Os09g0441900

2014-06-03T15:59:29Z

ZhuXiping: /* Function */

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==
===Function===

*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" />).'']]
*''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<ref name="ref3" />.

'''GO assignment(s):''' GO:0005882

*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 6)<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 7). DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
[[File:positonal cloning of dep1.jpg|right|thumb|300px|'''Figure 5.''' ''Positional cloning of dep1(from reference<ref name="ref1" />).'']]]]

===Mutation===
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''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 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''<ref name="ref1" />.
[[File:2 mutation.jpg|right|thumb|300px|'''Figure 3.''' ''Different nitrogen responses(from reference<ref name="ref2" />).'']]
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level(Figure 3)<ref name="ref2" />.
* dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
*DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).
*But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.
*The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
*Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I).The evidence of grain-fillinf failure in the presence of dep1 is unclear. Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

===Expression===
[[File:DEP expression2.jpg|right|thumb|300px|'''Figure 4.''' ''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 4)<ref name="ref1" />.
*Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c)<ref name="ref1" />.
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.

===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" />.
==Evolution==
Genetic diversity analysis suggests that ''DEP1'' has been subjected to artificial selection during ''Oryza sativa'' spp.''japonica'' rice domestication<ref name="ref2" />.
The allelic constitution at the DEP1 locus was explored by resequencing from a panel of widely cultivated Chinese varieties (69 japonica and 83 indica)<ref name="ref1" />. Several sequence variants at the DEP1 C terminus were present in the sample of indica types. The variety 93-11 differed from the japonica variety Nipponbare by three amino acids, whereas that of the variety Teqing differed by two amino acids. The Nipponbare sequence differed from that of an accession of Oryza rufipogon by one nucleotide at position 663, but this did not produce a variant peptide. We investigated the structure of the homologs of DEP1 in other smallgrain cereals[2]. Several truncated C-terminal deletions were observed in barley, and in bread wheat and its diploid wild progenitor Triticum urartu. To determine whether any novel gain-of-function was induced by the presence of these truncated genes, we generated a number of transgenic wheat plants carrying a pUbi:RNAi-TaDEP1 construct. The consequent downregulation of TaDEP1 resulted in an increase in the length of the ear, a less compact ear and a somewhat reduced number of spikelets. This suggests that a functionally equivalent mutation may have occurred early in the divergence of the wheat and barley lineages.

==Extension==
[[File:reponses to Cd.jpg|right|thumb|300px|'''Figure 5.''' ''Plant responses to Cd stress (from reference<ref name="ref4" />).'']]
*[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="ref5" />.G proteins typically consist of α, β and γ subunits<ref name="ref6" /><ref name="ref7" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />.
*[http://en.wikipedia.org/wiki/Cadmium 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<ref name="ref4" /><ref name="ref11" />. 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)<ref name="ref4" />.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<ref name="ref12" /><ref name="ref13" />.
==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>
<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"> 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.</ref>
<ref name="ref4">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.</ref>
<ref name="ref5">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="ref6">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.</ref>
<ref name="ref7">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.</ref>
<ref name="ref8">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="ref9">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="ref10">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.</ref>
<ref name="ref11">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.</ref>
<ref name="ref12"> 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.</ref>
<ref name="ref13">Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17064862..17069562|
CDS = 17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413 |
GCID = <gbrowseImage1>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>|
AA = <aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>|
DNA = <dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069822.1 RefSeq:Os09g0441900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0441900

2014-06-03T15:58:30Z

ZhuXiping: /* Evolution */

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==
===Function===

*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" />).'']]
*''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<ref name="ref3" />.

'''GO assignment(s):''' GO:0005882

*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 6)<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 7). DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
[[File:positonal cloning of dep1.jpg|right|thumb|300px|'''Figure 1.''' ''Positional cloning of dep1(from reference<ref name="ref3" />).'']]]]

===Mutation===
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''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 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''<ref name="ref1" />.
[[File:2 mutation.jpg|right|thumb|300px|'''Figure 3.''' ''Different nitrogen responses(from reference<ref name="ref2" />).'']]
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level(Figure 3)<ref name="ref2" />.
* dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
*DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).
*But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.
*The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
*Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I).The evidence of grain-fillinf failure in the presence of dep1 is unclear. Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

===Expression===
[[File:DEP expression2.jpg|right|thumb|300px|'''Figure 4.''' ''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 4)<ref name="ref1" />.
*Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c)<ref name="ref1" />.
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.

===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" />.
==Evolution==
Genetic diversity analysis suggests that ''DEP1'' has been subjected to artificial selection during ''Oryza sativa'' spp.''japonica'' rice domestication<ref name="ref2" />.
The allelic constitution at the DEP1 locus was explored by resequencing from a panel of widely cultivated Chinese varieties (69 japonica and 83 indica)<ref name="ref1" />. Several sequence variants at the DEP1 C terminus were present in the sample of indica types. The variety 93-11 differed from the japonica variety Nipponbare by three amino acids, whereas that of the variety Teqing differed by two amino acids. The Nipponbare sequence differed from that of an accession of Oryza rufipogon by one nucleotide at position 663, but this did not produce a variant peptide. We investigated the structure of the homologs of DEP1 in other smallgrain cereals[2]. Several truncated C-terminal deletions were observed in barley, and in bread wheat and its diploid wild progenitor Triticum urartu. To determine whether any novel gain-of-function was induced by the presence of these truncated genes, we generated a number of transgenic wheat plants carrying a pUbi:RNAi-TaDEP1 construct. The consequent downregulation of TaDEP1 resulted in an increase in the length of the ear, a less compact ear and a somewhat reduced number of spikelets. This suggests that a functionally equivalent mutation may have occurred early in the divergence of the wheat and barley lineages.

==Extension==
[[File:reponses to Cd.jpg|right|thumb|300px|'''Figure 5.''' ''Plant responses to Cd stress (from reference<ref name="ref4" />).'']]
*[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="ref5" />.G proteins typically consist of α, β and γ subunits<ref name="ref6" /><ref name="ref7" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />.
*[http://en.wikipedia.org/wiki/Cadmium 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<ref name="ref4" /><ref name="ref11" />. 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)<ref name="ref4" />.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<ref name="ref12" /><ref name="ref13" />.
==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>
<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"> 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.</ref>
<ref name="ref4">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.</ref>
<ref name="ref5">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="ref6">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.</ref>
<ref name="ref7">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.</ref>
<ref name="ref8">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="ref9">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="ref10">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.</ref>
<ref name="ref11">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.</ref>
<ref name="ref12"> 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.</ref>
<ref name="ref13">Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17064862..17069562|
CDS = 17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413 |
GCID = <gbrowseImage1>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>|
AA = <aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>|
DNA = <dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069822.1 RefSeq:Os09g0441900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0441900

2014-06-03T15:56:55Z

ZhuXiping: /* Expression */

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==
===Function===

*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" />).'']]
*''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<ref name="ref3" />.

'''GO assignment(s):''' GO:0005882

*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 6)<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 7). DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
[[File:positonal cloning of dep1.jpg|right|thumb|300px|'''Figure 1.''' ''Positional cloning of dep1(from reference<ref name="ref3" />).'']]]]

===Mutation===
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''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 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''<ref name="ref1" />.
[[File:2 mutation.jpg|right|thumb|300px|'''Figure 3.''' ''Different nitrogen responses(from reference<ref name="ref2" />).'']]
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level(Figure 3)<ref name="ref2" />.
* dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
*DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).
*But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.
*The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
*Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I).The evidence of grain-fillinf failure in the presence of dep1 is unclear. Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

===Expression===
[[File:DEP expression2.jpg|right|thumb|300px|'''Figure 4.''' ''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 4)<ref name="ref1" />.
*Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c)<ref name="ref1" />.
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.

===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" />.
==Evolution==
Genetic diversity analysis suggests that ''DEP1'' has been subjected to artificial selection during ''Oryza sativa'' spp.''japonica'' rice domestication<ref name="ref2" />.
==Extension==
[[File:reponses to Cd.jpg|right|thumb|300px|'''Figure 5.''' ''Plant responses to Cd stress (from reference<ref name="ref4" />).'']]
*[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="ref5" />.G proteins typically consist of α, β and γ subunits<ref name="ref6" /><ref name="ref7" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />.
*[http://en.wikipedia.org/wiki/Cadmium 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<ref name="ref4" /><ref name="ref11" />. 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)<ref name="ref4" />.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<ref name="ref12" /><ref name="ref13" />.
==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>
<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"> 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.</ref>
<ref name="ref4">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.</ref>
<ref name="ref5">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="ref6">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.</ref>
<ref name="ref7">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.</ref>
<ref name="ref8">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="ref9">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="ref10">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.</ref>
<ref name="ref11">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.</ref>
<ref name="ref12"> 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.</ref>
<ref name="ref13">Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17064862..17069562|
CDS = 17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413 |
GCID = <gbrowseImage1>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>|
AA = <aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>|
DNA = <dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069822.1 RefSeq:Os09g0441900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0441900

2014-06-03T15:55:56Z

ZhuXiping: /* Mutation */

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==
===Function===

*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" />).'']]
*''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<ref name="ref3" />.

'''GO assignment(s):''' GO:0005882

*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 6)<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 7). DEP1 is pleiotropically responsible for all three traits: dense panicle, high grain number per panicle and erect panicle.
[[File:positonal cloning of dep1.jpg|right|thumb|300px|'''Figure 1.''' ''Positional cloning of dep1(from reference<ref name="ref3" />).'']]]]

===Mutation===
[[File:1 dep-1.jpg|right|thumb|300px|'''Figure 2.''' ''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 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''<ref name="ref1" />.
[[File:2 mutation.jpg|right|thumb|300px|'''Figure 3.''' ''Different nitrogen responses(from reference<ref name="ref2" />).'']]
*The ''dep1-1'' and ''dep1-32'' alleles exhibit insensitive growth to nitrogen input level(Figure 3)<ref name="ref2" />.
* dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
*DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).
*But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.
*The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
*Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I).The evidence of grain-fillinf failure in the presence of dep1 is unclear. Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

===Expression===
[[File:DEP expression2.jpg|right|thumb|300px|'''Figure 4.''' ''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 4)<ref name="ref1" />.
*''DEP1'' transcript abundance was positively induced by the level of nitrogen supplied<ref name="ref2" />.
===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" />.
==Evolution==
Genetic diversity analysis suggests that ''DEP1'' has been subjected to artificial selection during ''Oryza sativa'' spp.''japonica'' rice domestication<ref name="ref2" />.
==Extension==
[[File:reponses to Cd.jpg|right|thumb|300px|'''Figure 5.''' ''Plant responses to Cd stress (from reference<ref name="ref4" />).'']]
*[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="ref5" />.G proteins typically consist of α, β and γ subunits<ref name="ref6" /><ref name="ref7" />.Gβγ acts as a functional monomer,and Gβ-mediated processes require a γ subunit<ref name="ref8" /><ref name="ref9" /><ref name="ref10" />.
*[http://en.wikipedia.org/wiki/Cadmium 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<ref name="ref4" /><ref name="ref11" />. 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)<ref name="ref4" />.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<ref name="ref12" /><ref name="ref13" />.
==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>
<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"> 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.</ref>
<ref name="ref4">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.</ref>
<ref name="ref5">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="ref6">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.</ref>
<ref name="ref7">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.</ref>
<ref name="ref8">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="ref9">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="ref10">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.</ref>
<ref name="ref11">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.</ref>
<ref name="ref12"> 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.</ref>
<ref name="ref13">Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily[J]. Dalton Transactions, 2008 (47): 6663-6675.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17064862..17069562|
CDS = 17065265..17065393,17066606..17066664,17067820..17067864,17067951..17067995,17068411..17069413 |
GCID = <gbrowseImage1>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17064862..17069562
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagataaatgagtttgttggtacaaaacatgacccactaataccaacaaagagaaggaggcacagatcttgccgtctttttcggtggatcggatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttga</cdnaseq>|
AA = <aaseq>MGEEAVVMEAPRPKSPPRYPDLCGRRRMQLEVQILSREITFLKD ELHFLEGAQPVSRSGCIKEINEFVGTKHDPLIPTKRRRHRSCRLFRWIGSKLCICISC LCYCCKCSPKCKRPRCLNCSCSSCCDEPCCKPNCSACCAGSCCSPDCCSCCKPNCSCC KTPSCCKPNCSCSCPSCSSCCDTSCCKPSCTCFNIFSCFKSLYSCFKIPSCFKSQCNC SSPNCCTCTLPSCSCKGCACPSCGCNGCGCPSCGCNGCGCPSCGCNGCGLPSCGCNGC GSCSCAQCKPDCGSCSTNCCSCKPSCNGCCGEQCCRCADCFSCSCPRCSSCFNIFKCS CAGCCSSLCKCPCTTQCFSCQSSCCKRQPSCCKCQSSCCEGQPSCCEGHCCSLPKPSC PECSCGCVWSCKNCTEGCRCPRCRNPCCLSGCLC</aaseq>|
DNA = <dnaseqindica>404..532#1745..1803#2959..3003#3090..3134#3550..4552#tctcttccctctctctctttctctctccaaaccccacgcacgccgcgtcgccgcctcctcctctccatctccgctgctattattgcccgcgcagacgcaggccaccatccttcctctcgctcacgctcgctgctatatgggggtcctcctcatcgcatcgcatcgcatcacctcgcacgggcgcgcgcgccgtgccgtgccgctagctcgatccgcctcgtacgccagctcgctcgctcgctcccccaccccgctgctgcacggctgcgcccgcgctgtcccctgtccccccgctcgccgcggcgatttatacccaccacgccccctgctgctgctataatgcccatgagtgaaggcggcgaggggtggttctgagttggccgttggcgtgctgcgtgtggagatgggggaggaggcggtggtgatggaggcgccgaggcccaagtcgccgccgaggtacccggacctgtgcggccggcggcggatgcagctggaggtgcagatcctgagccgcgagatcacgttcctcaaggtgagcgccccgcggcggcggcggctgcgtttttctctataggtttctctttcacactcgctcgctcgaaattctcggggcccgagctctacttgcttcgtcttcctttgactttaccgattaattttaaaaaaaaggagatccgattcgccgcgcatttttcaaaacccaagcggccgagtacggagctacccgctactgcaagtaggatgctgtgaagtgtacagtaatggcgttgttaattgcggtagctagtgctattctagtacttgtagtactgtttctaggcggaggtgaatcacggcgccatcaatccgaggctggcgagacaagcttggccctctttgggcgtggcgccatggctgtactacctttgtcgttgtttggttgggctcctcgttggagaaaagaagagcgtgggcatggacaactgacctgagtggccttgtcagggagagccatagcagtggacgtgtctatctccgccattgcttcgtcgacactggacgtgcagacggcatggccatgagggctttgcacgatgggtggtgccgtgttggtgttatgggctgccaccatggtttgaggcttttgatgttgctagattttgtgtttaacgagggagggaagaatgtgttgttcttgacactgtgctgtgcttttaaggagcagagatttcagaagctcttcagatatcagagaacttctttgtagtagtaatcaaatgcgctttagacatctttttatcgtttcttgcaaggtcagtccctgctttggtacccgatctcgcttttgtgcaacatcaaagttacacttacacagtaaagcaggaatctttatgggaccgttcgtactggtcaattactccaggctttgattaatgggttttaagttttaaccgcagatttggtacaagtaacaacctttatttactttttatttctgcaactgtgtcttttaacatgaaagaatccagctccattcaaaagtttagtttttattttccattgtggtgcatggtcactcagcctgcagtactgaattatcaaaattttcttttgtcatttctctcatgttaagtgcatagtctattttacttcaacaggtagaaaaacttttgtgggtttgtttctagctcaaggaggaaattcatgggtttgcatctagcacatgagagaacaatattggtctaacacaaagctccttttgtaggatgagcttcacttccttgaaggagctcagcccgtttctcgttctggatgcattaaagagtatgtactactgcccttcatgcattacagatattttgtttttaagtttttagaaatttgaagagcttatgtcaagtatgaaatgtcagcttaattttattgctgtccttatctaatgtcttatgctctgttttataaaatttggttgcattttctcccccagggaaaaatcttgtataagtgtgttatgtacttatgtgtataaaatcttgttgcacttgtatgtcacacttaggccctgtttagatcctccaaaatggcagtttgccattttgaagaaccttttgccattttggatctaaacactagtaacaaaacttggcaatttggcatttggcatttgctagtctatagtagcaaattgtgccaaaaagtgctttggaaccactctctctttctttctctctctcactttagtgctagaatggtaaaagtttaggatgcatctaaacaccaactagtacttttacaatactaaaacttttgccaccaaaacttttgccatttgccatttgctatttcaaatggatctaaacagggccttagcaaatcaccatatgttaaaattaccttgggatgaaaaagaaaaaggaaaccagcattgaagtcttgtttgaaatgcatatgtacttgtaccattacagaaattcttaaaactgctgtcttgacagctacttatcaaacagccccacctgcatcataacgttcctagtggtgcctataactctgcctcagttattattttgtggcccactggtccaacaatttgaaaaaaattatattgaactaaatatattgaacagtagtatgacgtcctctttgcttgagttccatattacagctcacagtcctgagatttgtttcaccgattctttccatgcgatgtgcacatattcttattcaatttaaaaaatgaaagcagattatttttaacaagtaacctatcacgttagcttaacattgtatatttgtggtggaattatgtaatattccgatatcgcatttgaagttttgaacatgtgtgctcaaattgagggacacatgactgtagtgaaagcaaatataaatgtctgagcaatggactatactttgtattcattactacaagttatgtccttttgcaggttgctaatgtcctcttacattacttgtcaggataaatgagtttgttggtacaaaacatgacccactaataccaacgtatggcctctaaactttcagttcccccattttaagcatgttcgctgtttatttacgagttttgacattgttttttccttttccagaaagagaaggaggcacagatcttgccgtctttttcggtggatcgggtatgttttgatccaatatagtttgctcgcaggttctgaggggcaagaacattcaaatatctataatgttttctgttggattcaacattcatcactatttccctcgaaaaaaaagcattcgtcactattggaattgaaagtctgaaagtgcctctagtccctttgtatgttaaaagtcaataaacaagcagtagttttctatatgccacattaatattattgacgcattttaaaaagcaaactagtccagggatgtaatcatctttgttatctaaaactaaaaaaggaaaaactagtgcttttttacattaacattgatttttttgcggctgaaattacatgtagaaactttggcataataatctgtactactgccaaactgagcttttacatggtgaaaatattttccctgcagatcaaaattgtgtatctgcatttcatgtctttgctactgttgcaagtgctcacccaagtgcaaaagaccaaggtgcctcaattgttcttgcagctcatgctgcgacgagccatgctgtaagccaaactgcagtgcgtgctgcgctgggtcatgctgtagtccagactgctgctcatgctgtaaacctaactgcagttgctgcaagaccccttcttgctgcaaaccgaactgctcgtgctcctgtccaagctgcagctcatgctgcgatacatcgtgctgcaaaccgagctgcacctgcttcaacatcttttcatgcttcaaatccctgtacagctgcttcaagatcccttcatgcttcaagtcccagtgcaactgctctagccccaattgctgcacttgcacccttccaagctgtagctgcaagggctgtgcctgtccaagctgtggatgcaacggctgtggctgtccaagctgcggatgcaacggttgtggctgtccaagctgcggttgcaacggctgtggccttccaagctgcggttgcaacggctgcggctcgtgctcttgcgcccaatgcaaacccgattgtggctcgtgctctaccaattgctgtagctgcaagccaagctgcaacggctgctgcggcgagcagtgctgccgctgcgcggactgcttctcctgctcgtgccctcgttgctccagctgcttcaacatcttcaaatgctcctgcgctggctgctgctcgagcctgtgcaagtgcccctgcacgacgcagtgcttcagctgccagtcgtcatgctgcaagcggcagccttcgtgctgcaagtgccagtcgtcttgctgcgaggggcagccttcctgctgcgagggacactgctgcagcctcccgaaaccgtcgtgccctgaatgttcctgtgggtgtgtctggtcttgcaagaattgtacagagggttgtcgatgcccacggtgtcgtaacccatgctgtctcagtggttgcttatgttgatctagatccttttttggttgttgtttttcttgtattttttagttgttaggcctttgattaagttcgaactttcataaatatatggtgtttatcctgtaaagaaatgatgatttcaaggatttttcatagctatgagacgaggttgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069822.1 RefSeq:Os09g0441900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

2014-06-03T14:49:27Z

ZhuXiping: /* Function */

==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[1,2].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.

[[

Figure 1. Positional cloning of dep1. (a) The gene was mapped to the interval between the molecular marker RM3700 and RM7424 on rice chromosome 9 on the basis of the genotyping of 210 F2 segregants. (b) The gene was further delimited to a B85-kb genomic region on Nipponbare BAC AP005419 using 1,311 F2 segregants. The number below line indicates the number of recombinants between DEP1 and the adjacent marker. An arrow indicates the site of predicted genes in the S2 to S11-2 interval. (c) Allelic variation of the DEP1 sequence.

Figure 2. The arrows indicate (A) an axillary meristem initiated from the axial of a leaf, (B) a tiller bud formed from the axillary meristem, (C) a tiller bud with the first leaf primordium, (D) the mature tiller buds with several young leaves, and (E) tillers outgrown from mature tiller buds

]]

===Mutation===
dep1 is the mutant DEP1 allele.The variant involves the replacement of a 637-bp stretch of the middle of exon 5 by 12-bp sequence,which has the effect of creatig a premature stop codon and consequently a loss of 230 residues from C termimus.As showed in Figure 1[2].
DEP1 acts as a dominant negative regulator of panicle architecture ad grain number.The near isogenic lines(NILs) carrying a mutated DEP1 (NIL-dep1) exhibit increased number of grain per panicle,shorter infloresence internodes, increased number of both primary and secondary panicle branches,which may result from the enhanced meristematic activity and cell proliferation through regulating OsCKX2[2](Fig 3. a).But they do not exhibit noticeable change in panical architecture. The experiments are taken as the following several aspects[2]. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c). Close examination of the shoot apex meristem (SAM) showed that the SAM of NIL-dep1 plants was larger than that of NIL-DEP1 plants (Fig 3. 2d). Cells in the uppermost internode of the mature NIL-dep1 culm were shorter than those in NIL-DEP1 plants (Fig 3. 2e). At the same time, cell number across the longitudinal axis of NIL-dep1 plants was higher than in NIL-DEP1 plants (Fig 3. 2f). Taken together, these observations suggest that the dep1 allele enhances meristematic activity and promotes cell proliferation. So dep1 allele enhances meristematic activity and promotes cell proliferation.The activity of axillary meristem in the shoot apex is important for the determination of the extent of panicle branching and hence grain number[3,4,5]. In NIL-dep1 plants, the Gn1a was clearly downregulated.Gn1a, a major grain number QTL, encodes a cytokinin oxidase/ dehydrogenase, and has been implicated in the regulation of meristematic activity, panicle branching and grain number through its effect on the level of cytokinin. ANIL-Gn1a line had the same number of primary branches as the control line but developed more secondary branches[6,7]. This suggests that dep1 genetically controls the number of both primary branches and secondary branches on primary branches at the panicle top, whereas Gn1a regulates the number of secondary branches on primary branches at the panicle base.
Preparing the field performation of DEP1 and dep1, the grain number per mian panicle is higher in the presence of dep1 (Fig 4.c) and there are clear differences in panicle architecture, influorescence internode and panicle length (Fig.b,e), and the number of both primary (Fig 4.b,f)and secondary (Fig 4.g) branches per panicle.Furthermore,he grain-weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig 4.h),but the overall grain yield per plant under field conditions was increased(+40.9%) (Fig 4.I). The evidence of grain-fillinf failure in the presence of dep1 is unclear. The vascular system of NIL-dep1 plants appeared rather better developed and their sclerenchyma cell walls were thicker at maturity than those in NIL-DEP1 plants. These traits are favorable for both water transport capacity and the mechanical strength of the stem, both of which are important factors for the breeding of high-yielding, lodging-resistant varieties.Through testing the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent. Thus, dep1 is a useful allele for increasing grain yield in rice.

===Expression===
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. Through GFP-expression fused with dep1, in NIL-dep1, dep1 and DEP1 was detected in nucleis of root,leaf, culm, meristem, with the highest expression in the meristem at the stage of primary and secondary rachis branch formation(Fig 3.b,c).
===Evolution===
Pedigree records show that many high-yielding Chinese japonica varieties, including Shennong 265, were derived from the Italian land race Balilla13,15, which was extensively cultivated in Italy in the 1970s and introduced into China in 1958[8]. The allelic constitution at the DEP1 locus was explored by resequencing from a panel of widely cultivated Chinese varieties (69 japonica and 83 indica). This truncated mutation was present in Balilla and all 36 japonica types having an erect or semierect panicle, including super high-yielding cultivars Liaojing 5 and Qianchonglang, but it was absent from all the other varieties. Thus, this natural allelic variation in DEP1 has clearly been exploited by japonica breeding programs in China. Several sequence variants at the DEP1 C terminus were present in the sample of indica types. The variety 93-11 differed from the japonica variety Nipponbare by three amino acids, whereas that of the variety Teqing differed by two amino acids. The Nipponbare sequence differed from that of an accession of Oryza rufipogon by one nucleotide at position 663, but this did not produce a variant peptide. We investigated the structure of the homologs of DEP1 in other smallgrain cereals. Several truncated C-terminal deletions were observed in barley, and in bread wheat and its diploid wild progenitor Triticum urartu. To determine whether any novel gain-of-function was induced by the presence of these truncated genes, we generated a number of transgenic wheat plants carrying a pUbi:RNAi-TaDEP1 construct. The consequent downregulation of TaDEP1 resulted in an increase in the length of the ear, a less compact ear and a somewhat reduced number of spikelets. This suggests that a functionally equivalent mutation may have occurred early in the divergence of the wheat and barley lineages.

==Reference==

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==Annotated Information==
===Function===
===Mutation===
===Expression===