PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G39860.1
Common NameBHLH136, BNQ1, MYH19.1, PRE1
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: 92aa    MW: 10514.9 Da    PI: 9.3615
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G39860.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH21.93.1e-0722591854
                 HHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS
          HLH 18 safeeLrellPk.askapskKlsKaeiLekAveYIksL 54
                 +  ++Lr++lP+   + +s K s + +L+++++YI++L
  AT5G39860.1 22 DLVSKLRQILPEiGQRRRSDKASASKVLQETCNYIRNL 59
                 55689*******999*********************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS508889.826459IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.104.7E-72175IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.36E-72279IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.8E-42259IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009640Biological Processphotomorphogenesis
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0009741Biological Processresponse to brassinosteroid
GO:0009742Biological Processbrassinosteroid mediated signaling pathway
GO:0009826Biological Processunidimensional cell growth
GO:0040008Biological Processregulation of growth
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
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:0000005anatomycultured plant cell
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0009066anatomyanther
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 92 aa     Download sequence    Send to blast
MSNRRSRQSS SAPRISDNQM IDLVSKLRQI LPEIGQRRRS DKASASKVLQ ETCNYIRNLN  60
REVDNLSERL SQLLESVDED SPEAAVIRSL LM
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible249383_at1e-143
Expression AtlasAT5G39860-
AtGenExpressAT5G39860-
ATTED-IIAT5G39860-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers. {ECO:0000269|PubMed:16527868}.
Functional Description ? help Back to Top
Source Description
TAIREncodes PRE1 (PACLOBUTRAZOL RESISTANCE1). PRE1 and IBH1 form a pair of antagonistic HLH/bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation. BNQ1 is directly and negatively regulated by AP3 and PI in petals.Required for appropriate regulation of flowering time.
UniProtAtypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development. Binds IBH1, forming a pair of antagonistic bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation. Regulates light responses by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance. May have a regulatory role in various aspects of gibberellin-dependent growth and development. {ECO:0000269|PubMed:16527868, ECO:0000269|PubMed:20009022, ECO:0000269|PubMed:20305124, ECO:0000269|PubMed:23161888, ECO:0000269|PubMed:23221598}.
Function -- GeneRIF ? help Back to Top
  1. PRE genes may have a regulatory role in gibberellin-dependent development in Arabidopsis thaliana
    [PMID: 16527868]
  2. PRE1-At IBH1 is a conserved pair of antagonistic HLH/bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation.
    [PMID: 20009022]
  3. PAR1-PRE1 and PAR1-PIF4 heterodimers form a complex HLH/bHLH network regulating cell elongation and plant development in response to light and hormones.
    [PMID: 22331621]
  4. The expression of IBH1 and PRE1 is regulated by brassinosteroid, gibberellins, and developmental phase dependent factors, indicating that two phytohormones and phase-dependent signals are integrated by this triantagonistic bHLH system.
    [PMID: 23161888]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G39860.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By gibberellin and epibrassinolide. {ECO:0000269|PubMed:16527868, ECO:0000269|PubMed:20009022}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G75080 (A)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G39860
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0882461e-155AY088246.1 Arabidopsis thaliana clone 4734 mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_198802.12e-58bHLH transcription factor PRE1
SwissprotQ9FLE93e-60PRE1_ARATH; Transcription factor PRE1
TrEMBLA0A087GTI32e-54A0A087GTI3_ARAAL; Uncharacterized protein
STRINGAT5G39860.17e-58(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM25928225
Representative plantOGRP18771240
Publications ? help Back to Top
  1. 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]
  2. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  3. 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]
  4. Hannah MA,Heyer AG,Hincha DK
    A global survey of gene regulation during cold acclimation in Arabidopsis thaliana.
    PLoS Genet., 2005. 1(2): p. e26
    [PMID:16121258]
  5. Lee S, et al.
    Overexpression of PRE1 and its homologous genes activates Gibberellin-dependent responses in Arabidopsis thaliana.
    Plant Cell Physiol., 2006. 47(5): p. 591-600
    [PMID:16527868]
  6. Hyun Y,Lee I
    KIDARI, encoding a non-DNA Binding bHLH protein, represses light signal transduction in Arabidopsis thaliana.
    Plant Mol. Biol., 2006. 61(1-2): p. 283-96
    [PMID:16786307]
  7. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
    [PMID:16920880]
  8. Kleine T,Kindgren P,Benedict C,Hendrickson L,Strand A
    Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance.
    Plant Physiol., 2007. 144(3): p. 1391-406
    [PMID:17478635]
  9. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  10. Zhang LY, et al.
    Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis.
    Plant Cell, 2009. 21(12): p. 3767-80
    [PMID:20009022]
  11. Wang H, et al.
    Regulation of Arabidopsis brassinosteroid signaling by atypical basic helix-loop-helix proteins.
    Plant Cell, 2009. 21(12): p. 3781-91
    [PMID:20023194]
  12. Mara CD,Huang T,Irish VF
    The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling.
    Plant Cell, 2010. 22(3): p. 690-702
    [PMID:20305124]
  13. Hao Y,Oh E,Choi G,Liang Z,Wang ZY
    Interactions between HLH and bHLH factors modulate light-regulated plant development.
    Mol Plant, 2012. 5(3): p. 688-97
    [PMID:22331621]
  14. Castelain M,Le Hir R,Bellini C
    The non-DNA-binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis.
    Physiol Plant, 2012. 145(3): p. 450-60
    [PMID:22339648]
  15. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
    [PMID:22995285]
  16. 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]
  17. Bai MY,Fan M,Oh E,Wang ZY
    A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4917-29
    [PMID:23221598]
  18. Ikeda M,Mitsuda N,Ohme-Takagi M
    ATBS1 INTERACTING FACTORs negatively regulate Arabidopsis cell elongation in the triantagonistic bHLH system.
    Plant Signal Behav, 2013. 8(3): p. e23448
    [PMID:23333962]
  19. 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]