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Os04g0271200

2014-06-10T08:01:06Z

Shfengna: /* Expression */

Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.

==Annotated Information==
===Function===
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" />

*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.

*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" />

*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" />

*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" />

*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" />

*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" />

*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" />

*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" />

[[File:1-s2.0-S1367593105001079-gr1.gif|right|thumb|360px|1-s2.0-S1367593105001079-gr1.'']]
 Proposed functions of yeast Sir2 and of mammalian SIRT1. (a) Yeast Sir2 histone deacetylation and silencing function. Acetyl-CoA-dependent histone acetyltransferases acetylate histones leading to transcriptional activation. The NAD+-dependent deacetylase Sir2 deacetylates histones and creates transcriptional silent chromatin. Nicotinamide is a product of the reaction and is a potent inhibitor of Sir2. OAADPr is a novel metabolite generated during deacetylation and may function in linked cellular pathways. An NAD+ salvage pathway depletes nicotinamide and funnels NAD+ to Sir2. (b) General chemical reaction catalyzed by sirtuins. Human SIRT1 is depicted with several reported acetylated protein targets and the pathways affected. 

===Expression===
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" />

*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" />

*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" />

*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" />

*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" />

*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" />

[[File:small.gif|right|thumb|360px|small''<ref name="ref1" />'']]
 Expression profiles of OsSRT1. A, Northern hybridization detection of OsSRT1 mRNA in different rice tissues or developmental stages. Actin transcripts were detected as controls. B, Nuclear localization of the OsSRT1-GFP fusion. Top, Onion skin cells transfected with OsSRT1-GFP photographed under a confocal microscope at 488 nm (left) and merged with the transmission image (right). Bottom, GFP alone. 
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]
 Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated. 

[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]
 Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. 

[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]
 Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.
 
 
 
 
 
 
 
 

===Evolution===
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.

*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" />

*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />.

*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" />

*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" />
[[File:F1.small.gif]]
 Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.

*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" />

*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" />

==Labs working on this gene==

*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of
*Institute of Plant Biology, National Taiwan University, Taipei
*University of Chinese Academy of Sciences, Beijing 100049, China
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France

==References==
<references>
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref>
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref>
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref>
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref>
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref>
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim
Subcellular localization of rice histone deacetylases in organelles
FEBS Lett., 583 (2009), pp. 2249–2254</ref>
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
Plant Physiol., 144 (2007), pp. 1508–1519</ref>
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu
Cell signaling during cold, drought, and salt stress
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref>
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref>
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref>
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref>
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref>
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref>
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref>
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref>
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref>
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref>
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os04g0271200|
Description = Silent information regulator protein Sir2 family protein|
Version = NM_001058879.1 GI:115457487 GeneID:4335343|
Length = 2712 bp|
Definition = Oryza sativa Japonica Group Os04g0271200, 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 4|Chromosome 4]]|
AP = Chromosome 4:11382902..11385613|
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581 ,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374 |
GCID = <gbrowseImage1>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:Small.gif

2014-06-10T08:00:16Z

Shfengna:

Os04g0271200

2014-06-10T07:59:52Z

Shfengna: /* Expression */

Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.

==Annotated Information==
===Function===
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" />

*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.

*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" />

*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" />

*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" />

*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" />

*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" />

*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" />

*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" />

[[File:1-s2.0-S1367593105001079-gr1.gif|right|thumb|360px|1-s2.0-S1367593105001079-gr1.'']]
 Proposed functions of yeast Sir2 and of mammalian SIRT1. (a) Yeast Sir2 histone deacetylation and silencing function. Acetyl-CoA-dependent histone acetyltransferases acetylate histones leading to transcriptional activation. The NAD+-dependent deacetylase Sir2 deacetylates histones and creates transcriptional silent chromatin. Nicotinamide is a product of the reaction and is a potent inhibitor of Sir2. OAADPr is a novel metabolite generated during deacetylation and may function in linked cellular pathways. An NAD+ salvage pathway depletes nicotinamide and funnels NAD+ to Sir2. (b) General chemical reaction catalyzed by sirtuins. Human SIRT1 is depicted with several reported acetylated protein targets and the pathways affected. 

===Expression===
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" />

*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" />

*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" />

*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" />

*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" />

*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" />

[[File:small.gif|right|thumb|360px|small''<ref name="ref1" />'']]
 Expression profiles of OsSRT1. A, Northern hybridization detection of OsSRT1 mRNA in different rice tissues or developmental stages. Actin transcripts were detected as controls. B, Nuclear localization of the OsSRT1-GFP fusion. Top, Onion skin cells transfected with OsSRT1-GFP photographed under a confocal microscope at 488 nm (left) and merged with the transmission image (right). Bottom, GFP alone. 
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]
 Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated. 

[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]
 Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. 

[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]
 Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.
 
 
 
 
 
 

===Evolution===
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.

*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" />

*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />.

*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" />

*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" />
[[File:F1.small.gif]]
 Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.

*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" />

*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" />

==Labs working on this gene==

*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of
*Institute of Plant Biology, National Taiwan University, Taipei
*University of Chinese Academy of Sciences, Beijing 100049, China
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France

==References==
<references>
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref>
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref>
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref>
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref>
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref>
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim
Subcellular localization of rice histone deacetylases in organelles
FEBS Lett., 583 (2009), pp. 2249–2254</ref>
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
Plant Physiol., 144 (2007), pp. 1508–1519</ref>
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu
Cell signaling during cold, drought, and salt stress
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref>
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref>
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref>
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref>
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref>
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref>
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref>
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref>
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref>
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref>
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os04g0271200|
Description = Silent information regulator protein Sir2 family protein|
Version = NM_001058879.1 GI:115457487 GeneID:4335343|
Length = 2712 bp|
Definition = Oryza sativa Japonica Group Os04g0271200, 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 4|Chromosome 4]]|
AP = Chromosome 4:11382902..11385613|
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581 ,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374 |
GCID = <gbrowseImage1>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0271200

2014-06-10T07:58:08Z

Shfengna: /* Expression */

Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.

==Annotated Information==
===Function===
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" />

*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.

*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" />

*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" />

*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" />

*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" />

*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" />

*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" />

*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" />

[[File:1-s2.0-S1367593105001079-gr1.gif|right|thumb|360px|1-s2.0-S1367593105001079-gr1.'']]
 Proposed functions of yeast Sir2 and of mammalian SIRT1. (a) Yeast Sir2 histone deacetylation and silencing function. Acetyl-CoA-dependent histone acetyltransferases acetylate histones leading to transcriptional activation. The NAD+-dependent deacetylase Sir2 deacetylates histones and creates transcriptional silent chromatin. Nicotinamide is a product of the reaction and is a potent inhibitor of Sir2. OAADPr is a novel metabolite generated during deacetylation and may function in linked cellular pathways. An NAD+ salvage pathway depletes nicotinamide and funnels NAD+ to Sir2. (b) General chemical reaction catalyzed by sirtuins. Human SIRT1 is depicted with several reported acetylated protein targets and the pathways affected. 

===Expression===
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" />

*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" />

*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" />

*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" />

*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" />

*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" />

[[File:F2.small.gif|right|thumb|360px|F2.small''<ref name="ref1" />'']]
 Expression profiles of OsSRT1. A, Northern hybridization detection of OsSRT1 mRNA in different rice tissues or developmental stages. Actin transcripts were detected as controls. B, Nuclear localization of the OsSRT1-GFP fusion. Top, Onion skin cells transfected with OsSRT1-GFP photographed under a confocal microscope at 488 nm (left) and merged with the transmission image (right). Bottom, GFP alone. 
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]
 Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated. 

[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]
 Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. 

[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]
 Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.
 
 
 
 
 
 

===Evolution===
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.

*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" />

*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />.

*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" />

*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" />
[[File:F1.small.gif]]
 Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.

*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" />

*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" />

==Labs working on this gene==

*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of
*Institute of Plant Biology, National Taiwan University, Taipei
*University of Chinese Academy of Sciences, Beijing 100049, China
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France

==References==
<references>
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref>
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref>
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref>
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref>
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref>
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim
Subcellular localization of rice histone deacetylases in organelles
FEBS Lett., 583 (2009), pp. 2249–2254</ref>
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
Plant Physiol., 144 (2007), pp. 1508–1519</ref>
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu
Cell signaling during cold, drought, and salt stress
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref>
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref>
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref>
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref>
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref>
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref>
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref>
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref>
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref>
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref>
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os04g0271200|
Description = Silent information regulator protein Sir2 family protein|
Version = NM_001058879.1 GI:115457487 GeneID:4335343|
Length = 2712 bp|
Definition = Oryza sativa Japonica Group Os04g0271200, 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 4|Chromosome 4]]|
AP = Chromosome 4:11382902..11385613|
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581 ,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374 |
GCID = <gbrowseImage1>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0271200

2014-06-10T07:50:42Z

Shfengna: /* Function */

Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.

==Annotated Information==
===Function===
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" />

*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.

*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" />

*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" />

*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" />

*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" />

*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" />

*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" />

*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" />

[[File:1-s2.0-S1367593105001079-gr1.gif|right|thumb|360px|1-s2.0-S1367593105001079-gr1.'']]
 Proposed functions of yeast Sir2 and of mammalian SIRT1. (a) Yeast Sir2 histone deacetylation and silencing function. Acetyl-CoA-dependent histone acetyltransferases acetylate histones leading to transcriptional activation. The NAD+-dependent deacetylase Sir2 deacetylates histones and creates transcriptional silent chromatin. Nicotinamide is a product of the reaction and is a potent inhibitor of Sir2. OAADPr is a novel metabolite generated during deacetylation and may function in linked cellular pathways. An NAD+ salvage pathway depletes nicotinamide and funnels NAD+ to Sir2. (b) General chemical reaction catalyzed by sirtuins. Human SIRT1 is depicted with several reported acetylated protein targets and the pathways affected. 

===Expression===
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" />

*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" />

*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" />

*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" />

*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" />

*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" />

[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]
 Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated. 

[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]
 Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. 

[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]
 Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.
 
 
 
 
 
 

===Evolution===
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.

*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" />

*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />.

*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" />

*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" />
[[File:F1.small.gif]]
 Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.

*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" />

*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" />

==Labs working on this gene==

*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of
*Institute of Plant Biology, National Taiwan University, Taipei
*University of Chinese Academy of Sciences, Beijing 100049, China
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France

==References==
<references>
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref>
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref>
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref>
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref>
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref>
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim
Subcellular localization of rice histone deacetylases in organelles
FEBS Lett., 583 (2009), pp. 2249–2254</ref>
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
Plant Physiol., 144 (2007), pp. 1508–1519</ref>
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu
Cell signaling during cold, drought, and salt stress
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref>
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref>
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref>
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref>
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref>
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref>
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref>
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref>
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref>
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref>
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os04g0271200|
Description = Silent information regulator protein Sir2 family protein|
Version = NM_001058879.1 GI:115457487 GeneID:4335343|
Length = 2712 bp|
Definition = Oryza sativa Japonica Group Os04g0271200, 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 4|Chromosome 4]]|
AP = Chromosome 4:11382902..11385613|
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581 ,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374 |
GCID = <gbrowseImage1>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:1-s2.0-S1367593105001079-gr1.gif

2014-06-10T07:48:44Z

Shfengna:

Os04g0271200

2014-06-10T07:47:56Z

Shfengna: /* Function */

Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.

==Annotated Information==
===Function===
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" />

*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.

*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" />

*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" />

*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" />

*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" />

*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" />

*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" />

*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" />

[[File:1-s2.0-S1367593105001079-gr1.gif|right|thumb|360px|1-s2.0-S1367593105001079-gr1.''<ref name="ref21" />'']]
 Proposed functions of yeast Sir2 and of mammalian SIRT1. (a) Yeast Sir2 histone deacetylation and silencing function. Acetyl-CoA-dependent histone acetyltransferases acetylate histones leading to transcriptional activation. The NAD+-dependent deacetylase Sir2 deacetylates histones and creates transcriptional silent chromatin. Nicotinamide is a product of the reaction and is a potent inhibitor of Sir2. OAADPr is a novel metabolite generated during deacetylation and may function in linked cellular pathways. An NAD+ salvage pathway depletes nicotinamide and funnels NAD+ to Sir2. (b) General chemical reaction catalyzed by sirtuins. Human SIRT1 is depicted with several reported acetylated protein targets and the pathways affected. 

===Expression===
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" />

*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" />

*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" />

*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" />

*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" />

*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" />

[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]
 Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated. 

[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]
 Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. 

[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]
 Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.
 
 
 
 
 
 

===Evolution===
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.

*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" />

*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />.

*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" />

*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" />
[[File:F1.small.gif]]
 Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.

*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" />

*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" />

==Labs working on this gene==

*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of
*Institute of Plant Biology, National Taiwan University, Taipei
*University of Chinese Academy of Sciences, Beijing 100049, China
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France

==References==
<references>
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref>
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref>
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref>
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref>
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref>
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim
Subcellular localization of rice histone deacetylases in organelles
FEBS Lett., 583 (2009), pp. 2249–2254</ref>
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
Plant Physiol., 144 (2007), pp. 1508–1519</ref>
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu
Cell signaling during cold, drought, and salt stress
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref>
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref>
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref>
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref>
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref>
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref>
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref>
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref>
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref>
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref>
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref>
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os04g0271200|
Description = Silent information regulator protein Sir2 family protein|
Version = NM_001058879.1 GI:115457487 GeneID:4335343|
Length = 2712 bp|
Definition = Oryza sativa Japonica Group Os04g0271200, 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 4|Chromosome 4]]|
AP = Chromosome 4:11382902..11385613|
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581 ,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374 |
GCID = <gbrowseImage1>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:11382902..11385613
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os05g0445900

2014-06-10T04:07:39Z

Shfengna:

Please input one-sentence summary here.

==Annotated Information==
===Function===
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. As well, there are some proteins coded for DNA demethylation. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation are DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3). Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1orthologs and twoDML3orthologs, but no DME orthologs.

1.It has been demonstrated that rice ROS1a protein is a bi-functional DNA glycosylase/lyase for 5-meC DNA demethylation, although biochemical characterization of the ROS1a enzyme remains to be performed to confirm this.Rice ROS1a is toxic to E. coli containing 5-meC in its genome. When ROS1a cDNA was expressed under the control of an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible promoter, ROS1a was toxic to an E. coli dcm+ strain containing 5-meC in an IPTG-dependent manner, and was less toxic to a dcm− mutant without 5-meC.

[[File:TPJ_5009_f2.gif]]

ROS1a is the most abundantly expressed gene in tissues. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds.And the null mutation, ros1a-GUS1, was hardly ever transmitted to progeny.Even in the presence of the wild-type paternal ROS1a allele, the maternal nullros1a-GUS1allele caused failure of early stage endosperm development, indicating non-equivalent contribution of maternal and paternal ROS1a to endosperm development.

[[File:TPJ_5009_f4.gif]]

Figure. Histochemical GUS staining patterns in ROS1a/ros1a-GUS1 plants. (a) Longitudinal section through basal shoot meristem region of mature plants. Insets are magnified views of shoot apical and lateral (upper) and inflorescence (lower) meristems. (b) Flowers. (c) Anthers. Approximately half of the pollen present showed GUS staining (see also Figure S7b). The inset is a magnified view. (d) Pistils. Insets are ovules before pollination exposed by removing the carpel. The upper and lower insets show a GUS-stained ovule and its sibling, which displayed no GUS staining, respectively. Before pollination, ovules containing gametes with the wild-type ROS1a allele were morphologically indistinguishable from those with ros1a-GUS1 allele. (e) Schematic representation of a rice female gametophyte enclosed by the maternal tissues of the ovule: ovary tissue (light brown), integument (dark brown), and nucellus (gray). The haploid female gametophyte consists of the egg apparatus (green), including the egg cell and two synergids, the central cell (white), which contains large vacuoles and thin lines of cytoplasm (pink), and antipodals (blue). (f,g) Differential interference contrast micrographs of GUS-stained female gametophytes of ROS1a/ros1a-GUS1 plants. To make the borders of different tissues clear, white lines are drawn on the image in (f), which corresponds to the area enclosed by the red line in (e). (h) Differential interference contrast micrograph of a sibling female gametophyte displaying no GUS staining. Arrows indicate GUS-stained meristems (a), pollen (b) and the probable egg apparatus (d). In (b), the arrowhead indicates the GUS-stained lodicule. AP, antipodals; PN, polar nuclei. The images in (g,h) correspond to the area enclosed by the blue line in (e). Scale bars = 1 mm [a,b, inset in (a)], 500 μm [c,d], 100 μm [inset in (d)] and 50 μm [inset in (c) and f-h].

===Expression===
Rice contains four ROS1 orthologs and two DML3 orthologs tentatively named ROS1a–d and DML3a and DML3b, that contain characteristic DNA glycosylase domains flanked by conserved domains of unknown functions. Of these, ROS1ais the longest gene, comprising 17 exons that encode a protein with 1952 amino acids, and 5¢ and 3¢ UTRs of 73 and 607 bp, respectively.RT-PCR analysis revealed thatROS1awas expressed in all vegetative and reproductive tissues tested . Quantitative RT-PCR analysis revealed that ROS1ais the most extensively expressed gene among the four genes(ROS1a, ROS1c, ROS1d and DML3a) expressed in five selected tissues examined, including anthers and pistils,whereas ROS1b and DML3bare scarcely expressed in these tissues. Interestingly, moderate levels of transcripts for ROS1c, ROS1dandDML3awere detected in pistils and immature seeds 2 days after pollination.
[[File:TPJ_5009_f1.gif]]

===Evolution===
Phylogenetic analysis revealed that the rice (Oryza sativa) genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1 orthologs and two DML3 orthologs, but no DME orthologs (Zemach et al., 2010). Rice endosperm DNA is hypomethylated in all sequence contexts, implying that hypomethylation in rice endosperm relies on some of these DNA glycosylases or alternative biochemical mechanisms (Zemach et al., 2010). In this study, to characterize the function of one of the four rice ROS1 orthologs, tentatively named ROS1a (LOC_Os01g11900.1), that resides on chromosome 1, we used homologous recombination-promoted knock-in targeting with positive/negative selection (Yamauchi et al., 2009) to obtain a mutant that disrupts ROS1a by fusion of its endogenous promoter with the GUS reporter gene encoding β-glucuronidase. We reproducibly obtained T0 plants with the null knock-in allele, ros1a-GUS1, in the heterozygous condition, and detected GUS expression in the T0 plants in the shoot apical, lateral and inflorescence meristems, as well as in both female and male gametophytes before fertilization. The ros1a-GUS1 allele was hardly transmitted to the next generation; neither the maternal nor the paternal ros1a-GUS1 allele was virtually found in the progeny. The results indicate that ROS1a, presumably through DNA demethylation, is indispensable in both gametophytes, and that the null allele of ROS1a is difficult to isolate by conventional mutagenesis techniques, in which mutants are usually obtained as segregants in the progeny population.
[[File:pnas.1009695107fig05.jpg]]

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

==References==
1.A. Zemach et al., Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107, 18729 (Oct 26, 2010).

2.A. Ono et al., A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71, 564 (Aug, 2012).

==Structured Information==
{{JaponicaGene|
GeneName = Os05g0445900|
Description = Similar to ROS1 (Fragment)|
Version = NM_001062220.1 GI:115464170 GeneID:4338940|
Length = 5779 bp|
Definition = Oryza sativa Japonica Group Os05g0445900, 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 5|Chromosome 5]]|
AP = Chromosome 5:21889157..21894935|
CDS = 21889581..21889708,21890545..21890583,21890664..21890778,21890883..21890948,21892020..21892159 ,21892239..21892302,21892380..21892416,21892564..21893001,21893713..21893795 ,21893897..21893933,21894150..21894218,21894322..21894413,21894487..21894571 ,21894906..21894934|
GCID = <gbrowseImage1>
name=NC_008398:21889157..21894935
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008398:21889157..21894935
source=RiceChromosome05
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>ttaagagatgttcctccagactcagcaaaggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtatgagttacattatcagatgattacttttggaaaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtttacgaacttccagattcacatcccctcatgcaacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggtctaacaactgaagaaatacagcactgcttctggagaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactga</cdnaseq>|
AA = <aaseq>LRDVPPDSAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVG RICVRLGWVPIQPLPESLQLHLLELYPVLETIQKYLWPRLCKLDQQTLYELHYQMITF GKVFCTKSKPNCNACPMRSECRHFASAFASARLALPSPQDKRLVNLSNQFAFHNGTMP TPNSTPLPQLEGSIHARDVHANNTNPIIEEPASPREEECRELLENDIEDFDEDTDEIP IIKLNMEAFSQNLENCIKESNKDFQSDDITKALVAISNEAASIPVPKLKNVHRLRTEH YVYELPDSHPLMQQLALDQREPDDPSPYLLAIWTPDELKDTREAPKPCCNPQTEGGLC SNEMCHNCVSERENQYRYVRGTVLVPCRTAMRGSFPLNGTYFQVNEVFADHSSSHNPI NIPREQLWNLHRRMVYFGTSVPTIFKGLTTEEIQHCFWRGFVCVRGFNMETRAPRPLC PHFHLAASKLRRSSKKAATEQTH</aaseq>|
DNA = <dnaseqindica>5228..5355#4353..4391#4158..4272#3988..4053#2777..2916#2634..2697#2520..2556#1935..2372#1141..1223#1003..1039#718..786#523..614#365..449#2..30#gttaagagatgttcctccagactcagcaaagtaagatactacacctgtattcaatatttacaaatcccattgccctgctgatgagatttttctagttctggaaatgataaatcaagtatcaaagaagtttgtgaaccaattaaatggagcaagctgatccaagaacttgccagttaatatctagaattaaatactatgagcaaagttctatgaaatgggcacgcagaacagaaaaggctgtataatgtatgacacatgatcgaagcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagtaagtttctgttggattaattctccttcacctgcagccaatttgaaatttacactacattgttgcaactcaggttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctgtaagaatgttgcattgtctactacagttgtataaatactctctgcaattttatacgatgatgtttcaatttgaatatattgattttgtttgtgccttcaaagataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtgagttataaccaattaaccatacccactcatagttgcccttcttattagtttttttttacgcaagcccttcttattagtttgtgtaacttctaggttatttctttttcatgcaaattacagtatttggaatcatgaataattaaggcaataaggagtaaataacataatttataactataaggaattattaacagagtttcatggttttcacaggtatgagttacattatcagatgattacttttggaaaggtacttcattagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaaggtattatggcaagcagaaaatgggagccttctggctgcaaggagacttacaaaataaacactatttgcttcagtagtcacttttttccgataaaggaagctttattaaaactcagtcaaatacaccaagatgatacattctaactgagccactcccggcctctgcatgaaatgcacaccgccacaaaacaggatctaactagaccctcaacacaaaacaaataaattagtgactatcaagccgtagactatatcgccacccatgctccagggtaaaaaactcctgtgccacctgatagtgcacagcaaaaaccacgagaaggatgtgctttcgttggtggagagaccgaattagctccattaacataatatgaccactaagagcgcaaaatagtgcttttgaagaataaaagggaaaatatgctaggagaaaaatcaatatatggttctagtacaccgccatggcactttgtgtagtctctgtctgcaacaaaatatatttgccgctttcacttatcttacctgggaattttgttatcacgtatttcctcgttccactatctttcttgttttgtttgtgcgcgcgcgcatgcctgatatatcttgctctttcagttgaccttacctgggagccttcattttgcatatttcttcatttgttattttttccttattaactctgttatattttgtttgacttttttaaatgaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtgtaagtgttggactgatattttatttagcttgaacatgtacctgtttaaacttacatttattatagagcccaccatctaagtaattctatacatcctgaacaaaatattttttaatttctattactgacttaaggttctgctcgcagttacgaacttccagattcacatcccctcatgcaacaggtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgattgcaaatgatcttacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggtaaatcaaccaacattatgtagcaatcatcaacattgaagagctgaacctctgcattagtcagctagtaaacaaaatattcattataatccaaacattggaatgaattcaggaattcaagaaaatgttgaagataacttttaatgaaaactagtgcttacaaagtgccaagcaaagctattctgttgtctgtgtaatctcttttcttgcatgaaatagcccactgtcttcactttaaacaataagaatagcatagattttgggtttccggctatacaacacatcttaatatgaacttttgtggaagtctaaaagagaacctctctgaacctttaaactgtacactatttaaccaacaatcaaagccgatcacttctcaacgtcattctgaattagctttgggcgatgtttcttaaccaggagatgtggtctgagattttagattttttttttcatctcctttatattagtagacgacttaaaattttctggaataatcttacttcgctgtgaagtatttataacccagataaatcggtaagattgaagtaaagtattattgtcccacgaaatttagtgtgtgaaagtagacaacatttttttctactgtccgattaaactttatttaactctgccccattttatctaggctataaatggtgatttcttctaggctatacggtttttcaatccaattttaccttattttgctttaccaaatttgtcaacattataatactttgtagtgcaagtgagattttttttttcaattttgttatgtcatttactaattttaaaattgaaaacctggttcagccttgggccattttgccacattagggacacatagtccaaagccactttaaatttgagacaaggttgaaaagcgcatggttttgatacttcaggttctgggttgaattgtgtccagttttctgctttggggttgtctctggactaacagaaaagttcagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacggttactggaacatgaacaggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttaggtctaacaactgaagaaatacagcactgcttctggagaggtattaacagtatttttttcactcgctgtttcagcgcattctcctctgggacatatcttgtttcctcatatgatcaaacaatttgcagaatgcagatgccatcatataatcacaatatgtttctacagttatatagcattcgtgtgattgtgtcaaggtgtccacacacttttcacaaaaacttactccccctgtcccataatataagggattttgagcttttgtttgcactgtttgaccattcgtcttattcaaaaaaatttagaattatattttttttctttgtgacttactttattatccaaaatactttaagcacaacttttcgttttttatatttgcacaaattttttgaataagacgagtggtcaaacattataatcaaaaaactcaaaatcccttgtattatgggacggagggagtagtattaagggtctaaaaggagcctgaatatttggttcagttagagtctatatctgagtccattttaattcctagtgctatggataaaggtgtcctccttcaataaataaataaaggtctctccagttattagtcaccagcatccaatataactgcctgataatatatgtggtaagttatatggtgccaaagaggcaaagatactgctaccatgactaaccccctttttttttctgagttaataagggtgttagcatacatatagcttccaaattggtttagttaggtggaaaaagtcgtcatttcaggatgcagatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactgatttcaacagggacatatcaattctataaaataatgttgatggtgattacatcagttctcgatctgtgcatgggtcatattagttcctgcaggacgatagccattcttctaggaaataaacagtggagttggaaacagttaactttaagatgtgggagccaattgggcacgagaaagcaccaatatttcatatgcacctctggggcaggtcggatgcggatcatcatcatcagttaacatgggcgtagaatatcattccgttttttttttctgtggctttggtgtatcttattcacttttcatttgttttatccattcaactagcttgccaagagaccttaccatctgttctcatgacatgttagtttttcagaacttatagcaggtagtaccttcatattgatgatatgactttgattttcatt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062220.1 RefSeq:Os05g0445900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 5]]
[[Category:Chromosome 5]]

2014-06-05T12:02:19Z

Shfengna: /* Function */

Please input one-sentence summary here.

SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues.
==Annotated Information==
===Function===
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']]
*Several plant SDGs have in vitro HMTase activities<ref name="ref8"/>. For instance, SDG714 in rice tends to choose core
histones as preferred substrates , but ArabidopsisSDG8, SDG26, and SDG25 prefer to methylate oligonucleosomes

*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.

*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.

*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.

===Expression===
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.

*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.

[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]
[[File:Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.jpg|300px|thumb|left|Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.''<ref name="ref1"/>'']]
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.

*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.

[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]

*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.

*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.

===Evolution===
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.

*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.

*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.

==Labs working on this gene==

*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China

*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China

*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

==References==
<references>
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref>

<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref>

<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref>

<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref>

<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref>

<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref>

<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref>
〈/references〉

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0307800|
Description = Nuclear protein SET domain containing protein|
Version = NM_001069362.1 GI:115478463 GeneID:4346677|
Length = 7580 bp|
Definition = Oryza sativa Japonica Group Os09g0307800, 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 9:8605019..8612598|
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917 ,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059 ,8611590..8611707,8612450..8612473|
GCID = <gbrowseImage1>
name=NC_008402:8605019..8612598
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:8605019..8612598
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0307800

2014-06-05T12:01:46Z

Shfengna: /* Function */

Please input one-sentence summary here.

SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues.
==Annotated Information==
===Function===
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']]
Several plant SDGs have in vitro HMTase activities<ref name="ref8"/>. For instance, SDG714 in rice tends to choose core
histones as preferred substrates , but ArabidopsisSDG8, SDG26, and SDG25 prefer to methylate oligonucleosomes

*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.

*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.

*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.

===Expression===
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.

*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.

[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]
[[File:Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.jpg|300px|thumb|left|Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.''<ref name="ref1"/>'']]
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.

*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.

[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]

*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.

*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.

===Evolution===
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.

*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.

*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.

==Labs working on this gene==

*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China

*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China

*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

==References==
<references>
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref>

<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref>

<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref>

<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref>

<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref>

<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref>

<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref>
〈/references〉

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0307800|
Description = Nuclear protein SET domain containing protein|
Version = NM_001069362.1 GI:115478463 GeneID:4346677|
Length = 7580 bp|
Definition = Oryza sativa Japonica Group Os09g0307800, 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 9:8605019..8612598|
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917 ,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059 ,8611590..8611707,8612450..8612473|
GCID = <gbrowseImage1>
name=NC_008402:8605019..8612598
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:8605019..8612598
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]