Difference between revisions of "Os09g0441900"

From RiceWiki
Jump to: navigation, search
Line 1: Line 1:
−
The rice Os09g0441900 was identified as DEP1 (DENSE AND ERECT PANICLE1) and qPE9-1 respectively in 2009 by researchers from China. (in chronological order).  
+
The rice ''Os09g0441900'' was identified as ''DEP1'' (DENSE AND ERECT PANICLE1) and ''qPE9-1'' respectively in 2009 by researchers from China<ref name="ref1" />.(in chronological order).
 
==Annotated Information==
 
==Annotated Information==
 
===Function===
 
===Function===
−
Please input function information here.
+
Natural variation at the ''DEP1'' locus enhances grain yield in rice<ref name="ref1" />.
 +
''DEP1'' regulates nitrogen uptake and metabolism and participates in determining the amount and direction of cell division,which in turn controls organ size and shape.It has been suggested to encode a plant-specific G protein γ subunit.The DEP1 protein interacts in vivo with both the Gα(RGA1)and Gβ(RGB1)subunits,and reduced RGA1 or enhanced RGB1 activity inhibits nitrogen responses.The plant G protein complex regulates nitrogen signaling and modulation of heterotrimeric G protein activity provides a strategy for environmentally sustainable increases in rice grain yield<ref name="ref2" />.
  
 +
'''GO assignment(s):''' GO:0005882
 +
===Mutation===
 +
[[File:1 dep-1.jpg|right|thumb|500px|'''Figure 1.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]
 +
*''dep1'' confers an increased number of grains per panicle (and a consequent increase in grain yield).Figure 1 shows the ''DEP1'' and ''dep1'' NIL line field performance.(a) Dense and erect panicle.(b)Increased panicle branching and reduced rachis length. (c)Grain number per main panicle was significantly higher in the presence of ''dep1''<ref name="ref1" />.
 +
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level<ref name="ref2" />.
 
===Expression===
 
===Expression===
−
Please input expression information here.
+
[[File:DEP expression2.jpg|right|thumb|500px|'''Figure 2.''' ''The expression profile of DEP1 during spikelet development from reference<ref name="ref1" />).'']]
−
 
+
*During reproductive development,''DEP1'' was preferentially expressed on the adaxial side of the bract primordium,as well as in the bract primordia of primary and secondary rachis-branches. Within the inflorescence meristem,''DEP1'' was expressed weakly in the carpel and stamen primordia, with patchy expression in the lemma and palea(Figure 2)<ref name="ref1" />.
−
===Evolution===
+
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.
−
Please input evolution information here.
+
===Cellular Location===
−
 
+
RGB1-GFP, DEP1-GFP,and dep1-1–GFP fusion proteins were detected both on the plasma membrane and within the nucleus of transgenic rice root cells<ref name="ref2" />.
−
You can also add sub-section(s) at will.
+
==Extension==
−
 
+
[http://en.wikipedia.org/wiki/Heterotrimeric_G_proteins Heterotrimeric G proteins] are multisubunit, integral membrane signal-transduction complexes that mediate intracellular responses to external stimuli in diverse eukaryotic organisms<ref name="ref3" />.G proteins typically consist of α, β and γ subunits<ref name="ref4" /><ref name="ref5" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref6" /><ref name="ref7" /><ref name="ref8" />.
 
==Labs working on this gene==
 
==Labs working on this gene==
−
Please input related labs here.
+
*The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China.
−
 
+
*The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
 +
*The State Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
 +
*Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
 +
*The State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
 
==References==
 
==References==
−
Please input cited references here.
+
<references>
 +
<ref name="ref1">
 +
Huang X, Qian Q, Liu Z, et al. Natural variation at the DEP1 locus enhances grain yield in rice[J]. Nature genetics, 2009, 41(4): 494-497.</ref>
 +
<ref name="ref2">Sun H, Qian Q, Wu K, et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice[J]. Nature genetics, 2014.</ref>
 +
<ref name="ref3">New D C, Wong J T Y. The evidence for G-protein-coupled receptors and heterotrimeric G proteins in protozoa and ancestral metazoa[J]. Neurosignals, 1998, 7(2): 98-108.</ref>
 +
<ref name="ref4">Perfus-Barbeoch L, Jones A M, Assmann S M. Plant heterotrimeric G protein function: insights from< i> Arabidopsis</i> and rice mutants[J]. Current opinion in plant biology, 2004, 7(6): 719-731.</ref>
 +
<ref name="ref5">Jones J C, Duffy J W, Machius M, et al. The crystal structure of a self-activating G protein {alpha} subunit reveals its distinct mechanism of signal initiation[J]. Science signaling, 2011, 4(159): ra8.</ref>
 +
<ref name="ref6">Ford C E, Skiba N P, Bae H, et al. Molecular basis for interactions of G protein βγ subunits with effectors[J]. Science, 1998, 280(5367): 1271-1274.</ref>
 +
<ref name="ref7">Ullah H, Chen J G, Young J C, et al. Modulation of cell proliferation by heterotrimeric G protein in Arabidopsis[J]. Science, 2001, 292(5524): 2066-2069.</ref>
 +
<ref name="ref8">Trusov Y, Rookes J E, Tilbrook K, et al. Heterotrimeric G protein γ subunits provide functional selectivity in Gβγ dimer signaling in Arabidopsis[J]. The Plant Cell Online, 2007, 19(4): 1235-1250.
  
 
==Structured Information==
 
==Structured Information==

Revision as of 18:25, 23 May 2014

The rice Os09g0441900 was identified as DEP1 (DENSE AND ERECT PANICLE1) and qPE9-1 respectively in 2009 by researchers from China[1].(in chronological order).

Annotated Information

Function

Natural variation at the DEP1 locus enhances grain yield in rice[1]. DEP1 regulates nitrogen uptake and metabolism and participates in determining the amount and direction of cell division,which in turn controls organ size and shape.It has been suggested to encode a plant-specific G protein γ subunit.The DEP1 protein interacts in vivo with both the Gα(RGA1)and Gβ(RGB1)subunits,and reduced RGA1 or enhanced RGB1 activity inhibits nitrogen responses.The plant G protein complex regulates nitrogen signaling and modulation of heterotrimeric G protein activity provides a strategy for environmentally sustainable increases in rice grain yield[2].

GO assignment(s): GO:0005882

Mutation

Figure 1. The phenotype of NIL-dep1 plants(from reference[1]).
  • dep1 confers an increased number of grains per panicle (and a consequent increase in grain yield).Figure 1 shows the DEP1 and dep1 NIL line field performance.(a) Dense and erect panicle.(b)Increased panicle branching and reduced rachis length. (c)Grain number per main panicle was significantly higher in the presence of dep1[1].
  • The dep1-1 and dep1-32 alleles exhibit insensitive growth to nitrogen input level[2].

Expression

Figure 2. The expression profile of DEP1 during spikelet development from reference[1]).
  • During reproductive development,DEP1 was preferentially expressed on the adaxial side of the bract primordium,as well as in the bract primordia of primary and secondary rachis-branches. Within the inflorescence meristem,DEP1 was expressed weakly in the carpel and stamen primordia, with patchy expression in the lemma and palea(Figure 2)[1].
  • DEP1 transcript abundance was positively induced by the level of nitrogen supplied[2].

Cellular Location

RGB1-GFP, DEP1-GFP,and dep1-1–GFP fusion proteins were detected both on the plasma membrane and within the nucleus of transgenic rice root cells[2].

Extension

Heterotrimeric G proteins are multisubunit, integral membrane signal-transduction complexes that mediate intracellular responses to external stimuli in diverse eukaryotic organisms[3].G proteins typically consist of α, β and γ subunits[4][5].Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit[6][7][8].

Labs working on this gene

  • The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China.
  • The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
  • The State Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
  • Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
  • The State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

References

<references> [1] [2] [3] [4] [5] [6] [7] <ref name="ref8">Trusov Y, Rookes J E, Tilbrook K, et al. Heterotrimeric G protein γ subunits provide functional selectivity in Gβγ dimer signaling in Arabidopsis[J]. The Plant Cell Online, 2007, 19(4): 1235-1250.

Structured Information

Gene Name

Os09g0441900

Description

Whey acidic protein, core region domain containing protein

Version

NM_001069822.1 GI:115479386 GeneID:4347178

Length

4701 bp

Definition

Oryza sativa Japonica Group Os09g0441900, complete gene.

Source

Oryza sativa Japonica Group 

 ORGANISM  Oryza sativa Japonica Group
           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
           Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
           clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome

Chromosome 9

Location

Chromosome 9:17064862..17069562

Sequence Coding Region

17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413

Expression

GEO Profiles:Os09g0441900

Genome Context

<gbrowseImage1> name=NC_008402:17064862..17069562 source=RiceChromosome09 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008402:17064862..17069562 source=RiceChromosome09 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>

Protein Sequence

<aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>

Gene Sequence

<dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>

External Link(s)

NCBI Gene:Os09g0441900, RefSeq:Os09g0441900

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Huang X, Qian Q, Liu Z, et al. Natural variation at the DEP1 locus enhances grain yield in rice[J]. Nature genetics, 2009, 41(4): 494-497.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Sun H, Qian Q, Wu K, et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice[J]. Nature genetics, 2014.
  3. ↑ 3.0 3.1 New D C, Wong J T Y. The evidence for G-protein-coupled receptors and heterotrimeric G proteins in protozoa and ancestral metazoa[J]. Neurosignals, 1998, 7(2): 98-108.
  4. ↑ 4.0 4.1 Perfus-Barbeoch L, Jones A M, Assmann S M. Plant heterotrimeric G protein function: insights from< i> Arabidopsis</i> and rice mutants[J]. Current opinion in plant biology, 2004, 7(6): 719-731.
  5. ↑ 5.0 5.1 Jones J C, Duffy J W, Machius M, et al. The crystal structure of a self-activating G protein {alpha} subunit reveals its distinct mechanism of signal initiation[J]. Science signaling, 2011, 4(159): ra8.
  6. ↑ 6.0 6.1 Ford C E, Skiba N P, Bae H, et al. Molecular basis for interactions of G protein βγ subunits with effectors[J]. Science, 1998, 280(5367): 1271-1274.
  7. ↑ 7.0 7.1 Ullah H, Chen J G, Young J C, et al. Modulation of cell proliferation by heterotrimeric G protein in Arabidopsis[J]. Science, 2001, 292(5524): 2066-2069.
  8. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref8
Retrieved from "https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0441900&oldid=171428"