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

AT4G34530.1

Common Name

BHLH63, CIB1, EN84, T4L20.110

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

bHLH

Protein Properties

Length: 335aa MW: 37540.4 Da PI: 5.6803

Description

cryptochrome-interacting basic-helix-loop-helix 1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G34530.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	30.6	6.1e-10	182	229	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +h+++Er RR++i +++ L++l+P + +k Ka +L + ++Y++sLq AT4G34530.1 182 SHSIAERVRREKISERMKFLQDLVPGC----DKITGKAGMLDEIINYVQSLQ 229 8***********************9....899***************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	5.30E-11	176	233	No hit	No description
SuperFamily	SSF47459	1.2E-16	176	246	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.593	178	228	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.9E-16	178	239	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.5E-7	182	229	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.0E-8	184	234	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006351	Biological Process	transcription, DNA-templated
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009637	Biological Process	response to blue light
GO:0009911	Biological Process	positive regulation of flower development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0005020	anatomy	vascular bundle

Sequence ? help Back to Top
Protein Sequence Length: 335 aa Download sequence Send to blast
MNGAIGGDLL LNFPDMSVLE RQRAHLKYLN PTFDSPLAGF FADSSMITGG EMDSYLSTAG 60 LNLPMMYGET TVEGDSRLSI SPETTLGTGN FKKRKFDTET KDCNEKKKKM TMNRDDLVEE 120 GEEEKSKITE QNNGSTKSIK KMKHKAKKEE NNFSNDSSKV TKELEKTDYI HVRARRGQAT 180 DSHSIAERVR REKISERMKF LQDLVPGCDK ITGKAGMLDE IINYVQSLQR QIEFLSMKLA 240 IVNPRPDFDM DDIFAKEVAS TPMTVVPSPE MVLSGYSHEM VHSGYSSEMV NSGYLHVNPM 300 QQVNTSSDPL SCFNNGEAPS MWDSHVQNLY GNLGV

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	92	108	KRKFDTETKDCNEKKKK

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42567392	0.0
Expression Atlas	AT4G34530	-
AtGenExpress	AT4G34530	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed constitutively in roots, leaves, and stems. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a transcription factor CIB1 (cryptochrome-interacting basic-helix-loop-helix). CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast and Arabidopsis cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 positively regulates FT expression.
UniProt	Transcription factor that binds DNA to G box 5'-CACGTG-3' and, to a lower extent, to E-box 5'-CANNTG-3' in vitro. Binds to chromatin DNA of the FT gene and promotes its expression, and thus triggers flowering in response to blue light. {ECO:0000269\|PubMed:18988809, ECO:0000269\|PubMed:24130508}.

Function -- GeneRIF ? help Back to Top
identification & characterization of CIB1 (At4g34530) protein; CIB1 interacts with CRY2 in a blue light-specific manner & acts with additional CIB1-related proteins to promote CRY2-dependent floral initiation; CIB1 stimulates FT messenger RNA expression. [PMID: 18988809] Data indicate that although cryptochrome 2 physically interacts with CIB1 in response to blue light, ZEITLUPE and LOV KELCH PROTEIN 2 are required for the function and blue-light suppression of degradation of CIB1. [PMID: 24101505] It describes minimal functional CRY2 and CIB1 domains maintaining light-dependent interaction and new signaling mutations affecting Arabidopsis thaliana cryptochrome 2 (AtCRY2) photocycle kinetics. [PMID: 27065233] CRY2-CIB1 and CRY2-CRY2 interactions are governed by well-separated protein interfaces at the two termini of CRY2. [PMID: 28916751] We also determined that CRY2 was recruited to the FT chromatin by CIB1 and CO and that all three proteins are bound to the same region within the FT promoter. Therefore, there is crosstalk between the CRY2-CO and CRY2-CIBs pathways, and CIB1 and CO act together to regulate FT transcription and flowering. [PMID: 30126927]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G34530.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Accumulates strongly in response to blue light due to reduced preventing 26S proteasome-mediated degradation in an ADO1/ZTL and ADO2/LKP2 dependent manner, but levels decrease in the absence of blue light via 26S proteasome degradation (at protein level). {ECO:0000269\|PubMed:24101505}.

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G48560, AT1G26260
IntAct	Search Q8GY61

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G34530

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK117846	0.0	AK117846.1 Arabidopsis thaliana At4g34530 mRNA for putative bHLH transcription factor (bHLH063), complete cds, clone: RAFL18-04-K08.
GenBank	BT005313	0.0	BT005313.1 Arabidopsis thaliana At4g34530 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_195179.2	0.0	cryptochrome-interacting basic-helix-loop-helix 1
Swissprot	Q8GY61	0.0	BH063_ARATH; Transcription factor bHLH63
TrEMBL	A0A178V495	0.0	A0A178V495_ARATH; CIB1
STRING	AT4G34530.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5947	25	43
Representative plant	OGRP58	16	313

Link Out ? help Back to Top
Phytozome	AT4G34530.1
Entrez Gene	829604
iHOP	AT4G34530
wikigenes	AT4G34530

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] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Thimmapuram J,Duan H,Liu L,Schuler MA Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome. RNA, 2005. 11(2): p. 128-38 [PMID:15659355] Andersson-Gunner Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J., 2006. 45(2): p. 144-65 [PMID:16367961] Kong H, et al. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J., 2007. 50(5): p. 873-85 [PMID:17470057] Liu H, et al. Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science, 2008. 322(5907): p. 1535-9 [PMID:18988809] Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Kennedy MJ, et al. Rapid blue-light-mediated induction of protein interactions in living cells. Nat. Methods, 2010. 7(12): p. 973-5 [PMID:21037589] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Li X, et al. Arabidopsis cryptochrome 2 (CRY2) functions by the photoactivation mechanism distinct from the tryptophan (trp) triad-dependent photoreduction. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(51): p. 20844-9 [PMID:22139370] Weidler G, et al. Degradation of Arabidopsis CRY2 is regulated by SPA proteins and phytochrome A. Plant Cell, 2012. 24(6): p. 2610-23 [PMID:22739826] Idevall-Hagren O,Dickson EJ,Hille B,Toomre DK,De Camilli P Optogenetic control of phosphoinositide metabolism. Proc. Natl. Acad. Sci. U.S.A., 2012. 109(35): p. E2316-23 [PMID:22847441] Hughes RM,Bolger S,Tapadia H,Tucker CL Light-mediated control of DNA transcription in yeast. Methods, 2012. 58(4): p. 385-91 [PMID:22922268] Ikeda M,Fujiwara S,Mitsuda N,Ohme-Takagi M A triantagonistic basic helix-loop-helix system regulates cell elongation in Arabidopsis. Plant Cell, 2012. 24(11): p. 4483-97 [PMID:23161888] Konermann S, et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature, 2013. 500(7463): p. 472-6 [PMID:23877069] Liu H, et al. Arabidopsis CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(43): p. 17582-7 [PMID:24101505] Liu Y,Li X,Li K,Liu H,Lin C Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in Arabidopsis. PLoS Genet., 2013. 9(10): p. e1003861 [PMID:24130508] Idevall-Hagren O,Decamilli P Manipulation of plasma membrane phosphoinositides using photoinduced protein-protein interactions. Methods Mol. Biol., 2014. 1148: p. 109-28 [PMID:24718798] Cui Y,Choudhury SR,Irudayaraj J Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools. Anal. Biochem., 2014. 458: p. 58-60 [PMID:24780222] Yang D,Zhao W,Meng Y,Li H,Liu B A CIB1-LIKE transcription factor GmCIL10 from soybean positively regulates plant flowering. Sci China Life Sci, 2015. 58(3): p. 261-9 [PMID:25651969] Duan L, et al. Optogenetic control of molecular motors and organelle distributions in cells. Chem. Biol., 2015. 22(5): p. 671-82 [PMID:25963241] Katsura Y, et al. An optogenetic system for interrogating the temporal dynamics of Akt. Sci Rep, 2015. 5: p. 14589 [PMID:26423353] Taslimi A, et al. Optimized second-generation CRY2-CIB dimerizers and photoactivatable Cre recombinase. Nat. Chem. Biol., 2016. 12(6): p. 425-30 [PMID:27065233] Liu Q, et al. The Blue Light-Dependent Polyubiquitination and Degradation of Arabidopsis Cryptochrome2 Requires Multiple E3 Ubiquitin Ligases. Plant Cell Physiol., 2016. 57(10): p. 2175-2186 [PMID:27516416] Pathak GP, et al. Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2. Nucleic Acids Res., 2017. 45(20): p. e167 [PMID:28431041] Duan L, et al. Understanding CRY2 interactions for optical control of intracellular signaling. Nat Commun, 2017. 8(1): p. 547 [PMID:28916751] Quejada JR, et al. Optimized light-inducible transcription in mammalian cells using Flavin Kelch-repeat F-box1/GIGANTEA and CRY2/CIB1. Nucleic Acids Res., 2017. 45(20): p. e172 [PMID:29040770] Liu Y, et al. CIB1 and CO interact to mediate CRY2-dependent regulation of flowering. EMBO Rep., 2019. [PMID:30126927]