PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G46640.1

Common Name

F12A12.160, LUX, PCL1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

G2-like

Protein Properties

Length: 323aa MW: 34648.9 Da PI: 5.6716

Description

G2-like family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G46640.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	G2-like	95.2	5e-30	144	197	1	55
G2-like 1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 +prl+Wtp+LH+rFv++v++L G+++A+Pkti++lm+v+gLt+e+v+SHLQkYRl AT3G46640.1 144 RPRLVWTPQLHKRFVDVVAHL-GIKNAVPKTIMQLMNVEGLTRENVASHLQKYRL 197 59*****************.******************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	10.252	139	200	IPR017930	Myb domain
SuperFamily	SSF46689	1.63E-19	141	201	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	3.5E-30	143	202	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	1.6E-23	145	197	IPR006447	Myb domain, plants
Pfam	PF00249	5.6E-8	147	196	IPR001005	SANT/Myb domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0042753	Biological Process	positive regulation of circadian rhythm
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000293	anatomy	guard cell

Sequence ? help Back to Top
Protein Sequence Length: 323 aa Download sequence Send to blast
MGEEVQMSDY DVSGDGDRVS EWEMGLPSDE DLASLSYSLI PPNLAMAFSI TPERSRTIQD 60 VNRASETTLS SLRGGSSGPN TSSSNNNVEE EDRVGSSSPG SDSKKQKTSN GDGDDGGGVD 120 PDSAMAAEEG DSGTEDLSGK TLKRPRLVWT PQLHKRFVDV VAHLGIKNAV PKTIMQLMNV 180 EGLTRENVAS HLQKYRLYLK RMQGLTNEGP SASDKLFSST PVPPQSFQDI GGGGGSSGNV 240 GVPIPGAYGT QQMMQMPVYA HHMGMQGYHH QNHNHDPYHQ NHRHHHGAGG NGAFESNPYM 300 MQQNKFGSMA SYPSVGGGSA NEN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5lxu_A	9e-36	144	200	1	57	Transcription factor LUX
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.47951	0.0	flower\| root\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	252475_s_at	0.0
Expression Atlas	AT3G46640	-
AtGenExpress	AT3G46640	-

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a myb family transcription factor with a single Myb DNA-binding domain (type SHAQKYF) that is unique to plants and is essential for circadian rhythms, specifically for transcriptional regulation within the circadian clock. LUX is required for normal rhythmic expression of multiple clock outputs in both constant light and darkness. It is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter.
UniProt	Transcription factor that is essential for the generation of the circadian clock oscillation. Is necessary for activation of CCA1 and LHY expression. Is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter. Directly regulates the expression of PRR9, a major component of the morning transcriptional feedback circuit, by binding specific sites on PRR9 promoter. Binds to its own promoter, inducing a negative auto-regulatory feedback loop within the core clock. Binds to ELF3 and associates with ELF4 in a diurnal complex which is required for the expression of the growth-promoting transcription factors PIF4 and PIF5 and subsequent hypocotyl growth in the early evening. {ECO:0000269\|PubMed:16006522, ECO:0000269\|PubMed:16164597, ECO:0000269\|PubMed:21236673, ECO:0000269\|PubMed:21753751, ECO:0000269\|PubMed:22311777}.

Function -- GeneRIF ? help Back to Top
LUX ARRHYTHMO (LUX) encodes a Myb domain protein essential for circadian rhythms. [LUX] [PMID: 16006522] The PCL1 gene is the clock oscillator gene essential to the generation of clock oscillation in the higher plant. [PCL1] [PMID: 16164597] The in vitro Dna-binding specificity of LUX, its role in the expression of PRR9, and its feedback properties are reported. [PMID: 21236673] identification of a protein complex composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth [PMID: 21753751] Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loops LHY and CCA1 expression by binding to their promoters. [PMID: 24267177] Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis. [PMID: 24954045] Data identified proteins that associate with the evening complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX). [PMID: 26545401] mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonas syringae challenge conditions as well as defense signaling mediated by salicylic and jasmonic acid, leading to compromised disease resistance. [PMID: 31186426]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00014	PBM	25378322	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G46640.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian oscillation with peaks at subjective dusk. {ECO:0000269\|PubMed:16006522, ECO:0000269\|PubMed:16164597, ECO:0000269\|PubMed:17132630, ECO:0000269\|PubMed:21753751}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G01060 (R), AT2G46830 (R), AT3G46640 (R), AT5G10140 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G01060(A), AT1G22770(R), AT2G40080(R), AT2G46830(A), AT3G46640(R), AT5G61380(R)

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Mutant plant flowering lacks a photoperiodic response. {ECO:0000269\|PubMed:16006522, ECO:0000269\|PubMed:16164597}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G46640

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB206576	0.0	AB206576.1 Arabidopsis thaliana PCL1 gene for PHYTOCLOCK 1, complete cds.
GenBank	AK227686	0.0	AK227686.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL14-26-J19.
GenBank	AL133314	0.0	AL133314.1 Arabidopsis thaliana DNA chromosome 3, BAC clone F12A12.
GenBank	BT006425	0.0	BT006425.1 Arabidopsis thaliana At3g46640 gene, complete cds.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001030823.1	0.0	Homeodomain-like superfamily protein
Refseq	NP_190248.1	0.0	Homeodomain-like superfamily protein
Swissprot	Q9SNB4	0.0	PCL1_ARATH; Transcription factor LUX
TrEMBL	F4J959	0.0	F4J959_ARATH; Homeodomain-like superfamily protein
STRING	AT3G46640.3	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT3G46640.1
Entrez Gene	823817
iHOP	AT3G46640
wikigenes	AT3G46640

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Hazen SP, et al. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc. Natl. Acad. Sci. U.S.A., 2005. 102(29): p. 10387-92 [PMID:16006522] Onai K,Ishiura M PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells, 2005. 10(10): p. 963-72 [PMID:16164597] Salom Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. Plant Cell, 2006. 18(1): p. 55-69 [PMID:16326927] Murakami M,Tago Y,Yamashino T,Mizuno T Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol., 2007. 48(1): p. 110-21 [PMID:17132630] Abe M,Fujiwara M,Kurotani K,Yokoi S,Shimamoto K Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP). Plant Cell Physiol., 2008. 49(3): p. 420-32 [PMID:18296724] Bieniawska Z, et al. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol., 2008. 147(1): p. 263-79 [PMID:18375597] Helfer A, et al. LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr. Biol., 2011. 21(2): p. 126-33 [PMID:21236673] Dai S, et al. BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock. Plant Cell, 2011. 23(3): p. 961-72 [PMID:21447790] Nusinow DA, et al. The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature, 2011. 475(7356): p. 398-402 [PMID:21753751] Chow BY,Helfer A,Nusinow DA,Kay SA ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock. Plant Signal Behav, 2012. 7(2): p. 170-3 [PMID:22307044] Sellaro R,Pac Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling. Mol Plant, 2012. 5(3): p. 619-28 [PMID:22311777] Herrero E, et al. EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. Plant Cell, 2012. 24(2): p. 428-43 [PMID:22327739] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Mizuno N,Nitta M,Sato K,Nasuda S A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat. Genes Genet. Syst., 2012. 87(6): p. 357-67 [PMID:23558642] Higham CF,Husmeier D A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana. BMC Bioinformatics, 2013. 14 Suppl 10: p. S3 [PMID:24267177] Chow BY, et al. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis. Curr. Biol., 2014. 24(13): p. 1518-24 [PMID:24954045] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Huang H, et al. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol. Cell Proteomics, 2016. 15(1): p. 201-17 [PMID:26545401] Huang H, et al. PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. Elife, 2016. 5: p. e13292 [PMID:26839287] Zhang C, et al. LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis. Nat Commun, 2019. 10(1): p. 2543 [PMID:31186426]