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

RrC11033_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 126aa MW: 14489 Da PI: 4.7286

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC11033_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	42.6	1.1e-13	64	115	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 ++++h +Er+RR+++N+ + Lr+l+P + k+ + a+i +veYI++Lq RrC11033_p1 64 QKMSHVNVERNRRKQMNEHLTVLRSLMPCF---YVKRGDQASIIGGVVEYISELQ 115 6899***********************9...9******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.25E-11	61	119	No hit	No description
SuperFamily	SSF47459	2.75E-17	62	124	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	7.6E-14	62	118	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.148	63	114	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.9E-11	64	115	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	5.7E-11	69	120	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: 126 aa Download sequence Send to blast
MAASTPKDGT TSSKELVKNQ NYETSSPKKK RKRLETGKEE EEEEEEEDED GEGEEEDNKQ 60 DGQQKMSHVN VERNRRKQMN EHLTVLRSLM PCFYVKRGDQ ASIIGGVVEY ISELQQVLQS 120 LEAKKQ

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	26	33	PKKKRKRL

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}.

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	AJ630498	1e-113	AJ630498.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g53210.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018455056.1	3e-67	PREDICTED: transcription factor SPEECHLESS-like
Swissprot	Q700C7	2e-61	SPCH_ARATH; Transcription factor SPEECHLESS
TrEMBL	A0A078FND9	1e-64	A0A078FND9_BRANA; BnaA10g06580D protein
TrEMBL	A0A397XMV8	1e-64	A0A397XMV8_BRACM; Uncharacterized protein
TrEMBL	A0A3P6D3M8	1e-64	A0A3P6D3M8_BRACM; Uncharacterized protein
STRING	Bra003073.1-P	2e-64	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53210.1	1e-62	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]