VIP4_ARATH
ID VIP4_ARATH Reviewed; 625 AA.
AC Q9FNQ0; B9DF97; Q8L5W5;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=Protein LEO1 homolog {ECO:0000305};
DE AltName: Full=Protein VERNALIZATION INDEPENDENCE 4 {ECO:0000303|PubMed:12207655};
GN Name=VIP4 {ECO:0000303|PubMed:12207655};
GN OrderedLocusNames=At5g61150 {ECO:0000312|Araport:AT5G61150};
GN ORFNames=MAF19.15 {ECO:0000312|EMBL:BAB10377.1};
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 [MRNA], FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=12207655; DOI=10.1046/j.1365-313x.2002.01380.x;
RA Zhang H., van Nocker S.;
RT "The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of
RT FLOWERING LOCUS C.";
RL Plant J. 31:663-673(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-531.
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP INTERACTION WITH VIP3 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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-203; SER-570; SER-600;
RP SER-605 AND SER-622, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-548; SER-600 AND SER-605, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-548; SER-600; SER-605 AND
RP SER-622, AND IDENTIFICATION BY 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 [10]
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 [11]
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).
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:12207655). Involved in the control of seed dormancy
CC and germination (PubMed:21799800). {ECO:0000269|PubMed:12207655,
CC ECO:0000269|PubMed:20363855, 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 (PubMed:20363855). Interacts with VIP3 and
CC VIP6 (PubMed:15472079). {ECO:0000269|PubMed:15472079,
CC ECO:0000269|PubMed:20363855}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences. {ECO:0000305};
CC Name=1;
CC IsoId=Q9FNQ0-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in roots, shoot apices, stems, cauline
CC leaves, inflorescence apices and flowers.
CC {ECO:0000269|PubMed:12207655}.
CC -!- DISRUPTION PHENOTYPE: Early flowering, defects in floral morphology in
CC whorls 1-3, but fully fertile flowers (PubMed:12207655). Reduced seed
CC dormancy and increased germination rate of freshly harvested seeds
CC (PubMed:21799800). {ECO:0000269|PubMed:12207655,
CC ECO:0000269|PubMed:21799800}.
CC -!- SIMILARITY: Belongs to the LEO1 family. {ECO:0000305}.
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DR EMBL; AF490422; AAM81969.1; -; mRNA.
DR EMBL; AB006696; BAB10377.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97427.1; -; Genomic_DNA.
DR EMBL; BT002058; AAN72069.1; -; mRNA.
DR EMBL; BT008386; AAP37745.1; -; mRNA.
DR EMBL; AK316687; BAH19414.1; -; mRNA.
DR RefSeq; NP_851237.1; NM_180906.2. [Q9FNQ0-1]
DR AlphaFoldDB; Q9FNQ0; -.
DR IntAct; Q9FNQ0; 2.
DR STRING; 3702.AT5G61150.1; -.
DR iPTMnet; Q9FNQ0; -.
DR PaxDb; Q9FNQ0; -.
DR PRIDE; Q9FNQ0; -.
DR ProteomicsDB; 234262; -. [Q9FNQ0-1]
DR EnsemblPlants; AT5G61150.1; AT5G61150.1; AT5G61150. [Q9FNQ0-1]
DR GeneID; 836236; -.
DR Gramene; AT5G61150.1; AT5G61150.1; AT5G61150. [Q9FNQ0-1]
DR KEGG; ath:AT5G61150; -.
DR Araport; AT5G61150; -.
DR TAIR; locus:2159466; AT5G61150.
DR eggNOG; KOG2428; Eukaryota.
DR InParanoid; Q9FNQ0; -.
DR OrthoDB; 675275at2759; -.
DR PhylomeDB; Q9FNQ0; -.
DR PRO; PR:Q9FNQ0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FNQ0; baseline and differential.
DR Genevisible; Q9FNQ0; AT.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
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:0016570; P:histone modification; IEA:InterPro.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:InterPro.
DR GO; GO:0010048; P:vernalization response; IMP:TAIR.
DR InterPro; IPR007149; Leo1.
DR PANTHER; PTHR23146; PTHR23146; 1.
DR Pfam; PF04004; Leo1; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Coiled coil; Flowering; Nucleus; Phosphoprotein;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..625
FT /note="Protein LEO1 homolog"
FT /id="PRO_0000432760"
FT REGION 1..214
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 415..625
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 415..539
FT /evidence="ECO:0000255"
FT COMPBIAS 52..66
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 80..162
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 186..214
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 436..450
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 469..491
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 581..625
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 203
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157"
FT MOD_RES 548
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT MOD_RES 570
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157"
FT MOD_RES 600
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19245862, ECO:0007744|PubMed:19376835"
FT MOD_RES 605
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19245862, ECO:0007744|PubMed:19376835"
FT MOD_RES 622
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19376835"
FT CONFLICT 27
FT /note="E -> Q (in Ref. 1; AAM81969)"
FT /evidence="ECO:0000305"
FT CONFLICT 206
FT /note="D -> H (in Ref. 1; AAM81969)"
FT /evidence="ECO:0000305"
FT CONFLICT 318
FT /note="T -> P (in Ref. 1; AAM81969)"
FT /evidence="ECO:0000305"
FT CONFLICT 474
FT /note="N -> T (in Ref. 1; AAM81969)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 625 AA; 71758 MW; 8073ED1C25B3504D CRC64;
MVKGEKRSEM MLNLFGDNSE EEEIESEHEC NRRQPNYASD EAEGGVEPEG EGEAEVEVHG
EAEAESDGEQ GDVELDPGES EGEREQSSQE ADPQEESEAR DSDSDNKEEE HGGRVAKKRR
QEVVESGSER SGEKHYESED EEVDQTRSPR SPSEEKEEVQ VAQSDVNIRN VFGSSDDEDA
EEYVRNDVEQ DEHRSPIEDE EGSEKDLRPD DMVLDDIIPE EDPQYESEAE HVEARYRERP
VGPPLEVEVP FRPPPGDPVK MNMIKVSNIM GIDPKPFDAK TFVEEDTFMT DEPGAKNRIR
LDNNIVRHRF VKSRDGKTYS ESNARFVRWS DGSLQLLIGN EVLNITEQDA KEDQNHLFIK
HEKGILQSQG RILKKMRFTP SSLTSNSHRL LTAIVESRQK KAFKVKNCVT DIDPEREKEK
REKAESQNLK ASTKLSQARE KIKRKYPLPV ERRQLSTGYL EDALDEDDED YRSNRGYEED
LEAEAQRERR ILNAKKSHKG IPGRSSMTSA RPSRRQMEYS ESEREESEYE TEEEEEEKSP
ARGRGKDSED EYEEDAEEDE EERGKSNRYS DEDEEEEEVA GGRAEKDHRG SGRKRKGIES
DEEESPPRKA PTHRRKAVID DSDED
