PAF1_ARATH
ID PAF1_ARATH Reviewed; 589 AA.
AC F4HQA1; Q8RW91; Q9CA82; Q9MA04;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Protein PAF1 homolog {ECO:0000305};
DE AltName: Full=Protein EARLY FLOWERING 7 {ECO:0000303|PubMed:15520273};
DE AltName: Full=Protein VERNALIZATION INDEPENDENCE 2 {ECO:0000303|PubMed:15472079};
GN Name=VIP2 {ECO:0000303|PubMed:15472079};
GN Synonyms=ELF7 {ECO:0000303|PubMed:15520273};
GN OrderedLocusNames=At1g79730 {ECO:0000312|Araport:AT1G79730};
GN ORFNames=F19K16.29 {ECO:0000312|EMBL:AAG52243.1},
GN F20B17.16 {ECO:0000312|EMBL:AAF68118.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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 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 FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=15520273; DOI=10.1101/gad.1244504;
RA He Y., Doyle M.R., Amasino R.M.;
RT "PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin
RT is required for the vernalization-responsive, winter-annual habit in
RT Arabidopsis.";
RL Genes Dev. 18:2774-2784(2004).
RN [6]
RP NOMENCLATURE.
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 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 [8]
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 repressors and MAD-box
CC genes FLC, AGL27/FLM and AGL31/MAF2. Required for histone H3
CC trimethylation on 'Lys-4' H3K4me3 at the FLC and AGL27/FLM loci
CC (PubMed:15520273). Involved in the control of seed dormancy and
CC germination (PubMed:21799800). {ECO:0000269|PubMed:15520273,
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. {ECO:0000269|PubMed:20363855}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves and shoot apex.
CC {ECO:0000269|PubMed:15520273}.
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). Reduced seed dormancy and increased germination rate
CC of freshly harvested seeds (PubMed:21799800).
CC {ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:21799800}.
CC -!- SIMILARITY: Belongs to the PAF1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF68118.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAG52243.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC010793; AAF68118.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC011717; AAG52243.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE36292.1; -; Genomic_DNA.
DR EMBL; AY093780; AAM10397.1; -; mRNA.
DR EMBL; BT002711; AAO11627.1; -; mRNA.
DR PIR; C96828; C96828.
DR RefSeq; NP_178091.2; NM_106622.5.
DR AlphaFoldDB; F4HQA1; -.
DR SMR; F4HQA1; -.
DR IntAct; F4HQA1; 3.
DR STRING; 3702.AT1G79730.1; -.
DR iPTMnet; F4HQA1; -.
DR PaxDb; F4HQA1; -.
DR PRIDE; F4HQA1; -.
DR ProteomicsDB; 248742; -.
DR EnsemblPlants; AT1G79730.1; AT1G79730.1; AT1G79730.
DR GeneID; 844312; -.
DR Gramene; AT1G79730.1; AT1G79730.1; AT1G79730.
DR KEGG; ath:AT1G79730; -.
DR Araport; AT1G79730; -.
DR TAIR; locus:2017879; AT1G79730.
DR eggNOG; KOG2478; Eukaryota.
DR HOGENOM; CLU_027299_0_0_1; -.
DR InParanoid; F4HQA1; -.
DR OMA; TQILFEC; -.
DR OrthoDB; 599989at2759; -.
DR PRO; PR:F4HQA1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; F4HQA1; baseline and differential.
DR Genevisible; F4HQA1; AT.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IBA:GO_Central.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0016571; P:histone methylation; IMP:TAIR.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:InterPro.
DR InterPro; IPR007133; RNA_pol_II-assoc_Paf1.
DR PANTHER; PTHR23188; PTHR23188; 1.
DR Pfam; PF03985; Paf1; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Flowering; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..589
FT /note="Protein PAF1 homolog"
FT /id="PRO_0000432758"
FT REGION 1..180
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 542..589
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 126..159
FT /evidence="ECO:0000255"
FT COMPBIAS 1..58
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 67..90
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 91..112
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 126..180
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 553..577
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 185
FT /note="E -> Q (in Ref. 3; AAM10397/AAO11627)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 589 AA; 67338 MW; 8909E557DED725A0 CRC64;
MASYRPPYPP LPQPPSQNSL APPPPPPSLP PPVPPPPPSH QPYSYPPPPP PPPHAYYQQG
PHYPQFNQLQ APPPPPPPSA PPPLVPDPPR HQGPNDHEKG ASKQVGRRER AKPDPSKHHH
RSHLPHSKKI ETEEERRLRK KRELEKQRQD EKHRQQMKNS HKSQMPKGHT EEKKPTPLLT
TDRVENRLKK PTTFICKLKF RNELPDPSAQ LKLMTIKRDK DQFTKYTITS LEKLWKPKIF
VEPDLGIPLD LLDLSVYNPP KVKAPLAPED EELLRDDDAV TPIKKDGIRR KERPTDKGMS
WLVKTQYISS INNESARQSL TEKQAKELRE MKGGINILHN LNNRERQIKD IEASFEACKS
RPVHATNKNL QPVEVLPLLP YFDRYDEQFV VANFDGAPIA DSEFFGKLDP SIRDAHESRA
ILKSYVVAGS DTANPEKFLA YMVPSLDELS KDIHDENEEI SYTWVREYLW DVQPNANDPG
TYLVSFDNGT ASYLPLPMRL NLRKKRAREG RSSDEIEHFP VPSRVTVRRR STVSVIEHKD
SGVYSSRVGA SSSKMRRLED EGGLGRSWKH EPEQDANQYS DGNEDDYSE
