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

cra_locus_16044_iso_2

Organism

Catharanthus roseus

Taxonomic ID

4058

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthinae; Catharanthus

Family

bHLH

Protein Properties

Length: 646aa MW: 73182.5 Da PI: 5.4998

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
cra_locus_16044_iso_2	genome	MPGR	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	39.4	1e-12	441	488	3	55
HHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 3 rahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r+h ++Er+RR+++ ++f L +l+P++ +K++K++iL ++eY+k+L+ cra_locus_16044_iso_2_len_2549_ver_3 441 RNHVMAERKRREKLHERFTLLGSLVPSS-----GKVDKVSILDDTIEYLKELE 488 589**********************9.....9**************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	3.3E-54	15	198	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	16.044	438	487	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	4.84E-17	441	504	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.3E-10	441	488	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.23E-10	441	485	No hit	No description
Gene3D	G3DSA:4.10.280.10	6.3E-17	442	499	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-15	444	493	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009957	Biological Process	epidermal cell fate specification
GO:0010091	Biological Process	trichome branching
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 646 aa Download sequence Send to blast
MEIQLQDQNG AAENLKRQLA LAVKSIQWSY AIFWSISSRQ PGVLEWGEGY YNGDIKTRKT 60 IQAGELSVDQ LGLQRSEQLR ELYESLSAAE SNPQAKRPSA ALSPEDLTDT EWYFLVCMSF 120 VFNIGQGLPG RSLAKNQAIW LCNAHQADSK VFTRSLLAKS ADIQTVFCFP YLGGIVELGV 180 TELVSEDRNL IQHIKTNFLD NPNAVISKIP NYVSNNPRND KDFMCANPVK DILEADFSPL 240 IECENVQVSS PKSSSNGFES NQPGEESFMI EAINGEASQV QSWQFMDDEI SNCIHNSMNS 300 SDCISQTYAN PKRMVPPLYD EKVNNNFLHD LHECNQKKLD SFDFKSDDVH YQNVLSTLLK 360 SSHQLILGPH CRKNNMESSF VNWKKERSVV FQKPRCATSQ RVLKKVLFEV TKMHGDLIPE 420 SSKENGKKES IWRPEADEID RNHVMAERKR REKLHERFTL LGSLVPSSGK VDKVSILDDT 480 IEYLKELERR VEELESQKEV GELEGRTRRR PQQEGTERIS DSYGSNRTAN NNNRKSLINK 540 RKASDVEEME HETECCMMIG GESSSEDVTV SVIDKNVLIE INCPWKESVL LEIMEGLTDL 600 NLESQAVQSS NTDGILSLTI KCKFKGSRIA SASMIRQALQ RIVRKS

Sequence ? help Back to Top

Protein Sequence Length: 646 aa Download sequence Send to blast

MEIQLQDQNG AAENLKRQLA LAVKSIQWSY AIFWSISSRQ PGVLEWGEGY YNGDIKTRKT  60
IQAGELSVDQ LGLQRSEQLR ELYESLSAAE SNPQAKRPSA ALSPEDLTDT EWYFLVCMSF  120
VFNIGQGLPG RSLAKNQAIW LCNAHQADSK VFTRSLLAKS ADIQTVFCFP YLGGIVELGV  180
TELVSEDRNL IQHIKTNFLD NPNAVISKIP NYVSNNPRND KDFMCANPVK DILEADFSPL  240
IECENVQVSS PKSSSNGFES NQPGEESFMI EAINGEASQV QSWQFMDDEI SNCIHNSMNS  300
SDCISQTYAN PKRMVPPLYD EKVNNNFLHD LHECNQKKLD SFDFKSDDVH YQNVLSTLLK  360
SSHQLILGPH CRKNNMESSF VNWKKERSVV FQKPRCATSQ RVLKKVLFEV TKMHGDLIPE  420
SSKENGKKES IWRPEADEID RNHVMAERKR REKLHERFTL LGSLVPSSGK VDKVSILDDT  480
IEYLKELERR VEELESQKEV GELEGRTRRR PQQEGTERIS DSYGSNRTAN NNNRKSLINK  540
RKASDVEEME HETECCMMIG GESSSEDVTV SVIDKNVLIE INCPWKESVL LEIMEGLTDL  600
NLESQAVQSS NTDGILSLTI KCKFKGSRIA SASMIRQALQ RIVRKS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rqw_A	1e-16	13	198	7	192	Transcription factor MYC3
4rqw_B	1e-16	13	198	7	192	Transcription factor MYC3
4rs9_A	1e-16	13	198	7	192	Transcription factor MYC3
4yz6_A	1e-16	13	198	7	192	Transcription factor MYC3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	446	451	ERKRRE
2	447	452	RKRREK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication. Regulates also trichome cell wall maturation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Activates the transcription of GL2. {ECO:0000269\|PubMed:11063707, ECO:0000269\|PubMed:12917293, ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14561633, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15590742}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By nitrogen deficiency and UV light. Negatively regulated by MYB66/WER, GL3 and BHLH2 in the developing non-hair cells, and positively regulated by CPC and TRY in the developing hair cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15590742, ECO:0000269\|PubMed:17053893}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027181560.1	0.0	transcription factor EGL1-like isoform X1
Refseq	XP_027181561.1	0.0	transcription factor EGL1-like isoform X1
Refseq	XP_027181562.1	0.0	transcription factor EGL1-like isoform X1
Swissprot	Q9FN69	0.0	GL3_ARATH; Transcription factor GLABRA 3
TrEMBL	A0A2U9IY29	0.0	A0A2U9IY29_CATRO; Transcription factor GLABRA 3
STRING	EOY24750	0.0	(Theobroma cacao)

Publications ? help Back to Top
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] Liu Z,Shi MZ,Xie DY Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. Planta, 2014. 239(4): p. 765-81 [PMID:24370633] Nemie-Feyissa D,Olafsdottir SM,Heidari B,Lillo C Nitrogen depletion and small R3-MYB transcription factors affecting anthocyanin accumulation in Arabidopsis leaves. Phytochemistry, 2014. 98: p. 34-40 [PMID:24388610] Nayidu NK, et al. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS ONE, 2014. 9(4): p. e95877 [PMID:24755905] Wada T,Kunihiro A,Tominaga-Wada R Arabidopsis CAPRICE (MYB) and GLABRA3 (bHLH) control tomato (Solanum lycopersicum) anthocyanin biosynthesis. PLoS ONE, 2014. 9(9): p. e109093 [PMID:25268379] Ranocha P,Francoz E,Burlat V,Dunand C Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Plant Signal Behav, 2014. 9(11): p. e977734 [PMID:25531128] Sun L, et al. GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis. New Phytol., 2015. 206(1): p. 220-30 [PMID:25640859] Nemie-Feyissa D,Heidari B,Blaise M,Lillo C Analysis of interactions between heterologously produced bHLH and MYB proteins that regulate anthocyanin biosynthesis: quantitative interaction kinetics by Microscale Thermophoresis. Phytochemistry, 2015. 111: p. 21-6 [PMID:25659750] Yu D, et al. RPN1a, a subunit of the 26S proteasome, controls trichome development in Arabidopsis. Plant Physiol. Biochem., 2015. 88: p. 82-8 [PMID:25676129] Huang M,Hu Y,Liu X,Li Y,Hou X Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development. Front Plant Sci, 2015. 6: p. 955 [PMID:26579186] Dai X, et al. A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3. Plant Cell Environ., 2016. 39(4): p. 897-907 [PMID:26667588] Pan Y,Bo K,Cheng Z,Weng Y The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1. BMC Plant Biol., 2015. 15: p. 302 [PMID:26714637] Alahakoon UI, et al. Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity. BMC Plant Biol., 2016. 16: p. 12 [PMID:26739276] Zheng K, et al. Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation. Sci Rep, 2016. 6: p. 19254 [PMID:26758286] Shangguan XX,Yang CQ,Zhang XF,Wang LJ Functional characterization of a basic helix-loop-helix (bHLH) transcription factor GhDEL65 from cotton (Gossypium hirsutum). Physiol Plant, 2016. 158(2): p. 200-12 [PMID:27080593] Petridis A,Döll S,Nichelmann L,Bilger W,Mock HP Arabidopsis thaliana G2-LIKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low-temperature regulators of flavonoid accumulation. New Phytol., 2016. 211(3): p. 912-25 [PMID:27125220] Gao C, et al. Genome-wide identification of GLABRA3 downstream genes for anthocyanin biosynthesis and trichome formation in Arabidopsis. Biochem. Biophys. Res. Commun., 2017. 485(2): p. 360-365 [PMID:28216162] Friede A, et al. The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves. Front Plant Sci, 2017. 8: p. 1382 [PMID:28848584] Gao C, et al. Brassica napusGLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana. Plant Biol (Stuttg), 2018. 20(1): p. 3-9 [PMID:28940939] Wen J, et al. The C-terminal domains of Arabidopsis GL3/EGL3/TT8 interact with JAZ proteins and mediate dimeric interactions. Plant Signal Behav, 2018. 13(1): p. e1422460 [PMID:29293407] Kim SY,Hyoung S,So WM,Shin JS The novel transcription factor TRP interacts with ZFP5, a trichome initiation-related transcription factor, and negatively regulates trichome initiation through gibberellic acid signaling. Plant Mol. Biol., 2018. 96(3): p. 315-326 [PMID:29335898]