular spaces where they serve to process dietary lipids into more simple forms that can be more easily absorbed and transported throughout the body.As biological membranes are integral to living cells and are largely composed of phospholipids, lipases also play important roles in cell biology.

===Expression===
Lipases are important biocatalysts showing many interesting properties with industrial applications. Previously, different isoforms of lipases, Lipase-I and Lipase-II from rice (Oryza sativa) have been purified and characterized. Lipase-II identified as the major lipase in rice bran is designated as rice bran lipase (RBL). An exploration of expression in four different E. coli expression systems analyzed: BL21(DE3)pLysS, RIL(DE3)pLysS, Rosetta(DE3)pLysS and Origami(DE3)pLysS indicated that E. coli was not a suitable host. Expression with supplement of rare codons in Rosetta (DE3)pLysS and RIL(DE3)pLysS resulted in highest expression as insoluble inclusion bodies. The hurdles of expression in E. coli were overcome by expression as a secretory protein in P. pastoris X-33. The expression of lipase in shake flasks was optimized to achieve the maximum recombinant lipase activity of 152.6 U/mL. The purified recombinant lipase had a specific activity of 998 U/mg toward triacetin. The pH and temperature optimum of native and recombinant enzymes were pH 7.4 and 25 ± 2 °C, respectively. Both the lipases showed higher activity toward short chain triacylglycerol and unsaturated fatty acid enriched oils. Computational modeling and molecular docking studies reveal that the catalytic efficiency of the lipase correlates with the distance of the nucleophilic Ser(175)-OH and the scissile ester bond. The shorter the distance, the greater is the turnover of the substrate.<ref name="ref4" />

===Evolution===
one study characterized a rice mutant, the most obvious phenotypes of which are high tillering, reduced height, and infertile spikelets (named this1). Similarly to the high tiller number and dwarf mutants in rice, the increased tiller number of this1 plants is ascribed to the release of tiller bud outgrowth rather than to increased tiller bud formation. In the this1 mutant, however, the accelerated rate of branching was delayed until the stem elongation stage, while other mutants lost the ability to control branching at all developmental stages. The seed-setting rate of this1 was less than half that of the wild type, owing to defects in pollen maturation, anther dehiscence, and flower opening. Histological analyses showed that the mutation in this1 resulted in anisotropic cell expansion and cell division. Using a map-based cloning approach, This1 was found to encode a class III lipase. Homology searches revealed that THIS1 is conserved in both monocots and eudicots, suggesting that it plays fundamental role in regulating branch and spikelet fertility, as well as other aspects of developmental control. The relative change in expression of marker genes highlighted the possibility that This1 is involved in phytohormone signalling pathways, such as those for strigolactone and auxin. Thus, This1 provides joint control between shoot branching and reproductive development.<ref name="ref5" />

==Labs working on this gene==
*Department of Biochemistry and Molecular Biology ,Oklahoma University Health Sciences Center, Oklahoma City, USA.

*Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20007, USA

*Department of Biological Sciences, Hunter College of City University of New York, 695 Park Ave, New York, NY 10021, USA

*Laboratory of Signal Transduction, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

*The Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112

*Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.

==References==
<references>
<ref name="ref1">Chi-Sun Wang, Jean A. Hartsuck. (1993)Bile salt-activated lipase. A multiple function lipolytic enzyme.Biochimica et Biophysics Acta, 1166: l-19.</ref>
<ref name="ref2">Spiegel S, Foster D, and R Kolesnick.(1996) Signal transduction through lipid second messengers. Current Opinion in Cell Biology 8(2): 159–67.</ref>
<ref name="ref3">Tjoelker LW, Eberhardt C, Unger J, Trong HL, Zimmerman GA, McIntyre TM, Stafforini DM, Prescott SM, and PW Gray.(1995) Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad. J Biol Chem 270(43): 25481–7.</ref>
<ref name="ref4">Vijayakumar KR, Gowda LR.(2013)Rice (Oryza sativa) lipase: molecular cloning, functional expression and substrate specificity.Protein Expr Purif.88(1):67-79.</ref>
<ref name="ref5">Liu W1, Zhang D, Tang M, Li D, Zhu Y, Zhu L, Chen C.(2013)THIS1 is a putative lipase that regulates tillering, plant height, and spikelet fertility in rice.J Exp Bot.64(14):4389-402.</ref>
</references>

==Structured Information==
 
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0567800

2017-03-27T11:35:27Z

Xysj1980: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
This gene encodes an lipolytic enzyme(lipase) involved in the degradation of fat,which will form fatty acids, glycerol and monoglyceride or diacylglycerol.<ref name="ref1" />lipolytic enzyme perform essential roles in the digestion, transport and processing of dietary lipids (e.g. triglycerides, fats, oils) in most, if not all, living organisms.Most lipases act at a specific position on the glycerol backbone of lipid substrate (A1, A2 or A3)(small intestine).
Lipases are involved in diverse biological processes ranging from routine metabolism of dietary triglycerides to cell signaling<ref name="ref2" /> and inflammation.<ref name="ref3" />Thus, some lipase activities are confined to specific compartments within cells while others work in extracellular spaces.Other lipase enzymes, such as pancreatic lipases, are secreted into extracellular spaces where they serve to process dietary lipids into more simple forms that can be more easily absorbed and transported throughout the body.As biological membranes are integral to living cells and are largely composed of phospholipids, lipases also play important roles in cell biology.

===Expression===
Lipases are important biocatalysts showing many interesting properties with industrial applications. Previously, different isoforms of lipases, Lipase-I and Lipase-II from rice (Oryza sativa) have been purified and characterized. Lipase-II identified as the major lipase in rice bran is designated as rice bran lipase (RBL). An exploration of expression in four different E. coli expression systems analyzed: BL21(DE3)pLysS, RIL(DE3)pLysS, Rosetta(DE3)pLysS and Origami(DE3)pLysS indicated that E. coli was not a suitable host. Expression with supplement of rare codons in Rosetta (DE3)pLysS and RIL(DE3)pLysS resulted in highest expression as insoluble inclusion bodies. The hurdles of expression in E. coli were overcome by expression as a secretory protein in P. pastoris X-33. The expression of lipase in shake flasks was optimized to achieve the maximum recombinant lipase activity of 152.6 U/mL. The purified recombinant lipase had a specific activity of 998 U/mg toward triacetin. The pH and temperature optimum of native and recombinant enzymes were pH 7.4 and 25 ± 2 °C, respectively. Both the lipases showed higher activity toward short chain triacylglycerol and unsaturated fatty acid enriched oils. Computational modeling and molecular docking studies reveal that the catalytic efficiency of the lipase correlates with the distance of the nucleophilic Ser(175)-OH and the scissile ester bond. The shorter the distance, the greater is the turnover of the substrate.<ref name="ref4" />

===Evolution===
one study characterized a rice mutant, the most obvious phenotypes of which are high tillering, reduced height, and infertile spikelets (named this1). Similarly to the high tiller number and dwarf mutants in rice, the increased tiller number of this1 plants is ascribed to the release of tiller bud outgrowth rather than to increased tiller bud formation. In the this1 mutant, however, the accelerated rate of branching was delayed until the stem elongation stage, while other mutants lost the ability to control branching at all developmental stages. The seed-setting rate of this1 was less than half that of the wild type, owing to defects in pollen maturation, anther dehiscence, and flower opening. Histological analyses showed that the mutation in this1 resulted in anisotropic cell expansion and cell division. Using a map-based cloning approach, This1 was found to encode a class III lipase. Homology searches revealed that THIS1 is conserved in both monocots and eudicots, suggesting that it plays fundamental role in regulating branch and spikelet fertility, as well as other aspects of developmental control. The relative change in expression of marker genes highlighted the possibility that This1 is involved in phytohormone signalling pathways, such as those for strigolactone and auxin. Thus, This1 provides joint control between shoot branching and reproductive development.<ref name="ref5" />

==Labs working on this gene==
*Department of Biochemistry and Molecular Biology ,Oklahoma University Health Sciences Center, Oklahoma City, USA.

*Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20007, USA

*Department of Biological Sciences, Hunter College of City University of New York, 695 Park Ave, New York, NY 10021, USA

*Laboratory of Signal Transduction, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

*The Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112

*Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.

==References==
<references>
<ref name="ref1">Chi-Sun Wang, Jean A. Hartsuck. (1993)Bile salt-activated lipase. A multiple function lipolytic enzyme.Biochimica et Biophysics Acta, 1166: l-19.</ref>
<ref name="ref2">Spiegel S, Foster D, and R Kolesnick.(1996) Signal transduction through lipid second messengers. Current Opinion in Cell Biology 8(2): 159–67.</ref>
<ref name="ref3">Tjoelker LW, Eberhardt C, Unger J, Trong HL, Zimmerman GA, McIntyre TM, Stafforini DM, Prescott SM, and PW Gray.(1995) Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad. J Biol Chem 270(43): 25481–7.</ref>
<ref name="ref4">Vijayakumar KR, Gowda LR.(2013)Rice (Oryza sativa) lipase: molecular cloning, functional expression and substrate specificity.Protein Expr Purif.88(1):67-79.</ref>
<ref name="ref5">Liu W1, Zhang D, Tang M, Li D, Zhu Y, Zhu L, Chen C.(2013)THIS1 is a putative lipase that regulates tillering, plant height, and spikelet fertility in rice.J Exp Bot.64(14):4389-402.</ref>

==Structured Information==
 
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os05g0486100

2017-03-27T11:33:35Z

Xysj1980:

Please input one-sentence summary here.

==Annotated Information==
[[File:x.jpg|right|thumb|350px|Fig.1 Top:1-week-old seedlings Bottom: 4-week-old seedlings]] [[File:F2.jpg|right|thumb|300px|Fig.2 Top: Roots of 10-day-old plants Bottom: Roots of 4-week-old plants ]] [[File:F3.jpg|right|thumb|300px|Fig.3 Top: Histology of root apex visualized on optical longitudinal sections of living embryonic primary roots Bottom: Longitudinal sections of primary root ]]

===Function===
This gene encodes a Ca2+-independent Ser/Thr kinase which is induced by auxin and abscisic acid (ABA). The novel leucine-rich-repeat receptor-like kinase affects the root system architecture by negatively regulating polar auxin transport in rice.<ref name="ref1" /> Knockdown of OsRPK1 promoted the growth of transgenic rice plants, and increased plant height and tiller numbers. In contrast, over-expressing plants showed undeveloped adventitious roots, lateral roots, and a reduced root apicalmeristem. OsRPK1 over-expression also inhibited the expression ofmost auxin efflux carrier OsPIN genes, which was accompanied by changes in PAT and endogenous free IAA distribution in the leaves and roots.
This study demonstrated a common regulatory pathway of root system development in higher plants, which might be initiated by external stimuli via upstream receptor-like kinases and downstream carriers for polar auxin transport.

===Wild Type VS. Mutant===

Three under-expressing lines:A5, A7, A9

Three over-expressing lines: O1, O7, O8

One week after germination, the growth of the primary embryonic root was delayed in the over-expressing lines, whereas the under-expressing lines had more adventitious root production compared with WT. At the seedling stage, over-expressing lines exhibited significant shorter shoot height and less fresh weight compared with the WT or under-expressing lines. From the seedling to the tillering stage, under-expressing lines had an increased tiller number compared with the WT and over-expressing lines. At the ripening stage, there were significant differences between WT and the transgenic lines in the total and effective tiller number per plant. ComparedwithWT, over-expressing lines showed a 25% decrease in the effective tiller number, leading to a 27% reduction in grain yield per plant(Fig.1)

Over-expressing lines had a smaller root system and fewer adventitious roots . Lateral root formation was severely defective in over-expressing lines. (Fig.2)

Under-expressing lines had well-developed meristems and elongation zones compared with WT, which were slightly defective
in over-expressing plants.(Fig.3)

===Expression===

This gene is predominantly expressed in root tips, leaf blades, and undifferentiated suspension cells, and is markedly induced by treatment with auxin or ABA.

The expression of OsRPK1 in different tissues was analyzed by realtime quantitative PCR. The results showed that OsRPK1 had a higher expression in root tips and leaf blades.Compared with the roots, the expression of OsRPK1 was reduced 5-fold in the stem and 2-fold in the leaf sheath. Real-time PCR analyses showed that the expression of OsRPK1 was induced mainly by exogenous auxin (2,4-D and IAA) and ABA within 12 h of treatment.<ref name="ref1" />(Fig.4)
[[File:34e.jpg|thumb|300px|Fig.4 Top:Tissue specific expression of OsRPK1 in wild-type rice plants Bottom: Relative expression levels of OsRPK1 in the roots of 2-week old wild type seedlings with reagents treatment for 0 h and 12 h]]

===Evolution===
Data revealed that OsRPK1, which was designated Osi000900.2 and belongs to the LRR-VIII subfamily of RLK/Pelle in rice, had no close homologues in any other plant genome . For example, OsRPK1 shows 68 and 58% identity with EES19713 from Sorghum bicolor and CCB55930 proteins from Vitis vinifera, respectively, and 56% identity with XP_003547844 from Glycine max. In the rice genome, Os03g0329700 and Os01g0816600 proteins share 58 and 56% identity with OsRPK1, respectively. In addition, the results demonstrated that OsRPK1 is a novel leucine-rich-repeat receptor-like kinase (LRRRLK), and no function had been assigned. OsRPK1 contains six periplasmic LRR motifs, one transmembrane domain, and one conserved cytoplasmic kinase domain . The kinase domain contained all 12 conserved sub-domains of the eukaryotic protein kinase, HRDIKSTN in the VIb sub-domain, and GTLGYLDPEY in the VIII sub-domain, indicating that OsRPK1 is a serine/threonine kinase

Receptor-like kinases (RLKs) are a family of transmembrane proteins with versatile N-terminal extracellular domains and C-terminal intracellular kinases.Analysis of four fungal, six metazoan, and two Plasmodium sp. genomes indicates that the family was represented in all but fungal genomes, indicating an ancient origin for the family with a more recent expansion only in the plant lineages.

None of the four fungal genomes examined contained recognizable RLK/Pelle family members. However, the presence of family members in Plasmodium sp. and animal genomes suggests an origin for the RLK/Pelle family in a common ancestor of all genomes examined. The consistently low gene numbers in genomes other than Arabidopsis suggest that a dramatic expansion occurred in the plant lineage. On the other hand, the absence of family members in the fungal genomes examined indicates the RLK/Pelle family may be lost in fungal lineages after fungus-metazoan split.<ref name="ref2" /> <ref name="ref3" />

==Labs working on this gene==
1.Dept. of Biochemistry & Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China

2.Japan Biological Information Research Center

3.EMBL Outstation–European Bioinformatics Institute, United Kingdom

4.Department of Biology, McGill University, Canada

5.Department of Genetics, The University of Georgia, USA

6.Center for Information Biology and DNA Data Bank of Japan

7.Graduate School of Information Science and Technology, Hokkaido University, Japan.

==References==
1.Yu Zou, Xiaoyu Liu, QingWang, Yu Chen, Cheng Liu, Yang Qiu,Wei Zhang, OsRPK1, a novel leucine-rich repeat receptor-like kinase, negatively regulates polar auxin transport and root development in rice, Biochimica et Biophysica Acta 1840 (2014) 1676–1685

2.Shin-Han Shiu and Anthony B. Bleecker, Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis, Plant Physiol. 132 (2003) 530–543.

3.S.H. Shiu, A.B. Bleecker, Plant receptor-like kinase gene family: diversity, function, and signaling, Sci. STKE 2001 (2001) RE22.

4.Cui-Cui Shi1, Cui-Cui Feng1, Mei-Mei Yang, Overexpression of the receptor-like protein kinase genes AtRPK1 andOsRPK1 reduces the salt tolerance of Arabidopsis thaliana, Plant Science 217– 218 (2014) 63– 70

5.Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Curated genome annotation of Oryza sativa ssp.japonica and comparative genome analysis with Arabidopsis thaliana, Genome Research 17:175–183 2007

6.Tsuyoshi Tanaka1, Baltazar A. Antonio1, Shoshi Kikuchi, The Rice Annotation Project Database (RAP-DB): 2008 update, Nucleic Acids Research, D1028–D1033 ( 2008)

<references>
<ref name="ref1">XXX</ref>
<ref name="ref2">XXX</ref>
<ref name="ref3">XXX</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

Os08g0114200

2017-03-27T03:05:47Z

Xysj1980:

'''''Os08g0114200''''' is OsGLU3 which is similar to CEL5=CELLULASE 5 coding a β-1,4-endoglucanase，playing an significant role in root elongation in rice
==Annotated Information==
===Introduce===
'''Endo-1,4-β-D-glucanases (EGases)''' form a large family of hydrolytic enzymes in prokaryotes and eukaryotes.In higher plants, potential substratesin vivo are xyloglucan and non-crystalline cellulose in the cell wall.Gene expression patterns suggest a role for EGases in various developmental processes such as leaf abscission,fruit ripening and cell expansion. Using Arabidopsis thaliana genetics, scientists demonstrate the requirement of a specialized member of the EGase family for the correct assembly of the walls of elongating cells.'''KORRIGAN(KOR)''' is identified by an extreme dwarf mutant with pronounced architectural alterations in the primary cell wall. The '''KORgene''' was isolated and encodes a membrane-anchored member of the EGase family, which is highly conserved between mono- and icotyledonous plants. '''KOR''' is located primarily in the plasma membrane and presumably acts at the plasma membrane–cell wall interface.'''KORmRNA''' was found in all organs examined, and in the developing darkgrown hypocotyl, mRNA levels were correlated with rapid cell elongation. Among plant growth factors involved in the control of hypocotyl elongation (auxin, gibberellins and ethylene) none significantly influenced KOR-mRNA levels. However, reducedKOR-mRNA levels were observed in det2, a mutant deficient for brassinosteroids. Although the in vivo substrate remains to be determined, the mutant phenotype is consistent with a central role for KOR in the assembly of the cellulose–hemicellulose network in the expanding cell wall (4).
===Function===
The gene OsGLU3 (Os08g0114200), a β-1,4-endoglucanase, can affect the cellulose synthesis for root elongation in rice. And the phosphate starvation induced root
elongation in rice depends on the function of OsGLU3 (Os08g0114200). Which was researched that OsGLU3 (Os08g0114200) is also dispensable for nitrogen starvation induced root elongation in rice.
The test:The Wild type (WT, SSBM) were grown for 10 d in media without nitrogen and transferred to low nitrogen media (2 mg/L nitrogen) or control media (40 mg/L nitrogen) for another 20d respectively. The nitrogen starvation stress leads to an around 20% increase of primary root elongation in WT as compared with that gro wn under the control condition, '''Fig1A'''). It showed that nitrogen starvation can lead to an increase of approximately 13% in rice root cell elongation ('''Fig1C and E''').It also found that the nitrogen starvation can lead to an approximately 15% increase in root cellulose content ('''Fig1D'''). It was iden tified phosphate starvation and the nitrogen starvation stimulate primary root elongation by inducing root cell elongation and activating root mitotic activity. It suggests that nitrogen starvation induced primary root elongation depends on the activity of OsGLU3 (Os08g0114200). An OsGLU3(Os08g0114200) dependant way affec t root cell wall cellulose synthesis by modulating root architectureboth in the phosphate or nitrogen starvation in rice.OsGLU3 (Os08g0114200)is a key player in the carbon partitioning system, as loss of function of it can abolish the response (1). The fully functional OsGLU3–GFP was detected in plasma membrane, and FM4-64-labeled compartments in the root meristem and elongation zones .In conclusion, it demonstrated that OsGLU3 was involved in the synthesis of root cellulose and thereby modulate root cell division and elongation in rice. Phosphate starvation, an environmental stress, induces root cellulose synthesis for root elongation, and OsGLU3 is a key player in this process(3).

===Mutation===
Screeningan ethylmethane sulfonate (EMS) mutagenized rice library, and isolated a short root mutant,Osglu3-1. The map-based cloning results showed that the mutant was due to a point mutation in OsGLU3, which encodes a putative membrane-bound endo-1,4-b-glucanase. Osglu3-1 displayed less crystalline cellulose content in its root cell wall, shorter root cell length, and a slightly smaller root meristem as visualized by restricted expression of OsCYCB1,1:GUS. Exogenous application of glucose can suppress both the lower root cell wall cellulose content and short root phenotypes ofOsglu3-1.The mutant resulted from a mutation in a rice KOR1 homolog OsGLU3, which encodes a putative membranebound endo-1,4-b-glucanase. OsGLU3 can affect root cell wall cellulose synthesis to modulate root elongation. Phosphate starvation, an environmental stress,can modulate root cell wall cellulose synthesis to induce root growth in an OsGLU3-dependent way. the cell length of mature epidermal cells was only one-third of those in the WT, while the root hair length of the mutant is similar to that of WT ('''Fig 3B and 3C''' ).The region expressing the OsCYCB1,1:GUSin the root meristem of mutant is about 90% of that in WT ('''Fig 3D and 3E'''). Together,these data suggest that the short root phenotype of Osglu3-1results from defects in both root cell elongation and division,particularly defect in cell elongation.the mutation of OsGLU3 might lead to an alteration of cell wall components in root tissue.The results showed that Osglu3-1 had almost the same concentration of cell wall cellulose as WT grown on medium with 3% exogenous glucose. Moreover, the cellulose content of WT and Osglu3-1 had statistically increased after the application of 3% glucose '''(Fig 3F)'''.The root growth response ofOsglu3-2to glucose treatment was also tested. As with the Osglu3-1 mutant, the application of 3% glucose suppressed the short root and short lateral root defect of Osglu3-2'''(Fig 3G)'''.Together, these data indicate that OsGLU3 modulates root cell wall cellulose synthesis and affects root cell elongation and division. The exogenous application of glucose can restore the root cell wall cellulose synthesis and rescue the root growth defects of Osglu3 mutants (3).

===Expression===
In the rice genome, endo-1,4-b-D-glucanases form a multiple gene family including OsGLU3 which share high sequence similarity with KOR1 (2). OsGLU3is ubiquitously expressed in various tissues with strong expression in root tip, lateral root, and crown root primodia. OsGLU3contains four exons and three introns (Fig 2B). The putative OsGLU3 was predicted to contain a transmembrane domain, a cytosolic domain, and a catalytic domain ('''Supplemental Fig 3A'''). The mutation is located in the catalytic domain, which is highly conserved among the plant KOR1 homologs ('''Supplemental Fig 3B'''). qRT–PCR showed that the OsGLU3 is highly expressed in root tissue and has relatively lower expression in the other tissues. The OsGLU3–GUS expression was observed ubiquitously in the rice plants included in leaf veins, excoemums,and roots. the OsGLU3–GFP protein may reflect the native OsGLU3.OsGLU3 localizes in the plasma member and endosomes, and the export of OsGLU3 to the PM depends on vesicle transport. Phosphate starvation could induce root elongation inOsglu3-1.The phosphate starvation-induced primary root elongation and cellulose-content increase are abolished in Osglu3-2, which suggests that phosphate starvation-induced primary root elongation depends on the activity of OsGLU3.Suggesting that a single recessive gene was responsible for the mutant phenotype. Using 1 000 F2 mutant seedlings selected from the population, the mutation was mapped to a 56-kb region between S4-24837K and S4-24893K on chromosome 4. This region contains 14 open reading frames (ORFs), including a b-1,4-endoglucanase (OsGLU3, LOC_Os04g41970)(3).

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

In rice genome, the putative membrane-anchored endo-b-1,4-D-glucanases were encoded by three genes: OsGLU1, OsGLU2, and OsGLU3.Recently,Libertiniet al.(2004) reported that 15 endoglucanase genes were present in rice genome.that these proteins could be classified into four main clusters. One cluster contained OsGLU4, OsGLU8, OsGLU12, OsGLU13,OsGLU14 and OsGLU15. Another cluster contained OsGLU1, OsGLU2, OsGLU3, KOR and CEL3. The third cluster contained OsGLU5,OsGLU6, OsGLU7, OsGLU9, OsGLU10 and OsGLU11.OsGLU1to OsGLU10 each gene had different numbers of introns and exons. All proteins of the OsGLU family contained the EGase domain. The
OsGLU1, OsGLU2 and OsGLU3 contained a predicted highly hydrophobic transmembrane motif in the N-terminal and belonged to the type II integral membrane protein anchored in the membrane. The results demonstrated thatOsGLU1, OsGLU2,OsGLU3 and OsGLU10 showed constitutive expression patterns in all the organs tested, and
the OsGLU4, OsGLU5, OsGLU6, OsGLU9were abundant in roots and developing flowers of plants. The other two genes OsGLU7 and OsGLU8 showed relatively higher expression in rachis and developing flowers. These different expression patterns indicated multiple functions of these genes in different processes of plant growth and development. Specific and combinational expression of these genes may be essential for the formation or function of a given organ（2）.
===Discussion===
The Osglu3-1 mutant has less cellulose in its roots and is defective in root cell elongation and division. However,theshoot development ofOsglu3-1seems ormal. In rice genome, the putative membrane-anchored endo-b-1,4-D-glucanases were encoded by three genes: OsGLU1, OsGLU2, and OsGLU3. Although all of them are
expressed ubiquitously in the rice plant,OsGLU1 showed high expression in shoot tissue whilstOsGLU3is highly expressed inroot tissue.This indicates that the different expression pattern of the gene members might explain the root elongation defect of Osglu3-1. Consistently with this,the mutation of OsGLU1 also resulted in a reduction in shoot cell growth(2). In our study, the exogenous glucose inhibits the primary root elongation in the WT, which might due to the osmotic stress or the glucose serving as a signal. However, it could completely restore the mutant phenotype ofOsglu3-1and partially restore the phenotype of Osglu3-2. There were two possible explanations for this phenomenon. One is that OsGLU3 might function in trimming sterol residues from nascent glucan primers. When glucose, the substrate of cellulose synthesis, is added, it leads to an increase in the glucan chain.The addition of the glucan chains together with the residual OsGLU3 enzymatic activity of the point mutation mutant could restore the phenotypic defects ofOsglu3-1. However, this explanation could not explain the partial complementation of the loss-of-function mutantOsglu3-2by the exogenous glucose. The other possibility is that OsGLU3 might hydrolyze the matrix polysaccharides or the links between matrix polysaccharides and, together with cell wall-loosening enzymes (such as expansins), create space for new synthesis cellulose.Exogenous glucose leads to an induction of cellulose synthesis,which needs more space(3).

==Labs working on this gene==
1.National Key Lab of Plant Genomics,People’s Republic of China.
2.Institute of Genetics and Developmental Biology, Chinese Academy of Sciences ,People’s Republic of China.
3.The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University,People’s Republic of China.
4.College of Science and Technology, Ningbo University, Ningbo, Zhejiang , China.
5.State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, People’s Republic of China.
6.Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou , People’s Republic of China.
7.Laboratoire de Biologie Cellulaire, Institut National de RechercheAgronomique
8.Universite´ de Rouen, CNRS UPRESA 6307, Faculte´ des Sciences
9.Centre de Physiologie Ve´ge´tale de l’Universite ´ Paul Sabatier, U.A.

==References==
1. Zhang J, Xu L, Wang F, Deng M, Yi K. Modulating the root elongation by phosphate/nitrogen starvation in an OsGLU3 dependant way in rice. Plant signaling & behavior. 2012;7(9):1144-5.
2. Zhou HL, He SJ, Cao YR, Chen T, Du BX, Chu CC, et al. OsGLU1, a putative membrane-bound endo-1,4-beta-D-glucanase from rice, affects plant internode elongation. Plant molecular biology. 2006;60(1):137-51.
3. Zhang JW, Xu L, Wu YR, Chen XA, Liu Y, Zhu SH, et al. OsGLU3, a putative membrane-bound endo-1,4-beta-glucanase, is required for root cell elongation and division in rice (Oryza sativa L.). Mol Plant. 2012;5(1):176-86.
4. Fre´de´ ric Nicol1, Isabelle His, Alain Jauneau, Samantha Vernhettes, Herve´ Canut, Herman Ho¨ fte. A plasma membrane-bound putative endo-1,4-betaD-glucanase is required for normal wall assembly and cell elongation inArabidopsis. The EMBO Journal. 1998;17(19):5563-76.

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os04g0473900

2017-03-27T02:52:59Z

Xysj1980:

''DWA1'' encodes an enzymatic megaprotein conserved in vascular plants，and ''DWA1'' controls drought resistance by regulating drought-induced cuticular wax deposition in rice.

==Annotated Information==
===Function===
''DWA1'' encodes an enzymatic megaprotein (2,391 aa in length) conserved in vascular plants, including an oxidoreductase-like domain, a prokaryotic nonribosomal peptide synthetase-like module, an AMP-binding domain, and an allene oxide synthase-like domain. The AMP-binding domain exhibits in vitro enzymatic activity in activating long-chain fatty acids to form acyl-CoA. Expression pattern analysis shows that ''DWA1'' is preferentially expressed in vascular tissues and epidermal layers and strongly induced by drought stress. The ''dwa1'' mutant was highly sensitive to drought stress compared to the WT and DWA1-functional complementation （DWA1-FC）plants restored drought resistance. Further dissections uncovers that the ''dwa1'' mutant was impaired in cuticular wax accumulation and significantly suppressed many wax-related genes expression under drought conditions and reduced levels of very-long-chain fatty acids. Conversely, plants overexpressing ''DWA1'' were significantly up-regulated many wax-related genes expression under drought conditions and elevated levels of very-long-chain fatty acids. The results suggest that ''DWA1'' controls drought resistance by regulating drought-induced cuticular wax deposition in rice<ref name="ref1"/>.

===Mutation===
[[File:dwa1.jpg|right|thumb|250px|Fig.1 Screening of mutants(from reference<ref name="ref1" />)]]
[[File:dwa2.jpg|right|thumb|250px|Fig.2 phenotypic analysis and the expression levels of wax-related rice genes in the ''dwa1'' mutant and WT(from reference<ref name="ref1" />)]]

'''(1)''' '''Screening of mutants(Identification of the drought-hypersensitive ''dwa1'' mutant in rice.)''' 
''dwa1'' mutant is observed by inserting T-DNA in the sixth exon of ''DWA1''(Fig.1A and B).RT-qPCR analysis of ''DWA1'' in WT and mutant tissues(leaf and panicle) indicate that ''dwa1'' is a loss of-function mutant because of no transcript found in the mutant(Fig.1C and D). 
'''(2)''' '''phenotypic analysis and the expression levels of wax-related rice genes in the ''dwa1'' mutant and WT''' 
During the course of drought treatment, the mutant wilted and exhibited leaf rolling earlier than the WT. After severe drought treatment followed by rewatering, more than 90% of the WT plants survive, whereas the ''dwa1'' mutant plants are almost dead(Fig.2A and C). Water loss rate of mutant is faster than WT(Fig.2B).Furthermore, SEM analysis indicate that the deposition of vertical plate-like wax crystals on the ''dwa1'' leaf cuticle is severely reduced under normal and drought conditions in contrast to WT leaf(Fig.2D). The contents of individual FA components is obvious difference between the ''dwa1'' mutant and WT. Among them, VLCFAs are significantly reduced, whereas the levels of are slightly higher in the ''dwa1'' mutant(Fig.2E). The gene expression levels of wax-related genes are obviously different under drought treatment(Fig.2F) 
'''(3) functional complementation assay analysis''' 
DWA1-functional complementation(DWA1-FC)lines which is inserted the full-length genomic fragment of ''DWA1'' into the ''dwa1'' mutant restore drought resistance(Fig.3). 
'''(4)''' '''Overexpression of ''DWA1'' analysis''' 
There are three independent overexpression plants(U7,U9 and U10) and a negative control (U4),and there is no visual differences in the epicuticular wax load compared with the control (Fig. 4B).But the VLCFA constituents increase in the overexpression lines compared with WT. However, the contents of LCFAs are significantly reduced in the overexpression plants. The alkanes and primary alcohols showed no significant changes (Fig. 4C). Under normal growth conditions, the expression levels of wax-related genes enhance in the overexpression plants (Fig.4D).

===Expression===
'''(1)'''qRCR results show that ''DWA1'' expression level is very low and undetectable at the vegetative stages but is relatively high at the reproductive stages(Fig.5A). 
'''(2)'''Using a GUS reporter gene driven by a ''DWA1'' promoter detects that ''DWA1'' expression is mainly in the mature organs, such as in mature leaves (Fig.5B1 and 2), axillary bud (Fig.5B3), young panicle (Fig.5B4),spikelet (Fig.5B5), stem (Fig.5B6), young panicle (Fig.5B7), pistil (Fig.5B8), stamen (Fig.5B9), young embryo (Fig.5B10), SEM picture of rice leaf cuticle (Fig.5B11), cross-sections of stem (Fig.5B12) and leaf (Fig.5B13),and semithin sections of leaf (Fig.5B14-15).In addition,SEM observation shows that the GUS staining in leaves is mainly distributed along the silica-cork cell lines in the cuticle.Cross-sections and semithin sections indicate that DWA1 is expressed mainly in vascular tissues and epidermal cell layers. 
'''(3)'''What's more,after various phytohormones treatment,''DWA1'' expresses higher,such as abscisic acid, jasmonic acid, indole-3-acetic acid, and
gibberellic acid (Fig.5C). 
'''(4)'''Under drought treatment,GUS staining shows that''DWA1'' is induced.For example,in Fig.6B,GUS staining in leaf before (1 and 3) and after (2 and 4) drought stress is shown. 

===Evolution===
At present,DWA1,likely to a megaenzyme,has five domains at least. The N terminus of DWA1 is an oxidoreductase-like domain,and closely followed by the AMP-binding domain(A domain)Then,two repeats of a phosphopantetheine-binding subdomain follow the A domain and feature a thiolation domain (T domain).An allene oxide synthase (AOS)-like domain is located between the second and third repeats of the left-handed β-helix (LbH) domain at the C-terminal region<ref name="ref1"/>(Fig.7).What's more,homologous sequences with ''DWA1''are all from microorganisms.Nonribosomal peptide synthetase(NRPS),a megaenzyme needed for nonribosomal peptides synthesis in bacteria and filamentous fungi<ref name="ref2"/>,is a major branch of the AMP-binding enzyme superfamily.More importantly,both these homologous sequences and ''DWA1'' have an NRPS module, including adenylation domain, followed by a thiolation domain catalyzing the activation and thiolation reaction of an amino acid instead of a carboxyl substrate for acyl-CoA synthetase.These features suggest that DWA1 and its plant homologs may be derived from a prokaryotic NRPS rather than the acyl-CoA synthetase family, which possesses only the A domain<ref name="ref1"/>.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan,China

==References==
<references>
<ref name="ref1">Xiaoyi Zhu, Lizhong Xiong.（2013）Putative megaenzyme DWA1 plays essential roles in drought resistance by regulating stress-induced wax
deposition in rice.PANS 110(44): 17790-17795.</ref>
<ref name="ref2">Marahiel MA, Stachelhaus T, Mootz HD.(1997) Modular peptide synthetases involved in nonribosomal peptide synthesis.Chem Rev 97(7):2651–2674.</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0473900

2017-03-27T02:52:38Z

Xysj1980:

''DWA1'' encodes an enzymatic megaprotein conserved in vascular plants，and ''DWA1'' controls drought resistance by regulating drought-induced cuticular wax deposition in rice.

==Annotated Information==
===Function===
''DWA1'' encodes an enzymatic megaprotein (2,391 aa in length) conserved in vascular plants, including an oxidoreductase-like domain, a prokaryotic nonribosomal peptide synthetase-like module, an AMP-binding domain, and an allene oxide synthase-like domain. The AMP-binding domain exhibits in vitro enzymatic activity in activating long-chain fatty acids to form acyl-CoA. Expression pattern analysis shows that ''DWA1'' is preferentially expressed in vascular tissues and epidermal layers and strongly induced by drought stress. The ''dwa1'' mutant was highly sensitive to drought stress compared to the WT and DWA1-functional complementation （DWA1-FC）plants restored drought resistance. Further dissections uncovers that the ''dwa1'' mutant was impaired in cuticular wax accumulation and significantly suppressed many wax-related genes expression under drought conditions and reduced levels of very-long-chain fatty acids. Conversely, plants overexpressing ''DWA1'' were significantly up-regulated many wax-related genes expression under drought conditions and elevated levels of very-long-chain fatty acids. The results suggest that ''DWA1'' controls drought resistance by regulating drought-induced cuticular wax deposition in rice<ref name="ref1"/>.

===Mutation===
[[File:dwa1.jpg|right|thumb|250px|Fig.1 Screening of mutants(from reference<ref name="ref1" />)]]
[[File:dwa2.jpg|right|thumb|250px|Fig.2 phenotypic analysis and the expression levels of wax-related rice genes in the ''dwa1'' mutant and WT(from reference<ref name="ref1" />)]]
[[File:dwa3.jpg|right|thumb|250px|Fig.3 functional complementation assay analysis(from reference<ref name="ref1" />)]]
'''(1)''' '''Screening of mutants(Identification of the drought-hypersensitive ''dwa1'' mutant in rice.)''' 
''dwa1'' mutant is observed by inserting T-DNA in the sixth exon of ''DWA1''(Fig.1A and B).RT-qPCR analysis of ''DWA1'' in WT and mutant tissues(leaf and panicle) indicate that ''dwa1'' is a loss of-function mutant because of no transcript found in the mutant(Fig.1C and D). 
'''(2)''' '''phenotypic analysis and the expression levels of wax-related rice genes in the ''dwa1'' mutant and WT''' 
During the course of drought treatment, the mutant wilted and exhibited leaf rolling earlier than the WT. After severe drought treatment followed by rewatering, more than 90% of the WT plants survive, whereas the ''dwa1'' mutant plants are almost dead(Fig.2A and C). Water loss rate of mutant is faster than WT(Fig.2B).Furthermore, SEM analysis indicate that the deposition of vertical plate-like wax crystals on the ''dwa1'' leaf cuticle is severely reduced under normal and drought conditions in contrast to WT leaf(Fig.2D). The contents of individual FA components is obvious difference between the ''dwa1'' mutant and WT. Among them, VLCFAs are significantly reduced, whereas the levels of are slightly higher in the ''dwa1'' mutant(Fig.2E). The gene expression levels of wax-related genes are obviously different under drought treatment(Fig.2F) 
'''(3) functional complementation assay analysis''' 
DWA1-functional complementation(DWA1-FC)lines which is inserted the full-length genomic fragment of ''DWA1'' into the ''dwa1'' mutant restore drought resistance(Fig.3). 
'''(4)''' '''Overexpression of ''DWA1'' analysis''' 
There are three independent overexpression plants(U7,U9 and U10) and a negative control (U4),and there is no visual differences in the epicuticular wax load compared with the control (Fig. 4B).But the VLCFA constituents increase in the overexpression lines compared with WT. However, the contents of LCFAs are significantly reduced in the overexpression plants. The alkanes and primary alcohols showed no significant changes (Fig. 4C). Under normal growth conditions, the expression levels of wax-related genes enhance in the overexpression plants (Fig.4D).

===Expression===
'''(1)'''qRCR results show that ''DWA1'' expression level is very low and undetectable at the vegetative stages but is relatively high at the reproductive stages(Fig.5A). 
'''(2)'''Using a GUS reporter gene driven by a ''DWA1'' promoter detects that ''DWA1'' expression is mainly in the mature organs, such as in mature leaves (Fig.5B1 and 2), axillary bud (Fig.5B3), young panicle (Fig.5B4),spikelet (Fig.5B5), stem (Fig.5B6), young panicle (Fig.5B7), pistil (Fig.5B8), stamen (Fig.5B9), young embryo (Fig.5B10), SEM picture of rice leaf cuticle (Fig.5B11), cross-sections of stem (Fig.5B12) and leaf (Fig.5B13),and semithin sections of leaf (Fig.5B14-15).In addition,SEM observation shows that the GUS staining in leaves is mainly distributed along the silica-cork cell lines in the cuticle.Cross-sections and semithin sections indicate that DWA1 is expressed mainly in vascular tissues and epidermal cell layers. 
'''(3)'''What's more,after various phytohormones treatment,''DWA1'' expresses higher,such as abscisic acid, jasmonic acid, indole-3-acetic acid, and
gibberellic acid (Fig.5C). 
'''(4)'''Under drought treatment,GUS staining shows that''DWA1'' is induced.For example,in Fig.6B,GUS staining in leaf before (1 and 3) and after (2 and 4) drought stress is shown. 

===Evolution===
At present,DWA1,likely to a megaenzyme,has five domains at least. The N terminus of DWA1 is an oxidoreductase-like domain,and closely followed by the AMP-binding domain(A domain)Then,two repeats of a phosphopantetheine-binding subdomain follow the A domain and feature a thiolation domain (T domain).An allene oxide synthase (AOS)-like domain is located between the second and third repeats of the left-handed β-helix (LbH) domain at the C-terminal region<ref name="ref1"/>(Fig.7).What's more,homologous sequences with ''DWA1''are all from microorganisms.Nonribosomal peptide synthetase(NRPS),a megaenzyme needed for nonribosomal peptides synthesis in bacteria and filamentous fungi<ref name="ref2"/>,is a major branch of the AMP-binding enzyme superfamily.More importantly,both these homologous sequences and ''DWA1'' have an NRPS module, including adenylation domain, followed by a thiolation domain catalyzing the activation and thiolation reaction of an amino acid instead of a carboxyl substrate for acyl-CoA synthetase.These features suggest that DWA1 and its plant homologs may be derived from a prokaryotic NRPS rather than the acyl-CoA synthetase family, which possesses only the A domain<ref name="ref1"/>.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan,China

==References==
<references>
<ref name="ref1">Xiaoyi Zhu, Lizhong Xiong.（2013）Putative megaenzyme DWA1 plays essential roles in drought resistance by regulating stress-induced wax
deposition in rice.PANS 110(44): 17790-17795.</ref>
<ref name="ref2">Marahiel MA, Stachelhaus T, Mootz HD.(1997) Modular peptide synthetases involved in nonribosomal peptide synthesis.Chem Rev 97(7):2651–2674.</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os11g0208900

2017-03-27T01:36:39Z

Xysj1980:

''Os05g0107700'', named as ''xa5'', is a recessive gene associated with resistance to rice bacterial leaf blight.

==Annotated Information==
===Function===
Xa3/Xa26 mediates resistance to bacterial blight, a disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which is a significant agronomic problem in rice-growing regions.The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.). This family encodes leucine-rich repeat (LRR) receptor kinasetype proteins. Asian-cultivated rice consists of two major subspecies, indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica).

===Expression===
The indica plants carrying Xa3/Xa26 were highly susceptible in four-leaf stage, but become resistant or moderately resistant to these Xoo races at booting stage. The development-controlled Xa3/Xa26 activity is also associated with its expression level (Cao et al. 2007).
===Evolution===
The orthologs (alleles) of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza species O. officinalis (CC genome) and O. minuta (BBCC genome), respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91–99% sequence identity and 94–99% sequence similarity.

== Knowledge Extension ==

Xa3/Xa26 was first identified in the indica rice cultivar Minghui 63 and named Xa26. Further study revealed that Xa3, an R gene conferring resistance against Xoo, and Xa26 are actually the same gene and then it was renamed Xa3/Xa26. Xa3/Xa26 has been an important resistance gene for both indica and japonica rice production in China for a long time.

==Labs working on this gene==
* Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA.

==References==
<references>
* <ref name="ref1">
Iyer AS, McCouch SR. The rice bacterial blight resistance gene xa5 encodes a
novel form of disease resistance. Mol Plant Microbe Interact. 2004
Dec;17(12):1348-54. PubMed PMID: 15597740.
</ref>

</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 11]]

Os01g0185300

2017-03-27T01:31:11Z

Xysj1980: /* References */

Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. <ref name="ref1" />

==Annotated Information==
===Function===
*Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. The FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves.
*The members of the PF02458 family may encode for putative arabinoxylan feruloyl transferases (AFT) and be involved in acylating arabinoxylans with FA.
 

===Expression===
*No significant differences in transcript levels of the highly expressed genes were detected between pAFT-A transgenic events A5 and A11 or between pAFT-B transgenic events B1 and B11,when the tissues were studied separately or when they were combined in the statistical analyses. Therefore, the following statistical analyses combine the two events examined for each construct, whereas the results for the individual events and tissues are presented in Fig. 3.
[[File:12-f3.png |center |thumb |10000px |''''''Fig. 3 Transcript levels of genes targeted by a pAFT-A or b pAFT-B constructs in transgenic and control plants in experiment 2. a Transcript levels of genes from group I in the transgenic events A5 and A11 compared with the control. b, c The expression levels of groups III (b), IV (c) genes in the transgenic events B1 and B11 compared with the control. Values in the Y axes are normalized and calibrated values using the formula (1 ? efficiency)-DDCT method(Livak and Schmittgen 2001). All values were divided by 1,000 to simplify the graphs. The same calibrator was used for all genes so values are comparable across genes. Error bars are SE of the means'''''']]
 
==Labs working on this gene==
*Department of Plant Sciences, University of California,
*Dept. de Agronomı ´a y Mejora Gene ´tica Vegetal,Instituto de Agricultura Sostenible, CSIC,
*Department of Crop Genetics, John Innes Centre,
 

==References==
<references>
<ref name="ref1">Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation
of four putative arabinoxylan feruloyl transferase genes from family PF02458
reduces ester-linked ferulate content in rice cell walls. Planta. 2010
Feb;231(3):677-91. doi: 10.1007/s00425-009-1077-1. PubMed PMID: 20012086; PubMed
Central PMCID: PMC2806532.</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0185300

2017-03-27T01:31:01Z

Xysj1980: /* References */

Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. <ref name="ref1" />

==Annotated Information==
===Function===
*Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. The FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves.
*The members of the PF02458 family may encode for putative arabinoxylan feruloyl transferases (AFT) and be involved in acylating arabinoxylans with FA.
 

===Expression===
*No significant differences in transcript levels of the highly expressed genes were detected between pAFT-A transgenic events A5 and A11 or between pAFT-B transgenic events B1 and B11,when the tissues were studied separately or when they were combined in the statistical analyses. Therefore, the following statistical analyses combine the two events examined for each construct, whereas the results for the individual events and tissues are presented in Fig. 3.
[[File:12-f3.png |center |thumb |10000px |''''''Fig. 3 Transcript levels of genes targeted by a pAFT-A or b pAFT-B constructs in transgenic and control plants in experiment 2. a Transcript levels of genes from group I in the transgenic events A5 and A11 compared with the control. b, c The expression levels of groups III (b), IV (c) genes in the transgenic events B1 and B11 compared with the control. Values in the Y axes are normalized and calibrated values using the formula (1 ? efficiency)-DDCT method(Livak and Schmittgen 2001). All values were divided by 1,000 to simplify the graphs. The same calibrator was used for all genes so values are comparable across genes. Error bars are SE of the means'''''']]
 
==Labs working on this gene==
*Department of Plant Sciences, University of California,
*Dept. de Agronomı ´a y Mejora Gene ´tica Vegetal,Instituto de Agricultura Sostenible, CSIC,
*Department of Crop Genetics, John Innes Centre,
 

==References==
<references>
<ref name="ref1">Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation
of four putative arabinoxylan feruloyl transferase genes from family PF02458
reduces ester-linked ferulate content in rice cell walls. Planta. 2010
Feb;231(3):677-91. doi: 10.1007/s00425-009-1077-1. PubMed PMID: 20012086; PubMed
Central PMCID: PMC2806532.</ref>
<references>
 
==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0185300

2017-03-27T01:30:48Z

Xysj1980:

Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. <ref name="ref1" />

==Annotated Information==
===Function===
*Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. The FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves.
*The members of the PF02458 family may encode for putative arabinoxylan feruloyl transferases (AFT) and be involved in acylating arabinoxylans with FA.
 

===Expression===
*No significant differences in transcript levels of the highly expressed genes were detected between pAFT-A transgenic events A5 and A11 or between pAFT-B transgenic events B1 and B11,when the tissues were studied separately or when they were combined in the statistical analyses. Therefore, the following statistical analyses combine the two events examined for each construct, whereas the results for the individual events and tissues are presented in Fig. 3.
[[File:12-f3.png |center |thumb |10000px |''''''Fig. 3 Transcript levels of genes targeted by a pAFT-A or b pAFT-B constructs in transgenic and control plants in experiment 2. a Transcript levels of genes from group I in the transgenic events A5 and A11 compared with the control. b, c The expression levels of groups III (b), IV (c) genes in the transgenic events B1 and B11 compared with the control. Values in the Y axes are normalized and calibrated values using the formula (1 ? efficiency)-DDCT method(Livak and Schmittgen 2001). All values were divided by 1,000 to simplify the graphs. The same calibrator was used for all genes so values are comparable across genes. Error bars are SE of the means'''''']]
 
==Labs working on this gene==
*Department of Plant Sciences, University of California,
*Dept. de Agronomı ´a y Mejora Gene ´tica Vegetal,Instituto de Agricultura Sostenible, CSIC,
*Department of Crop Genetics, John Innes Centre,
 

==References==
<references>
<ref name="ref1">Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation
of four putative arabinoxylan feruloyl transferase genes from family PF02458
reduces ester-linked ferulate content in rice cell walls. Planta. 2010
Feb;231(3):677-91. doi: 10.1007/s00425-009-1077-1. PubMed PMID: 20012086; PubMed
Central PMCID: PMC2806532.</ref>
<references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0185300

2017-03-27T01:30:08Z

Xysj1980: /* References */

Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges.

==Annotated Information==
===Function===
*Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. The FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves.
*The members of the PF02458 family may encode for putative arabinoxylan feruloyl transferases (AFT) and be involved in acylating arabinoxylans with FA.
 

===Expression===
*No significant differences in transcript levels of the highly expressed genes were detected between pAFT-A transgenic events A5 and A11 or between pAFT-B transgenic events B1 and B11,when the tissues were studied separately or when they were combined in the statistical analyses. Therefore, the following statistical analyses combine the two events examined for each construct, whereas the results for the individual events and tissues are presented in Fig. 3.
[[File:12-f3.png |center |thumb |10000px |''''''Fig. 3 Transcript levels of genes targeted by a pAFT-A or b pAFT-B constructs in transgenic and control plants in experiment 2. a Transcript levels of genes from group I in the transgenic events A5 and A11 compared with the control. b, c The expression levels of groups III (b), IV (c) genes in the transgenic events B1 and B11 compared with the control. Values in the Y axes are normalized and calibrated values using the formula (1 ? efficiency)-DDCT method(Livak and Schmittgen 2001). All values were divided by 1,000 to simplify the graphs. The same calibrator was used for all genes so values are comparable across genes. Error bars are SE of the means'''''']]
 
==Labs working on this gene==
*Department of Plant Sciences, University of California,
*Dept. de Agronomı ´a y Mejora Gene ´tica Vegetal,Instituto de Agricultura Sostenible, CSIC,
*Department of Crop Genetics, John Innes Centre,
 

==References==
<references>
<ref name="ref1">Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation
of four putative arabinoxylan feruloyl transferase genes from family PF02458
reduces ester-linked ferulate content in rice cell walls. Planta. 2010
Feb;231(3):677-91. doi: 10.1007/s00425-009-1077-1. PubMed PMID: 20012086; PubMed
Central PMCID: PMC2806532.</ref>
<references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0185300

2017-03-27T01:29:17Z

Xysj1980: /* References */

Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges.

==Annotated Information==
===Function===
*Ferulates (FA) can crosslink different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. The FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves.
*The members of the PF02458 family may encode for putative arabinoxylan feruloyl transferases (AFT) and be involved in acylating arabinoxylans with FA.
 

===Expression===
*No significant differences in transcript levels of the highly expressed genes were detected between pAFT-A transgenic events A5 and A11 or between pAFT-B transgenic events B1 and B11,when the tissues were studied separately or when they were combined in the statistical analyses. Therefore, the following statistical analyses combine the two events examined for each construct, whereas the results for the individual events and tissues are presented in Fig. 3.
[[File:12-f3.png |center |thumb |10000px |''''''Fig. 3 Transcript levels of genes targeted by a pAFT-A or b pAFT-B constructs in transgenic and control plants in experiment 2. a Transcript levels of genes from group I in the transgenic events A5 and A11 compared with the control. b, c The expression levels of groups III (b), IV (c) genes in the transgenic events B1 and B11 compared with the control. Values in the Y axes are normalized and calibrated values using the formula (1 ? efficiency)-DDCT method(Livak and Schmittgen 2001). All values were divided by 1,000 to simplify the graphs. The same calibrator was used for all genes so values are comparable across genes. Error bars are SE of the means'''''']]
 
==Labs working on this gene==
*Department of Plant Sciences, University of California,
*Dept. de Agronomı ´a y Mejora Gene ´tica Vegetal,Instituto de Agricultura Sostenible, CSIC,
*Department of Crop Genetics, John Innes Centre,
 

==References==
*Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation
of four putative arabinoxylan feruloyl transferase genes from family PF02458
reduces ester-linked ferulate content in rice cell walls. Planta. 2010
Feb;231(3):677-91. doi: 10.1007/s00425-009-1077-1. PubMed PMID: 20012086; PubMed
Central PMCID: PMC2806532.

 

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]

Os01g0307500

2017-03-27T01:24:38Z

Xysj1980: /* References */

The introduction of the gene SKC1.
==Annotated Information==
===Function===
This gene control the express of the protein HKT family. The HKT family of Na+ and Na+/K+ transporters is implicated in plant salinity tolerance. The cereal HKT1;4 and HKT1;5 are responsible for Na+ exclusion from photosynthetic tissues, a key mechanism for plant salinity tolerance.
We previously mapped a rice QTL, SKC1, that maintained K+ homeostasis in the salt-tolerant variety under salt stress<ref name="pmid:14513218"/>, consistent with the earlier finding that K+ homeostasis is important in salt tolerance <ref name="pmid:15347782"/>.
It encoded a member of HKT-type transporters. SKC1 is preferentially expressed in the parenchyma cells surrounding the xylem vessels. Voltage-clamp.
SKC1 protein functions as a Na+-selective transporter. Physiological analysis suggested that SKC1 is involved in regulating K+/Na+ homeostasis under salt stress, providing a potential tool for improving salt tolerance in crops.
Up-regulation of OsNRT1;2, a gene coding nitrate transporter, might contribute to the accumulation of NO3 - in the old leaves of salt stressed-rice. Salt stress clearly up-regulated the expression of OsGDH2.

===Expression===
The work described here provides evidence for a crucial amino acid substitution which determines Na+ transport efficiency of OsHKT1;5. The recently solved structure of a highly similar TrkH K+ transporter<ref name="pmid:21317882"/>provided the basis for three-dimensional(3D) molecular modeling of OsHKT1;5 and OsHKT1;4.
Different HKT members may have different transport properties.The founding member of the HKT family, TaHKT1, mediates K+/Na+symport and Na+ transport whereas AtHKT1 selectively transportsNa+. In rice, OsHKT1, like AtHKT1, transports Na+only and OsHKT2 mediates TaHKT1-like K+/Na+ symport. Toassess the functional property of SKC1.<ref name="pmid:7502075"/>,<ref name="pmid:8953248"/>. NSKC1 is a more active allele than KSKC1,which might contribute to the difference in ionic homeostasis and salt tolerance, a salt-sensitive allele of AtHKT1 encodes a mutant protein with lower transport activity<ref name="pmid:12727868 " />.The KSKC1 allele encodes a protein with lower transport activity that also leads to a salt sensitive phenotype in rice seedlings.

===Evolution===
Comparison of the genomic and cDNA sequences of the Nona Bokra allele of SKC1 identified three exons and two introns. SKC1 is predicted to encode a 554–amino acid polypeptide of B60 kDa. Database searches showed substantial similarity between SKC1 and the HKT-type transporters found in plants, bacteria and fungi8–10. SKC1 protein showed 44%, 48%, 44%, and 41% identity to wheat TaHKT1, Arabidopsis thaliana AtHKT1 <ref name="pmid: 10759522"/> and rice OsHKT1 and OsHKT4, respectively. Seven HKT members and two pseudo genes have been identified from the rice genomic database by homology search12. SKC1 corresponded to OsHKT8. The physiological function of HKT members in rice has not previously been studied.SKC1 also controlled Na+ accumulation and encoded a Na+ transporter belonging to the HKT family.

==Labs working on this gene==
Nature Publishing Group, Australian Centre for Plant Functional Genomics,University of Adelaide, Adelaide, South Australia, Australia, Key laboratory of Molecular Epigenetics of MOE,Northeast Normal University, Changchun 130024 Jilin Province, China,Northeast Institute of Geography and Agricultural Ecology,Chinese Academy of Sciences.

==References==
<references>

<ref name="pmid:14513218">Lin, H.X. et al. QTLs for Na+ and K+ uptake of shoot and root controlling rice salt tolerance. Theor. Appl. Genet. 108, 253–260 (2004). </ref>
<ref name="pmid:15347782">Qi, Z. & Spalding, E.P. Protection of plasma membrane K+ transport by the salt overlysensitive1 Na+/H+ antiporter during salinity stress. Plant Physiol. 136, 2548–2555
(2004). </ref>
<ref name="pmid:21317882">Cao Y, Jin X, Huang H, Derebe MG, Levin EJ, et al. (2011) Crystal structure of a potassium ion transporter, TrkH. Nature 471: 336–340. </ref>.
<ref name="pmid:7502075">Rubio, F., Gassmann, W. & Schroeder, J.I. Sodium-driven potassium uptake by theplant potassium transporter HKT1 and mutations conferring salt tolerance. Science
270, 1660–1663 (1995). </ref>
<ref name="pmid:8953248">Gassman, W., Rubio, F. & Schroeder, J.I. Alkali cation selectivity of the wheat root highaffinity potassium transporter HKT1. Plant J. 10, 869–882 (1996). </ref>
<ref name="pmid:12727868">Berthomieu, P. et al. Functional analysis of AtHKT1 in Arabidopsis shows that Na+recirculation by the phloem is crucial for salt tolerance. EMBO J. 22, 2004–2014 (2003). </ref>
<ref name="pmid: 10759522">Uozumi, N. et al. The Arabidopsis HKT1 gene homolog mediates inward Na+ currents in Xenopus laevis Oocytes and Na+ uptake in Saccharomyces cerevisiae. Plant Physiol.122, 1249–1259 (2000). </ref>
</references>

Os01g0307500

2017-03-27T01:24:10Z

Xysj1980:

Os07g0227800

2017-03-27T01:20:35Z

Xysj1980: /* Subcellular localization */

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
* Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />.
* Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.

[[File:abc1-table.jpg|right|thumb|330px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
* ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />.
[[File:motif10.jpg|right|thumb|330px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]

===Expression===
* The real-time PCR results show that 14 genes express mainly in leaves.

===Subcellular localization===
* The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0227800

2017-03-27T01:20:18Z

Xysj1980: /* Function */

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
* Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />.
* Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.

[[File:abc1-table.jpg|right|thumb|330px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
* ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />.
[[File:motif10.jpg|right|thumb|330px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]

===Expression===
* The real-time PCR results show that 14 genes express mainly in leaves.

===Subcellular localization===
The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0227800

2017-03-27T01:19:58Z

Xysj1980: /* Function */

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
* Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />.
* Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.

[[File:abc1-table.jpg|right|thumb|330px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
* ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />. The XaXasX2QV segment that functions as a nucleotide-binding motif for protein kinases is highly conserved in ABC1 domain as well as lysine residue in N-terminal that as a binding site for chemical groups. In addition, other conserved amino acid valine and aspartate acid in the middle of the domain and glutamate acid in the C-terminal. It is also suggested that there are 10 putative motifs in rice ABC1 proteins (Fig1).
[[File:motif10.jpg|right|thumb|330px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]

===Expression===
* The real-time PCR results show that 14 genes express mainly in leaves.

===Subcellular localization===
The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0227800

2017-03-27T01:19:15Z

Xysj1980:

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
* Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />.
* Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.
There are 15 non-redundant ABC1genes distributed on all rice chromosomes randomly except chromosomes 3, 8, 10, and 12 in rice, and were named from OsABC1-1 to OsABC1-15 according to their chromosomal location (table 1). However, there are 17 members of ABC1 family in ''Arabidopsis''. All of these genes contain introns and the number of intron varies greatly, and intron gain was an important event accompanying the recent evolution of the rice ABC1 family <ref name="ref4" />.
[[File:abc1-table.jpg|middle|thumb|530px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
* ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />. The XaXasX2QV segment that functions as a nucleotide-binding motif for protein kinases is highly conserved in ABC1 domain as well as lysine residue in N-terminal that as a binding site for chemical groups. In addition, other conserved amino acid valine and aspartate acid in the middle of the domain and glutamate acid in the C-terminal. It is also suggested that there are 10 putative motifs in rice ABC1 proteins (Fig1).
[[File:motif10.jpg|middle|thumb|430px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]

===Expression===
* The real-time PCR results show that 14 genes express mainly in leaves.

===Subcellular localization===
The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0227800

2017-03-27T01:17:46Z

Xysj1980: /* Evolution */

Please input one-sentence summary here.

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />. Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.
There are 15 non-redundant ABC1genes distributed on all rice chromosomes randomly except chromosomes 3, 8, 10, and 12 in rice, and were named from OsABC1-1 to OsABC1-15 according to their chromosomal location (table 1). However, there are 17 members of ABC1 family in ''Arabidopsis''. All of these genes contain introns and the number of intron varies greatly, and intron gain was an important event accompanying the recent evolution of the rice ABC1 family <ref name="ref4" />.
[[File:abc1-table.jpg|middle|thumb|530px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />. The XaXasX2QV segment that functions as a nucleotide-binding motif for protein kinases is highly conserved in ABC1 domain as well as lysine residue in N-terminal that as a binding site for chemical groups. In addition, other conserved amino acid valine and aspartate acid in the middle of the domain and glutamate acid in the C-terminal. It is also suggested that there are 10 putative motifs in rice ABC1 proteins (Fig1).
[[File:motif10.jpg|middle|thumb|430px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]
The real-time PCR results show that 14 genes express mainly in leaves. The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0227800

2017-03-27T01:17:29Z

Xysj1980: /* Expression */

Please input one-sentence summary here.

''OsABC1-9'' contains 13 extrons and is located in chromosome 7, and this gene encodes a proteins with 793 amino acids.
==Annotated Information==
===Function===
Members of the activity of bc1 complex (ABC1) family are widely existed in prokaryotes and eukaryotes as protein kinases. These protein kinase members were initially isolated from Saccharomyces cerevisiae and were responsible to suppress a defect in mRNA translation of cytochrome b and maintain the activity of the bc1 complex in the mitochondrial respiratory chain <ref name="ref1" />. Mitochondrial and chloroplast ABC1 proteins is associated in respiratory electron transport system and as a lipid-soluble antioxidant in ''yeast'', ''Escherichia col'', and human <ref name="ref2" /><ref name="ref3" />.
There are 15 non-redundant ABC1genes distributed on all rice chromosomes randomly except chromosomes 3, 8, 10, and 12 in rice, and were named from OsABC1-1 to OsABC1-15 according to their chromosomal location (table 1). However, there are 17 members of ABC1 family in ''Arabidopsis''. All of these genes contain introns and the number of intron varies greatly, and intron gain was an important event accompanying the recent evolution of the rice ABC1 family <ref name="ref4" />.
[[File:abc1-table.jpg|middle|thumb|530px|'''Table.1'' Basic information of the rice ABC1 genes.(from reference) <ref name="ref4" />.]]
ABC1 domain is an important part of the ABC1 proteins, and aligned results show that the domains of all proteins were from 102–126 amino acids, except the OsABC1-14 and OsABC1-15 proteins. The length of the domain in OsABC1-14 and OsABC1-15 is 92 amino acids and 184 amino acids, respectively <ref name="ref4" />. The XaXasX2QV segment that functions as a nucleotide-binding motif for protein kinases is highly conserved in ABC1 domain as well as lysine residue in N-terminal that as a binding site for chemical groups. In addition, other conserved amino acid valine and aspartate acid in the middle of the domain and glutamate acid in the C-terminal. It is also suggested that there are 10 putative motifs in rice ABC1 proteins (Fig1).
[[File:motif10.jpg|middle|thumb|430px|'''Fig.1'' Motif composition of rice ABC1 proteins.(from reference) <ref name="ref4" />.]]
The real-time PCR results show that 14 genes express mainly in leaves. The subcellular localization is predicted that OsABC1-1 and OsABC1-8 were localized in the cytoplasm, OsABC1-3 and OsABC1-6 in the plasma membrane, OsABC1-10 in mitochondria, OsABC1-14 in vacuoles and the others in chloroplasts <ref name="ref4" />.
Members of this family participate in the extensive abiotic stress response and may play roles in the tolerance of plants to adverse environments. Furthermore, some of the rice ABC1 genes may be involved in the oxidative stress response and ABA signaling<ref name="ref4" />.

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

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

==Labs working on this gene==
*Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology
*Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, China

==References==
<references>
<ref name="ref1"> Bousquet I, Dujardin G, Slonimski P P. 1991. ABC1, a novel yeast nuclear gene has a dual function in mitochondria: It suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. EMBO J, 10(8): 2023–2031.</ref>
<ref name="ref2"> Villalba J M, Navas P. 2000. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2(2): 213–230.</ref>
<ref name="ref3"> Ernster L, Forsmark-Andree P. 1993. Ubiquinol: an endogenous antioxidant in aerobic organisms. Clin Investig, 71(8 Suppl): S60–S65.</ref>
<ref name="ref4">GAOQing-song, ZHANGDan, XULiang, XUChen-wu. Systematic Identification of Rice ABC1Gene Family and Its Response to Abiotic Stress. Rice Science, 2011, 18(2).</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os08g0445700

2017-03-27T01:07:43Z

Xysj1980:

The rice '''''Os08g0445700''''' was reported as '''''OsTPS1''''' in 2011 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Function===
* Trehalose-6-phosphate synthase (TPS) is a key enzyme for trehalose biosynthesis.
* Overexpression of the trehalose-6-phosphate synthase gene '''''OsTPS1''''' enhances abiotic stress tolerance in rice
* Trehalose plays an important role in metabolic regulation and abiotic stress tolerance in a variety of organisms.
* In plants, its biosynthesis is catalyzed by two key enzymes: trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). The genome of rice (Oryza sativa) contains 11 OsTPS genes, and only OsTPS1 shows TPS activity.

===Phenotypic analysis===
* Leaves of OsTPS1 knockout (KO) plants were more sensitive to drought or cold stress than were the wild types.
* Furthermore, transgenic rice of UBI::CBF1 had high expression OsTPS1 mRNA, suggesting that '''''OsTPS1''''' is regulated by the CBF/DREB transcription factor.
* '''''OsTPS1''''' overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes

===Expression===
* Reverse transcriptase-PCR analysis of OsTPS1 showed that OsTPS1 is inducible by drought, salt, cold, and ABA.

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

==Labs working on this gene==
* Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, People's Republic of China.

==References==
<references>
* <ref name="ref1">
Li HW, Zang BS, Deng XW, Wang XP. Overexpression of the trehalose-6-phosphate
synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta. 2011
Nov;234(5):1007-18. doi: 10.1007/s00425-011-1458-0. PubMed PMID: 21698458.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0445700

2017-03-27T01:06:30Z

Xysj1980: /* Labs working on this gene */

Os08g0445700

2017-03-27T01:06:12Z

Xysj1980: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
* Trehalose-6-phosphate synthase (TPS) is a key enzyme for trehalose biosynthesis.
* Trehalose plays an important role in metabolic regulation and abiotic stress tolerance in a variety of organisms.
* In plants, its biosynthesis is catalyzed by two key enzymes: trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). The genome of rice (Oryza sativa) contains 11 OsTPS genes, and only OsTPS1 shows TPS activity.

===Phenotypic analysis===
* Leaves of OsTPS1 knockout (KO) plants were more sensitive to drought or cold stress than were the wild types.
* Furthermore, transgenic rice of UBI::CBF1 had high expression OsTPS1 mRNA, suggesting that '''''OsTPS1''''' is regulated by the CBF/DREB transcription factor.
* '''''OsTPS1''''' overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes

===Expression===
* Reverse transcriptase-PCR analysis of OsTPS1 showed that OsTPS1 is inducible by drought, salt, cold, and ABA.

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

==Labs working on this gene==
To understand the function of the TPS gene, we identified the T-DNA insertion in a TPSgene of rice.<fil.1>
To demonstrate the physiological function of OsTPS1, we introduced it into rice and found that OsTPS1 overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes.<fil.2>

==References==
<references>
* <ref name="ref1">
Li HW, Zang BS, Deng XW, Wang XP. Overexpression of the trehalose-6-phosphate
synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta. 2011
Nov;234(5):1007-18. doi: 10.1007/s00425-011-1458-0. PubMed PMID: 21698458.
</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0445700

2017-03-27T01:04:37Z

Xysj1980: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
* Trehalose-6-phosphate synthase (TPS) is a key enzyme for trehalose biosynthesis.
* Trehalose plays an important role in metabolic regulation and abiotic stress tolerance in a variety of organisms.
* In plants, its biosynthesis is catalyzed by two key enzymes: trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). The genome of rice (Oryza sativa) contains 11 OsTPS genes, and only OsTPS1 shows TPS activity.

===Phenotypic analysis===
* Leaves of OsTPS1 knockout (KO) plants were more sensitive to drought or cold stress than were the wild types.
* Furthermore, transgenic rice of UBI::CBF1 had high expression OsTPS1 mRNA, suggesting that '''''OsTPS1''''' is regulated by the CBF/DREB transcription factor.
* '''''OsTPS1''''' overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes

===Expression===
* Reverse transcriptase-PCR analysis of OsTPS1 showed that OsTPS1 is inducible by drought, salt, cold, and ABA.

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

==Labs working on this gene==
To understand the function of the TPS gene, we identified the T-DNA insertion in a TPSgene of rice.<fil.1>
To demonstrate the physiological function of OsTPS1, we introduced it into rice and found that OsTPS1 overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes.<fil.2>

==References==
1. Baisheng Zang;Haowen Li;Wenjun Li;Xing Wang Deng;Xiping Wang
Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice
Plant Molecular Biology, 2011, 76(6): 507-522
2. Hao-Wen Li;Bai-Sheng Zang;Xing-Wang Deng;Xi-Ping Wang
Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice
Planta, 2011, 234(5): 1007-1018
3. Richard A. Wilson;Robert P. Gibson;Cristian F. Quispe;Jennifer A. Littlechild;Nicholas J. Talbot
An NADPH-dependent genetic switch regulates plant infection by the rice blast fungus
Proceedings of the National Academy of Sciences, 2010, 107(50): 21902-21907
4. Soo-Jin Kim;Dong-Hoon Jeong;Gynheung An;Seong-Ryong Kim
Characterization of a drought-responsive gene, OsTPS1 , identified by the T-DNA Gene-Trap system in rice
Journal of Plant Biology, 2005, 48(4): 371-379

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os06g0499500

2017-03-25T14:33:02Z

Xysj1980: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The GH3 is a class of genes that respond to Auxin in some species of plants. The GH3 proteins in Arabidopsis have been shown to be involved in plant growth and development, photomorphogenesis, light- and auxin-signaling, and auxin homeostasis. GH3 proteins from Arabidopsis and rice could be divided into three and two groups, respectively. GH3 proteins classified in the same groups may have the similar functions in events common to both monocot and dicot plants. Group III GH3 proteins may have dicot-specific functions as they could not be identified from rice or other monocots. Organ-specific differential expression suggests diverse roles of these proteins during plant growth and development. The effect of light and auxin treatment on the transcript levels of OsGH3 genes implies their role in light and auxin signal transduction.
The phenotypes of the insertion mutants of some GH3 genes showed dwarfism, sterility, vivipary, and leaf withering. From these phenotypes, it can be speculated that these genes may play a role in different metabolic pathways and cellular processes influenced by light and auxin. But whether the assumption
that these phenotype changes are specific to insertional mutagenesis of OsGH3 gene still remains to be proven experimentally.
===Expression===
The expression of all the 12 OsGH3 genes was verified experimentally and quantitated by real-time PCR analysis in the present study. Many of the GH3 genes in Arabidopsis, soybean, and tobacco were found to be differentially expressed in different tissues or in response to exogenous auxin and light stimuli. To determine the organ-specific expression pattern of each OsGH3 gene, real-time PCR was performed with total RNA isolated from etiolated shoots, green shoots, roots, flowers, and callus. This analysis revealed that OsGH3 genes are differentially expressed in various tissues/organs. The transcription of OsGH3-12 was found to be root-specific and was hardly detectable in other tissues examined. However, OsGH3-10 was found to be expressed at very low levels in all the tissues. In contrast, other OsGH3 genes were found to be expressed in almost all the tissues examined but at different levels. Also, significant differences were found in the transcript abundance of OsGH3 genes in etiolated and green shoots, indicating their light regulation. The transcript levels of most of the OsGH3 genes were upregulated by auxin treatment, although to varying degree. The effect is more pronounced on OsGH3-1, -2, -4 and, to some extent, on OsGH3-8 too. The difference in the inducibility of individual GH3 genes is likely due to a variety of factors such as kinetics of induction, tissue-specific auxin reception, cell type-dependent and differential regulation of free auxin concentrations, or differentmodes of auxin-dependent transcriptional and posttranscriptional regulation.

===Evolution===
Two major groups (groups I and II), with very strong boot-strap support, were observed, which included four and eight OsGH3 proteins, respectively. Twelve OsGH3 proteins formed only three sister pairs. The sister pair OsGH3-1 and -4 was found to be present on duplicated chromosomal block 1 present between chromosomes 1 and 5 as described by Paterson et al (2004). However, the sister pair OsGH3-9 and -10 may represent a local duplication event. The third sister pair (OsGH3-3 and -12) may also be present on unidentified duplicated chromosomal block. Taken together, these observations throw some light on the diversification of rice GH3 genes during evolution. The Arabidopsis GH3 proteins have been classified into three groups on the basis of their protein structure and specificity to adenylate plant hormones (Staswick et al 2002). To examine protein relationships of rice and Arabidopsis. GH3 proteins, an unrooted tree was constructed from alignments of their full-length GH3 protein sequences. Based upon the sequence homology, all the rice and Arabidopsis GH3 proteins clustered distinctly into three groups (I, II, and III). Group I consisted of only six members, four from rice cluster, i.e., OsGH3-3, -5, -6, and -12, along with AtGH-10 and -11. AtGH3-11 (JAR1/FIN219) has been shown to adenylate jasmonic acid (JA) (Staswick et al. 2002). Seven of the OsGH3 proteins belonged to group II AtGH3 proteins, which are involved in IAA adenylation (Staswick et al. 2002). The group II Arabidopsis GH3 genes encode IAA-amido synthetases that conjugate amino acids to IAA and regulate plant growth and development (Staswick et al. 2005). However, group III included only Arabidopsis GH3 proteins with unknown function, which do not adenylate IAA, JA, or SA. Surprisingly, no group III GH3 protein could be identified in rice sequence databases searched. It can be speculated that group III GH3 proteins were lost in rice after divergence of monocots and dicots or evolved in dicots after the divergence from monocots and may perform dicot-specific functions. However, OsGH3-7 grouped with group II rice GH3 proteins, but did not group with Arabidopsis group II GH3 proteins.

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

==References==
The auxin-responsive GH3 gene family in rice (Oryza sativa) Functional & Integrative Genomics, 2006, 6(1): 36-46

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os02g0666200

2017-03-25T14:18:05Z

Xysj1980: /* References */

One of most highly expressed aquaporin gene in the leaves and roots of rice, highly responsible to environmental stresses.<ref name="ref1" />

==Annotated Information==
===Introduction===
According to the nomenclature of ''PIP'' genes in maize, this gene has been designated as ''OsPIP1-1''.'' PIP'' genes are the protein encoding genes of plasma membrane intrinsic proteins (PIPs) -- a subfamily of aquaporins that enable fast and controlled translocation of water across the membrane. There are recently 10 designated ''PIP'' genes in the gnome of rice, they are classified into two groups, that is ''OsPIP1-1'' to ''OsPIP1-3'' and ''OsPIP2-1'' to ''OsPIP2-7'', based on the similarity of their amino acid sequences.<ref name="ref2" /> The ubiquitously expression of ''OsPIP1-1'' gene in rice leaves and roots indicates its important physiological role.

===Function===
Experiments show that when transiently expressed as EGFP-OsPIP1 in rice cell protoplasts, it is mainly distributed in cytoplasm, While co-expressing with EGFP-OsPIP1 make it re
-translocate to plasma membrane. This observation is further confirmed by the water permeability measuring experiment.<ref name="ref1" />

==== ''Seed germination'' ====
Transgenic rice seeds with overexpressed OsPIP1 exhibit a significant higher germination rate than the control, this is consistent with the higher α-amylase activity in transgenic seeds.<ref name="ref1" />

==== ''Salt tolerance'' ====
Experiments show that when not overexpressed at high level,OsPIP1 will efficiently promote salt resistance in rice, but when has high OsPIP1 expression level, rice will become more sensitive to
high salt environment than control.<ref name="ref1" />

==== ''Seed yield'' ====

Transgenic rice plants with various OsPIP1 express level show that, appropriate low level of overexpressed OsPIP1 will increase seed yield, while high level of OsPIP1 expression will decrease seed yield, and extremely high expression will even make rice sterile.<ref name="ref1" />

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 2]]

===Evolution===
Aquaporin family occur in greatest numbers and with the greatest diversity in plants. Angiosperm species have ~30 different aquaporins grouped into four subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs), and small, basic intrinsic proteins (SIPs). An EST library of the moss Physcomitrella patens reveals that its aquaporins fall into the same subfamilies, indicating that the main radiation of plant aquaporins was already established when land plant evolution began.<ref name="ref3" />

The partial identification of Physcomitrella aquaporins demonstrates that the diversification into PIP, TIP, NIP and SIP subfamilies, as well as the differentiation into PIP1 and PIP2 classes, pre-dates the divergence of bryophytes and tracheophytes, whereas the differentiation of α-, γ- and δ-TIPs must have occurred during the evolution of tracheophytes. Identification of aquaporins in charophytes should elucidate to what degree the plant aquaporins had diversified before the algal ancestors invaded the land.<ref name="ref3" />

[[File:diversification.png|600px|"diversification of aquaporins (from reference <ref name="ref3"/>)."]]

==Labs working on this gene==
Graduate School of Bioresource Sciences, Akita Prefectural University, Shimoshinjo, Akita 010-0195, Japan

Institute of Plant Science and Resources, Okayama University, Kuashiki 710-0046, Japan

College of Life Science, Northeast Agricultural University, Harbin 150030, China

Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, National Laboratory for Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China

==References==
<references>
<ref name="ref1">Liu C, Fukumoto T, Matsumoto T, Gena P, Frascaria D, Kaneko T, Katsuhara M, et al. (2013) Aquaporin OsPIP1;1 promotes rice salt resistance and seed germination. Plant Physiol Biochem.63:151-8.</ref>
<ref name="ref2">Guo L, Wang ZY, Lin H, Cui WE, et al.(2006) Expression and functional analysis of the rice plasma-membrane intrinsic protein gene family. Cell Res. 16(3):277-86.</ref>
<ref name="ref3">Borstlap AC. (2002) Early diversification of plant aquaporins. Trends Plant Sci. 7(12):529-30.</ref>
</references>

==Structured Information==

[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

Os09g0541000

2017-03-25T14:16:44Z

Xysj1980: /* Labs working on this gene */

The rice '''''Os09g0541000''''' was reported as '''''OsPIP2;7''''' in 2008 <ref name="ref1" /> by researchers from China.

==Annotated Information==
===Gene Symbol===
*'''''Os09g0541000''''' '''''<=>''''' '''''OsPIP2;7, PIP2.7, PIP2-7, OsPIP2-6'''''

===Function===
* '''''OsPIP2;7''''' was involved in rapid water transport and maintenance of the water balance in cells, and ultimately improves the tolerance of yeast and rice to low temperature stress.

===Phenotypic analysis===
* Yeast cells overexpressing OsPIP2;7 showed a higher survival rate after freeze–thaw stress.
* Furthermore, OsPIP2;7 enhanced the transpiration rate and tolerance to low temperature when overexpressed in rice.

===Expression===
* '''''OsPIP2;7''''' was generally up-regulated in roots but down-regulated in shoots at the early stage of chilling stress.

===Subcellular localization===
* '''''OsPIP2;7''''' was localized mainly in mesophyll cells of leaves.
* In roots '''''OsPIP2;7''''' was detected in the vascular tissues, epidermis cells and exodermis cells at the elongation zone, as well as in the epidermis cells, exodermis cells and root hair at the maturation zone.

==Labs working on this gene==
* Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, PR China

==References==
<references>
* <ref name="ref1">
Li GW, Zhang MH, Cai WM, Sun WN, Su WA. Characterization of OsPIP2;7, a water
channel protein in rice. Plant Cell Physiol. 2008 Dec;49(12):1851-8. doi:
10.1093/pcp/pcn166. PubMed PMID: 18988636.

</ref>

</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 9]]

Os04g0186800

2017-03-25T14:07:28Z

Xysj1980: /* References */

The rice '''''Os04g0186800''''' was reported as '''''PT13''''' in 2012 <ref name="ref1" /> by researchers from Switzerland, Denmark, Japan, USA and Philippines.

==Annotated Information==
===Gene Symbol===
*'''''Os04g0186800''''' '''<=>''' '''''OsPT13,PT13,OsPht1;13,PHT1;13'''''
===Function===
* '''''OsPT13''''' is a member of the '''''PHOSPHATE TRANSPORTER1 (PHT1)''''' gene family in rice
* The '''''OsPT11''''' lineage of proteins from mono- and dicotyledons is most closely related to homologs from the ancient moss, indicating an early evolutionary origin.
* By contrast, '''''OsPT13''''' arose in the Poaceae, suggesting that grasses acquired a particular strategy for the acquisition of symbiotic Pi.
* Surprisingly, mutations in either '''''OsPT11''''' or '''''OsPT13''''' affected the development of the symbiosis, demonstrating that both genes are important for AM symbiosis.
* For symbiotic Pi uptake, however, only '''''PT13''''' is not necessary and sufficient.

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

==Labs working on this gene==
* Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
* Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-4000 Roskilde, Denmark
* University of Bern, Institute of Plant Sciences, CH-3013, Switzerland
* National Institute of Agrobiological Sciences, Agronomics Research Center, Tsukuba, Ibaraki 305-8602, Japan
* Department of Plant Biology and Plant Sciences, University of California, Davis, California 95616
* Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
* Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro, Manila, 1301 Philippines

==References==
<references>
* <ref name="ref1">
Yang SY, Grønlund M, Jakobsen I, Grotemeyer MS, Rentsch D, Miyao A, Hirochika
H, Kumar CS, Sundaresan V, Salamin N, Catausan S, Mattes N, Heuer S, Paszkowski
U. Nonredundant regulation of rice arbuscular mycorrhizal symbiosis by two
members of the phosphate transporter1 gene family. Plant Cell. 2012
Oct;24(10):4236-51. doi: 10.1105/tpc.112.104901. PubMed PMID: 23073651; PubMed
Central PMCID: PMC3517247.
</ref>
</references>

==Structured Information==
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 4]]