PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G34530.1
Common NameBHLH63, CIB1, EN84, T4L20.110
Organism
Taxonomic ID
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
AT4G34530.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH30.66.1e-10182229455
                  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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000835.30E-11176233No hitNo description
SuperFamilySSF474591.2E-16176246IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.593178228IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.103.9E-16178239IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.5E-7182229IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.0E-8184234IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006351Biological Processtranscription, DNA-templated
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009637Biological Processresponse to blue light
GO:0009911Biological Processpositive regulation of flower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0005020anatomyvascular 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
NLS
No. Start End Sequence
192108KRKFDTETKDCNEKKKK
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425673920.0
Expression AtlasAT4G34530-
AtGenExpressAT4G34530-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, and stems. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes 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.
UniProtTranscription 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
  1. 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]
  2. 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]
  3. 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]
  4. CRY2-CIB1 and CRY2-CRY2 interactions are governed by well-separated protein interfaces at the two termini of CRY2.
    [PMID: 28916751]
  5. 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
SourceLink
PlantRegMapAT4G34530.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G48560, AT1G26260
IntActSearch Q8GY61
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G34530
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1178460.0AK117846.1 Arabidopsis thaliana At4g34530 mRNA for putative bHLH transcription factor (bHLH063), complete cds, clone: RAFL18-04-K08.
GenBankBT0053130.0BT005313.1 Arabidopsis thaliana At4g34530 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_195179.20.0cryptochrome-interacting basic-helix-loop-helix 1
SwissprotQ8GY610.0BH063_ARATH; Transcription factor bHLH63
TrEMBLA0A178V4950.0A0A178V495_ARATH; CIB1
STRINGAT4G34530.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM59472543
Representative plantOGRP5816313
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  3. 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]
  4. 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]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. Konermann S, et al.
    Optical control of mammalian endogenous transcription and epigenetic states.
    Nature, 2013. 500(7463): p. 472-6
    [PMID:23877069]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. Duan L, et al.
    Optogenetic control of molecular motors and organelle distributions in cells.
    Chem. Biol., 2015. 22(5): p. 671-82
    [PMID:25963241]
  26. Katsura Y, et al.
    An optogenetic system for interrogating the temporal dynamics of Akt.
    Sci Rep, 2015. 5: p. 14589
    [PMID:26423353]
  27. 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]
  28. 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]
  29. 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]
  30. Duan L, et al.
    Understanding CRY2 interactions for optical control of intracellular signaling.
    Nat Commun, 2017. 8(1): p. 547
    [PMID:28916751]
  31. 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]
  32. Liu Y, et al.
    CIB1 and CO interact to mediate CRY2-dependent regulation of flowering.
    EMBO Rep., 2019.
    [PMID:30126927]