PIF5_ARATH
ID PIF5_ARATH Reviewed; 444 AA.
AC Q84LH8; Q8RXG4; Q8S3D7; Q9LYT0;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Transcription factor PIF5;
DE AltName: Full=Basic helix-loop-helix protein 65;
DE Short=AtbHLH65;
DE Short=bHLH 65;
DE AltName: Full=Phytochrome interacting factor-like 6;
DE AltName: Full=Phytochrome-interacting factor 5;
DE AltName: Full=Transcription factor EN 103;
DE AltName: Full=bHLH transcription factor bHLH065;
GN Name=PIF5; Synonyms=BHLH65, EN103, PIL6; OrderedLocusNames=At3g59060;
GN ORFNames=F17J16.110;
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 2), TISSUE SPECIFICITY, GENE FAMILY,
RP 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 [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, INDUCTION, AND
RP INTERACTION WITH TOC1/APRR1.
RC STRAIN=cv. Columbia;
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
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 3).
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 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 [7]
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 [8]
RP FUNCTION, MUTAGENESIS OF GLU-31; LEU-32; GLY-37 AND GLN-38, AND INTERACTION
RP WITH PHYB.
RX PubMed=15486100; DOI=10.1105/tpc.104.025643;
RA Khanna R., Huq E., Kikis E.A., Al-Sady B., Lanzatella C., Quail P.H.;
RT "A novel molecular recognition motif necessary for targeting photoactivated
RT phytochrome signaling to specific basic helix-loop-helix transcription
RT factors.";
RL Plant Cell 16:3033-3044(2004).
RN [9]
RP FUNCTION, DEVELOPMENTAL STAGE, AND INTERACTION WITH TOC1/APRR1 AND PIF3.
RX PubMed=15356333; DOI=10.1093/pcp/pch124;
RA Fujimori T., Yamashino T., Kato T., Mizuno T.;
RT "Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in
RT light-signal transduction in Arabidopsis thaliana.";
RL Plant Cell Physiol. 45:1078-1086(2004).
RN [10]
RP FUNCTION, AND INDUCTION.
RX PubMed=17589502; DOI=10.1038/nature05946;
RA Nozue K., Covington M.F., Duek P.D., Lorrain S., Fankhauser C.,
RA Harmer S.L., Maloof J.N.;
RT "Rhythmic growth explained by coincidence between internal and external
RT cues.";
RL Nature 448:358-361(2007).
RN [11]
RP FUNCTION, AND MUTAGENESIS OF GLY-37.
RX PubMed=18065691; DOI=10.1105/tpc.107.051508;
RA Khanna R., Shen Y., Marion C.M., Tsuchisaka A., Theologis A., Schaefer E.,
RA Quail P.H.;
RT "The basic helix-loop-helix transcription factor PIF5 acts on ethylene
RT biosynthesis and phytochrome signaling by distinct mechanisms.";
RL Plant Cell 19:3915-3929(2007).
RN [12]
RP PHOSPHORYLATION.
RX PubMed=17827270; DOI=10.1104/pp.107.105601;
RA Shen Y., Khanna R., Carle C.M., Quail P.H.;
RT "Phytochrome induces rapid PIF5 phosphorylation and degradation in response
RT to red-light activation.";
RL Plant Physiol. 145:1043-1051(2007).
RN [13]
RP FUNCTION, PHOSPHORYLATION, AND INDUCTION.
RX PubMed=18047474; DOI=10.1111/j.1365-313x.2007.03341.x;
RA Lorrain S., Allen T., Duek P.D., Whitelam G.C., Fankhauser C.;
RT "Phytochrome-mediated inhibition of shade avoidance involves degradation of
RT growth-promoting bHLH transcription factors.";
RL Plant J. 53:312-323(2008).
RN [14]
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 [15]
RP INTERACTION WITH TOPP4, AND PHOSPHORYLATION.
RX PubMed=26704640; DOI=10.1104/pp.15.01729;
RA Yue J., Qin Q., Meng S., Jing H., Gou X., Li J., Hou S.;
RT "TOPP4 regulates the stability of PHYTOCHROME INTERACTING FACTOR5 during
RT photomorphogenesis in Arabidopsis.";
RL Plant Physiol. 170:1381-1397(2016).
CC -!- FUNCTION: Transcription factor acting negatively in the phytochrome B
CC signaling pathway to promote the shade-avoidance response. Regulates
CC PHYB abundance at the post-transcriptional level, possibly via the
CC ubiquitin-proteasome pathway. Promotes ethylene activity in the dark.
CC May regulate the expression of a subset of genes by binding to the G-
CC box motif. Might be involved in the integration of light-signals to
CC control both circadian and photomorphogenic processes. Activated by
CC CRY1 and CRY2 in response to low blue light (LBL) by direct binding at
CC chromatin on E-box variant 5'-CA[CT]GTG-3' to stimulate specific gene
CC expression to adapt global physiology (e.g. hypocotyl elongation in low
CC blue light) (PubMed:26724867). {ECO:0000269|PubMed:12826627,
CC ECO:0000269|PubMed:15356333, ECO:0000269|PubMed:15486100,
CC ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474,
CC ECO:0000269|PubMed:18065691, ECO:0000269|PubMed:26724867}.
CC -!- SUBUNIT: Homodimer (Probable). Interacts specifically with the Pfr form
CC of phytochrome B and with TOC1/APRR1. May form a heterodimer with PIF3.
CC Interacts with PHYB, CRY1 and CRY2 in the nucleus in response to low
CC blue light (LBL) (PubMed:26724867). Interacts with TOPP4
CC (PubMed:26704640). {ECO:0000269|PubMed:12826627,
CC ECO:0000269|PubMed:15356333, ECO:0000269|PubMed:15486100,
CC ECO:0000269|PubMed:26704640, ECO:0000269|PubMed:26724867, ECO:0000305}.
CC -!- INTERACTION:
CC Q84LH8; Q9FE22: HFR1; NbExp=3; IntAct=EBI-631622, EBI-626001;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00981,
CC ECO:0000269|PubMed:26724867}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q84LH8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q84LH8-2; Sequence=VSP_032846;
CC Name=3;
CC IsoId=Q84LH8-3; Sequence=VSP_032844, VSP_032845;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, and flowers.
CC {ECO:0000269|PubMed:12679534}.
CC -!- DEVELOPMENTAL STAGE: Circadian-controlled expression.
CC {ECO:0000269|PubMed:15356333}.
CC -!- INDUCTION: Follow a free-running robust circadian rhythm, with higher
CC levels during the light phase. Rapidly induced by light in etiolated
CC plants. Up-regulated by white light. Rapid degradation after red light
CC exposure (at protein level). Accumulates to high levels in the dark, is
CC selectively degraded in response to red light and remains at high
CC levels under shade-mimicking conditions. {ECO:0000269|PubMed:12826627,
CC ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474}.
CC -!- DOMAIN: The active phytochrome binding (APB) motif (26-39) is involved
CC in interaction with PHYB and is required for proteasome-mediated
CC degradation.
CC -!- PTM: Phosphorylated. Additional phosphorylations induced within 60
CC seconds following phytochrome B photoactivation.
CC {ECO:0000269|PubMed:17827270, ECO:0000269|PubMed:18047474}.
CC -!- PTM: Dephosphorylated by TOPP4 during photomorphogenesis, leading to
CC subsequent degradation of PIF5 by the proteasomal pathway.
CC {ECO:0000269|PubMed:26704640}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
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DR EMBL; AF488598; AAM10954.1; -; mRNA.
DR EMBL; AB103112; BAC56978.1; -; Transcribed_RNA.
DR EMBL; AL163527; CAB86934.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79868.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79869.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79870.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79871.1; -; Genomic_DNA.
DR EMBL; AY081271; AAL91160.1; -; mRNA.
DR EMBL; BT000049; AAN15368.1; -; mRNA.
DR PIR; T47788; T47788.
DR RefSeq; NP_001030889.1; NM_001035812.2. [Q84LH8-1]
DR RefSeq; NP_001030890.1; NM_001035813.2. [Q84LH8-1]
DR RefSeq; NP_191465.3; NM_115768.5. [Q84LH8-1]
DR RefSeq; NP_851021.1; NM_180690.2. [Q84LH8-2]
DR AlphaFoldDB; Q84LH8; -.
DR SMR; Q84LH8; -.
DR BioGRID; 10390; 11.
DR IntAct; Q84LH8; 4.
DR MINT; Q84LH8; -.
DR STRING; 3702.AT3G59060.4; -.
DR iPTMnet; Q84LH8; -.
DR PaxDb; Q84LH8; -.
DR PRIDE; Q84LH8; -.
DR ProteomicsDB; 235112; -. [Q84LH8-1]
DR EnsemblPlants; AT3G59060.1; AT3G59060.1; AT3G59060. [Q84LH8-2]
DR EnsemblPlants; AT3G59060.2; AT3G59060.2; AT3G59060. [Q84LH8-1]
DR EnsemblPlants; AT3G59060.3; AT3G59060.3; AT3G59060. [Q84LH8-1]
DR EnsemblPlants; AT3G59060.4; AT3G59060.4; AT3G59060. [Q84LH8-1]
DR GeneID; 825075; -.
DR Gramene; AT3G59060.1; AT3G59060.1; AT3G59060. [Q84LH8-2]
DR Gramene; AT3G59060.2; AT3G59060.2; AT3G59060. [Q84LH8-1]
DR Gramene; AT3G59060.3; AT3G59060.3; AT3G59060. [Q84LH8-1]
DR Gramene; AT3G59060.4; AT3G59060.4; AT3G59060. [Q84LH8-1]
DR KEGG; ath:AT3G59060; -.
DR Araport; AT3G59060; -.
DR TAIR; locus:2077680; AT3G59060.
DR eggNOG; ENOG502QTIX; Eukaryota.
DR InParanoid; Q84LH8; -.
DR OMA; ECQSEFA; -.
DR PhylomeDB; Q84LH8; -.
DR PRO; PR:Q84LH8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q84LH8; baseline and differential.
DR Genevisible; Q84LH8; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
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:0009693; P:ethylene biosynthetic process; IMP:TAIR.
DR GO; GO:0009585; P:red, far-red light phototransduction; IMP:TAIR.
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; Phosphoprotein;
KW Phytochrome signaling pathway; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..444
FT /note="Transcription factor PIF5"
FT /id="PRO_0000328935"
FT DOMAIN 256..305
FT /note="bHLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 26..39
FT /note="Involved in interaction with phyB"
FT REGION 154..265
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 416..444
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 154..175
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 184..207
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 208..223
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 224..253
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 437
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8GZM7"
FT VAR_SEQ 289..300
FT /note="TDKASILDEAID -> IKLRYWMKQLIT (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_032844"
FT VAR_SEQ 301..444
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_032845"
FT VAR_SEQ 405..406
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12679534"
FT /id="VSP_032846"
FT MUTAGEN 31
FT /note="E->A: Loss of binding to PHYB."
FT /evidence="ECO:0000269|PubMed:15486100"
FT MUTAGEN 32
FT /note="L->A: Loss of binding to PHYB."
FT /evidence="ECO:0000269|PubMed:15486100"
FT MUTAGEN 37
FT /note="G->A: Loss of binding to PHYB."
FT /evidence="ECO:0000269|PubMed:15486100,
FT ECO:0000269|PubMed:18065691"
FT MUTAGEN 38
FT /note="Q->A: Loss of binding to PHYB."
FT /evidence="ECO:0000269|PubMed:15486100"
FT CONFLICT 126
FT /note="T -> M (in Ref. 1; AAM10954)"
FT /evidence="ECO:0000305"
FT CONFLICT 174
FT /note="S -> N (in Ref. 5; AAN15368/AAL91160)"
FT /evidence="ECO:0000305"
FT CONFLICT 371
FT /note="Q -> L (in Ref. 1; AAM10954)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 444 AA; 49302 MW; 593D72C1F2ED86C7 CRC64;
MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQET
LRKPNNIFLD NQETVQKPNY AALDDQETVS WIQYPPDDVI DPFESEFSSH FFSSIDHLGG
PEKPRTIEET VKHEAQAMAP PKFRSSVITV GPSHCGSNQS TNIHQATTLP VSMSDRSKNV
EERLDTSSGG SSGCSYGRNN KETVSGTSVT IDRKRKHVMD ADQESVSQSD IGLTSTDDQT
MGNKSSQRSG STRRSRAAEV HNLSERRRRD RINERMKALQ ELIPHCSRTD KASILDEAID
YLKSLQMQLQ VMWMGSGMAA AAAAAASPMM FPGVQSSPYI NQMAMQSQMQ LSQFPVMNRS
APQNHPGLVC QNPVQLQLQA QNQILSEQLA RYMGGIPQMP PAGNQMQTVQ QQPADMLGFG
SPAGPQSQLS APATTDSLHM GKIG
