VIL1_ARATH
ID VIL1_ARATH Reviewed; 602 AA.
AC Q9LHF5;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=VIN3-like protein 1;
DE AltName: Full=Protein VERNALIZATION 5;
GN Name=VIL1; Synonyms=VRN5; OrderedLocusNames=At3g24440; ORFNames=MXP5.1;
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, DISRUPTION PHENOTYPE, INTERACTION
RP WITH VIN3 AND VIL2, AND INDUCTION BY COLD.
RC STRAIN=cv. Columbia;
RX PubMed=17114575; DOI=10.1101/gad.1493306;
RA Sung S., Schmitz R.J., Amasino R.M.;
RT "A PHD finger protein involved in both the vernalization and photoperiod
RT pathways in Arabidopsis.";
RL Genes Dev. 20:3244-3248(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
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 FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH VIN3, TISSUE SPECIFICITY,
RP AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17174094; DOI=10.1016/j.cub.2006.11.052;
RA Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R.,
RA Dean C.;
RT "The PHD finger protein VRN5 functions in the epigenetic silencing of
RT Arabidopsis FLC.";
RL Curr. Biol. 17:73-78(2007).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBUNIT, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=18854416; DOI=10.1073/pnas.0808687105;
RA De Lucia F., Crevillen P., Jones A.M.E., Greb T., Dean C.;
RT "A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of
RT FLC during vernalization.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:16831-16836(2008).
CC -!- FUNCTION: Involved in both the vernalization and photoperiod pathways
CC by regulating expression of the related floral repressors FLOWERING
CC LOCUS C (FLC) and FLOWERING LOCUS M (FLM). Together with VIN3, required
CC during vernalization for the modifications of FLC and FLM chromatin
CC that are associated with an epigenetically silenced state (e.g.
CC chromatin modifications, histone deacetylation, and trimethylated H3
CC 'Lys-4' H3K4me3 and 'Lys-27' H3K27me3) and with acquisition of
CC competence to flower. Promotes flowering in short days (SD=8 hours
CC light/16 hours dark). Associates dynamically at FLC locus; during
CC vernalization, binds to specific sites, but when in warm conditions,
CC distributed along the whole locus. {ECO:0000269|PubMed:17114575,
CC ECO:0000269|PubMed:17174094, ECO:0000269|PubMed:18854416}.
CC -!- SUBUNIT: Interacts with VIN3 and VIL2. The heterodimer made of VIN3 and
CC VIL1 is required for establishing the vernalization-induced epigenetic
CC silencing of FLC. Component of the plant homeodomain / polycomb
CC repressive complex 2 (PHD-PRC2) large complex during prolonged cold,
CC composed of core PRC2 components (VRN2, EZA1, FIE and MSI1), and three
CC related PHD finger proteins (VIL1, VIL2 and VIN3) that mediates histone
CC H3 trimethylation on 'Lys-27' (H3K27me3). {ECO:0000269|PubMed:17114575,
CC ECO:0000269|PubMed:17174094, ECO:0000269|PubMed:18854416}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17174094}. Nucleus
CC speckle {ECO:0000269|PubMed:17174094}. Note=Probably DNA-associated.
CC {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Accumulates in shoot and root apices, and in
CC leaves. {ECO:0000269|PubMed:17174094}.
CC -!- INDUCTION: Expressed at higher levels in short days (SD=8 hours
CC light/16 hours dark) than in long days (LD=16 hours light/8 hours
CC dark). Slightly induced by long cold exposure (e.g. 40 days at 4
CC degrees Celsius). {ECO:0000269|PubMed:17114575}.
CC -!- DISRUPTION PHENOTYPE: Impaired vernalization response with incomplete
CC repression of FLC during and after cold exposure, due to a reduction in
CC vernalization-induced histone H3 deacetylation and methylation (e.g.
CC H3K4me3 and H3K27me3). Delayed flowering in short days (SD=8 hours
CC light/16 hours dark) conditions but not in long days (LD=16 hours
CC light/8 hours dark); enhanced FLM levels dur to an enhance level of
CC chromatin acetylation. {ECO:0000269|PubMed:17114575,
CC ECO:0000269|PubMed:17174094, ECO:0000269|PubMed:18854416}.
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DR EMBL; EF064791; ABL01538.1; -; mRNA.
DR EMBL; AP002048; BAB01947.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76898.1; -; Genomic_DNA.
DR RefSeq; NP_189087.1; NM_113351.3.
DR AlphaFoldDB; Q9LHF5; -.
DR BioGRID; 7366; 4.
DR DIP; DIP-48608N; -.
DR IntAct; Q9LHF5; 6.
DR STRING; 3702.AT3G24440.1; -.
DR PaxDb; Q9LHF5; -.
DR PRIDE; Q9LHF5; -.
DR ProteomicsDB; 228533; -.
DR EnsemblPlants; AT3G24440.1; AT3G24440.1; AT3G24440.
DR GeneID; 822034; -.
DR Gramene; AT3G24440.1; AT3G24440.1; AT3G24440.
DR KEGG; ath:AT3G24440; -.
DR Araport; AT3G24440; -.
DR TAIR; locus:2094859; AT3G24440.
DR eggNOG; ENOG502QSVB; Eukaryota.
DR HOGENOM; CLU_016873_1_0_1; -.
DR InParanoid; Q9LHF5; -.
DR OMA; VKCSNSW; -.
DR OrthoDB; 331273at2759; -.
DR PhylomeDB; Q9LHF5; -.
DR PRO; PR:Q9LHF5; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LHF5; baseline and differential.
DR Genevisible; Q9LHF5; AT.
DR GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0016571; P:histone methylation; IMP:TAIR.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:0061087; P:positive regulation of histone H3-K27 methylation; IMP:UniProtKB.
DR GO; GO:0051571; P:positive regulation of histone H3-K4 methylation; IMP:UniProtKB.
DR GO; GO:0031062; P:positive regulation of histone methylation; IMP:TAIR.
DR GO; GO:0009409; P:response to cold; IEP:UniProtKB.
DR GO; GO:0048572; P:short-day photoperiodism; IMP:UniProtKB.
DR GO; GO:0048575; P:short-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0010048; P:vernalization response; IMP:UniProtKB.
DR CDD; cd00063; FN3; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR003961; FN3_dom.
DR InterPro; IPR036116; FN3_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR032881; Oberon_PHD.
DR InterPro; IPR044514; VIN3-like.
DR PANTHER; PTHR46286; PTHR46286; 1.
DR Pfam; PF00041; fn3; 1.
DR Pfam; PF07227; PHD_Oberon; 1.
DR SUPFAM; SSF49265; SSF49265; 1.
DR PROSITE; PS50853; FN3; 1.
PE 1: Evidence at protein level;
KW Flowering; Metal-binding; Nucleus; Reference proteome; Repressor;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..602
FT /note="VIN3-like protein 1"
FT /id="PRO_0000422539"
FT DOMAIN 242..340
FT /note="Fibronectin type-III"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00316"
FT ZN_FING 67..137
FT /note="PHD-type"
FT REGION 1..38
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 430..470
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 502..602
FT /note="VIN3-Interacting Domain (VID)"
FT MOTIF 144..151
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250"
FT COMPBIAS 455..470
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 602 AA; 66851 MW; 093EF96A7AEDD197 CRC64;
MDSSSTKSKI SHSRKTNKKS NKKHESNGKQ QQQQDVDGGG GCLRSSWICK NASCRANVPK
EDSFCKRCSC CVCHNFDENK DPSLWLVCEP EKSDDVEFCG LSCHIECAFR EVKVGVIALG
NLMKLDGCFC CYSCGKVSQI LGCWKKQLVA AKEARRRDGL CYRIDLGYRL LNGTSRFSEL
HEIVRAAKSM LEDEVGPLDG PTARTDRGIV SRLPVAANVQ ELCTSAIKKA GELSANAGRD
LVPAACRFHF EDIAPKQVTL RLIELPSAVE YDVKGYKLWY FKKGEMPEDD LFVDCSRTER
RMVISDLEPC TEYTFRVVSY TEAGIFGHSN AMCFTKSVEI LKPVDGKEKR TIDLVGNAQP
SDREEKSSIS SRFQIGQLGK YVQLAEAQEE GLLEAFYNVD TEKICEPPEE ELPPRRPHGF
DLNVVSVPDL NEEFTPPDSS GGEDNGVPLN SLAEADGGDH DDNCDDAVSN GRRKNNNDCL
VISDGSGDDT GFDFLMTRKR KAISDSNDSE NHECDSSSID DTLEKCVKVI RWLEREGHIK
TTFRVRFLTW FSMSSTAQEQ SVVSTFVQTL EDDPGSLAGQ LVDAFTDVVS TKRPNNGVMT
SH
