PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G02340.1
Common NameBHLH26, EN68, FBI1, HFR1, REP1, RSF1, T6A9_13, T6A9.4
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: 292aa    MW: 33615 Da    PI: 7.5839
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G02340.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH30.75.5e-101441841055
                  HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH  10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  rrR +++ +++ +L++l+P++      K +K+++L k++eY+k+Lq
  AT1G02340.1 144 RRRDEKMSNKMRKLQQLVPNC-----HKTDKVSVLDKTIEYMKNLQ 184
                  666679**************9.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088813.802134183IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.69E-10135188No hitNo description
SMARTSM003535.3E-9139189IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000104.3E-7144184IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.105.8E-13144191IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474598.11E-14144194IPR011598Myc-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:0009585Biological Processred, far-red light phototransduction
GO:0009642Biological Processresponse to light intensity
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0009785Biological Processblue light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003712Molecular Functiontranscription cofactor activity
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000293anatomyguard cell
PO:0009001anatomyfruit
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
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:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 292 aa     Download sequence    Send to blast
MSNNQAFMEL GWRNDVGSLA VKDQGMMSER ARSDEDRLIN GLKWGYGYFD HDQTDNYLQI  60
VPEIHKEVEN AKEDLLVVVP DEHSETDDHH HIKDFSERSD HRFYLRNKHE NPKKRRIQVL  120
SSDDESEEFT REVPSVTRKG SKRRRRDEKM SNKMRKLQQL VPNCHKTDKV SVLDKTIEYM  180
KNLQLQLQMM STVGVNPYFL PATLGFGMHN HMLTAMASAH GLNPANHMMP SPLIPALNWP  240
LPPFTNISFP HSSSQSLFLT TSSPASSPQS LHGLVPYFPS FLDFSSHAMR RL
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.247950.0leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO131836430.0
Genevisible259417_at0.0
Expression AtlasAT1G02340-
AtGenExpressAT1G02340-
ATTED-IIAT1G02340-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1.
UniProtAtypical bHLH transcription factor that regulates photomorphogenesis through modulation of phytochrome (e.g. PHYA) and cryptochrome signalings (Ref.4, PubMed:11090209, PubMed:10995393, PubMed:19482971). Suppresses the transcriptional regulation activity of PIF4 by forming non-DNA-binding heterodimer. {ECO:0000269|PubMed:10995393, ECO:0000269|PubMed:11090209, ECO:0000269|PubMed:19482971, ECO:0000269|Ref.4}.
Function -- GeneRIF ? help Back to Top
  1. in addition to their independent functions in phyA signaling, LAF1 and HFR1 also cooperate post-translationally to stabilize each other through inhibition of ubiquitination by COP1, thereby enhancing phyA photoresponses
    [PMID: 17699755]
  2. CKII-mediated phosphorylation represents an important post-translational modification influencing the stability and signaling activity of Arabidopsis HFR1
    [PMID: 18556661]
  3. HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling.
    [PMID: 18974779]
  4. OWL1 interacts with the basic helix-loop-helix HFR1 (LONG HYPOCOTYL IN FAR-RED) transcription factor. Both proteins are involved in the agravitropic response under far-red light.
    [PMID: 19808946]
  5. The HLH and the adjacent C-terminal domain are required for biological activity of HFR1.
    [PMID: 21205034]
  6. HY5 transmits phyA signals through an FHY1/FHL-independent pathway but it may also modulate FHY1/FHL signal through its interaction with HFR1 and LAF1.
    [PMID: 23503597]
  7. HFR1 prevents PIF1 from binding to its target genes and antagonistically regulates PIF1-mediated gene expression. HFR1 and PIF1 are the major transcription regulators responsible for light-directed Transcriptome changes in seed germination.
    [PMID: 24179122]
  8. light inactivates DET1, elevating HFR1 to sequester PIF1's suppression on seed germination
    [PMID: 25775589]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G02340.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Twofold induction by far-red light and 14-fold suppression by red light.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G26945 (R), AT2G46970 (A), AT4G16780 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G29910(A), AT4G16780(R), AT5G13930(R)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT1G02340HFR1 interacts with another molecule of HFR1.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G02340, AT1G26945
IntActSearch Q9FE22
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Partially blind to far-red (FR). Impaired inhibition of hypocotyl elongation and cotyledons expansion under continuous FR light conditions. {ECO:0000269|PubMed:19482971}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G02340
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3242450.0AF324245.1 Arabidopsis thaliana bHLH-like protein HFR1 mRNA, complete cds.
GenBankAF3231820.0AF323182.1 Arabidopsis thaliana basic helix-loop-helix FBI1 protein (FBI1) mRNA, complete cds.
GenBankAF2882870.0AF288287.1 Aarabidopsis thaliana reduced phytochrome signaling 1 (REP1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_563650.10.0transcription factor HFR1
SwissprotQ9FE220.0HFR1_ARATH; Transcription factor HFR1
TrEMBLR0GQW81e-156R0GQW8_9BRAS; Uncharacterized protein (Fragment)
STRINGAT1G02340.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM140151624
Representative plantOGRP25816128
Publications ? help Back to Top
  1. Fankhauser C,Chory J
    RSF1, an Arabidopsis locus implicated in phytochrome A signaling.
    Plant Physiol., 2000. 124(1): p. 39-45
    [PMID:10982420]
  2. Fairchild CD,Schumaker MA,Quail PH
    HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction.
    Genes Dev., 2000. 14(18): p. 2377-91
    [PMID:10995393]
  3. Soh MS,Kim YM,Han SJ,Song PS
    REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in arabidopsis.
    Plant Cell, 2000. 12(11): p. 2061-74
    [PMID:11090209]
  4. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  5. Spiegelman JI, et al.
    Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography.
    Plant Cell, 2000. 12(12): p. 2485-2498
    [PMID:11148292]
  6. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  7. Kim YM,Woo JC,Song PS,Soh MS
    HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana.
    Plant J., 2002. 30(6): p. 711-9
    [PMID:12061902]
  8. Wang H, et al.
    Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.
    Plant J., 2002. 32(5): p. 723-33
    [PMID:12472688]
  9. 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]
  10. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
    [PMID:12826627]
  11. 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]
  12. Yang KY,Kim YM,Lee S,Song PS,Soh MS
    Overexpression of a mutant basic helix-loop-helix protein HFR1, HFR1-deltaN105, activates a branch pathway of light signaling in Arabidopsis.
    Plant Physiol., 2003. 133(4): p. 1630-42
    [PMID:14645731]
  13. Duek PD,Elmer MV,van Oosten VR,Fankhauser C
    The degradation of HFR1, a putative bHLH class transcription factor involved in light signaling, is regulated by phosphorylation and requires COP1.
    Curr. Biol., 2004. 14(24): p. 2296-301
    [PMID:15620659]
  14. Yang J, et al.
    Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis.
    Plant Cell, 2005. 17(3): p. 804-21
    [PMID:15705947]
  15. Jang IC,Yang JY,Seo HS,Chua NH
    HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling.
    Genes Dev., 2005. 19(5): p. 593-602
    [PMID:15741320]
  16. Yang J, et al.
    Repression of light signaling by Arabidopsis SPA1 involves post-translational regulation of HFR1 protein accumulation.
    Plant J., 2005. 43(1): p. 131-41
    [PMID:15960622]
  17. Sessa G, et al.
    A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis.
    Genes Dev., 2005. 19(23): p. 2811-5
    [PMID:16322556]
  18. Kang X,Ni M
    Arabidopsis SHORT HYPOCOTYL UNDER BLUE1 contains SPX and EXS domains and acts in cryptochrome signaling.
    Plant Cell, 2006. 18(4): p. 921-34
    [PMID:16500988]
  19. 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]
  20. Yang J,Wang H
    The central coiled-coil domain and carboxyl-terminal WD-repeat domain of Arabidopsis SPA1 are responsible for mediating repression of light signaling.
    Plant J., 2006. 47(4): p. 564-76
    [PMID:16813572]
  21. Jang IC,Yang SW,Yang JY,Chua NH
    Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling.
    Genes Dev., 2007. 21(16): p. 2100-11
    [PMID:17699755]
  22. Park HJ,Ding L,Dai M,Lin R,Wang H
    Multisite phosphorylation of Arabidopsis HFR1 by casein kinase II and a plausible role in regulating its degradation rate.
    J. Biol. Chem., 2008. 283(34): p. 23264-73
    [PMID:18556661]
  23. Zhang XN, et al.
    HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.
    PLoS ONE, 2008. 3(10): p. e3563
    [PMID:18974779]
  24. Yang SW,Jang IC,Henriques R,Chua NH
    FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation.
    Plant Cell, 2009. 21(5): p. 1341-59
    [PMID:19482971]
  25. Lorrain S,Trevisan M,Pradervand S,Fankhauser C
    Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.
    Plant J., 2009. 60(3): p. 449-61
    [PMID:19619162]
  26. Gong W, et al.
    The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.
    Mol Plant, 2008. 1(1): p. 27-41
    [PMID:19802365]
  27. Kneissl J,Wachtler V,Chua NH,Bolle C
    OWL1: an Arabidopsis J-domain protein involved in perception of very low light fluences.
    Plant Cell, 2009. 21(10): p. 3212-25
    [PMID:19808946]
  28. Hornitschek P,Lorrain S,Zoete V,Michielin O,Fankhauser C
    Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers.
    EMBO J., 2009. 28(24): p. 3893-902
    [PMID:19851283]
  29. 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]
  30. 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]
  31. Pokhilko A, et al.
    Ubiquitin ligase switch in plant photomorphogenesis: A hypothesis.
    J. Theor. Biol., 2011. 270(1): p. 31-41
    [PMID:21093457]
  32. Galstyan A,Cifuentes-Esquivel N,Bou-Torrent J,Martinez-Garcia JF
    The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors.
    Plant J., 2011. 66(2): p. 258-67
    [PMID:21205034]
  33. Foreman J, et al.
    Light receptor action is critical for maintaining plant biomass at warm ambient temperatures.
    Plant J., 2011. 65(3): p. 441-52
    [PMID:21265897]
  34. Zhao R, et al.
    The Arabidopsis Ca(2+) -dependent protein kinase CPK12 negatively regulates abscisic acid signaling in seed germination and post-germination growth.
    New Phytol., 2011. 192(1): p. 61-73
    [PMID:21692804]
  35. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
    [PMID:21928113]
  36. Jang IC,Niu QW,Deng S,Zhao P,Chua NH
    Enhancing protein stability with retained biological function in transgenic plants.
    Plant J., 2012. 72(2): p. 345-54
    [PMID:22631228]
  37. Li W,Dai L,Wang GL
    PUB13, a U-box/ARM E3 ligase, regulates plant defense, cell death, and flowering time.
    Plant Signal Behav, 2012. 7(8): p. 898-900
    [PMID:22827949]
  38. Rolauffs S,Fackendahl P,Sahm J,Fiene G,Hoecker U
    Arabidopsis COP1 and SPA genes are essential for plant elongation but not for acceleration of flowering time in response to a low red light to far-red light ratio.
    Plant Physiol., 2012. 160(4): p. 2015-27
    [PMID:23093358]
  39. Hong SY, et al.
    A competitive peptide inhibitor KIDARI negatively regulates HFR1 by forming nonfunctional heterodimers in Arabidopsis photomorphogenesis.
    Mol. Cells, 2013. 35(1): p. 25-31
    [PMID:23224238]
  40. Jang IC,Henriques R,Chua NH
    Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A.
    Plant Cell Physiol., 2013. 54(6): p. 907-16
    [PMID:23503597]
  41. Shi H, et al.
    HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis.
    Plant Cell, 2013. 25(10): p. 3770-84
    [PMID:24179122]
  42. Liu Y,Liu Q,Yan Q,Shi L,Fang Y
    Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model.
    Mol. Biol. Cell, 2014. 25(8): p. 1366-73
    [PMID:24554768]
  43. 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]
  44. Shi H, et al.
    Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(12): p. 3817-22
    [PMID:25775589]