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Transcription factor PIF3 (Basic helix-loop-helix protein 8) (AtbHLH8) (bHLH 8) (Phytochrome-associated protein 3) (Phytochrome-interacting factor 3) (Transcription factor EN 100) (bHLH transcription factor bHLH008)

 PIF3_ARATH              Reviewed;         524 AA.
O80536; A5Y7A2; A5Y7A3; A5Y7A4; A5Y7A5; A5Y7A6; A5Y7A7; A5Y7A8;
A5Y7A9; A5Y7B0; A5Y7B1; A5Y7B2; A5Y7B3; A5Y7B4; A5Y7B5; A5Y7B6;
Q9SBC5;
10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
01-NOV-1998, sequence version 1.
12-SEP-2018, entry version 153.
RecName: Full=Transcription factor PIF3;
AltName: Full=Basic helix-loop-helix protein 8;
Short=AtbHLH8;
Short=bHLH 8;
AltName: Full=Phytochrome-associated protein 3;
AltName: Full=Phytochrome-interacting factor 3;
AltName: Full=Transcription factor EN 100;
AltName: Full=bHLH transcription factor bHLH008;
Name=PIF3; Synonyms=BHLH8, EN100, PAP3; OrderedLocusNames=At1g09530;
ORFNames=F14J9.19;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
STRAIN=cv. Columbia;
PubMed=9845368; DOI=10.1016/S0092-8674(00)81636-0;
Ni M., Tepperman J.M., Quail P.H.;
"PIF3, a phytochrome-interacting factor necessary for normal
photoinduced signal transduction, is a novel basic helix-loop-helix
protein.";
Cell 95:657-667(1998).
[2]
NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY UV LIGHT, GENE FAMILY, AND
NOMENCLATURE.
STRAIN=cv. Columbia;
PubMed=12679534; DOI=10.1093/molbev/msg088;
Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C.;
"The basic helix-loop-helix transcription factor family in plants: a
genome-wide study of protein structure and functional diversity.";
Mol. Biol. Evol. 20:735-747(2003).
[3]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=cv. Columbia;
Lee J., Yi H., Shin B., Song P.-S., Choi G.;
"Identification and characterization of three phytochrome-associated
proteins.";
Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[5]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=11910074; DOI=10.1126/science.1071006;
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
Shibata K., Shinagawa A., Shinozaki K.;
"Functional annotation of a full-length Arabidopsis cDNA collection.";
Science 296:141-145(2002).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-272, AND VARIANTS ASP-124;
ASN-141; HIS-176; LYS-186; LEU-209; ILE-220 AND ILE-236.
STRAIN=cv. An-2, cv. Bla-6, cv. Br-0, cv. Bu-2, cv. Columbia,
cv. Di-1, cv. Et-0, cv. Kl-1, cv. Li-5:3, cv. Ma-2, cv. Mt-0,
cv. Pa-2, cv. Pi-0, cv. Su-0, and cv. Tsu-1;
PubMed=17614917; DOI=10.1111/j.1365-294X.2007.03298.x;
Brock M.T., Tiffin P., Weinig C.;
"Sequence diversity and haplotype associations with phenotypic
responses to crowding: GIGANTEA affects fruit set in Arabidopsis
thaliana.";
Mol. Ecol. 16:3050-3062(2007).
[8]
FUNCTION.
PubMed=10466729; DOI=10.1038/23500;
Ni M., Tepperman J.M., Quail P.H.;
"Binding of phytochrome B to its nuclear signalling partner PIF3 is
reversibly induced by light.";
Nature 400:781-784(1999).
[9]
FUNCTION.
PubMed=10797009; DOI=10.1126/science.288.5467.859;
Martinez-Garcia J.F., Huq E., Quail P.H.;
"Direct targeting of light signals to a promoter element-bound
transcription factor.";
Science 288:859-863(2000).
[10]
INTERACTION WITH APRR1.
PubMed=11828023; DOI=10.1093/pcp/pcf005;
Makino S., Matsushika A., Kojima M., Yamashino T., Mizuno T.;
"The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis
thaliana: I. Characterization with APRR1-overexpressing plants.";
Plant Cell Physiol. 43:58-69(2002).
[11]
GENE FAMILY, AND INTERACTION WITH PIF4.
PubMed=12897250; DOI=10.1105/tpc.013839;
Toledo-Ortiz G., Huq E., Quail P.H.;
"The Arabidopsis basic/helix-loop-helix transcription factor family.";
Plant Cell 15:1749-1770(2003).
[12]
GENE FAMILY, AND NOMENCLATURE.
PubMed=14600211; DOI=10.1105/tpc.151140;
Bailey P.C., Martin C., Toledo-Ortiz G., Quail P.H., Huq E.,
Heim M.A., Jakoby M., Werber M., Weisshaar B.;
"Update on the basic helix-loop-helix transcription factor gene family
in Arabidopsis thaliana.";
Plant Cell 15:2497-2502(2003).
[13]
INTERACTION WITH APRR1.
PubMed=12826627; DOI=10.1093/pcp/pcg078;
Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S.,
Mizuno T.;
"A link between circadian-controlled bHLH factors and the APRR1/TOC1
quintet in Arabidopsis thaliana.";
Plant Cell Physiol. 44:619-629(2003).
[14]
INTERACTION WITH PIA2, AND PHOSPHORYLATION BY PHYA.
STRAIN=cv. Columbia;
PubMed=27143545; DOI=10.1093/jb/mvw031;
Yoo J., Cho M.-H., Lee S.-W., Bhoo S.H.;
"Phytochrome-interacting ankyrin repeat protein 2 modulates
phytochrome A-mediated PIF3 phosphorylation in light signal
transduction.";
J. Biochem. 160:243-249(2016).
[15]
INTERACTION WITH TOPP4, AND PHOSPHORYLATION.
PubMed=26704640; DOI=10.1104/pp.15.01729;
Yue J., Qin Q., Meng S., Jing H., Gou X., Li J., Hou S.;
"TOPP4 regulates the stability of PHYTOCHROME INTERACTING FACTOR5
during photomorphogenesis in Arabidopsis.";
Plant Physiol. 170:1381-1397(2016).
-!- FUNCTION: Transcription factor acting positively in the
phytochrome signaling pathway. Activates transcription by binding
to the G box (5'-CACGTG-3'). {ECO:0000269|PubMed:10466729,
ECO:0000269|PubMed:10797009}.
-!- SUBUNIT: Homodimer (Probable). Can form a heterodimer with REP1
and PIF4. Phytochrome B binds specifically to DNA-bound PIF3, but
only upon red light induced conversion to the Pfr form (PfrB).
Reconversion to Pr form causes rapid dissociation. Interacts with
APRR1/TOC1. Binds to PIA2; this interaction may trigger the
repression of PHYA-mediated phosphorylation (PubMed:27143545).
Interacts with TOPP4 (PubMed:26704640).
{ECO:0000269|PubMed:11828023, ECO:0000269|PubMed:12826627,
ECO:0000269|PubMed:12897250, ECO:0000269|PubMed:26704640,
ECO:0000269|PubMed:27143545, ECO:0000305}.
-!- INTERACTION:
Self; NbExp=3; IntAct=EBI-625701, EBI-625701;
Q9FE22:HFR1; NbExp=6; IntAct=EBI-625701, EBI-626001;
P14712:PHYA; NbExp=8; IntAct=EBI-625701, EBI-624446;
P14713:PHYB; NbExp=22; IntAct=EBI-625701, EBI-300727;
Q8GZM7:PIF1; NbExp=6; IntAct=EBI-625701, EBI-630400;
Q8W2F3-2:PIF4; NbExp=3; IntAct=EBI-625701, EBI-625732;
Q9SLH3:RGA; NbExp=6; IntAct=EBI-625701, EBI-963624;
-!- SUBCELLULAR LOCATION: Nucleus.
-!- INDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
-!- PTM: Phosphorylated by PHYA; this phosphorylation is repressed by
PIA2. {ECO:0000269|PubMed:27143545}.
-!- PTM: Dephosphorylated by TOPP4 during photomorphogenesis, leading
to subsequent degradation of PIF3 by the proteasomal pathway.
{ECO:0000269|PubMed:26704640}.
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EMBL; AF100166; AAC95156.1; -; mRNA.
EMBL; AF251693; AAL55715.1; -; mRNA.
EMBL; AF088280; AAC99771.1; -; mRNA.
EMBL; AC003970; AAC33213.1; -; Genomic_DNA.
EMBL; CP002684; AEE28457.1; -; Genomic_DNA.
EMBL; CP002684; AEE28458.1; -; Genomic_DNA.
EMBL; CP002684; ANM60410.1; -; Genomic_DNA.
EMBL; CP002684; ANM60411.1; -; Genomic_DNA.
EMBL; CP002684; ANM60412.1; -; Genomic_DNA.
EMBL; CP002684; ANM60413.1; -; Genomic_DNA.
EMBL; AK117255; BAC41930.1; -; mRNA.
EMBL; EF193482; ABP96435.1; -; Genomic_DNA.
EMBL; EF193483; ABP96436.1; -; Genomic_DNA.
EMBL; EF193484; ABP96437.1; -; Genomic_DNA.
EMBL; EF193485; ABP96438.1; -; Genomic_DNA.
EMBL; EF193486; ABP96439.1; -; Genomic_DNA.
EMBL; EF193487; ABP96440.1; -; Genomic_DNA.
EMBL; EF193488; ABP96441.1; -; Genomic_DNA.
EMBL; EF193489; ABP96442.1; -; Genomic_DNA.
EMBL; EF193490; ABP96443.1; -; Genomic_DNA.
EMBL; EF193491; ABP96444.1; -; Genomic_DNA.
EMBL; EF193492; ABP96445.1; -; Genomic_DNA.
EMBL; EF193493; ABP96446.1; -; Genomic_DNA.
EMBL; EF193494; ABP96447.1; -; Genomic_DNA.
EMBL; EF193495; ABP96448.1; -; Genomic_DNA.
EMBL; EF193496; ABP96449.1; -; Genomic_DNA.
PIR; H86228; H86228.
RefSeq; NP_001318964.1; NM_001331836.1.
RefSeq; NP_001318965.1; NM_001331837.1.
RefSeq; NP_001322700.1; NM_001331838.1.
RefSeq; NP_001322701.1; NM_001331839.1.
RefSeq; NP_172424.1; NM_100824.3.
RefSeq; NP_849626.1; NM_179295.3.
UniGene; At.10926; -.
ProteinModelPortal; O80536; -.
SMR; O80536; -.
BioGrid; 22720; 33.
DIP; DIP-33892N; -.
IntAct; O80536; 18.
STRING; 3702.AT1G09530.1; -.
PaxDb; O80536; -.
PRIDE; O80536; -.
EnsemblPlants; AT1G09530.1; AT1G09530.1; AT1G09530.
EnsemblPlants; AT1G09530.2; AT1G09530.2; AT1G09530.
EnsemblPlants; AT1G09530.3; AT1G09530.3; AT1G09530.
EnsemblPlants; AT1G09530.4; AT1G09530.4; AT1G09530.
EnsemblPlants; AT1G09530.5; AT1G09530.5; AT1G09530.
EnsemblPlants; AT1G09530.6; AT1G09530.6; AT1G09530.
GeneID; 837479; -.
Gramene; AT1G09530.1; AT1G09530.1; AT1G09530.
Gramene; AT1G09530.2; AT1G09530.2; AT1G09530.
Gramene; AT1G09530.3; AT1G09530.3; AT1G09530.
Gramene; AT1G09530.4; AT1G09530.4; AT1G09530.
Gramene; AT1G09530.5; AT1G09530.5; AT1G09530.
Gramene; AT1G09530.6; AT1G09530.6; AT1G09530.
KEGG; ath:AT1G09530; -.
Araport; AT1G09530; -.
TAIR; locus:2012345; AT1G09530.
eggNOG; ENOG410IV8V; Eukaryota.
eggNOG; ENOG4111SYS; LUCA.
InParanoid; O80536; -.
KO; K12126; -.
OMA; VACSSVC; -.
OrthoDB; EOG093605W3; -.
PhylomeDB; O80536; -.
PRO; PR:O80536; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; O80536; baseline and differential.
Genevisible; O80536; AT.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0003677; F:DNA binding; IDA:TAIR.
GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
GO; GO:0044212; F:transcription regulatory region DNA binding; IPI:TAIR.
GO; GO:0000976; F:transcription regulatory region sequence-specific DNA binding; IPI:TAIR.
GO; GO:0009704; P:de-etiolation; IMP:TAIR.
GO; GO:0009740; P:gibberellic acid mediated signaling pathway; IMP:TAIR.
GO; GO:0031539; P:positive regulation of anthocyanin metabolic process; IMP:TAIR.
GO; GO:0010017; P:red or far-red light signaling pathway; IMP:TAIR.
GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
GO; GO:0009639; P:response to red or far red light; IMP:TAIR.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00083; HLH; 1.
Gene3D; 4.10.280.10; -; 1.
InterPro; IPR011598; bHLH_dom.
InterPro; IPR036638; HLH_DNA-bd_sf.
Pfam; PF00010; HLH; 1.
SMART; SM00353; HLH; 1.
SUPFAM; SSF47459; SSF47459; 1.
PROSITE; PS50888; BHLH; 1.
1: Evidence at protein level;
Complete proteome; DNA-binding; Nucleus; Phosphoprotein;
Phytochrome signaling pathway; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 524 Transcription factor PIF3.
/FTId=PRO_0000127428.
DOMAIN 343 392 bHLH. {ECO:0000255|PROSITE-
ProRule:PRU00981}.
COMPBIAS 353 358 Poly-Arg.
COMPBIAS 422 428 Poly-Ala.
VARIANT 124 124 E -> D (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 141 141 K -> N (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 176 176 Q -> H (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 186 186 Q -> K (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 209 209 F -> L (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 220 220 T -> I (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
VARIANT 236 236 V -> I (in strain: cv. An-2 and cv. Su-
0). {ECO:0000269|PubMed:17614917}.
CONFLICT 15 15 E -> D (in Ref. 3; AAC99771).
{ECO:0000305}.
CONFLICT 344 344 S -> L (in Ref. 3; AAC99771).
{ECO:0000305}.
SEQUENCE 524 AA; 56990 MW; 1044AC01D598DE7C CRC64;
MPLFELFRLT KAKLESAQDR NPSPPVDEVV ELVWENGQIS TQSQSSRSRN IPPPQANSSR
AREIGNGSKT TMVDEIPMSV PSLMTGLSQD DDFVPWLNHH PSLDGYCSDF LRDVSSPVTV
NEQESDMAVN QTAFPLFQRR KDGNESAPAA SSSQYNGFQS HSLYGSDRAR DLPSQQTNPD
RFTQTQEPLI TSNKPSLVNF SHFLRPATFA KTTNNNLHDT KEKSPQSPPN VFQTRVLGAK
DSEDKVLNES VASATPKDNQ KACLISEDSC RKDQESEKAV VCSSVGSGNS LDGPSESPSL
SLKRKHSNIQ DIDCHSEDVE EESGDGRKEA GPSRTGLGSK RSRSAEVHNL SERRRRDRIN
EKMRALQELI PNCNKVDKAS MLDEAIEYLK SLQLQVQIMS MASGYYLPPA VMFPPGMGHY
PAAAAAMAMG MGMPYAMGLP DLSRGGSSVN HGPQFQVSGM QQQPVAMGIP RVSGGGIFAG
SSTIGNGSTR DLSGSKDQTT TNNNSNLKPI KRKQGSSDQF CGSS


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