Reviewed, UniProtKB/Swiss-Prot Q8W2F3 (PIF4_ARATH)

Names and origin

Protein names

Recommended name:
    Transcription factor PIF4
Alternative name(s):
    Phytochrome-interacting factor 4
    Transcription factor EN 102
    bHLH transcription factor bHLH009
    Basic helix-loop-helix protein 9
      Short name=bHLH 9
      Short name=AtbHLH9
    Short under red-light 2

Gene names

Name:	PIF4
Synonyms:	BHLH9, EN102, SRL2
Ordered Locus Names:	At2g43010
ORF Names:	MFL8.13

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	430 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Transcription factor acting negatively in the phytochrome B signaling pathway. May regulate the expression of a subset of genes involved in cell expansion by binding to the G-box motif.
Subunit structure	Interacts preferentially with the Pfr form of phytochrome B (phyB). Binds DNA as a homodimer, but once bound to DNA, loses its capacity to interact with phyB. Interacts with APRR1/TOC1 and PIF3. Ref.6 Ref.7
Subcellular location	Nucleus.
Induction	By UV treatment. Follow a free-running robust circadian rhythm, with higher levels during the light phase. Rapidly induced by light in etiolated plants. Sixfold induction by both red and far-red light. Ref.7 Ref.2
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.

Ontologies

Keywords
Biological process	Phytochrome signaling pathway Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	DNA-binding
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	de-etiolation Inferred from mutant phenotype. Source: TAIR red light signaling pathway Ref.1 Inferred from genetic interaction. Source: TAIR red, far-red light phototransduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Ref.1 Inferred from direct assay. Source: TAIR
Molecular function	DNA binding Ref.1 Inferred from direct assay. Source: TAIR protein binding Ref.1 Ref.6 Inferred from physical interaction. Source: IntAct transcription regulator activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PHYA	P14712	2	EBI-625732,EBI-624446
PHYB	P14713	3	EBI-625732,EBI-300727
PIF3	O80536	1	EBI-625732,EBI-625701

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform Long (identifier: Q8W2F3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Short (identifier: Q8W2F3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     268-279: RRRDRINERMKA → VLHRFVYIIYNI
     280-430: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 430	430	Transcription factor PIF4		PRO_0000127429
Regions
	Domain	271 – 311	41	Helix-loop-helix motif
	DNA binding	254 – 270	17	Basic motif By similarity
	Compositional bias	78 – 137	60	Pro-rich
Natural variations
	Alternative sequence	268 – 279	12	RRRDR…ERMKA → VLHRFVYIIYNI in isoform Short.		VSP_002146
	Alternative sequence	280 – 430	151	Missing in isoform Short.		VSP_002147
	Natural variant	231	1	H → D in strain: cv. Bla-6, cv. Et-0, cv. Li-5:3, cv. Mt-0, cv. Pa-2 and cv. Tsu-1. Ref.5
Experimental info
	Sequence conflict	204	1	G → S in AAK25931. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Long [UniParc]. Last modified March 1, 2002. Version 1. Checksum: B4C081D0BF907C26	FASTA	430	48,363
	10 20 30 40 50 60 MEHQGWSFEE NYSLSTNRRS IRPQDELVEL LWRDGQVVLQ SQTHREQTQT QKQDHHEEAL 70 80 90 100 110 120 RSSTFLEDQE TVSWIQYPPD EDPFEPDDFS SHFFSTMDPL QRPTSETVKP KSSPEPPQVM 130 140 150 160 170 180 VKPKACPDPP PQVMPPPKFR LTNSSSGIRE TEMEQYSVTT VGPSHCGSNP SQNDLDVSMS 190 200 210 220 230 240 HDRSKNIEEK LNPNASSSSG GSSGCSFGKD IKEMASGRCI TTDRKRKRIN HTDESVSLSD 250 260 270 280 290 300 AIGNKSNQRS GSNRRSRAAE VHNLSERRRR DRINERMKAL QELIPHCSKT DKASILDEAI 310 320 330 340 350 360 DYLKSLQLQL QVMWMGSGMA AAAASAPMMF PGVQPQQFIR QIQSPVQLPR FPVMDQSAIQ 370 380 390 400 410 420 NNPGLVCQNP VQNQIISDRF ARYIGGFPHM QAATQMQPME MLRFSSPAGQ QSQQPSSVPT 430 KTTDGSRLDH
	Isoform Short. Checksum: B722C3E8EB999D44	FASTA	279	31,647
	10 20 30 40 50 60 MEHQGWSFEE NYSLSTNRRS IRPQDELVEL LWRDGQVVLQ SQTHREQTQT QKQDHHEEAL 70 80 90 100 110 120 RSSTFLEDQE TVSWIQYPPD EDPFEPDDFS SHFFSTMDPL QRPTSETVKP KSSPEPPQVM 130 140 150 160 170 180 VKPKACPDPP PQVMPPPKFR LTNSSSGIRE TEMEQYSVTT VGPSHCGSNP SQNDLDVSMS 190 200 210 220 230 240 HDRSKNIEEK LNPNASSSSG GSSGCSFGKD IKEMASGRCI TTDRKRKRIN HTDESVSLSD 250 260 270 AIGNKSNQRS GSNRRSRAAE VHNLSERVLH RFVYIIYNI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis." Huq E., Quail P.H. EMBO J. 21:2441-2450(2002) [PubMed: 12006496] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG). Strain: cv. Wassilewskija.
[2]	"The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity." Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C. Mol. Biol. Evol. 20:735-747(2003) [PubMed: 12679534] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG), INDUCTION BY UV LIGHT, GENE FAMILY, NOMENCLATURE. Strain: cv. Columbia.
[3]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C. Nature 402:761-768(1999) [PubMed: 10617197] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM SHORT). Strain: cv. Columbia.
[5]	"Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana." Brock M.T., Tiffin P., Weinig C. Mol. Ecol. 16:3050-3062(2007) [PubMed: 17614917] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 56-306, VARIANT ASP-231. Strain: cv. An-2, cv. Bla-6, cv. Br-0, cv. Bu-2, cv. Columbia, 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.
[6]	"The Arabidopsis basic/helix-loop-helix transcription factor family." Toledo-Ortiz G., Huq E., Quail P.H. Plant Cell 15:1749-1770(2003) [PubMed: 12897250] [Abstract] Cited for: GENE FAMILY, INTERACTION WITH PIF3.
[7]	"A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana." Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S., Mizuno T. Plant Cell Physiol. 44:619-629(2003) [PubMed: 12826627] [Abstract] Cited for: INTERACTION WITH APRR1, INDUCTION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AJ440755 mRNA. Translation: CAD29449.1. AF251694 mRNA. Translation: AAL55716.1. AC006224 Genomic DNA. Translation: AAD22130.2. AY142625 mRNA. Translation: AAN13083.1. AF360221 mRNA. Translation: AAK25931.1. EF193514 Genomic DNA. Translation: ABP96467.1. EF193515 Genomic DNA. Translation: ABP96468.1. EF193516 Genomic DNA. Translation: ABP96469.1. EF193517 Genomic DNA. Translation: ABP96470.1. EF193518 Genomic DNA. Translation: ABP96471.1. EF193519 Genomic DNA. Translation: ABP96472.1. EF193520 Genomic DNA. Translation: ABP96473.1. EF193521 Genomic DNA. Translation: ABP96474.1. EF193522 Genomic DNA. Translation: ABP96475.1. EF193523 Genomic DNA. Translation: ABP96476.1. EF193524 Genomic DNA. Translation: ABP96477.1. EF193525 Genomic DNA. Translation: ABP96478.1. EF193526 Genomic DNA. Translation: ABP96479.1. EF193527 Genomic DNA. Translation: ABP96480.1.
IPI	IPI00520232. IPI00534557.
PIR	H84860.
RefSeq	NP_565991.2.
UniGene	At.19015
3D structure databases
HSSP	HSSP built from PDB template 1AN4 based on UniProtKB P22415.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8W2F3. 3 interactions.
Genome annotation databases
GeneID	818903.
GenomeReviews	Gene locus AT2G43010 in contig CT485783_GR.
KEGG	ath:AT2G43010.
NMPDR	fig|3702.1.peg.29059.
Organism-specific databases
TAIR	At2g43010.
Gene expression databases
ArrayExpress	Q8W2F3.
GermOnline	AT2G43010. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001092. HLH_basic. IPR011598. HLH_DNA_bd. [Graphical view]
Gene3D	G3DSA:4.10.280.10. HLH_DNA_bd. 1 hit.
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
PROSITE	PS50888. HLH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PIF4_ARATH

Accession

Primary (citable) accession number: Q8W2F3
Secondary accession number(s): A5Y7D4 , A5Y7D5, A5Y7D6, A5Y7D7, A5Y7D8, A5Y7D9, A5Y7E0, A5Y7E1, A5Y7E2, A5Y7E3, A5Y7E4, A5Y7E5, A5Y7E6, A5Y7E7, Q9C5I8, Q9SKX6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 2003
Last sequence update:	March 1, 2002
Last modified:	June 16, 2009
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)