Difference between revisions of "Os09g0441900"

From RiceWiki
Jump to: navigation, search
(→‎Function)
Line 2: Line 2:
 
==Annotated Information==
 
==Annotated Information==
 
===Function===
 
===Function===
 +
*DEP1 (Dense and Erect Panicle1) gene is identified to be an approximately 85 kb segment of the Nipponbare BAC AP005419 between newly developed markers S2 and S11-2, which locates the interval between the molecular marker RM3700 and RM7424 on rice chromosome 9, as showed in Figure 1<ref name="ref1" />.This gene encodes an unknown protein containing the PEBP (phosphatidylethanolamine-binding protein) domain which share some homology with the N terminus of GS3. In the case of the rice plant, more tillering equates to more grain-bearing branches. Rice branching determines the number of panicle and grain number per panicle ,and then control the grain yield.We can see the rice tillering at Figure 2. DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
 +
 
*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" />.
 
*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" />.
 
[[File:cd tolerance.jpg|right|thumb|300px|'''Figure 1.''' ''Impact of the C-terminal half of OsDEP1 on yeast Cd tolerance(from reference<ref name="ref3" />).'']]
 
[[File:cd tolerance.jpg|right|thumb|300px|'''Figure 1.''' ''Impact of the C-terminal half of OsDEP1 on yeast Cd tolerance(from reference<ref name="ref3" />).'']]
Line 7: Line 9:
  
 
'''GO assignment(s):''' GO:0005882
 
'''GO assignment(s):''' GO:0005882
 +
 
===Mutation===
 
===Mutation===
 
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]
 
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''The phenotype of NIL-dep1 plants(from reference<ref name="ref1" />).'']]

Revision as of 15:45, 3 June 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

  • DEP1 (Dense and Erect Panicle1) gene is identified to be an approximately 85 kb segment of the Nipponbare BAC AP005419 between newly developed markers S2 and S11-2, which locates the interval between the molecular marker RM3700 and RM7424 on rice chromosome 9, as showed in Figure 1[1].This gene encodes an unknown protein containing the PEBP (phosphatidylethanolamine-binding protein) domain which share some homology with the N terminus of GS3. In the case of the rice plant, more tillering equates to more grain-bearing branches. Rice branching determines the number of panicle and grain number per panicle ,and then control the grain yield.We can see the rice tillering at Figure 2. DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
  • 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].
Figure 1. Impact of the C-terminal half of OsDEP1 on yeast Cd tolerance(from reference[3]).
  • OsDEP1 encoded a highly cysteine (Cys)-rich G protein γ subunit composed of 426 aa. The OsDEP1(170–426) region is necessary and sufficient to confer cadmium (Cd)tolerance on host yeast cells(Figure 1).The Cd responses of transgenic Arabidopsis plants constitutively expressing OsDEP1,OsDEP1(1–169) or OsDEP1(170–426),were similar to the observations in yeast cells, with OsDEP1 and OsDEP1(170–426) transgenic plants displaying Cd tolerance but OsDEP1(1–169) plants showing no such tolerance[3].

GO assignment(s): GO:0005882

Mutation

Figure 2. 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 2 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].
Figure 3. Different nitrogen responses(from reference[2]).
  • The dep1-1 and dep1-32 alleles exhibit insensitive growth to nitrogen input level(Figure 3)[2].

Expression

Figure 4. 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 4)[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].

Evolution

Genetic diversity analysis suggests that DEP1 has been subjected to artificial selection during Oryza sativa spp.japonica rice domestication[2].

Extension

Figure 5. Plant responses to Cd stress (from reference[4]).
  • Heterotrimeric G proteins are multisubunit, integral membrane signal-transduction complexes that mediate intracellular responses to external stimuli in diverse eukaryotic organisms[5].G proteins typically consist of α, β and γ subunits[6][7].Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit[8][9][10].
  • Cadmium (Cd)is one of the transition metals that is non-essential for almost all living organisms.It is also a noxious compound that inactivates and denatures structural and functional proteins of organisms by binding to free sulfhydryl groups,thereby inhibiting their growth and development.Another aspect of Cd toxicity is derived from its chemical similarity to metal co-factors or coordinated metals, such as Zn,Fe,and Ca, of enzymes,signalling intermediates,and transcription factors,especially the zinc-finger type[4][11]. To cope with Cd toxicity effects,plants are known to be equipped with the potential to chelate and extrude Cd,to sequester Cd into vacuoles, and to dissipate reactive oxygen species triggered by Cd(Figure 5)[4].For the chelation of heavy metals, including Cd,various cysteine (Cys)-rich proteins are employed by plants.Small Cys-rich peptides,called metallothioneins (MTs),are the major chelators of Cd[12][13].

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.
  • Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan.
  • National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
  • Faculty of Bioresource Sciences, Akita Prefectural University, 241-7 Kaidobata Nishi, Akita 010-1095, Japan.
  • Biodiversity and Climate Research Center (BiK-F), D-60323 Frankfurt, Germany.

References

<references> [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]

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 1.7 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 2.5 2.6 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 3.2 Kunihiro S, Saito T, Matsuda T, et al. Rice DEP1, encoding a highly cysteine-rich G protein γ subunit, confers cadmium tolerance on yeast cells and plants[J]. Journal of experimental botany, 2013, 64(14): 4517-4527.
  4. ↑ 4.0 4.1 4.2 4.3 DalCorso G, Farinati S, Maistri S, et al. How plants cope with cadmium: staking all on metabolism and gene expression[J]. Journal of integrative plant biology, 2008, 50(10): 1268-1280.
  5. ↑ 5.0 5.1 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.
  6. ↑ 6.0 6.1 Perfus-Barbeoch L, Jones A M, Assmann S M. Plant heterotrimeric G protein function: insights from Arabidopsis and rice mutants[J]. Current opinion in plant biology, 2004, 7(6): 719-731.
  7. ↑ 7.0 7.1 Jones J C, Duffy J W, Machius M, et al. The crystal structure of a self-activating G protein α subunit reveals its distinct mechanism of signal initiation[J]. Science signaling, 2011, 4(159): ra8.
  8. ↑ 8.0 8.1 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.
  9. ↑ 9.0 9.1 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.
  10. ↑ 10.0 10.1 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.
  11. ↑ 11.0 11.1 Verbruggen N, Hermans C, Schat H. Mechanisms to cope with arsenic or cadmium excess in plants[J]. Current opinion in plant biology, 2009, 12(3): 364-372.
  12. ↑ 12.0 12.1 Ecker D J, Butt T R, Sternberg E J, et al. Yeast metallothionein function in metal ion detoxification[J]. Journal of Biological Chemistry, 1986, 261(36): 16895-16900.
  13. ↑ 13.0 13.1 Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.
Retrieved from "https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0441900&oldid=177037"