VIP3_ARATH
ID VIP3_ARATH Reviewed; 321 AA.
AC Q9SZQ5;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=WD repeat-containing protein VIP3 {ECO:0000305};
DE AltName: Full=Protein BOUQUET-1 {ECO:0000303|PubMed:23134555};
DE Short=boq-1 {ECO:0000303|PubMed:23134555};
DE AltName: Full=Protein SKI8 homolog {ECO:0000303|PubMed:16716192};
DE AltName: Full=Protein VERNALIZATION INDEPENDENCE 3 {ECO:0000303|PubMed:12750345};
DE AltName: Full=Protein ZWERGERL {ECO:0000303|PubMed:22511887};
DE Short=zwg;
GN Name=VIP3 {ECO:0000303|PubMed:12750345};
GN Synonyms=SKI8 {ECO:0000303|PubMed:16716192};
GN OrderedLocusNames=At4g29830 {ECO:0000312|Araport:AT4G29830};
GN ORFNames=F27B13.70 {ECO:0000312|EMBL:CAB43658.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 FUNCTION, AND 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 INTERACTION WITH VIP4 AND VIP6.
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 FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16716192; DOI=10.1111/j.1365-2443.2006.00972.x;
RA Jolivet S., Vezon D., Froger N., Mercier R.;
RT "Non conservation of the meiotic function of the Ski8/Rec103 homolog in
RT Arabidopsis.";
RL Genes Cells 11:615-622(2006).
RN [7]
RP FUNCTION.
RX PubMed=18725930; DOI=10.1371/journal.pgen.1000077;
RA Oh S., Park S., van Nocker S.;
RT "Genic and global functions for Paf1C in chromatin modification and gene
RT expression in Arabidopsis.";
RL PLoS Genet. 4:E1000077-E1000077(2008).
RN [8]
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 [9]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RX PubMed=21571540; DOI=10.1016/j.plaphy.2011.04.012;
RA Shigeta T., Yasuda D., Mori T., Yoshimitsu Y., Nakamura Y., Yoshida S.,
RA Asami T., Okamoto S., Matsuo T.;
RT "Characterization of brassinosteroid-regulated proteins in a nuclear-
RT enriched fraction of Arabidopsis suspension-cultured cells.";
RL Plant Physiol. Biochem. 49:985-995(2011).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23134555; DOI=10.1111/gtc.12014;
RA Takagi N., Ueguchi C.;
RT "Enhancement of meristem formation by bouquet-1, a mis-sense allele of the
RT vernalization independence 3 gene encoding a WD40 repeat protein in
RT Arabidopsis thaliana.";
RL Genes Cells 17:982-993(2012).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT, AND SUBCELLULAR
RP LOCATION.
RX PubMed=22511887; DOI=10.1371/journal.pgen.1002652;
RA Dorcey E., Rodriguez-Villalon A., Salinas P., Santuari L., Pradervand S.,
RA Harshman K., Hardtke C.S.;
RT "Context-dependent dual role of SKI8 homologs in mRNA synthesis and
RT turnover.";
RL PLoS Genet. 8:E1002652-E1002652(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 repressor and MADS box
CC gene FLC (PubMed:12750345, PubMed:18725930). Required for histone H3
CC trimethylation on 'Lys-4' (H3K4me3) and histone dimethylation on 'Lys-
CC 36' (H3K36me2) at the FLC locus. Prevents trimethylation on 'Lys-27'
CC (H3K27me3) at the same locus (PubMed:18725930). Not required for
CC meiotic recombination or progression (PubMed:16716192). Component of
CC the SKI complex which is thought to be involved in exosome-mediated RNA
CC decay and associates with transcriptionally active genes in a manner
CC dependent on PAF1 complex (PAF1C) (PubMed:22511887). Required for
CC proper progression of cell differentiation process (PubMed:23134555).
CC {ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:16716192,
CC ECO:0000269|PubMed:18725930, ECO:0000269|PubMed:20363855,
CC ECO:0000269|PubMed:22511887, ECO:0000269|PubMed:23134555}.
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 (PubMed:20363855). Component of the
CC cytoplasmic SKI complex, which consists of SKI2, SKI3 and VIP3/SKI8
CC (PubMed:22511887). Interacts with VIP4 and VIP6 (PubMed:15472079).
CC {ECO:0000269|PubMed:15472079, ECO:0000269|PubMed:20363855,
CC ECO:0000269|PubMed:22511887}.
CC -!- INTERACTION:
CC Q9SZQ5; Q9M0V3: DDB1A; NbExp=2; IntAct=EBI-1632819, EBI-1632780;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855,
CC ECO:0000269|PubMed:21571540, ECO:0000269|PubMed:22511887}. Cytoplasm
CC {ECO:0000269|PubMed:22511887}.
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, PubMed:16716192). Growth defects due to extra shoot
CC apical meristem (SAM) formation (PubMed:23134555).
CC {ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:16716192,
CC ECO:0000269|PubMed:23134555}.
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DR EMBL; AL050352; CAB43658.1; -; Genomic_DNA.
DR EMBL; AL161575; CAB79741.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85683.1; -; Genomic_DNA.
DR EMBL; BT008333; AAP37692.1; -; mRNA.
DR PIR; T08544; T08544.
DR RefSeq; NP_194712.1; NM_119129.3.
DR AlphaFoldDB; Q9SZQ5; -.
DR SMR; Q9SZQ5; -.
DR IntAct; Q9SZQ5; 1.
DR STRING; 3702.AT4G29830.1; -.
DR PaxDb; Q9SZQ5; -.
DR PRIDE; Q9SZQ5; -.
DR ProteomicsDB; 233010; -.
DR EnsemblPlants; AT4G29830.1; AT4G29830.1; AT4G29830.
DR GeneID; 829105; -.
DR Gramene; AT4G29830.1; AT4G29830.1; AT4G29830.
DR KEGG; ath:AT4G29830; -.
DR Araport; AT4G29830; -.
DR TAIR; locus:2123929; AT4G29830.
DR eggNOG; KOG4155; Eukaryota.
DR HOGENOM; CLU_000288_57_11_1; -.
DR InParanoid; Q9SZQ5; -.
DR OMA; VGFSPCN; -.
DR OrthoDB; 1052423at2759; -.
DR PhylomeDB; Q9SZQ5; -.
DR PRO; PR:Q9SZQ5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SZQ5; baseline and differential.
DR Genevisible; Q9SZQ5; AT.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
DR GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; IPI:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0010452; P:histone H3-K36 methylation; IMP:TAIR.
DR GO; GO:0051568; P:histone H3-K4 methylation; IMP:TAIR.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
DR GO; GO:1904278; P:positive regulation of wax biosynthetic process; IGI:TAIR.
DR GO; GO:0016441; P:post-transcriptional gene silencing; IMP:TAIR.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR024977; Apc4_WD40_dom.
DR InterPro; IPR020472; G-protein_beta_WD-40_rep.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR019775; WD40_repeat_CS.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR Pfam; PF12894; ANAPC4_WD40; 1.
DR Pfam; PF00400; WD40; 4.
DR PRINTS; PR00320; GPROTEINBRPT.
DR SMART; SM00320; WD40; 7.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 6.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Flowering; Nucleus; Reference proteome; Repeat; Transcription;
KW Transcription regulation; WD repeat.
FT CHAIN 1..321
FT /note="WD repeat-containing protein VIP3"
FT /id="PRO_0000432759"
FT REPEAT 12..55
FT /note="WD 1"
FT /evidence="ECO:0000255"
FT REPEAT 58..97
FT /note="WD 2"
FT /evidence="ECO:0000255"
FT REPEAT 100..140
FT /note="WD 3"
FT /evidence="ECO:0000255"
FT REPEAT 156..195
FT /note="WD 4"
FT /evidence="ECO:0000255"
FT REPEAT 198..238
FT /note="WD 5"
FT /evidence="ECO:0000255"
FT REPEAT 241..280
FT /note="WD 6"
FT /evidence="ECO:0000255"
FT REPEAT 283..319
FT /note="WD 7"
FT /evidence="ECO:0000255"
SQ SEQUENCE 321 AA; 34260 MW; 0C71AB5E2B6968F3 CRC64;
MKLAGLKSIE NAHEDSVWAA TWVPATEDRP ALLLTGSLDE TVKLWRPDEL DLVRTNTGHS
LGVAALAAHP SGIIAASSSI DSFVRVFDVD TNATIAVLEA PPSEVWGMQF EPKGTILAVA
GGSSASVKLW DTASWRLIST LSIPRPDAPK PSDKTSSKKF VLSVAWSPNG KRLACGSMDG
TICVFDVDRS KLLHQLEGHN MPVRSLVFSP VDPRVLFSGS DDGHVNMHDA EGKTLLGSMS
GHTSWVLSVD ASPDGGAIAT GSSDRTVRLW DLKMRAAIQT MSNHNDQVWS VAFRPPGGTG
VRAGRLASVS DDKSVSLYDY S
