PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G24140.1
Common NameBHLH97, EN14, FAMA, FMA, MUJ8.4
Organism
Arabidopsis thaliana
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: 414aa    MW: 46407.7 Da    PI: 5.1165
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G24140.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH382.9e-12195246155
                  CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  +r++h ++Er+RR+++N+ +  Lr+l+P +   + ++ + a+i   A+e++++L+
  AT3G24140.1 195 QRMTHIAVERNRRKQMNEHLRVLRSLMPGS---YVQRGDQASIIGGAIEFVRELE 246
                  79****************************...9*****************9995 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.101.5E-13193249IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.08E-12193250No hitNo description
PROSITE profilePS5088815.428194245IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.36E-16194259IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.3E-9195246IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.4E-9200251IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd048730.00198328392No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010377Biological Processguard cell fate commitment
GO:0045597Biological Processpositive regulation of cell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051782Biological Processnegative regulation of cell division
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:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0000351anatomyguard mother cell
PO:0008019anatomyleaf lamina base
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:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020137anatomyleaf apex
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: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: 414 aa     Download sequence    Send to blast
MDKDYSAPNF LGESSGGNDD NSSGMIDYMF NRNLQQQQKQ SMPQQQQHQL SPSGFGATPF  60
DKMNFSDVMQ FADFGSKLAL NQTRNQDDQE TGIDPVYFLK FPVLNDKIED HNQTQHLMPS  120
HQTSQEGGEC GGNIGNVFLE EKEDQDDDND NNSVQLRFIG GEEEDRENKN VTKKEVKSKR  180
KRARTSKTSE EVESQRMTHI AVERNRRKQM NEHLRVLRSL MPGSYVQRGD QASIIGGAIE  240
FVRELEQLLQ CLESQKRRRI LGETGRDMTT TTTSSSSPIT TVANQAQPLI ITGNVTELEG  300
GGGLREETAE NKSCLADVEV KLLGFDAMIK ILSRRRPGQL IKTIAALEDL HLSILHTNIT  360
TMEQTVLYSF NVKITSETRF TAEDIASSIQ QIFSFIHANT NISGSSNLGN IVFT
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1195206RMTHIAVERNRR
2255259KRRRI
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.375860.0inflorescence| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible257247_at0.0
Expression AtlasAT3G24140-
AtGenExpressAT3G24140-
ATTED-IIAT3G24140-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Not expressed in meristemoids, but strongly expressed in guard mother cells (GMCs) and in young guard cells (at protein level) (PubMed:17088607). Expressed at the transition to terminal stomatal differentiation, just before and after the symmetric division of stomatal differentiation, being confined to late-stage GMC and to young, still differentiating guard cells (PubMed:24571519). {ECO:0000269|PubMed:17088607, ECO:0000269|PubMed:24571519}.
UniprotTISSUE SPECIFICITY: Resctricted to stomatal cell lineages (at protein level). Expressed in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:17088607}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a basic helix-loop-helix transcription factor whose activity is required to promote differentiation of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Both transcript and protein are expressed in and are required for halting divisions at the end of the stomatal lineage. It also has a role in the promotion of guard cell fate and in controlling the transition from guard mother cell to guard cell.
UniProtTranscription activator (PubMed:17088607, PubMed:17183265, PubMed:17183267). Together with MYB88 and MYB124, ensures that stomata contain just two guard cells (GCs) by enforcing a single symmetric precursor cell division before stomatal maturity (PubMed:24571519). Together with SPCH and MUTE, regulates the stomata formation. Required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Mediates the formation of stomata (PubMed:17088607, PubMed:17183265, PubMed:17183267). Prevents histone H3K27me3 marks and derepresses stem cell gene expression (PubMed:24654956). {ECO:0000269|PubMed:17088607, ECO:0000269|PubMed:17183265, ECO:0000269|PubMed:17183267, ECO:0000269|PubMed:24571519, ECO:0000269|PubMed:24654956}.
Function -- GeneRIF ? help Back to Top
  1. regulates cell-cell interaction involved in stomatal development.
    [PMID: 18453151]
  2. Transcriptional changes in response to inducible expression of Arabidopsis FAMA, a basic helix-loop-helix protein whose actions during the final stage in stomatal development regulate both cell division and cell fate, is reported.
    [PMID: 21245191]
  3. Low humidity induces DNA methylation and transcription repression of SPCH and FAMA.
    [PMID: 22442411]
  4. Data indicate that MYB transcription factor FOUR LIPS (FLP) and bHLH transcription factor FAMA complement respective mutant phenotypes.
    [PMID: 24571519]
  5. Data indicate that bHLH transcription factor FAMA and MYB transcription factor FOUR LIPS (FLP) genes stabilize guard cell fate.
    [PMID: 24654956]
  6. Irreversible cell fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RBR interaction.
    [PMID: 25303364]
  7. Data indicate that loss of the basic helix-loop-helix transcription factor FAMA function abolishes myrosin idioblasts (MIs) fate as well as the expression of the myrosinase genes TGG1 and TGG2.
    [PMID: 25304201]
  8. Data indicate that the basic helix-loop-helix transcription factor FAMA as an essential component for myrosin cell development along leaf veins.
    [PMID: 25304202]
  9. FAMA-overexpressed plants displayed enhanced resistance to B. cinerea infection and increased expression levels of defensin genes following B. cinerea treatment. Genetic analysis of MED8 and FAMA suggested that FAMA-regulated pathogen resistance was dependent on MED8. In addition, MED8 and FAMA were both associated with the G-box region in the promoter of ORA59.
    [PMID: 29513733]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G24140.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Inhibited by low relative humidity (LRH) via epigenetic CG methylation, thus leading to a reduced stomatal index. {ECO:0000269|PubMed:22442411}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G25710, AT3G26744, AT5G46690, AT5G65640, AT1G12860, AT1G62990
IntActSearch Q56YJ8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G24140
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2213240.0AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBankBT0289610.0BT028961.1 Arabidopsis thaliana At3g24140 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_189056.20.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ56YJ80.0FAMA_ARATH; Transcription factor FAMA
TrEMBLA0A178VKX80.0A0A178VKX8_ARATH; FMA
STRINGAT3G24140.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM55482649
Representative plantOGRP25315131
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. 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]
  3. 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]
  4. Ohashi-Ito K,Bergmann DC
    Arabidopsis FAMA controls the final proliferation/differentiation switch during stomatal development.
    Plant Cell, 2006. 18(10): p. 2493-505
    [PMID:17088607]
  5. MacAlister CA,Ohashi-Ito K,Bergmann DC
    Transcription factor control of asymmetric cell divisions that establish the stomatal lineage.
    Nature, 2007. 445(7127): p. 537-40
    [PMID:17183265]
  6. Pillitteri LJ,Sloan DB,Bogenschutz NL,Torii KU
    Termination of asymmetric cell division and differentiation of stomata.
    Nature, 2007. 445(7127): p. 501-5
    [PMID:17183267]
  7. Pillitteri LJ,Torii KU
    Breaking the silence: three bHLH proteins direct cell-fate decisions during stomatal development.
    Bioessays, 2007. 29(9): p. 861-70
    [PMID:17691100]
  8. Serna L
    bHLH proteins know when to make a stoma.
    Trends Plant Sci., 2007. 12(11): p. 483-5
    [PMID:17928257]
  9. Ohashi-Ito K
    [Three bHLH master regulators and cell-cell interaction involved in stomatal development]
    Tanpakushitsu Kakusan Koso, 2008. 53(6): p. 747-52
    [PMID:18453151]
  10. Kanaoka MM, et al.
    SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.
    Plant Cell, 2008. 20(7): p. 1775-85
    [PMID:18641265]
  11. Serna L
    Emerging parallels between stomatal and muscle cell lineages.
    Plant Physiol., 2009. 149(4): p. 1625-31
    [PMID:19201912]
  12. Boccalandro HE, et al.
    Phytochrome B enhances photosynthesis at the expense of water-use efficiency in Arabidopsis.
    Plant Physiol., 2009. 150(2): p. 1083-92
    [PMID:19363093]
  13. Liu T,Ohashi-Ito K,Bergmann DC
    Orthologs of Arabidopsis thaliana stomatal bHLH genes and regulation of stomatal development in grasses.
    Development, 2009. 136(13): p. 2265-76
    [PMID:19502487]
  14. Torii KU,Kanaoka MM,Pillitteri LJ,Bogenschutz NL
    Stomatal development: three steps for cell-type differentiation.
    Plant Signal Behav, 2007. 2(4): p. 311-3
    [PMID:19704632]
  15. Kang CY,Lian HL,Wang FF,Huang JR,Yang HQ
    Cryptochromes, phytochromes, and COP1 regulate light-controlled stomatal development in Arabidopsis.
    Plant Cell, 2009. 21(9): p. 2624-41
    [PMID:19794114]
  16. Peterson KM,Rychel AL,Torii KU
    Out of the mouths of plants: the molecular basis of the evolution and diversity of stomatal development.
    Plant Cell, 2010. 22(2): p. 296-306
    [PMID:20179138]
  17. 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]
  18. Hachez C,Ohashi-Ito K,Dong J,Bergmann DC
    Differentiation of Arabidopsis guard cells: analysis of the networks incorporating the basic helix-loop-helix transcription factor, FAMA.
    Plant Physiol., 2011. 155(3): p. 1458-72
    [PMID:21245191]
  19. MacAlister CA,Bergmann DC
    Sequence and function of basic helix-loop-helix proteins required for stomatal development in Arabidopsis are deeply conserved in land plants.
    Evol. Dev., 2011 Mar-Apr. 13(2): p. 182-92
    [PMID:21410874]
  20. Serna L
    Stomatal development in Arabidopsis and grasses: differences and commonalities.
    Int. J. Dev. Biol., 2011. 55(1): p. 5-10
    [PMID:21425077]
  21. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  22. Yang J,Isabel Ordiz M,Jaworski JG,Beachy RN
    Induced accumulation of cuticular waxes enhances drought tolerance in Arabidopsis by changes in development of stomata.
    Plant Physiol. Biochem., 2011. 49(12): p. 1448-55
    [PMID:22078383]
  23. Tricker PJ,Gibbings JG,Rodr
    Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development.
    J. Exp. Bot., 2012. 63(10): p. 3799-813
    [PMID:22442411]
  24. Tricker PJ,L
    Transgenerational, dynamic methylation of stomata genes in response to low relative humidity.
    Int J Mol Sci, 2013. 14(4): p. 6674-89
    [PMID:23531533]
  25. Lee E,Lucas JR,Sack FD
    Deep functional redundancy between FAMA and FOUR LIPS in stomatal development.
    Plant J., 2014. 78(4): p. 555-65
    [PMID:24571519]
  26. Lee E,Lucas JR,Goodrich J,Sack FD
    Arabidopsis guard cell integrity involves the epigenetic stabilization of the FLP and FAMA transcription factor genes.
    Plant J., 2014. 78(4): p. 566-77
    [PMID:24654956]
  27. Matos JL, et al.
    Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module.
    Elife, 2015.
    [PMID:25303364]
  28. Li M,Sack FD
    Myrosin idioblast cell fate and development are regulated by the Arabidopsis transcription factor FAMA, the auxin pathway, and vesicular trafficking.
    Plant Cell, 2014. 26(10): p. 4053-66
    [PMID:25304201]
  29. Shirakawa M, et al.
    FAMA is an essential component for the differentiation of two distinct cell types, myrosin cells and guard cells, in Arabidopsis.
    Plant Cell, 2014. 26(10): p. 4039-52
    [PMID:25304202]
  30. Chen L, et al.
    NRPB3, the third largest subunit of RNA polymerase II, is essential for stomatal patterning and differentiation in Arabidopsis.
    Development, 2016. 143(9): p. 1600-11
    [PMID:26989174]
  31. Lee JH,Jung JH,Park CM
    Light Inhibits COP1-Mediated Degradation of ICE Transcription Factors to Induce Stomatal Development in Arabidopsis.
    Plant Cell, 2017. 29(11): p. 2817-2830
    [PMID:29070509]
  32. Han X, et al.
    Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons.
    Plant Physiol., 2018. 176(4): p. 2871-2885
    [PMID:29496884]
  33. Li X,Yang R,Chen H
    The Arabidopsis thaliana Mediator subunit MED8 regulates plant immunity to Botrytis Cinerea through interacting with the basic helix-loop-helix (bHLH) transcription factor FAMA.
    PLoS ONE, 2018. 13(3): p. e0193458
    [PMID:29513733]