VIP5_ARATH
ID VIP5_ARATH Reviewed; 643 AA.
AC Q9C950; Q8RWR3;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 25-MAY-2022, entry version 124.
DE RecName: Full=Protein RTF1 homolog {ECO:0000305};
DE AltName: Full=Protein VERNALIZATION INDEPENDENCE 5 {ECO:0000303|PubMed:15472079};
GN Name=VIP5 {ECO:0000303|PubMed:15472079};
GN OrderedLocusNames=At1g61040 {ECO:0000312|Araport:AT1G61040};
GN ORFNames=T7P1.17 {ECO:0000312|EMBL:AAG51642.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=12750345; DOI=10.1093/genetics/164.1.347;
RA Zhang H., Ransom C., Ludwig P., van Nocker S.;
RT "Genetic analysis of early flowering mutants in Arabidopsis defines a class
RT of pleiotropic developmental regulator required for expression of the
RT flowering-time switch flowering locus C.";
RL Genetics 164:347-358(2003).
RN [5]
RP FUNCTION.
RX PubMed=15472079; DOI=10.1105/tpc.104.026062;
RA Oh S., Zhang H., Ludwig P., van Nocker S.;
RT "A mechanism related to the yeast transcriptional regulator Paf1c is
RT required for expression of the Arabidopsis FLC/MAF MADS box gene family.";
RL Plant Cell 16:2940-2953(2004).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-87, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [7]
RP IDENTIFICATION IN THE PAF1 COMPLEX, FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=20363855; DOI=10.1104/pp.110.155838;
RA Park S., Oh S., Ek-Ramos J., van Nocker S.;
RT "PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex and
RT assists in regulating expression of genes within H3K27ME3-enriched
RT chromatin.";
RL Plant Physiol. 153:821-831(2010).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=21799800; DOI=10.1371/journal.pone.0022241;
RA Liu Y., Geyer R., van Zanten M., Carles A., Li Y., Horold A.,
RA van Nocker S., Soppe W.J.;
RT "Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role
RT for the polymerase associated factor 1 complex in seed dormancy.";
RL PLoS ONE 6:E22241-E22241(2011).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT GLY-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Component of the PAF1 complex (PAF1C) which is involved in
CC histone modifications such as methylation on histone H3 'Lys-4'
CC (H3K4me3) (PubMed:20363855). Involved in regulation of flowering time.
CC Required for the expression of the flowering repressors and FLC and
CC MADS-box genes of the MAF family (PubMed:15472079). Involved in the
CC control of seed dormancy and germination (PubMed:21799800).
CC {ECO:0000269|PubMed:15472079, ECO:0000269|PubMed:20363855,
CC ECO:0000269|PubMed:21799800}.
CC -!- SUBUNIT: Component of the nuclear PAF1 complex (PAF1C), which consists
CC of VIP2/ELF7/PAF1, VIP3/SKI8/WDR61, VIP4/LEO1, VIP5/RTF1,
CC VIP6/ELF8/CTR9 and CDC73. {ECO:0000269|PubMed:20363855}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855}.
CC -!- DISRUPTION PHENOTYPE: Early flowering, reduced plant size and defects
CC in floral morphology in whorls 1-3, but fully fertile flowers
CC (PubMed:12750345). Reduced seed dormancy and increased germination rate
CC of freshly harvested seeds (PubMed:21799800).
CC {ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:21799800}.
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DR EMBL; AC018908; AAG51642.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33770.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60373.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60374.1; -; Genomic_DNA.
DR EMBL; AY091764; AAM10312.1; -; mRNA.
DR PIR; A96636; A96636.
DR RefSeq; NP_001322666.1; NM_001333927.1.
DR RefSeq; NP_001322667.1; NM_001333926.1.
DR RefSeq; NP_176299.1; NM_104784.4.
DR AlphaFoldDB; Q9C950; -.
DR SMR; Q9C950; -.
DR STRING; 3702.AT1G61040.1; -.
DR iPTMnet; Q9C950; -.
DR PaxDb; Q9C950; -.
DR PRIDE; Q9C950; -.
DR ProteomicsDB; 246452; -.
DR EnsemblPlants; AT1G61040.1; AT1G61040.1; AT1G61040.
DR EnsemblPlants; AT1G61040.2; AT1G61040.2; AT1G61040.
DR EnsemblPlants; AT1G61040.3; AT1G61040.3; AT1G61040.
DR GeneID; 842395; -.
DR Gramene; AT1G61040.1; AT1G61040.1; AT1G61040.
DR Gramene; AT1G61040.2; AT1G61040.2; AT1G61040.
DR Gramene; AT1G61040.3; AT1G61040.3; AT1G61040.
DR KEGG; ath:AT1G61040; -.
DR Araport; AT1G61040; -.
DR TAIR; locus:2205996; AT1G61040.
DR eggNOG; KOG2402; Eukaryota.
DR HOGENOM; CLU_018644_1_1_1; -.
DR InParanoid; Q9C950; -.
DR OMA; SGCKSAV; -.
DR OrthoDB; 720071at2759; -.
DR PhylomeDB; Q9C950; -.
DR PRO; PR:Q9C950; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9C950; baseline and differential.
DR Genevisible; Q9C950; AT.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IBA:GO_Central.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:TAIR.
DR Gene3D; 3.90.70.200; -; 1.
DR InterPro; IPR004343; Plus-3_dom.
DR InterPro; IPR036128; Plus3-like_sf.
DR Pfam; PF03126; Plus-3; 1.
DR SMART; SM00719; Plus3; 1.
DR SUPFAM; SSF159042; SSF159042; 1.
DR PROSITE; PS51360; PLUS3; 1.
PE 1: Evidence at protein level;
KW Acetylation; Flowering; Nucleus; Phosphoprotein; Reference proteome;
KW Transcription; Transcription regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..643
FT /note="Protein RTF1 homolog"
FT /id="PRO_0000432761"
FT DOMAIN 261..396
FT /note="Plus3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00693"
FT REGION 1..107
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 124..262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..53
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 64..107
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 124..153
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 173..208
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 210..248
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylglycine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES 87
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT CONFLICT 22
FT /note="R -> S (in Ref. 3; AAM10312)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 643 AA; 71320 MW; A098B6F38CE8C4AD CRC64;
MGDLENLLLE AAGRTNSAGR SRHPPSSRRR EGSYSDGSSD SRDDSDEDRG YASRKPSGSQ
VPLKKRLEAE REDRAARVEG GYGDGPSDRE GDSSEESDFG DDLYKNEEDR QKLAGMTEFQ
REMILSERAD KKGDKNFTEK LRSKRESEKT PVSKKETQPL PASRGVRSSA RSADRAAAKD
DALNELRAKR MKQQDPAALR KLRDASKGGS GSRDFSSTKR KPLASSNLSS SSQSDSDSRS
QSDDEGSNGG MLDSDDDRSD VPTFEDVKEV TIRRSKLAKW LMEPFFEELI VGCFVRVGIG
RSKSGPIYRL CWVKNVDATD PDKTYKLENK TTHKYLNVVW GNETSAARWQ MAMISDGHPL
EEEYRQWIRE VERTNGRMPT KQDISEKKEA IQRTNSFVYS AETVKQMLQE KKSASVRPMN
VAAEKDRLRK ELEIAQSKND EAGVERIKSK IKQLDASRNK KGVDKKALKL AEMNKKNRAE
NFKNASEVKS ITASLKAGEA GYDPFSRRWT RSSNYYNGKN KGKDGEENEA AVAAAVETNG
ADAGAGVEAT EAALEAAAEA GKLIDTRAPI GQGAEHNQLH NFELSLSLTA LQKYGGPQGV
QKAFMARKQL TEATVGCRVA ENDGKRHGLT LTVSDYKRRR GLL
