VIL2_ARATH
ID VIL2_ARATH Reviewed; 714 AA.
AC Q9SUM4; B9DFL9; F4JPJ8; F4JPK1; Q2QJG1; Q8GUH6;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 138.
DE RecName: Full=VIN3-like protein 2;
DE AltName: Full=Vernalization5/VIN3-like protein 1;
GN Name=VIL2; Synonyms=VEL1; OrderedLocusNames=At4g30200; ORFNames=F9N11.50;
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Itoh R.;
RT "Arabidopsis thaliana AT4g30200 gene for nuclear coiled-coil protein.";
RL Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBUNIT, INTERACTION WITH VIN3 AND
RP VIL1, 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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-266 (ISOFORMS 1/3/4).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
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 [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 503-713 (ISOFORMS 1/2/3).
RX PubMed=16117846; DOI=10.1038/sj.cr.7290326;
RA Sehnke P.C., Laughner B.J., Lyerly Linebarger C.R., Gurley W.B., Ferl R.J.;
RT "Identification and characterization of GIP1, an Arabidopsis thaliana
RT protein that enhances the DNA binding affinity and reduces the oligomeric
RT state of G-box binding factors.";
RL Cell Res. 15:567-575(2005).
RN [8]
RP SUBUNIT, AND IDENTIFICATION BY MASS 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).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF TRP-182 AND CYS-204, AND
RP INDUCTION BY PHOTOPERIODISM.
RX PubMed=20837520; DOI=10.1073/pnas.1010834107;
RA Kim D.-H., Sung S.;
RT "The plant homeo domain finger protein, VIN3-LIKE 2, is necessary for
RT photoperiod-mediated epigenetic regulation of the floral repressor, MAF5.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:17029-17034(2010).
RN [10]
RP REVIEW.
RX PubMed=21150261; DOI=10.4161/psb.5.12.14035;
RA Kim D.-H., Sung S.;
RT "Role of VIN3-LIKE 2 in facultative photoperiodic flowering response in
RT Arabidopsis.";
RL Plant Signal. Behav. 5:1672-1673(2010).
CC -!- FUNCTION: Maybe involved in both the vernalization and photoperiod
CC pathways by regulating gene expression. Binds preferentially to
CC dimethylated histone H3 'Lys-9' (H3K9me2). Promotes flowering in non-
CC inductive photoperiods (e.g. short days) through the maintenance of the
CC epigenetically repressed state of MAF5 via H3K9me2 and plant
CC homeodomain / polycomb repressive complex 2 (PHD-PRC2)-dependent
CC H3K27me3. {ECO:0000269|PubMed:20837520}.
CC -!- SUBUNIT: Self-interacts. Interacts with VIN3 and VIL1. Component of the
CC plant homeodomain / polycomb repressive complex 2 (PHD-PRC2) large
CC complex during prolonged cold, composed of core PRC2 components (VRN2,
CC EZA1, FIE and MSI1), and three related PHD finger proteins (VIL1, VIL2
CC and VIN3) that mediates histone H3 trimethylation on 'Lys-27'
CC (H3K27me3). {ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:18854416}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Note=Probably DNA-
CC associated. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q9SUM4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SUM4-2; Sequence=VSP_046533, VSP_046534;
CC Name=3;
CC IsoId=Q9SUM4-3; Sequence=VSP_046534;
CC Name=4;
CC IsoId=Q9SUM4-4; Sequence=VSP_046535, VSP_046536;
CC -!- INDUCTION: By cold (e.g. 4 degrees Celsius). Levels follow a diurnal
CC regulation with an accumulation during the dark period and reduced
CC levels upon exposure to light (at protein level).
CC {ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:20837520}.
CC -!- DISRUPTION PHENOTYPE: Delayed flowering in short days but not in long
CC days conditions, associated with high expression of MAF5, a floral
CC repressor, due to a reduced H3K9me2 status of MAF5 locus.
CC {ECO:0000269|PubMed:20837520}.
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DR EMBL; AB050977; BAB17836.1; -; mRNA.
DR EMBL; EF064792; ABL01539.1; -; mRNA.
DR EMBL; AL109796; CAB52464.1; -; Genomic_DNA.
DR EMBL; AL161576; CAB81013.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85733.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85734.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85735.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85736.1; -; Genomic_DNA.
DR EMBL; BT002499; AAO00859.1; -; mRNA.
DR EMBL; BT008428; AAP37787.1; -; mRNA.
DR EMBL; AK316824; BAH19536.1; -; mRNA.
DR EMBL; DQ067323; AAZ30055.1; -; mRNA.
DR PIR; T14080; T14080.
DR RefSeq; NP_001190871.1; NM_001203942.1. [Q9SUM4-4]
DR RefSeq; NP_194749.1; NM_119166.5. [Q9SUM4-1]
DR RefSeq; NP_849471.1; NM_179140.2. [Q9SUM4-2]
DR RefSeq; NP_974639.1; NM_202910.4. [Q9SUM4-3]
DR AlphaFoldDB; Q9SUM4; -.
DR BioGRID; 14430; 2.
DR DIP; DIP-48609N; -.
DR IntAct; Q9SUM4; 3.
DR STRING; 3702.AT4G30200.2; -.
DR iPTMnet; Q9SUM4; -.
DR PaxDb; Q9SUM4; -.
DR PRIDE; Q9SUM4; -.
DR ProteomicsDB; 243199; -. [Q9SUM4-1]
DR EnsemblPlants; AT4G30200.1; AT4G30200.1; AT4G30200. [Q9SUM4-2]
DR EnsemblPlants; AT4G30200.2; AT4G30200.2; AT4G30200. [Q9SUM4-1]
DR EnsemblPlants; AT4G30200.3; AT4G30200.3; AT4G30200. [Q9SUM4-3]
DR EnsemblPlants; AT4G30200.4; AT4G30200.4; AT4G30200. [Q9SUM4-4]
DR GeneID; 829143; -.
DR Gramene; AT4G30200.1; AT4G30200.1; AT4G30200. [Q9SUM4-2]
DR Gramene; AT4G30200.2; AT4G30200.2; AT4G30200. [Q9SUM4-1]
DR Gramene; AT4G30200.3; AT4G30200.3; AT4G30200. [Q9SUM4-3]
DR Gramene; AT4G30200.4; AT4G30200.4; AT4G30200. [Q9SUM4-4]
DR KEGG; ath:AT4G30200; -.
DR Araport; AT4G30200; -.
DR TAIR; locus:2128946; AT4G30200.
DR eggNOG; ENOG502QR8D; Eukaryota.
DR InParanoid; Q9SUM4; -.
DR OMA; KWSHGAS; -.
DR OrthoDB; 191691at2759; -.
DR PhylomeDB; Q9SUM4; -.
DR PRO; PR:Q9SUM4; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SUM4; baseline and differential.
DR Genevisible; Q9SUM4; AT.
DR GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR GO; GO:0031519; C:PcG protein complex; IDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:TAIR.
DR GO; GO:0032922; P:circadian regulation of gene expression; IEP:UniProtKB.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:1900111; P:positive regulation of histone H3-K9 dimethylation; IDA:UniProtKB.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IEA:InterPro.
DR GO; GO:0048587; P:regulation of short-day photoperiodism, flowering; IMP:TAIR.
DR GO; GO:0009409; P:response to cold; IEP:UniProtKB.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IPI:TAIR.
DR GO; GO:0010048; P:vernalization response; IEA:InterPro.
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; PF07227; PHD_Oberon; 1.
DR SUPFAM; SSF49265; SSF49265; 1.
DR PROSITE; PS50853; FN3; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Flowering; Metal-binding; Nucleus;
KW Reference proteome; Repressor; Stress response; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..714
FT /note="VIN3-like protein 2"
FT /id="PRO_0000422540"
FT DOMAIN 366..463
FT /note="Fibronectin type-III"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00316"
FT ZN_FING 164..232
FT /note="PHD-type"
FT REGION 478..530
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 602..714
FT /note="VIN3-Interacting Domain (VID)"
FT /evidence="ECO:0000250"
FT MOTIF 239..246
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250"
FT COMPBIAS 478..519
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..17
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_046533"
FT VAR_SEQ 349..360
FT /note="Missing (in isoform 2 and isoform 3)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_046534"
FT VAR_SEQ 620..624
FT /note="SGLEH -> ISDLV (in isoform 4)"
FT /evidence="ECO:0000305"
FT /id="VSP_046535"
FT VAR_SEQ 625..714
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000305"
FT /id="VSP_046536"
FT MUTAGEN 182
FT /note="W->A: Abolished histone-binding."
FT /evidence="ECO:0000269|PubMed:20837520"
FT MUTAGEN 204
FT /note="C->A: Abolished histone-binding."
FT /evidence="ECO:0000269|PubMed:20837520"
FT CONFLICT 119
FT /note="A -> T (in Ref. 6; BAH19536)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 714 AA; 78770 MW; D1762500E53B0B48 CRC64;
MDSSLDGAAG DSSKCSEMSV DEKRQLVYEL SKQSHLAAEV LQAWSRQEIL QILCAEMGKE
RKYTGLTKVK IIETLLKIVS EKNSGECEGK KRDSDCLPIQ RNTKRQRKVD NPSRYVIPAT
NIVTSNNASG SCSSVNTKGE STTIYCKNLA CRAVLRQEDS FCRRCSCCIC RKYDDNKDPS
LWLTCSSDPP FEGESCGFSC HLECAFNTEK SGLGKDKQSE GCCFYCVSCG KANSLLECWK
KQLTIAKETR RVEVLCYRLF LVQKLLKSST KYRNLCEVVD EAVKTLEADV GPLTGLPMKM
GRGIVNRLHS GPDVQKLCSS ALESLETIAT TPPDVAALPS PRSSKMQQDC SYVLSNEISA
DTATTGSTKI RFEDVNATSL TVVLASNEIP SPPNIVHYSI WHRKVPEKDY PEKSTCTLFI
PNTRFVVSGL APASEYCFKV VSYSGTREMG VDEINVLTRS AEEGANCSSA VERSVSPLTN
CSTLSSNPSS VEAESNNDYI VPKKPSSKNE DNNSPSVDES AAKRMKRTTD SDIVQIEKDV
EQIVLLDDEE QEAVLDKTES ETPVVVTTKS LVGNRNSSDA SLPITPFRSD EIKNRQARIE
ISMKDNCNNG DHSANGGTES GLEHCVKIIR QLECSGHIDK NFRQKFLTWY SLRATSQEIR
VVKIFIDTFI DDPMALAEQL IDTFDDRVSI KRSAVGGSGA SAVVPSGFCM KLWH
