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 AT5G53210.1
Common NameBHLH98, EN19, MFH8.15, SPCH
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: 364aa    MW: 40169.4 Da    PI: 4.9835
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G53210.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  ++++h  +Er+RR+++N+ +  Lr+l+P     + k+ + a+i   +veYI++Lq
                  6899*************************9...9********************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000832.82E-1297155No hitNo description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.83E-1798175IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088814.93999150IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.0E-10100151IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.0E-11105156IPR011598Myc-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:0010374Biological Processstomatal complex development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000017anatomyvascular leaf primordium
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0006016anatomyleaf epidermis
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 364 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT5G53210-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First observed in a subset of undifferentiated epidermal cells, often by pair of neighboring cells. Later confined to small epidermal cells, including cells that have recently divided next to stomatal lineage cells. Also expressed in stomatal lineage cells, fading out progressively during meristemoid determination. {ECO:0000269|PubMed:17183265, ECO:0000269|PubMed:18641265, ECO:0000269|PubMed:19008449}.
UniprotTISSUE SPECIFICITY: Expressed in developing leaf epidermis (PubMed:17183265). Reduced accumulation in the stomatal lineage ground cells (SLGCs) where BASL is polarized in the cell cortex (PubMed:27746029). Observed in small cells of non-protruding hypocotyl cell files and of developing cotyledon epidermis (PubMed:22466366). Restricted to meristemoids (stomatal precursor cell) in leaves epidermis, mostly in dividing cells of non-protruding cell files (PubMed:25680231, PubMed:18641265, PubMed:19008449). {ECO:0000269|PubMed:17183265, ECO:0000269|PubMed:18641265, ECO:0000269|PubMed:19008449, ECO:0000269|PubMed:22466366, ECO:0000269|PubMed:25680231, ECO:0000269|PubMed:27746029}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a basic helix-loop-helix (bHLH) transcription factor that is necessary and sufficient for the asymmetric divisions that establish the stomatal lineage in Arabidopsis thaliana. Expression of SPCH in young epidermal cells allows these cells to make asymmetric divisions. SPCH is a substrate of a kinase MPK3 and MPK6.
UniProtTranscription factor acting as an integration node for stomata and brassinosteroid (BR) signaling pathways to control stomatal initiation and development (PubMed:22466366, PubMed:28507175). Activates transcription when in the presence of SCRM/ICE1 (PubMed:28507175). Functions as a dimer with SCRM or SCRM2 during stomatal initiation (PubMed:18641265). Required for the initiation, the spacing and the formation of stomata, by promoting the first asymmetric cell divisions (PubMed:25843888, PubMed:25680231, PubMed:19008449). Together with FMA and MUTE, modulates the stomata formation. Involved in the regulation of growth reduction under osmotic stress (e.g. mannitol), associated with a quick decrease of meristemoid mother cells (MMCs) number lower stomatal index and density (PubMed:25381317). {ECO:0000269|PubMed:17183265, ECO:0000269|PubMed:17183267, ECO:0000269|PubMed:18641265, ECO:0000269|PubMed:19008449, ECO:0000269|PubMed:22466366, ECO:0000269|PubMed:25381317, ECO:0000269|PubMed:25680231, ECO:0000269|PubMed:25843888, ECO:0000269|PubMed:28507175}.
Function -- GeneRIF ? help Back to Top
  1. regulates cell-cell interaction involved in stomatal development.
    [PMID: 18453151]
  2. study found that a unique domain in basic helix-loop-helix (bHLH) stomatal initiating factor, SPEECHLESS, renders it a mitogen-activated protein kinase phosphorylation target in vitro and modulates its function in vivo
    [PMID: 19008449]
  3. findings show that limited stem cell behavior of stomatal precursors depends on maintenance of the SPEECHLESS transcription factor in single daughter cells
    [PMID: 21903812]
  4. Low humidity induces DNA methylation and transcription repression of SPCH and FAMA.
    [PMID: 22442411]
  5. demonstrate that through phosphorylation inputs from both MAPKs and BIN2, SPCH serves as an integration node for stomata and BR signalling pathways to control stomatal development in Arabidopsis
    [PMID: 22466366]
  6. EPF1 and EPF2 are able to activate the MAP kinase MPK6, and that both EPF1 and EPF2 are able to decrease the SPCH level, whereas stomagen is able to increase it.
    [PMID: 23686240]
  7. Arabidopsis reduces growth under stress by integrating the osmotic stress signal into the MAPK-SPEECHLESS core developmental pathway.
    [PMID: 25381317]
  8. Phosphorylation at Serine 186 is positively required for SPCH function in regulating stomatal development.
    [PMID: 25680231]
  9. BASL polarization leads to elevated nuclear MPK6 signaling and lowered SPCH abundance in one of the two daughter cells. Therefore, two daughter cells are differentiated by BASL polarity-mediated differential suppression of SPCH, which may provide developmental plasticity in plant stem cell asymmetric cell division.
    [PMID: 27746029]
  10. SPCH role in stomatal development
    [PMID: 28507175]
  11. The expression regulation of ERECTA and SPEECHLESS gene families are critical for molecular control of stomatal development. (Review)
    [PMID: 29386377]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by brassinazole (BRZ), thus leading to a reduced number of stomata in hypocotyls (PubMed:25680231). Inhibited by low relative humidity (LRH) via epigenetic CG methylation, thus leading to a reduced stomatal index (PubMed:22442411). Repressed by YDA (at protein level) (PubMed:19008449). Post-transcriptional decrease of protein level in response to osmotic stress (e.g. mannitol), through the action of a mitogen-activated protein kinase (MAPK) cascade; this repression is reversed by the MAPK kinase inhibitor PD98059 (PubMed:25381317). {ECO:0000269|PubMed:19008449, ECO:0000269|PubMed:22442411, ECO:0000269|PubMed:25381317, ECO:0000269|PubMed:25680231}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G12860 (A), AT3G26744 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT3G26744(A)
Interaction ? help Back to Top
Source Intact With
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G53210
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ8683730.0DQ868373.1 Arabidopsis thaliana SPEECHLESS (SPCH) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_200133.20.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ700C70.0SPCH_ARATH; Transcription factor SPEECHLESS
STRINGAT5G53210.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
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
  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
  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
  4. 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
  5. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
  6. 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
  7. Pillitteri LJ,Sloan DB,Bogenschutz NL,Torii KU
    Termination of asymmetric cell division and differentiation of stomata.
    Nature, 2007. 445(7127): p. 501-5
  8. Gray JE
    Plant development: three steps for stomata.
    Curr. Biol., 2007. 17(6): p. R213-5
  9. Pillitteri LJ,Torii KU
    Breaking the silence: three bHLH proteins direct cell-fate decisions during stomatal development.
    Bioessays, 2007. 29(9): p. 861-70
  10. Serna L
    bHLH proteins know when to make a stoma.
    Trends Plant Sci., 2007. 12(11): p. 483-5
  11. Casson S,Gray JE
    Influence of environmental factors on stomatal development.
    New Phytol., 2008. 178(1): p. 9-23
  12. Ohashi-Ito K
    [Three bHLH master regulators and cell-cell interaction involved in stomatal development]
    Tanpakushitsu Kakusan Koso, 2008. 53(6): p. 747-52
  13. 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
  14. Macgregor DR,Deak KI,Ingram PA,Malamy JE
    Root system architecture in Arabidopsis grown in culture is regulated by sucrose uptake in the aerial tissues.
    Plant Cell, 2008. 20(10): p. 2643-60
  15. Lampard GR,Macalister CA,Bergmann DC
    Arabidopsis stomatal initiation is controlled by MAPK-mediated regulation of the bHLH SPEECHLESS.
    Science, 2008. 322(5904): p. 1113-6
  16. Serna L
    Emerging parallels between stomatal and muscle cell lineages.
    Plant Physiol., 2009. 149(4): p. 1625-31
  17. 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
  18. Serna L
    Cell fate transitions during stomatal development.
    Bioessays, 2009. 31(8): p. 865-73
  19. 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
  20. 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
  21. Lampard GR
    The missing link?: Arabidopsis SPCH is a MAPK specificity factor that controls entry into the stomatal lineage.
    Plant Signal Behav, 2009. 4(5): p. 425-7
  22. 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
  23. 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
  24. 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
  25. Serna L
    Stomatal development in Arabidopsis and grasses: differences and commonalities.
    Int. J. Dev. Biol., 2011. 55(1): p. 5-10
  26. Robinson S, et al.
    Generation of spatial patterns through cell polarity switching.
    Science, 2011. 333(6048): p. 1436-40
  27. Pillitteri LJ,Peterson KM,Horst RJ,Torii KU
    Molecular profiling of stomatal meristemoids reveals new component of asymmetric cell division and commonalities among stem cell populations in Arabidopsis.
    Plant Cell, 2011. 23(9): p. 3260-75
  28. 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
  29. Iwata E, et al.
    GIGAS CELL1, a novel negative regulator of the anaphase-promoting complex/cyclosome, is required for proper mitotic progression and cell fate determination in Arabidopsis.
    Plant Cell, 2011. 23(12): p. 4382-93
  30. 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
  31. Kong D, et al.
    Regulation of plasmodesmatal permeability and stomatal patterning by the glycosyltransferase-like protein KOBITO1.
    Plant Physiol., 2012. 159(1): p. 156-68
  32. Gudesblat GE, et al.
    SPEECHLESS integrates brassinosteroid and stomata signalling pathways.
    Nat. Cell Biol., 2012. 14(5): p. 548-54
  33. Kim C,Apel K
    Arabidopsis light-dependent NADPH: protochlorophyllide oxidoreductase A (PORA) is essential for normal plant growth and development: an addendum.
    Plant Mol. Biol., 2012. 80(2): p. 237-40
  34. Fuentes S,Ca
    Relationship between brassinosteroids and genes controlling stomatal production in the Arabidopsis hypocotyl.
    Int. J. Dev. Biol., 2012. 56(9): p. 675-80
  35. Tanaka Y,Nose T,Jikumaru Y,Kamiya Y
    ABA inhibits entry into stomatal-lineage development in Arabidopsis leaves.
    Plant J., 2013. 74(3): p. 448-57
  36. 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
  37. Jewaria PK, et al.
    Differential effects of the peptides Stomagen, EPF1 and EPF2 on activation of MAP kinase MPK6 and the SPCH protein level.
    Plant Cell Physiol., 2013. 54(8): p. 1253-62
  38. Yang K,Jiang M,Le J
    A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell.
    J Integr Plant Biol, 2014. 56(6): p. 539-49
  39. Balcerowicz M,Ranjan A,Rupprecht L,Fiene G,Hoecker U
    Auxin represses stomatal development in dark-grown seedlings via Aux/IAA proteins.
    Development, 2014. 141(16): p. 3165-76
  40. Lau OS, et al.
    Direct roles of SPEECHLESS in the specification of stomatal self-renewing cells.
    Science, 2014. 345(6204): p. 1605-9
  41. Davies KA,Bergmann DC
    Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(43): p. 15585-90
  42. Kumari A,Jewaria PK,Bergmann DC,Kakimoto T
    Arabidopsis reduces growth under osmotic stress by decreasing SPEECHLESS protein.
    Plant Cell Physiol., 2014. 55(12): p. 2037-46
  43. Yang KZ, et al.
    Phosphorylation of Serine 186 of bHLH Transcription Factor SPEECHLESS Promotes Stomatal Development in Arabidopsis.
    Mol Plant, 2015. 8(5): p. 783-95
  44. 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
  45. Zhang Y,Wang P,Shao W,Zhu JK,Dong J
    The BASL polarity protein controls a MAPK signaling feedback loop in asymmetric cell division.
    Dev. Cell, 2015. 33(2): p. 136-49
  46. de Marcos A, et al.
    Transcriptional profiles of Arabidopsis stomataless mutants reveal developmental and physiological features of life in the absence of stomata.
    Front Plant Sci, 2015. 6: p. 456
  47. Horst RJ, et al.
    Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage.
    PLoS Genet., 2015. 11(7): p. e1005374
  48. Klermund C, et al.
    LLM-Domain B-GATA Transcription Factors Promote Stomatal Development Downstream of Light Signaling Pathways in Arabidopsis thaliana Hypocotyls.
    Plant Cell, 2016. 28(3): p. 646-60
  49. Gu F, et al.
    Arabidopsis CSLD5 Functions in Cell Plate Formation in a Cell Cycle-Dependent Manner.
    Plant Cell, 2016. 28(7): p. 1722-37
  50. Raissig MT,Abrash E,Bettadapur A,Vogel JP,Bergmann DC
    Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(29): p. 8326-31
  51. Castorina G,Fox S,Tonelli C,Galbiati M,Conti L
    A novel role for STOMATAL CARPENTER 1 in stomata patterning.
    BMC Plant Biol., 2016. 16(1): p. 172
  52. Fu ZW,Wang YL,Lu YT,Yuan TT
    Nitric oxide is involved in stomatal development by modulating the expression of stomatal regulator genes in Arabidopsis.
    Plant Sci., 2016. 252: p. 282-289
  53. Zhang Y,Guo X,Dong J
    Phosphorylation of the Polarity Protein BASL Differentiates Asymmetric Cell Fate through MAPKs and SPCH.
    Curr. Biol., 2016. 26(21): p. 2957-2965
  54. Sakai Y, et al.
    The chemical compound bubblin induces stomatal mispatterning in Arabidopsis by disrupting the intrinsic polarity of stomatal lineage cells.
    Development, 2017. 144(3): p. 499-506
  55. de Marcos A, et al.
    A Mutation in the bHLH Domain of the SPCH Transcription Factor Uncovers a BR-Dependent Mechanism for Stomatal Development.
    Plant Physiol., 2017. 174(2): p. 823-842
  56. Dow GJ,Berry JA,Bergmann DC
    Disruption of stomatal lineage signaling or transcriptional regulators has differential effects on mesophyll development, but maintains coordination of gas exchange.
    New Phytol., 2017. 216(1): p. 69-75
  57. 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
  58. Zoulias N,Harrison EL,Casson SA,Gray JE
    Molecular control of stomatal development.
    Biochem. J., 2018. 475(2): p. 441-454
  59. Han X, et al.
    Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons.
    Plant Physiol., 2018. 176(4): p. 2871-2885
  60. Houbaert A, et al.
    POLAR-guided signalling complex assembly and localization drive asymmetric cell division.
    Nature, 2018. 563(7732): p. 574-578