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WD repeat-containing protein VIP3 (Protein BOUQUET-1) (boq-1) (Protein SKI8 homolog) (Protein VERNALIZATION INDEPENDENCE 3) (Protein ZWERGERL) (zwg)

 VIP3_ARATH              Reviewed;         321 AA.
Q9SZQ5;
29-APR-2015, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
07-JUN-2017, entry version 132.
RecName: Full=WD repeat-containing protein VIP3 {ECO:0000305};
AltName: Full=Protein BOUQUET-1 {ECO:0000303|PubMed:23134555};
Short=boq-1 {ECO:0000303|PubMed:23134555};
AltName: Full=Protein SKI8 homolog {ECO:0000303|PubMed:16716192};
AltName: Full=Protein VERNALIZATION INDEPENDENCE 3 {ECO:0000303|PubMed:12750345};
AltName: Full=Protein ZWERGERL {ECO:0000303|PubMed:22511887};
Short=zwg;
Name=VIP3 {ECO:0000303|PubMed:12750345};
Synonyms=SKI8 {ECO:0000303|PubMed:16716192};
OrderedLocusNames=At4g29830 {ECO:0000312|Araport:AT4G29830};
ORFNames=F27B13.70 {ECO:0000312|EMBL:CAB43658.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=12750345;
Zhang H., Ransom C., Ludwig P., van Nocker S.;
"Genetic analysis of early flowering mutants in Arabidopsis defines a
class of pleiotropic developmental regulator required for expression
of the flowering-time switch flowering locus C.";
Genetics 164:347-358(2003).
[5]
INTERACTION WITH VIP4 AND VIP6.
PubMed=15472079; DOI=10.1105/tpc.104.026062;
Oh S., Zhang H., Ludwig P., van Nocker S.;
"A mechanism related to the yeast transcriptional regulator Paf1c is
required for expression of the Arabidopsis FLC/MAF MADS box gene
family.";
Plant Cell 16:2940-2953(2004).
[6]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=16716192; DOI=10.1111/j.1365-2443.2006.00972.x;
Jolivet S., Vezon D., Froger N., Mercier R.;
"Non conservation of the meiotic function of the Ski8/Rec103 homolog
in Arabidopsis.";
Genes Cells 11:615-622(2006).
[7]
FUNCTION.
PubMed=18725930; DOI=10.1371/journal.pgen.1000077;
Oh S., Park S., van Nocker S.;
"Genic and global functions for Paf1C in chromatin modification and
gene expression in Arabidopsis.";
PLoS Genet. 4:E1000077-E1000077(2008).
[8]
IDENTIFICATION IN THE PAF1 COMPLEX, FUNCTION, AND SUBCELLULAR
LOCATION.
PubMed=20363855; DOI=10.1104/pp.110.155838;
Park S., Oh S., Ek-Ramos J., van Nocker S.;
"PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex
and assists in regulating expression of genes within H3K27ME3-enriched
chromatin.";
Plant Physiol. 153:821-831(2010).
[9]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
PubMed=21571540; DOI=10.1016/j.plaphy.2011.04.012;
Shigeta T., Yasuda D., Mori T., Yoshimitsu Y., Nakamura Y.,
Yoshida S., Asami T., Okamoto S., Matsuo T.;
"Characterization of brassinosteroid-regulated proteins in a nuclear-
enriched fraction of Arabidopsis suspension-cultured cells.";
Plant Physiol. Biochem. 49:985-995(2011).
[10]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=23134555; DOI=10.1111/gtc.12014;
Takagi N., Ueguchi C.;
"Enhancement of meristem formation by bouquet-1, a mis-sense allele of
the vernalization independence 3 gene encoding a WD40 repeat protein
in Arabidopsis thaliana.";
Genes Cells 17:982-993(2012).
[11]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT, AND
SUBCELLULAR LOCATION.
PubMed=22511887; DOI=10.1371/journal.pgen.1002652;
Dorcey E., Rodriguez-Villalon A., Salinas P., Santuari L.,
Pradervand S., Harshman K., Hardtke C.S.;
"Context-dependent dual role of SKI8 homologs in mRNA synthesis and
turnover.";
PLoS Genet. 8:E1002652-E1002652(2012).
-!- FUNCTION: Component of the PAF1 complex (PAF1C) which is involved
in histone modifications such as methylation on histone H3 'Lys-4'
(H3K4me3) (PubMed:20363855). Involved in regulation of flowering
time. Required for the expression of the flowering repressor and
MADS box gene FLC (PubMed:12750345, PubMed:18725930). Required for
histone H3 trimethylation on 'Lys-4' (H3K4me3) and histone
dimethylation on 'Lys-36' (H3K36me2) at the FLC locus. Prevents
trimethylation on 'Lys-27' (H3K27me3) at the same locus
(PubMed:18725930). Not required for meiotic recombination or
progression (PubMed:16716192). Component of the SKI complex which
is thought to be involved in exosome-mediated RNA decay and
associates with transcriptionally active genes in a manner
dependent on PAF1 complex (PAF1C) (PubMed:22511887). Required for
proper progression of cell differentiation process
(PubMed:23134555). {ECO:0000269|PubMed:12750345,
ECO:0000269|PubMed:16716192, ECO:0000269|PubMed:18725930,
ECO:0000269|PubMed:20363855, ECO:0000269|PubMed:22511887,
ECO:0000269|PubMed:23134555}.
-!- SUBUNIT: Component of the nuclear PAF1 complex (PAF1C), which
consists of VIP2/ELF7/PAF1, VIP3/SKI8/WDR61, VIP4/LEO1, VIP5/RTF1,
VIP6/ELF8/CTR9 and CDC73 (PubMed:20363855). Component of the
cytoplasmic SKI complex, which consists of SKI2, SKI3 and
VIP3/SKI8 (PubMed:22511887). Interacts with VIP4 and VIP6
(PubMed:15472079). {ECO:0000269|PubMed:15472079,
ECO:0000269|PubMed:20363855, ECO:0000269|PubMed:22511887}.
-!- INTERACTION:
Q9M0V3:DDB1A; NbExp=2; IntAct=EBI-1632819, EBI-1632780;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855,
ECO:0000269|PubMed:21571540, ECO:0000269|PubMed:22511887}.
Cytoplasm {ECO:0000269|PubMed:22511887}.
-!- DISRUPTION PHENOTYPE: Early flowering, reduced plant size and
defects in floral morphology in whorls 1-3, but fully fertile
flowers (PubMed:12750345, PubMed:16716192). Growth defects due to
extra shoot apical meristem (SAM) formation (PubMed:23134555).
{ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:16716192,
ECO:0000269|PubMed:23134555}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AL050352; CAB43658.1; -; Genomic_DNA.
EMBL; AL161575; CAB79741.1; -; Genomic_DNA.
EMBL; CP002687; AEE85683.1; -; Genomic_DNA.
EMBL; BT008333; AAP37692.1; -; mRNA.
PIR; T08544; T08544.
RefSeq; NP_194712.1; NM_119129.3.
UniGene; At.23602; -.
UniGene; At.72983; -.
ProteinModelPortal; Q9SZQ5; -.
IntAct; Q9SZQ5; 1.
STRING; 3702.AT4G29830.1; -.
PaxDb; Q9SZQ5; -.
PRIDE; Q9SZQ5; -.
EnsemblPlants; AT4G29830.1; AT4G29830.1; AT4G29830.
GeneID; 829105; -.
Gramene; AT4G29830.1; AT4G29830.1; AT4G29830.
KEGG; ath:AT4G29830; -.
Araport; AT4G29830; -.
TAIR; locus:2123929; AT4G29830.
eggNOG; KOG4155; Eukaryota.
eggNOG; ENOG410XP1Z; LUCA.
HOGENOM; HOG000036765; -.
KO; K12602; -.
OMA; ERKCLHT; -.
OrthoDB; EOG09360GXL; -.
PhylomeDB; Q9SZQ5; -.
Reactome; R-ATH-429958; mRNA decay by 3' to 5' exoribonuclease.
PRO; PR:Q9SZQ5; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q9SZQ5; baseline and differential.
Genevisible; Q9SZQ5; AT.
GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; IPI:TAIR.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
GO; GO:0010452; P:histone H3-K36 methylation; IMP:TAIR.
GO; GO:0051568; P:histone H3-K4 methylation; IMP:TAIR.
GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
GO; GO:0016441; P:posttranscriptional gene silencing; IMP:TAIR.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 2.130.10.10; -; 1.
InterPro; IPR024977; Apc4_WD40_dom.
InterPro; IPR020472; G-protein_beta_WD-40_rep.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom.
InterPro; IPR001680; WD40_repeat.
InterPro; IPR019775; WD40_repeat_CS.
InterPro; IPR017986; WD40_repeat_dom.
Pfam; PF12894; ANAPC4_WD40; 1.
Pfam; PF00400; WD40; 4.
PRINTS; PR00320; GPROTEINBRPT.
SMART; SM00320; WD40; 7.
SUPFAM; SSF50978; SSF50978; 1.
PROSITE; PS00678; WD_REPEATS_1; 1.
PROSITE; PS50082; WD_REPEATS_2; 6.
PROSITE; PS50294; WD_REPEATS_REGION; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Flowering; Nucleus; Reference proteome;
Repeat; Transcription; Transcription regulation; WD repeat.
CHAIN 1 321 WD repeat-containing protein VIP3.
/FTId=PRO_0000432759.
REPEAT 12 55 WD 1. {ECO:0000255}.
REPEAT 58 97 WD 2. {ECO:0000255}.
REPEAT 100 140 WD 3. {ECO:0000255}.
REPEAT 156 195 WD 4. {ECO:0000255}.
REPEAT 198 238 WD 5. {ECO:0000255}.
REPEAT 241 280 WD 6. {ECO:0000255}.
REPEAT 283 319 WD 7. {ECO:0000255}.
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


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