Reviewed, UniProtKB/Swiss-Prot Q8L5W8 (PIL1_ARATH)

Names and origin

Protein names

Recommended name:
    Transcription factor PIL1
Alternative name(s):
    Protein PHYTOCHROME INTERACTING FACTOR 3-LIKE 1
    Transcription factor EN 110
    bHLH transcription factor bHLH124
    Basic helix-loop-helix protein 124
      Short name=bHLH 124
      Short name=AtbHLH124

Gene names

Name:	PIL1
Synonyms:	BHLH124, EN110
Ordered Locus Names:	At2g46970
ORF Names:	F14M4.20

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

General annotation (Comments)

Function	Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. Ref.6 Ref.9 Ref.10
Subunit structure	Homodimer Probable. Interacts with APRR1/TOC1.
Subcellular location	Nucleus. Ref.9
Tissue specificity	Etiolated seedlings. Ref.8
Induction	Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. Ref.6 Ref.9 Ref.10
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.
Sequence caution	The sequence AAC34226.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Coiled coil
Ligand	DNA-binding
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	red or far red light signaling pathway Ref.9 Inferred from mutant phenotype. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW shade avoidance Ref.10 Inferred from expression pattern. Source: TAIR transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding 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
APRR1	Q9LKL2	3	EBI-630752,EBI-618423

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 416	416	Transcription factor PIL1		PRO_0000358853
Regions
	Domain	243 – 283	41	Helix-loop-helix motif
	DNA binding	219 – 242	24	Basic motif By similarity
	Coiled coil	95 – 124	30	Potential
Experimental info
	Sequence conflict	302	1	H → K in AAO37214. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q8L5W8-1 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 69B86687CC1901CF	FASTA	416	46,580
	10 20 30 40 50 60 MEAKPLASSS SEPNMISPSS NIKPKLKDED YMELVCENGQ ILAKIRRPKN NGSFQKQRRQ 70 80 90 100 110 120 SLLDLYETEY SEGFKKNIKI LGDTQVVPVS QSKPQQDKET NEQMNNNKKK LKSSKIEFER 130 140 150 160 170 180 NVSKSNKCVE SSTLIDVSAK GPKNVEVTTA PPDEQSAAVG RSTELYFASS SKFSRGTSRD 190 200 210 220 230 240 LSCCSLKRKY GDIEEEESTY LSNNSDDESD DAKTQVHART RKPVTKRKRS TEVHKLYERK 250 260 270 280 290 300 RRDEFNKKMR ALQDLLPNCY KDDKASLLDE AIKYMRTLQL QVQMMSMGNG LIRPPTMLPM 310 320 330 340 350 360 GHYSPMGLGM HMGAAATPTS IPQFLPMNVQ ATGFPGMNNA PPQMLSFLNH PSGLIPNTPI 370 380 390 400 410 FSPLENCSQP FVVPSCVSQT QATSFTQFPK SASASNLEDA MQYRGSNGFS YYRSPN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants." Makino S., Matsushika A., Kojima M., Yamashino T., Mizuno T. Plant Cell Physiol. 43:58-69(2002) [PubMed: 11828023] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH APRR1/TOC1.
[2]	"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.
[3]	"Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis." Xiao Y.-L., Malik M., Whitelaw C.A., Town C.D. Plant Physiol. 130:2118-2128(2002) [PubMed: 12481096] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	Underwood B.A., Xiao Y., Moskal W., Monaghan E., Wang W., Redman J., Wu H.C., Utterback T., Town C.D. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"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: GENE FAMILY, NOMENCLATURE.
[6]	"Gating of the rapid shade-avoidance response by the circadian clock in plants." Salter M.G., Franklin K.A., Whitelam G.C. Nature 426:680-683(2003) [PubMed: 14668869] [Abstract] Cited for: FUNCTION, INDUCTION.
[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: 12897250] [Abstract] Cited for: GENE FAMILY.
[8]	"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, TISSUE SPECIFICITY.
[9]	"Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation." Khanna R., Shen Y., Toledo-Ortiz G., Kikis E.A., Johannesson H., Hwang Y.-S., Quail P.H. Plant Cell 18:2157-2171(2006) [PubMed: 16891401] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION.
[10]	"Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis." Roig-Villanova I., Bou J., Sorin C., Devlin P.F., Martinez-Garcia J.F. Plant Physiol. 141:85-96(2006) [PubMed: 16565297] [Abstract] Cited for: FUNCTION, INDUCTION BY FAR-RED LIGHT.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AB090873 Transcribed RNA. Translation: BAC10689.1. AC004411 Genomic DNA. Translation: AAC34226.1. Sequence problems. AY219127 mRNA. Translation: AAO37214.1. AY954840 mRNA. Translation: AAX55166.1.
IPI	IPI00545843.
PIR	T02190.
RefSeq	NP_182220.2.
UniGene	At.36425
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8L5W8. 1 interaction.
Genome annotation databases
GeneID	819311.
GenomeReviews	Gene locus AT2G46970 in contig CT485783_GR.
KEGG	ath:AT2G46970.
NMPDR	fig|3702.1.peg.11885.
Organism-specific databases
TAIR	At2g46970.
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

PIL1_ARATH

Accession

Primary (citable) accession number: Q8L5W8
Secondary accession number(s): O80727, Q84WY4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 16, 2008
Last sequence update:	October 1, 2002
Last modified:	June 16, 2009
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)