Reviewed, UniProtKB/Swiss-Prot Q8GZM7 (PIF1_ARATH)

Names and origin

Protein names

Recommended name:
    Transcription factor PIF1
Alternative name(s):
    Protein PHY-INTERACTING FACTOR 1
    Protein PHYTOCHROME INTERACTING FACTOR 3-LIKE 5
    Transcription factor EN 101
    bHLH transcription factor bHLH015
    Basic helix-loop-helix protein 15
      Short name=bHLH 15
      Short name=AtbHLH15

Gene names

Name:	PIF1
Synonyms:	BHLH15, EN101, PIL5
Ordered Locus Names:	At2g20180
ORF Names:	T2G17.2

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

General annotation (Comments)

Function	Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA). Ref.8 Ref.9 Ref.10 Ref.11 Ref.12
Subunit structure	Homodimer Probable. Interacts with the photoactivated conformer (Pfr) of phytochromes A and B, PHYA and PHYB. Interacts also with APRR1/TOC1.
Subcellular location	Nucleus. Ref.8 Ref.9
Tissue specificity	Expressed constitutively in roots, leaves, stems, and flowers. Ref.1
Induction	Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner. Ref.8
Post-translational modification	Phosphorylated and ubiquitinated after an exposure to light (especially red and far-red), in a phytochrome-dependent manner. Modified proteins undergo a proteasome-dependent degradation. Its stability and degradation plays a central role in photomorphogenesis of seedlings. Ref.12
Disruption phenotype	Plants overaccumulate free protochlorophyllide in the darkness and exhibit photooxidative damage (bleaching) in subsequent light, probably caused by the photosensitizing activity of this tetrapyrrole intermediate. Ref.8 Ref.11
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.
Sequence caution	The sequence AAD24380.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	DNA-binding
Molecular function	Activator
PTM	Ubl conjugation
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	chlorophyll biosynthetic process Ref.8 Inferred from mutant phenotype. Source: TAIR gibberellic acid mediated signaling Inferred from mutant phenotype. Source: TAIR heme biosynthetic process Ref.11 Inferred from mutant phenotype. Source: TAIR negative gravitropism Ref.9 Inferred from mutant phenotype. Source: TAIR negative regulation of photomorphogenesis Ref.12 Inferred from mutant phenotype. Source: TAIR negative regulation of seed germination Inferred from mutant phenotype. Source: TAIR red light signaling pathway Ref.12 Inferred from direct assay. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Ref.9 Inferred from direct assay. Source: TAIR
Molecular function	phytochrome binding Inferred from direct assay. Source: TAIR transcription factor activity Ref.9 Traceable author statement. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PHYA	P14712	1	EBI-630400,EBI-624446
PHYA3	P06593	1	EBI-630400,EBI-630413	From a different organism.
PHYB	P14713	2	EBI-630400,EBI-300727

Alternative products

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

Isoform 1 (identifier: Q8GZM7-1)

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 2 (identifier: Q8GZM7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-71: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 478	478	Transcription factor PIF1		PRO_0000358829
Regions
	Domain	298 – 338	41	Helix-loop-helix motif
	DNA binding	281 – 297	17	Basic motif By similarity
	Compositional bias	339 – 382	44	Met-rich
Sites
	Site	47	1	Pfr PHYB binding
	Site	95	1	Pfr PHYA binding
	Site	144	1	Pfr PHYA binding
Natural variations
	Alternative sequence	1 – 71	71	Missing in isoform 2.		VSP_036107
Experimental info
	Mutagenesis	1 – 50	50	Missing: Normal interaction with PHYA (Pfr form).
	Mutagenesis	41	1	E → A: Loss of interaction with PHYB (Pfr form). Ref.12
	Mutagenesis	42	1	L → A: Loss of interaction with PHYB (Pfr form). Ref.12
	Mutagenesis	44	1	W → A: Reduced interaction with PHYB (Pfr form). Ref.12
	Mutagenesis	47	1	G → A: Loss of interaction with PHYB (Pfr form). Ref.12
	Mutagenesis	85 – 95	11	Missing: Reduced interaction with PHYA (Pfr form). Ref.12
	Mutagenesis	95	1	L → A: Reduced interaction with PHYA (Pfr form). Reduced interaction with PHYA (Pfr form); when associated with A-123, A-153, or A-160. Loss of interaction with PHYA (Pfr form); when associated with A-144. Ref.12
	Mutagenesis	118 – 160	43	Missing: Reduced interaction with PHYA (Pfr form). Ref.12
	Mutagenesis	123	1	S → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. Ref.12
	Mutagenesis	144	1	N → A: Loss of interaction with PHYA (Pfr form); when associated with A-95. Ref.12
	Mutagenesis	148	1	F → A: Normal interaction with PHYA (Pfr form). Ref.12
	Mutagenesis	153	1	G → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. Ref.12
	Mutagenesis	155	1	F → A: Normal interaction with PHYA (Pfr form). Ref.12
	Mutagenesis	160	1	G → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. Ref.12
	Sequence conflict	102	1	D → G in BAF00716. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: 93572A0D4669D350	FASTA	478	52,864
	10 20 30 40 50 60 MHHFVPDFDT DDDYVNNHNS SLNHLPRKSI TTMGEDDDLM ELLWQNGQVV VQNQRLHTKK 70 80 90 100 110 120 PSSSPPKLLP SMDPQQQPSS DQNLFIQEDE MTSWLHYPLR DDDFCSDLLF SAAPTATATA 130 140 150 160 170 180 TVSQVTAARP PVSSTNESRP PVRNFMNFSR LRGDFNNGRG GESGPLLSKA VVRESTQVSP 190 200 210 220 230 240 SATPSAAASE SGLTRRTDGT DSSAVAGGGA YNRKGKAVAM TAPAIEITGT SSSVVSKSEI 250 260 270 280 290 300 EPEKTNVDDR KRKEREATTT DETESRSEET KQARVSTTST KRSRAAEVHN LSERKRRDRI 310 320 330 340 350 360 NERMKALQEL IPRCNKSDKA SMLDEAIEYM KSLQLQIQMM SMGCGMMPMM YPGMQQYMPH 370 380 390 400 410 420 MAMGMGMNQP IPPPSFMPFP NMLAAQRPLP TQTHMAGSGP QYPVHASDPS RVFVPNQQYD 430 440 450 460 470 PTSGQPQYPA GYTDPYQQFR GLHPTQPPQF QNQATSYPSS SRVSSSKESE DHGNHTTG
	Isoform 2. Checksum: 3A26031912741C41	FASTA	407	44,715
	10 20 30 40 50 60 MDPQQQPSSD QNLFIQEDEM TSWLHYPLRD DDFCSDLLFS AAPTATATAT VSQVTAARPP 70 80 90 100 110 120 VSSTNESRPP VRNFMNFSRL RGDFNNGRGG ESGPLLSKAV VRESTQVSPS ATPSAAASES 130 140 150 160 170 180 GLTRRTDGTD SSAVAGGGAY NRKGKAVAMT APAIEITGTS SSVVSKSEIE PEKTNVDDRK 190 200 210 220 230 240 RKEREATTTD ETESRSEETK QARVSTTSTK RSRAAEVHNL SERKRRDRIN ERMKALQELI 250 260 270 280 290 300 PRCNKSDKAS MLDEAIEYMK SLQLQIQMMS MGCGMMPMMY PGMQQYMPHM AMGMGMNQPI 310 320 330 340 350 360 PPPSFMPFPN MLAAQRPLPT QTHMAGSGPQ YPVHASDPSR VFVPNQQYDP TSGQPQYPAG 370 380 390 400 YTDPYQQFRG LHPTQPPQFQ NQATSYPSSS RVSSSKESED HGNHTTG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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 1), TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE. Strain: cv. Columbia. Tissue: Leaf.
[2]	"A link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet of Arabidopsis thaliana." Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S., Mizuno T. Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[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]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[5]	"Arabidopsis ORF clones." Bautista V.R., Kim C.J., Chen H., Wu S.Y., De Los Reyes C., Ecker J.R. Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[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.
[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/TOC1.
[8]	"Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis." Huq E., Al-Sady B., Hudson M., Kim C., Apel K., Quail P.H. Science 305:1937-1941(2004) [PubMed: 15448264] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INDUCTION BY RED AND FAR-RED LIGHTS, INTERACTION WITH PHYA AND PHYB.
[9]	"PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis." Shen H., Moon J., Huq E. Plant J. 44:1023-1035(2005) [PubMed: 16359394] [Abstract] Cited for: FUNCTION, UBIQUITINATION, SUBCELLULAR LOCATION.
[10]	"SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5." Kim D.H., Yamaguchi S., Lim S., Oh E., Park J., Hanada A., Kamiya Y., Choi G. Plant Cell 20:1260-1277(2008) [PubMed: 18487351] [Abstract] Cited for: FUNCTION.
[11]	"PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis." Moon J., Zhu L., Shen H., Huq E. Proc. Natl. Acad. Sci. U.S.A. 105:9433-9438(2008) [PubMed: 18591656] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[12]	"Light-induced phosphorylation and degradation of the negative regulator PHYTOCHROME-INTERACTING FACTOR1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes." Shen H., Zhu L., Castillon A., Majee M., Downie B., Huq E. Plant Cell 20:1586-1602(2008) [PubMed: 18539749] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF 1-MET--VAL-50; GLU-41; LEU-42; TRP-44; GLY-47; 85-PHE--LEU-95; LEU-95; 118-ALA--GLY-160; SER-123; ASN-144; PHE-148; GLY-153; PHE-155 AND GLY-160, INTERACTION WITH PHYA AND PHYB, PHOSPHORYLATION, UBIQUITINATION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF488560 mRNA. Translation: AAN78308.1. AB103113 Transcribed RNA. Translation: BAC56979.1. AC006081 Genomic DNA. Translation: AAD24380.1. Sequence problems. AK228820 mRNA. Translation: BAF00716.1. BT029775 mRNA. Translation: ABM06045.1.
IPI	IPI00527244. IPI00537020.
PIR	A84586.
RefSeq	NP_179608.2.
UniGene	At.43003
3D structure databases
HSSP	HSSP built from PDB template 1HLO based on UniProtKB P61244.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8GZM7. 3 interactions.
Genome annotation databases
GeneID	816538.
GenomeReviews	Gene locus AT2G20180 in contig CT485783_GR.
KEGG	ath:AT2G20180.
Organism-specific databases
TAIR	At2g20180.
Phylogenomic databases
OMA	Q8GZM7. QELIPRC.
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

PIF1_ARATH

Accession

Primary (citable) accession number: Q8GZM7
Secondary accession number(s): Q0WQ83, Q3EBY0, Q9SL63

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 16, 2008
Last sequence update:	March 1, 2003
Last modified:	June 16, 2009
This is version 39 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)