PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

XP_013605973.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

bHLH

Protein Properties

Length: 353aa MW: 38932.9 Da PI: 4.7832

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013605973.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	40	7.1e-13	101	152	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 ++++h +Er+RR+++N+ + Lr+l+P + k+ + a+i +veYI++Lq XP_013605973.1 101 QKMSHVNVERNRRKQMNEHLTVLRSLMPCF---YVKRGDQASIIGGVVEYISELQ 152 6899***********************9...9******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.88E-12	98	156	No hit	No description
SuperFamily	SSF47459	1.96E-17	99	176	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	5.5E-13	99	155	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.148	100	151	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.6E-10	101	152	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	5.7E-11	106	157	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 353 aa Download sequence Send to blast
MQETILDFLE ECEFVDTSLA GDDLFAILES LEGAGEISPT AASTPKDGTT SSKELVKNQN 60 YEASSAKKKR KRLETGKEEE DDDDGEGEEE EEEDNKQDGQ QKMSHVNVER NRRKQMNEHL 120 TVLRSLMPCF YVKRGDQASI IGGVVEYISE LQQVLQSLEA KKERKTYAEV LSPRLVPSPR 180 PSPPVLSPRK PPISPRISHQ HLLLHPISPR TPLPTSPYGG HPPQLPLIPQ PPRSYSLGDP 240 PPYSPASSSS SPSVSSNHES SLINELVANS KSALADVEVK FSGANVLLKT VSHKIPGQVM 300 KIIAALEDLS LEILQVNINT VEETMLYSFT IKIGIECQLS AEELAQQIQQ TFC

Sequence ? help Back to Top

Protein Sequence Length: 353 aa Download sequence Send to blast

MQETILDFLE ECEFVDTSLA GDDLFAILES LEGAGEISPT AASTPKDGTT SSKELVKNQN  60
YEASSAKKKR KRLETGKEEE DDDDGEGEEE EEEDNKQDGQ QKMSHVNVER NRRKQMNEHL  120
TVLRSLMPCF YVKRGDQASI IGGVVEYISE LQQVLQSLEA KKERKTYAEV LSPRLVPSPR  180
PSPPVLSPRK PPISPRISHQ HLLLHPISPR TPLPTSPYGG HPPQLPLIPQ PPRSYSLGDP  240
PPYSPASSSS SPSVSSNHES SLINELVANS KSALADVEVK FSGANVLLKT VSHKIPGQVM  300
KIIAALEDLS LEILQVNINT VEETMLYSFT IKIGIECQLS AEELAQQIQQ TFC

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL 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}.
Uniprot	TISSUE 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
UniProt	Transcription 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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013605973.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353209	0.0	AK353209.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-L21.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013605973.1	0.0	PREDICTED: transcription factor SPEECHLESS-like
Refseq	XP_013605974.1	0.0	PREDICTED: transcription factor SPEECHLESS-like
Refseq	XP_013605975.1	0.0	PREDICTED: transcription factor SPEECHLESS-like
Refseq	XP_013714033.1	0.0	transcription factor SPEECHLESS
Refseq	XP_022565610.1	0.0	transcription factor SPEECHLESS-like
Swissprot	Q700C7	1e-169	SPCH_ARATH; Transcription factor SPEECHLESS
TrEMBL	A0A078G3V8	0.0	A0A078G3V8_BRANA; BnaC09g29480D protein
TrEMBL	A0A0D3EAK9	0.0	A0A0D3EAK9_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6ELC5	0.0	A0A3P6ELC5_BRAOL; Uncharacterized protein
STRING	Bo9g110960.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7895	27	40

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53210.1	1e-157	bHLH family protein

Publications ? help Back to Top
Casson S,Gray JE Influence of environmental factors on stomatal development. New Phytol., 2008. 178(1): p. 9-23 [PMID:18266617] 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] 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 [PMID:24386951] 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 [PMID:25063454] Lau OS, et al. Direct roles of SPEECHLESS in the specification of stomatal self-renewing cells. Science, 2014. 345(6204): p. 1605-9 [PMID:25190717] 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 [PMID:25304637] 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 [PMID:25843888] 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 [PMID:26157447] 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 [PMID:26203655] 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 [PMID:26917680] 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 [PMID:27354558] 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 [PMID:27382177] 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 [PMID:27484174] 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 [PMID:27717464] 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 [PMID:27746029] 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 [PMID:28087627] 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 [PMID:28507175] 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 [PMID:28833173] 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] Zoulias N,Harrison EL,Casson SA,Gray JE Molecular control of stomatal development. Biochem. J., 2018. 475(2): p. 441-454 [PMID:29386377] Han X, et al. Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons. Plant Physiol., 2018. 176(4): p. 2871-2885 [PMID:29496884] Houbaert A, et al. POLAR-guided signalling complex assembly and localization drive asymmetric cell division. Nature, 2018. 563(7732): p. 574-578 [PMID:30429609]