HFR1_ARATH
ID HFR1_ARATH Reviewed; 292 AA.
AC Q9FE22; Q8GZ25; Q9FZ26;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Transcription factor HFR1 {ECO:0000303|PubMed:10995393};
DE AltName: Full=Basic helix-loop-helix protein 26 {ECO:0000303|PubMed:12679534};
DE Short=AtbHLH26 {ECO:0000303|PubMed:12679534};
DE Short=bHLH 26 {ECO:0000303|PubMed:12679534};
DE AltName: Full=Protein LONG HYPOCOTYL IN FAR-RED 1 {ECO:0000303|PubMed:10995393};
DE AltName: Full=Protein REDUCED PHYTOCHROME SIGNALING {ECO:0000303|PubMed:11090209};
DE AltName: Full=Reduced sensitivity to far-red light {ECO:0000303|PubMed:11148292};
DE AltName: Full=Transcription factor EN 68;
DE AltName: Full=bHLH transcription factor bHLH026 {ECO:0000303|PubMed:12679534};
GN Name=HFR1 {ECO:0000303|PubMed:10995393};
GN Synonyms=BHLH26 {ECO:0000303|PubMed:12679534}, EN68,
GN FBI1 {ECO:0000303|Ref.4}, REP1 {ECO:0000303|PubMed:11090209},
GN RSF1 {ECO:0000303|PubMed:11148292}; OrderedLocusNames=At1g02340;
GN ORFNames=T6A9.4, T6A9_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], AND FUNCTION.
RX PubMed=11090209; DOI=10.2307/3871105;
RA Soh M.-S., Kim Y.-M., Han S.-J., Song P.-S.;
RT "REP1, a basic helix-loop-helix protein, is required for a branch pathway
RT of phytochrome A signaling in Arabidopsis.";
RL Plant Cell 12:2061-2074(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RC STRAIN=cv. Landsberg erecta; TISSUE=Hypocotyl;
RX PubMed=10995393;
RA Fairchild C.D., Schumaker M.A., Quail P.H.;
RT "HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal
RT transduction.";
RL Genes Dev. 14:2377-2391(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=11148292; DOI=10.2307/3871243;
RA Spiegelman J.I., Mindrinos M.N., Fankhauser C., Richards D., Lutes J.,
RA Chory J., Oefner P.J.;
RT "Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on
RT high-density DNA arrays and denaturing high-performance liquid
RT chromatography.";
RL Plant Cell 12:2485-2498(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RA Wu Y., Liu D., Yang H., Tang R., Cashmore A.R.;
RT "FBI1, an Arabidopsis bHLH protein involved in both cryptochrome 1 and
RT phytochrome A signaling.";
RL Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 150-292.
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [8]
RP TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
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 [9]
RP GENE FAMILY.
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 [10]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=14600211; DOI=10.1105/tpc.151140;
RA Bailey P.C., Martin C., Toledo-Ortiz G., Quail P.H., Huq E., Heim M.A.,
RA Jakoby M., Werber M., Weisshaar B.;
RT "Update on the basic helix-loop-helix transcription factor gene family in
RT Arabidopsis thaliana.";
RL Plant Cell 15:2497-2502(2003).
RN [11]
RP INTERACTION WITH PRE6.
RX PubMed=16786307; DOI=10.1007/s11103-006-0010-2;
RA Hyun Y., Lee I.;
RT "KIDARI, encoding a non-DNA binding bHLH protein, represses light signal
RT transduction in Arabidopsis thaliana.";
RL Plant Mol. Biol. 61:283-296(2006).
RN [12]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP PHYA; FHY1 AND FHL.
RC STRAIN=cv. Columbia;
RX PubMed=19482971; DOI=10.1105/tpc.109.067215;
RA Yang S.W., Jang I.-C., Henriques R., Chua N.-H.;
RT "FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis
RT transcription factors LAF1 and HFR1 to transmit phytochrome A signals for
RT inhibition of hypocotyl elongation.";
RL Plant Cell 21:1341-1359(2009).
RN [13]
RP INTERACTION WITH PRE1; PRE2 AND PRE4.
RX PubMed=20305124; DOI=10.1105/tpc.109.065946;
RA Mara C.D., Huang T., Irish V.F.;
RT "The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA
RT negatively regulate the BANQUO genes implicated in light signaling.";
RL Plant Cell 22:690-702(2010).
RN [14]
RP INTERACTION WITH PRE6 AND PIF4, AND SUBCELLULAR LOCATION.
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).
CC -!- FUNCTION: Atypical bHLH transcription factor that regulates
CC photomorphogenesis through modulation of phytochrome (e.g. PHYA) and
CC cryptochrome signalings (Ref.4, PubMed:11090209, PubMed:10995393,
CC PubMed:19482971). Suppresses the transcriptional regulation activity of
CC PIF4 by forming non-DNA-binding heterodimer.
CC {ECO:0000269|PubMed:10995393, ECO:0000269|PubMed:11090209,
CC ECO:0000269|PubMed:19482971, ECO:0000269|Ref.4}.
CC -!- SUBUNIT: Binds to FHY1 and FHL. Forms PHYA/FHY1/HFR1 complex
CC (PubMed:19482971). Homodimer and heterodimer with PIF3. Do not interact
CC alone with either phytochrome A (phyA) or B (phyB), but REP1/PIF3
CC complex binds to phyA and phyB, preferentially to the Pfr forms. Forms
CC non-functional heterodimer with PRE6, causing liberation of PIF4 from
CC the transcriptionally inactive complex HFR1-PIF4. Repressed when bound
CC to PRE1, PRE2 and PRE4. {ECO:0000269|PubMed:16786307,
CC ECO:0000269|PubMed:19482971, ECO:0000269|PubMed:20305124,
CC ECO:0000269|PubMed:23224238}.
CC -!- INTERACTION:
CC Q9FE22; Q39079: ATJ13; NbExp=3; IntAct=EBI-626001, EBI-2461966;
CC Q9FE22; P43254: COP1; NbExp=6; IntAct=EBI-626001, EBI-301649;
CC Q9FE22; Q9M0K4: LAF1; NbExp=6; IntAct=EBI-626001, EBI-1543309;
CC Q9FE22; Q8GZM7: PIF1; NbExp=3; IntAct=EBI-626001, EBI-630400;
CC Q9FE22; O80536: PIF3; NbExp=6; IntAct=EBI-626001, EBI-625701;
CC Q9FE22; Q8W2F3: PIF4; NbExp=2; IntAct=EBI-626001, EBI-625716;
CC Q9FE22; Q84LH8: PIF5; NbExp=3; IntAct=EBI-626001, EBI-631622;
CC Q9FE22; Q9SYX2: SPA1; NbExp=3; IntAct=EBI-626001, EBI-626992;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00981,
CC ECO:0000269|PubMed:19482971, ECO:0000269|PubMed:23224238}.
CC -!- TISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems,
CC and flowers. {ECO:0000269|PubMed:12679534}.
CC -!- INDUCTION: Twofold induction by far-red light and 14-fold suppression
CC by red light.
CC -!- DISRUPTION PHENOTYPE: Partially blind to far-red (FR). Impaired
CC inhibition of hypocotyl elongation and cotyledons expansion under
CC continuous FR light conditions. {ECO:0000269|PubMed:19482971}.
CC -!- CAUTION: Contains a degenerate basic motif not likely to bind DNA.
CC {ECO:0000255|PROSITE-ProRule:PRU00981}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG00886.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF288287; AAG45733.1; -; mRNA.
DR EMBL; AF324245; AAG40617.1; -; mRNA.
DR EMBL; AF323182; AAK15282.1; -; mRNA.
DR EMBL; AC064879; AAG00886.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27418.1; -; Genomic_DNA.
DR EMBL; AK117248; BAC41923.1; -; mRNA.
DR PIR; G86153; G86153.
DR RefSeq; NP_563650.1; NM_100115.3.
DR PDB; 6QTV; X-ray; 1.31 A; B=57-66.
DR PDBsum; 6QTV; -.
DR AlphaFoldDB; Q9FE22; -.
DR SMR; Q9FE22; -.
DR BioGRID; 24535; 26.
DR IntAct; Q9FE22; 22.
DR MINT; Q9FE22; -.
DR STRING; 3702.AT1G02340.1; -.
DR iPTMnet; Q9FE22; -.
DR PaxDb; Q9FE22; -.
DR PRIDE; Q9FE22; -.
DR EnsemblPlants; AT1G02340.1; AT1G02340.1; AT1G02340.
DR GeneID; 839300; -.
DR Gramene; AT1G02340.1; AT1G02340.1; AT1G02340.
DR KEGG; ath:AT1G02340; -.
DR Araport; AT1G02340; -.
DR TAIR; locus:2204898; AT1G02340.
DR HOGENOM; CLU_970936_0_0_1; -.
DR InParanoid; Q9FE22; -.
DR OMA; YSEYNRR; -.
DR OrthoDB; 1083485at2759; -.
DR PhylomeDB; Q9FE22; -.
DR PRO; PR:Q9FE22; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FE22; baseline and differential.
DR Genevisible; Q9FE22; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0003712; F:transcription coregulator activity; IMP:TAIR.
DR GO; GO:0009738; P:abscisic acid-activated signaling pathway; IMP:TAIR.
DR GO; GO:0009785; P:blue light signaling pathway; TAS:TAIR.
DR GO; GO:0009585; P:red, far-red light phototransduction; TAS:TAIR.
DR GO; GO:0010218; P:response to far red light; IDA:UniProtKB.
DR GO; GO:0009642; P:response to light intensity; IEP:TAIR.
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 3D-structure; DNA-binding; Nucleus; Phytochrome signaling pathway;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..292
FT /note="Transcription factor HFR1"
FT /id="PRO_0000127430"
FT DOMAIN 134..183
FT /note="bHLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 114..153
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 134..147
FT /note="Basic motif; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 148..183
FT /note="Helix-loop-helix motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT MOTIF 141..148
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 114..137
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 292 AA; 33615 MW; BC75C5EB26E10A20 CRC64;
MSNNQAFMEL GWRNDVGSLA VKDQGMMSER ARSDEDRLIN GLKWGYGYFD HDQTDNYLQI
VPEIHKEVEN AKEDLLVVVP DEHSETDDHH HIKDFSERSD HRFYLRNKHE NPKKRRIQVL
SSDDESEEFT REVPSVTRKG SKRRRRDEKM SNKMRKLQQL VPNCHKTDKV SVLDKTIEYM
KNLQLQLQMM STVGVNPYFL PATLGFGMHN HMLTAMASAH GLNPANHMMP SPLIPALNWP
LPPFTNISFP HSSSQSLFLT TSSPASSPQS LHGLVPYFPS FLDFSSHAMR RL
