PIF4_ARATH
ID PIF4_ARATH Reviewed; 430 AA.
AC Q8W2F3; A5Y7D4; A5Y7D5; A5Y7D6; A5Y7D7; A5Y7D8; A5Y7D9; A5Y7E0; A5Y7E1;
AC A5Y7E2; A5Y7E3; A5Y7E4; A5Y7E5; A5Y7E6; A5Y7E7; Q9C5I8; Q9SKX6;
DT 01-FEB-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 25-MAY-2022, entry version 159.
DE RecName: Full=Transcription factor PIF4;
DE AltName: Full=Basic helix-loop-helix protein 9;
DE Short=AtbHLH9;
DE Short=bHLH 9;
DE AltName: Full=Phytochrome-interacting factor 4;
DE AltName: Full=Short under red-light 2;
DE AltName: Full=Transcription factor EN 102;
DE AltName: Full=bHLH transcription factor bHLH009;
GN Name=PIF4; Synonyms=BHLH9, EN102, SRL2; OrderedLocusNames=At2g43010;
GN ORFNames=MFL8.13;
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 LONG).
RC STRAIN=cv. Wassilewskija;
RX PubMed=12006496; DOI=10.1093/emboj/21.10.2441;
RA Huq E., Quail P.H.;
RT "PIF4, a phytochrome-interacting bHLH factor, functions as a negative
RT regulator of phytochrome B signaling in Arabidopsis.";
RL EMBO J. 21:2441-2450(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG), INDUCTION BY UV LIGHT, GENE
RP FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=12679534; DOI=10.1093/molbev/msg088;
RA Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C.;
RT "The basic helix-loop-helix transcription factor family in plants: a
RT genome-wide study of protein structure and functional diversity.";
RL Mol. Biol. Evol. 20:735-747(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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 SHORT).
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 [GENOMIC DNA] OF 56-306, AND VARIANT ASP-231.
RC STRAIN=cv. An-2, cv. Bla-6, cv. Br-0, cv. Bu-2, cv. Columbia, cv. Et-0,
RC cv. Kl-1, cv. Li-5:3, cv. Ma-2, cv. Mt-0, cv. Pa-2, cv. Pi-0, cv. Su-0, and
RC cv. Tsu-1;
RX PubMed=17614917; DOI=10.1111/j.1365-294x.2007.03298.x;
RA Brock M.T., Tiffin P., Weinig C.;
RT "Sequence diversity and haplotype associations with phenotypic responses to
RT crowding: GIGANTEA affects fruit set in Arabidopsis thaliana.";
RL Mol. Ecol. 16:3050-3062(2007).
RN [7]
RP GENE FAMILY, AND INTERACTION WITH PIF3.
RX PubMed=12897250; DOI=10.1105/tpc.013839;
RA Toledo-Ortiz G., Huq E., Quail P.H.;
RT "The Arabidopsis basic/helix-loop-helix transcription factor family.";
RL Plant Cell 15:1749-1770(2003).
RN [8]
RP INTERACTION WITH APRR1, AND INDUCTION.
RX PubMed=12826627; DOI=10.1093/pcp/pcg078;
RA Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S.,
RA Mizuno T.;
RT "A link between circadian-controlled bHLH factors and the APRR1/TOC1
RT quintet in Arabidopsis thaliana.";
RL Plant Cell Physiol. 44:619-629(2003).
RN [9]
RP INTERACTION WITH RGL2 AND RGA.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=20093430; DOI=10.1093/molbev/msq012;
RA Gallego-Bartolome J., Minguet E.G., Marin J.A., Prat S., Blazquez M.A.,
RA Alabadi D.;
RT "Transcriptional diversification and functional conservation between DELLA
RT proteins in Arabidopsis.";
RL Mol. Biol. Evol. 27:1247-1256(2010).
RN [10]
RP INTERACTION WITH HFR1.
RX PubMed=23224238; DOI=10.1007/s10059-013-2159-2;
RA Hong S.Y., Seo P.J., Ryu J.Y., Cho S.H., Woo J.C., Park C.M.;
RT "A competitive peptide inhibitor KIDARI negatively regulates HFR1 by
RT forming nonfunctional heterodimers in Arabidopsis photomorphogenesis.";
RL Mol. Cells 35:25-31(2013).
RN [11]
RP FUNCTION, AND INTERACTION WITH PHYB; CRY1 AND CRY2.
RX PubMed=26724867; DOI=10.1016/j.cell.2015.12.018;
RA Pedmale U.V., Huang S.S., Zander M., Cole B.J., Hetzel J., Ljung K.,
RA Reis P.A., Sridevi P., Nito K., Nery J.R., Ecker J.R., Chory J.;
RT "Cryptochromes interact directly with PIFs to control plant growth in
RT limiting blue light.";
RL Cell 164:233-245(2016).
RN [12]
RP INTERACTION WITH FYPP1 AND FYPP3.
RX PubMed=31527236; DOI=10.1073/pnas.1907540116;
RA Yu X., Dong J., Deng Z., Jiang Y., Wu C., Qin X., Terzaghi W., Chen H.,
RA Dai M., Deng X.W.;
RT "Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress
RT photomorphogenesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 116:20218-20225(2019).
CC -!- FUNCTION: Transcription factor acting negatively in the phytochrome B
CC signaling pathway. May regulate the expression of a subset of genes
CC involved in cell expansion by binding to the G-box motif (By
CC similarity). Activated by CRY1 and CRY2 in response to low blue light
CC (LBL) by direct binding at chromatin on E-box variant 5'-CA[CT]GTG-3'
CC to stimulate specific gene expression to adapt global physiology (e.g.
CC hypocotyl elongation in low blue light) (PubMed:26724867).
CC {ECO:0000250|UniProtKB:Q84LH8, ECO:0000269|PubMed:26724867}.
CC -!- SUBUNIT: Interacts preferentially with the Pfr form of phytochrome B
CC (phyB). Binds DNA as a homodimer, but once bound to DNA, loses its
CC capacity to interact with phyB. Interacts with APRR1/TOC1 and PIF3.
CC Binds to RGL2 and RGA. Forms non-functional heterodimer with HFR1.
CC Interacts with PHYB, CRY1 and CRY2 in the nucleus in response to low
CC blue light (LBL) (PubMed:26724867, PubMed:12826627, PubMed:12897250,
CC PubMed:20093430, PubMed:23224238). Interacts with FYPP1 and FYPP3
CC (PubMed:31527236). {ECO:0000269|PubMed:12826627,
CC ECO:0000269|PubMed:12897250, ECO:0000269|PubMed:20093430,
CC ECO:0000269|PubMed:23224238, ECO:0000269|PubMed:26724867,
CC ECO:0000269|PubMed:31527236}.
CC -!- INTERACTION:
CC Q8W2F3; Q8S307: BZR1; NbExp=4; IntAct=EBI-625716, EBI-1803261;
CC Q8W2F3; Q9FE22: HFR1; NbExp=2; IntAct=EBI-625716, EBI-626001;
CC Q8W2F3; Q9SLH3: RGA; NbExp=4; IntAct=EBI-625716, EBI-963624;
CC Q8W2F3-2; P14712: PHYA; NbExp=2; IntAct=EBI-625732, EBI-624446;
CC Q8W2F3-2; P14713: PHYB; NbExp=3; IntAct=EBI-625732, EBI-300727;
CC Q8W2F3-2; O80536: PIF3; NbExp=3; IntAct=EBI-625732, EBI-625701;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:26724867}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=Long;
CC IsoId=Q8W2F3-1; Sequence=Displayed;
CC Name=Short;
CC IsoId=Q8W2F3-2; Sequence=VSP_002146, VSP_002147;
CC -!- INDUCTION: By UV treatment. Follow a free-running robust circadian
CC rhythm, with higher levels during the light phase. Rapidly induced by
CC light in etiolated plants. Sixfold induction by both red and far-red
CC light. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:12826627}.
CC -!- SIMILARITY: Belongs to the bHLH protein family. {ECO:0000305}.
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DR EMBL; AJ440755; CAD29449.1; -; mRNA.
DR EMBL; AF251694; AAL55716.1; -; mRNA.
DR EMBL; AC006224; AAD22130.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC10197.1; -; Genomic_DNA.
DR EMBL; AY142625; AAN13083.1; -; mRNA.
DR EMBL; AF360221; AAK25931.1; -; mRNA.
DR EMBL; EF193514; ABP96467.1; -; Genomic_DNA.
DR EMBL; EF193515; ABP96468.1; -; Genomic_DNA.
DR EMBL; EF193516; ABP96469.1; -; Genomic_DNA.
DR EMBL; EF193517; ABP96470.1; -; Genomic_DNA.
DR EMBL; EF193518; ABP96471.1; -; Genomic_DNA.
DR EMBL; EF193519; ABP96472.1; -; Genomic_DNA.
DR EMBL; EF193520; ABP96473.1; -; Genomic_DNA.
DR EMBL; EF193521; ABP96474.1; -; Genomic_DNA.
DR EMBL; EF193522; ABP96475.1; -; Genomic_DNA.
DR EMBL; EF193523; ABP96476.1; -; Genomic_DNA.
DR EMBL; EF193524; ABP96477.1; -; Genomic_DNA.
DR EMBL; EF193525; ABP96478.1; -; Genomic_DNA.
DR EMBL; EF193526; ABP96479.1; -; Genomic_DNA.
DR EMBL; EF193527; ABP96480.1; -; Genomic_DNA.
DR PIR; H84860; H84860.
DR RefSeq; NP_565991.2; NM_129862.3. [Q8W2F3-1]
DR AlphaFoldDB; Q8W2F3; -.
DR SMR; Q8W2F3; -.
DR BioGRID; 4240; 23.
DR DIP; DIP-33903N; -.
DR IntAct; Q8W2F3; 12.
DR MINT; Q8W2F3; -.
DR STRING; 3702.AT2G43010.1; -.
DR PaxDb; Q8W2F3; -.
DR ProteomicsDB; 236753; -. [Q8W2F3-1]
DR EnsemblPlants; AT2G43010.1; AT2G43010.1; AT2G43010. [Q8W2F3-1]
DR GeneID; 818903; -.
DR Gramene; AT2G43010.1; AT2G43010.1; AT2G43010. [Q8W2F3-1]
DR KEGG; ath:AT2G43010; -.
DR Araport; AT2G43010; -.
DR TAIR; locus:2053733; AT2G43010.
DR eggNOG; ENOG502QTIX; Eukaryota.
DR InParanoid; Q8W2F3; -.
DR PhylomeDB; Q8W2F3; -.
DR PRO; PR:Q8W2F3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8W2F3; baseline and differential.
DR Genevisible; Q8W2F3; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:1990841; F:promoter-specific chromatin binding; IPI:TAIR.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0009704; P:de-etiolation; IMP:TAIR.
DR GO; GO:0009638; P:phototropism; IMP:TAIR.
DR GO; GO:0010161; P:red light signaling pathway; IGI:TAIR.
DR GO; GO:0010017; P:red or far-red light signaling pathway; IMP:TAIR.
DR GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
DR GO; GO:0010600; P:regulation of auxin biosynthetic process; IDA:TAIR.
DR GO; GO:0010928; P:regulation of auxin mediated signaling pathway; IDA:TAIR.
DR GO; GO:0010244; P:response to low fluence blue light stimulus by blue low-fluence system; IDA:UniProtKB.
DR Gene3D; 4.10.280.10; -; 1.
DR InterPro; IPR031066; bHLH_ALC-like_plant.
DR InterPro; IPR011598; bHLH_dom.
DR InterPro; IPR036638; HLH_DNA-bd_sf.
DR PANTHER; PTHR45855; PTHR45855; 1.
DR Pfam; PF00010; HLH; 1.
DR SMART; SM00353; HLH; 1.
DR SUPFAM; SSF47459; SSF47459; 1.
DR PROSITE; PS50888; BHLH; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; Nucleus; Phytochrome signaling pathway;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..430
FT /note="Transcription factor PIF4"
FT /id="PRO_0000127429"
FT DOMAIN 257..306
FT /note="bHLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 42..71
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 97..136
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 160..183
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 223..266
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 405..430
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 48..64
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 97..112
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 116..136
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 160..177
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 235..254
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 405..423
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 268..279
FT /note="RRRDRINERMKA -> VLHRFVYIIYNI (in isoform Short)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_002146"
FT VAR_SEQ 280..430
FT /note="Missing (in isoform Short)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_002147"
FT VARIANT 231
FT /note="H -> D (in strain: cv. Bla-6, cv. Et-0, cv. Li-5:3,
FT cv. Mt-0, cv. Pa-2 and cv. Tsu-1)"
FT /evidence="ECO:0000269|PubMed:17614917"
FT CONFLICT 204
FT /note="G -> S (in Ref. 5; AAK25931)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 430 AA; 48363 MW; B4C081D0BF907C26 CRC64;
MEHQGWSFEE NYSLSTNRRS IRPQDELVEL LWRDGQVVLQ SQTHREQTQT QKQDHHEEAL
RSSTFLEDQE TVSWIQYPPD EDPFEPDDFS SHFFSTMDPL QRPTSETVKP KSSPEPPQVM
VKPKACPDPP PQVMPPPKFR LTNSSSGIRE TEMEQYSVTT VGPSHCGSNP SQNDLDVSMS
HDRSKNIEEK LNPNASSSSG GSSGCSFGKD IKEMASGRCI TTDRKRKRIN HTDESVSLSD
AIGNKSNQRS GSNRRSRAAE VHNLSERRRR DRINERMKAL QELIPHCSKT DKASILDEAI
DYLKSLQLQL QVMWMGSGMA AAAASAPMMF PGVQPQQFIR QIQSPVQLPR FPVMDQSAIQ
NNPGLVCQNP VQNQIISDRF ARYIGGFPHM QAATQMQPME MLRFSSPAGQ QSQQPSSVPT
KTTDGSRLDH
