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Protein

Transcription factor PIF1

Gene

PIF1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).5 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei47 – 471Pfr PHYB binding
Sitei95 – 951Pfr PHYA binding
Sitei144 – 1441Pfr PHYA binding

GO - Molecular functioni

  • DNA binding Source: TAIR
  • identical protein binding Source: IntAct
  • phytochrome binding Source: TAIR
  • transcription factor activity, sequence-specific DNA binding Source: TAIR

GO - Biological processi

  • chlorophyll biosynthetic process Source: TAIR
  • gibberellic acid mediated signaling pathway Source: TAIR
  • heme biosynthetic process Source: TAIR
  • negative gravitropism Source: TAIR
  • negative regulation of photomorphogenesis Source: TAIR
  • negative regulation of seed germination Source: TAIR
  • red light signaling pathway Source: TAIR
  • regulation of photomorphogenesis Source: TAIR
  • regulation of seed germination Source: TAIR
  • regulation of transcription, DNA-templated Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor PIF1
Alternative name(s):
Basic helix-loop-helix protein 15
Short name:
AtbHLH15
Short name:
bHLH 15
Protein PHY-INTERACTING FACTOR 1
Protein PHYTOCHROME INTERACTING FACTOR 3-LIKE 5
Transcription factor EN 101
bHLH transcription factor bHLH015
Gene namesi
Name:PIF1
Synonyms:BHLH15, EN101, PIL5
Ordered Locus Names:At2g20180
ORF Names:T2G17.2
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G20180.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation2 Publications

GO - Cellular componenti

  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

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.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1 – 5050Missing : Normal interaction with PHYA (Pfr form). 1 PublicationAdd
BLAST
Mutagenesisi41 – 411E → A: Loss of interaction with PHYB (Pfr form). 1 Publication
Mutagenesisi42 – 421L → A: Loss of interaction with PHYB (Pfr form). 1 Publication
Mutagenesisi44 – 441W → A: Reduced interaction with PHYB (Pfr form). 1 Publication
Mutagenesisi47 – 471G → A: Loss of interaction with PHYB (Pfr form). 1 Publication
Mutagenesisi85 – 9511Missing : Reduced interaction with PHYA (Pfr form). 1 PublicationAdd
BLAST
Mutagenesisi95 – 951L → 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. 1 Publication
Mutagenesisi118 – 16043Missing : Reduced interaction with PHYA (Pfr form). 1 PublicationAdd
BLAST
Mutagenesisi123 – 1231S → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. 1 Publication
Mutagenesisi144 – 1441N → A: Loss of interaction with PHYA (Pfr form); when associated with A-95. 1 Publication
Mutagenesisi148 – 1481F → A: Normal interaction with PHYA (Pfr form). 1 Publication
Mutagenesisi153 – 1531G → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. 1 Publication
Mutagenesisi155 – 1551F → A: Normal interaction with PHYA (Pfr form). 1 Publication
Mutagenesisi160 – 1601G → A: Reduced interaction with PHYA (Pfr form); when associated with A-95. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 478478Transcription factor PIF1PRO_0000358829Add
BLAST

Post-translational modificationi

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.2 Publications

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiQ8GZM7.
PRIDEiQ8GZM7.

PTM databases

iPTMnetiQ8GZM7.

Expressioni

Tissue specificityi

Expressed constitutively in roots, leaves, stems, and flowers.1 Publication

Inductioni

Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner.1 Publication

Gene expression databases

GenevisibleiQ8GZM7. AT.

Interactioni

Subunit structurei

Homodimer (Probable). Interacts with the photoactivated conformer (Pfr) of phytochromes A and B, PHYA and PHYB. Interacts also with APRR1/TOC1. Binds to RGL2, RGA and FHY3 (via N-terminus).Curated5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-630400,EBI-630400
HFR1Q9FE223EBI-630400,EBI-626001
PHYBP147133EBI-630400,EBI-300727
PIF3O805366EBI-630400,EBI-625701

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • phytochrome binding Source: TAIR

Protein-protein interaction databases

BioGridi1892. 23 interactions.
IntActiQ8GZM7. 9 interactions.
STRINGi3702.AT2G20180.2.

Structurei

3D structure databases

ProteinModelPortaliQ8GZM7.
SMRiQ8GZM7. Positions 293-336.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini284 – 33350bHLHPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi339 – 38244Met-richAdd
BLAST

Sequence similaritiesi

Contains 1 bHLH (basic helix-loop-helix) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IWC4. Eukaryota.
ENOG41116VE. LUCA.
HOGENOMiHOG000240264.
InParanoidiQ8GZM7.
OMAiMMYPGMQ.
PhylomeDBiQ8GZM7.

Family and domain databases

Gene3Di4.10.280.10. 1 hit.
InterProiIPR011598. bHLH_dom.
[Graphical view]
PfamiPF00010. HLH. 1 hit.
[Graphical view]
SMARTiSM00353. HLH. 1 hit.
[Graphical view]
SUPFAMiSSF47459. SSF47459. 1 hit.
PROSITEiPS50888. BHLH. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8GZM7-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MHHFVPDFDT DDDYVNNHNS SLNHLPRKSI TTMGEDDDLM ELLWQNGQVV
60 70 80 90 100
VQNQRLHTKK PSSSPPKLLP SMDPQQQPSS DQNLFIQEDE MTSWLHYPLR
110 120 130 140 150
DDDFCSDLLF SAAPTATATA TVSQVTAARP PVSSTNESRP PVRNFMNFSR
160 170 180 190 200
LRGDFNNGRG GESGPLLSKA VVRESTQVSP SATPSAAASE SGLTRRTDGT
210 220 230 240 250
DSSAVAGGGA YNRKGKAVAM TAPAIEITGT SSSVVSKSEI EPEKTNVDDR
260 270 280 290 300
KRKEREATTT DETESRSEET KQARVSTTST KRSRAAEVHN LSERKRRDRI
310 320 330 340 350
NERMKALQEL IPRCNKSDKA SMLDEAIEYM KSLQLQIQMM SMGCGMMPMM
360 370 380 390 400
YPGMQQYMPH MAMGMGMNQP IPPPSFMPFP NMLAAQRPLP TQTHMAGSGP
410 420 430 440 450
QYPVHASDPS RVFVPNQQYD PTSGQPQYPA GYTDPYQQFR GLHPTQPPQF
460 470
QNQATSYPSS SRVSSSKESE DHGNHTTG
Length:478
Mass (Da):52,864
Last modified:March 1, 2003 - v1
Checksum:i93572A0D4669D350
GO
Isoform 2 (identifier: Q8GZM7-2) [UniParc]FASTAAdd to basket

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

Note: May be due to a competing acceptor splice site. No experimental confirmation available.
Show »
Length:407
Mass (Da):44,715
Checksum:i3A26031912741C41
GO

Sequence cautioni

The sequence AAD24380.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021D → G in BAF00716 (Ref. 5) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 7171Missing in isoform 2. 2 PublicationsVSP_036107Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF488560 mRNA. Translation: AAN78308.1.
AB103113 Transcribed RNA. Translation: BAC56979.1.
AC006081 Genomic DNA. Translation: AAD24380.1. Sequence problems.
CP002685 Genomic DNA. Translation: AEC06977.1.
CP002685 Genomic DNA. Translation: AEC06978.1.
CP002685 Genomic DNA. Translation: AEC06979.1.
AK228820 mRNA. Translation: BAF00716.1.
BT029775 mRNA. Translation: ABM06045.1.
PIRiA84586.
RefSeqiNP_001189559.1. NM_001202630.1. [Q8GZM7-1]
NP_179608.2. NM_127577.3. [Q8GZM7-1]
NP_849996.1. NM_179665.2. [Q8GZM7-2]
UniGeneiAt.43003.
At.69322.

Genome annotation databases

EnsemblPlantsiAT2G20180.2; AT2G20180.2; AT2G20180. [Q8GZM7-1]
AT2G20180.3; AT2G20180.3; AT2G20180. [Q8GZM7-1]
GeneIDi816538.
KEGGiath:AT2G20180.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF488560 mRNA. Translation: AAN78308.1.
AB103113 Transcribed RNA. Translation: BAC56979.1.
AC006081 Genomic DNA. Translation: AAD24380.1. Sequence problems.
CP002685 Genomic DNA. Translation: AEC06977.1.
CP002685 Genomic DNA. Translation: AEC06978.1.
CP002685 Genomic DNA. Translation: AEC06979.1.
AK228820 mRNA. Translation: BAF00716.1.
BT029775 mRNA. Translation: ABM06045.1.
PIRiA84586.
RefSeqiNP_001189559.1. NM_001202630.1. [Q8GZM7-1]
NP_179608.2. NM_127577.3. [Q8GZM7-1]
NP_849996.1. NM_179665.2. [Q8GZM7-2]
UniGeneiAt.43003.
At.69322.

3D structure databases

ProteinModelPortaliQ8GZM7.
SMRiQ8GZM7. Positions 293-336.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1892. 23 interactions.
IntActiQ8GZM7. 9 interactions.
STRINGi3702.AT2G20180.2.

PTM databases

iPTMnetiQ8GZM7.

Proteomic databases

PaxDbiQ8GZM7.
PRIDEiQ8GZM7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G20180.2; AT2G20180.2; AT2G20180. [Q8GZM7-1]
AT2G20180.3; AT2G20180.3; AT2G20180. [Q8GZM7-1]
GeneIDi816538.
KEGGiath:AT2G20180.

Organism-specific databases

TAIRiAT2G20180.

Phylogenomic databases

eggNOGiENOG410IWC4. Eukaryota.
ENOG41116VE. LUCA.
HOGENOMiHOG000240264.
InParanoidiQ8GZM7.
OMAiMMYPGMQ.
PhylomeDBiQ8GZM7.

Miscellaneous databases

PROiQ8GZM7.

Gene expression databases

GenevisibleiQ8GZM7. AT.

Family and domain databases

Gene3Di4.10.280.10. 1 hit.
InterProiIPR011598. bHLH_dom.
[Graphical view]
PfamiPF00010. HLH. 1 hit.
[Graphical view]
SMARTiSM00353. HLH. 1 hit.
[Graphical view]
SUPFAMiSSF47459. SSF47459. 1 hit.
PROSITEiPS50888. BHLH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [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 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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH APRR1/TOC1.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "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.
  6. "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.
  7. "The Arabidopsis basic/helix-loop-helix transcription factor family."
    Toledo-Ortiz G., Huq E., Quail P.H.
    Plant Cell 15:1749-1770(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.
  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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.
  13. "Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis."
    Gallego-Bartolome J., Minguet E.G., Marin J.A., Prat S., Blazquez M.A., Alabadi D.
    Mol. Biol. Evol. 27:1247-1256(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RGL2 AND RGA.
    Strain: cv. Landsberg erecta.
  14. "Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis."
    Tang W., Wang W., Chen D., Ji Q., Jing Y., Wang H., Lin R.
    Plant Cell 24:1984-2000(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH FHY3.

Entry informationi

Entry nameiPIF1_ARATH
AccessioniPrimary (citable) accession number: Q8GZM7
Secondary accession number(s): Q0WQ83, Q3EBY0, Q9SL63
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 16, 2008
Last sequence update: March 1, 2003
Last modified: April 13, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.