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

AT5G46760.1

Common Name

ATR2, BHLH5, EN36, MYC3, MZA15.18

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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: 592aa MW: 64991.9 Da PI: 4.9775

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G46760.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	39.4	1e-12	415	460	4	54
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 +h e+Er+RR+++N++f Lr ++P+ K++Ka+ L A+ YI++L AT5G46760.1 415 NHVEAERQRREKLNQRFYSLRAVVPNV-----SKMDKASLLGDAISYINEL 460 799*********************6.....5*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	5.3E-55	52	235	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	17.282	411	460	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.88E-18	414	480	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.05E-14	414	465	No hit	No description
Gene3D	G3DSA:4.10.280.10	6.0E-18	415	479	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.8E-10	415	460	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	9.8E-17	417	466	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006952	Biological Process	defense response
GO:0009718	Biological Process	anthocyanin-containing compound biosynthetic process
GO:0009753	Biological Process	response to jasmonic acid
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043425	Molecular Function	bHLH transcription factor binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000003	anatomy	whole plant
PO:0000005	anatomy	cultured plant cell
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 592 aa Download sequence Send to blast
MNGTTSSINF LTSDDDASAA AMEAFIGTNH HSSLFPPPPQ QPPQPQFNED TLQQRLQALI 60 ESAGENWTYA IFWQISHDFD SSTGDNTVIL GWGDGYYKGE EDKEKKKNNT NTAEQEHRKR 120 VIRELNSLIS GGIGVSDESN DEEVTDTEWF FLVSMTQSFV NGVGLPGESF LNSRVIWLSG 180 SGALTGSGCE RAGQGQIYGL KTMVCIATQN GVVELGSSEV ISQSSDLMHK VNNLFNFNNG 240 GGNNGVEASS WGFNLNPDQG ENDPALWISE PTNTGIESPA RVNNGNNSNS NSKSDSHQIS 300 KLEKNDISSV ENQNRQSSCL VEKDLTFQGG LLKSNETLSF CGNESSKKRT SVSKGSNNDE 360 GMLSFSTVVR SAANDSDHSD LEASVVKEAI VVEPPEKKPR KRGRKPANGR EEPLNHVEAE 420 RQRREKLNQR FYSLRAVVPN VSKMDKASLL GDAISYINEL KSKLQQAESD KEEIQKKLDG 480 MSKEGNNGKG CGSRAKERKS SNQDSTASSI EMEIDVKIIG WDVMIRVQCG KKDHPGARFM 540 EALKELDLEV NHASLSVVND LMIQQATVKM GSQFFNHDQL KVALMTKVGE NY

Sequence ? help Back to Top

Protein Sequence Length: 592 aa Download sequence Send to blast

MNGTTSSINF LTSDDDASAA AMEAFIGTNH HSSLFPPPPQ QPPQPQFNED TLQQRLQALI  60
ESAGENWTYA IFWQISHDFD SSTGDNTVIL GWGDGYYKGE EDKEKKKNNT NTAEQEHRKR  120
VIRELNSLIS GGIGVSDESN DEEVTDTEWF FLVSMTQSFV NGVGLPGESF LNSRVIWLSG  180
SGALTGSGCE RAGQGQIYGL KTMVCIATQN GVVELGSSEV ISQSSDLMHK VNNLFNFNNG  240
GGNNGVEASS WGFNLNPDQG ENDPALWISE PTNTGIESPA RVNNGNNSNS NSKSDSHQIS  300
KLEKNDISSV ENQNRQSSCL VEKDLTFQGG LLKSNETLSF CGNESSKKRT SVSKGSNNDE  360
GMLSFSTVVR SAANDSDHSD LEASVVKEAI VVEPPEKKPR KRGRKPANGR EEPLNHVEAE  420
RQRREKLNQR FYSLRAVVPN VSKMDKASLL GDAISYINEL KSKLQQAESD KEEIQKKLDG  480
MSKEGNNGKG CGSRAKERKS SNQDSTASSI EMEIDVKIIG WDVMIRVQCG KKDHPGARFM  540
EALKELDLEV NHASLSVVND LMIQQATVKM GSQFFNHDQL KVALMTKVGE NY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rru_A	1e-175	5	242	1	238	Transcription factor MYC3
4ywc_A	1e-175	5	242	1	238	Transcription factor MYC3
4ywc_B	1e-175	5	242	1	238	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	396	404	KKPRKRGRK

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	248864_at	0.0
Expression Atlas	AT5G46760	-
AtGenExpress	AT5G46760	-
ATTED-II	AT5G46760	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Constitutively expressed in roots, stems, leaves, flowers, and seedlings. {ECO:0000269\|PubMed:12136026, ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:21335373}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. With MYC2 and MYC4, controls additively subsets of JA-dependent responses. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the G-box (5'-CACGTG-3') of promoters. Activates multiple TIFY/JAZ promoters. {ECO:0000269\|PubMed:12136026, ECO:0000269\|PubMed:21242320, ECO:0000269\|PubMed:21321051, ECO:0000269\|PubMed:21335373, ECO:0000269\|PubMed:23943862}.

Function -- GeneRIF ? help Back to Top
results suggest that MYC3 (At5g46760) and MYC4 are JAZ-interacting transcription factors that regulate jasmonate responses [PMID: 21321051] MYC3 and MYC4, act additively with MYC2 in the activation of jasmonic acid responses. [PMID: 21335373] MYC2/MYC3/MYC4 are necessary for direct transcriptional activation of GS biosynthesis genes. [PMID: 23943862] regulator of glucosinolate biosynthesis [PMID: 25049362] JAZ1 and JAZ10 were the only JAZ proteins still showing interaction with the mutant MYC proteins, due to a second MYC interaction domain, besides the classical Jas domain. [PMID: 25817565] MYC3 undergoes pronounced conformational changes when bound to the conserved Jas motif of the JAZ9 repressor [PMID: 26258305] The function of MYC2, MYC3, and MYC4 in seed development and seed storage protein accumulation [PMID: 27415132]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00085	PBM	26531826	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G46760.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Barely up-regulated by jasmonic acid. {ECO:0000269\|PubMed:21242320, ECO:0000269\|PubMed:21335373}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G46760, AT5G60890, AT5G61420, AT1G18570, AT1G32640, AT1G74080

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Minor effect on jasmonic acid response and no effect on glucosinolate biosynthesis. Myc2 and myc3 double mutant has an increased insensitivity to jasmonic acid. Myc2, myc3 and myc4 triple mutant has no jasmonate-related defense response, is devoid of glucosinolates and is extremely susceptible to generalist herbivores. {ECO:0000269\|PubMed:21321051, ECO:0000269\|PubMed:21335373, ECO:0000269\|PubMed:23943862}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G46760

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB016882	0.0	AB016882.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MZA15.
GenBank	CP002688	0.0	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_199488.1	0.0	Basic helix-loop-helix (bHLH) DNA-binding family protein
Swissprot	Q9FIP9	0.0	MYC3_ARATH; Transcription factor MYC3
TrEMBL	A0A178UPV4	0.0	A0A178UPV4_ARATH; MYC3
STRING	AT5G46760.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1265	28	96
Representative plant	OGRP3733	12	24

Link Out ? help Back to Top
Phytozome	AT5G46760.1
Entrez Gene	834719
iHOP	AT5G46760
wikigenes	AT5G46760

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Smolen GA,Pawlowski L,Wilensky SE,Bender J Dominant alleles of the basic helix-loop-helix transcription factor ATR2 activate stress-responsive genes in Arabidopsis. Genetics, 2002. 161(3): p. 1235-46 [PMID:12136026] Abe H, et al. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell, 2003. 15(1): p. 63-78 [PMID:12509522] 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] 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] 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 [PMID:14600211] Lorenzo O,Chico JM,S JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell, 2004. 16(7): p. 1938-50 [PMID:15208388] Thilmony R,Underwood W,He SY Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7. Plant J., 2006. 46(1): p. 34-53 [PMID:16553894] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] 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] Gong W, et al. The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant, 2008. 1(1): p. 27-41 [PMID:19802365] Pauwels L, et al. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature, 2010. 464(7289): p. 788-91 [PMID:20360743] Cheng Z, et al. The bHLH transcription factor MYC3 interacts with the Jasmonate ZIM-domain proteins to mediate jasmonate response in Arabidopsis. Mol Plant, 2011. 4(2): p. 279-88 [PMID:21242320] Niu Y,Figueroa P,Browse J Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis. J. Exp. Bot., 2011. 62(6): p. 2143-54 [PMID:21321051] Fern The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell, 2011. 23(2): p. 701-15 [PMID:21335373] Tominaga-Wada R,Iwata M,Nukumizu Y,Wada T Analysis of IIId, IIIe and IVa group basic-helix-loop-helix proteins expressed in Arabidopsis root epidermis. Plant Sci., 2011. 181(4): p. 471-8 [PMID:21889054] Figueroa P,Browse J The Arabidopsis JAZ2 promoter contains a G-Box and thymidine-rich module that are necessary and sufficient for jasmonate-dependent activation by MYC transcription factors and repression by JAZ proteins. Plant Cell Physiol., 2012. 53(2): p. 330-43 [PMID:22173100] MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis. Plant Physiol., 2012. 160(1): p. 541-55 [PMID:22822211] Meinke DW A survey of dominant mutations in Arabidopsis thaliana. Trends Plant Sci., 2013. 18(2): p. 84-91 [PMID:22995285] Kazan K,Manners JM MYC2: the master in action. Mol Plant, 2013. 6(3): p. 686-703 [PMID:23142764] Moreno JE, et al. Negative feedback control of jasmonate signaling by an alternative splice variant of JAZ10. Plant Physiol., 2013. 162(2): p. 1006-17 [PMID:23632853] Schweizer F, et al. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell, 2013. 25(8): p. 3117-32 [PMID:23943862] Song S, et al. Interaction between MYC2 and ETHYLENE INSENSITIVE3 modulates antagonism between jasmonate and ethylene signaling in Arabidopsis. Plant Cell, 2014. 26(1): p. 263-79 [PMID:24399301] Chico JM, et al. Repression of Jasmonate-Dependent Defenses by Shade Involves Differential Regulation of Protein Stability of MYC Transcription Factors and Their JAZ Repressors in Arabidopsis. Plant Cell, 2014. 26(5): p. 1967-1980 [PMID:24824488] Frerigmann H,Berger B,Gigolashvili T bHLH05 is an interaction partner of MYB51 and a novel regulator of glucosinolate biosynthesis in Arabidopsis. Plant Physiol., 2014. 166(1): p. 349-69 [PMID:25049362] Goossens J,Swinnen G,Vanden Bossche R,Pauwels L,Goossens A Change of a conserved amino acid in the MYC2 and MYC3 transcription factors leads to release of JAZ repression and increased activity. New Phytol., 2015. 206(4): p. 1229-37 [PMID:25817565] Qi T,Huang H,Song S,Xie D Regulation of Jasmonate-Mediated Stamen Development and Seed Production by a bHLH-MYB Complex in Arabidopsis. Plant Cell, 2015. 27(6): p. 1620-33 [PMID:26002869] Gasperini D, et al. Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth. PLoS Genet., 2015. 11(6): p. e1005300 [PMID:26070206] Qi T, et al. Regulation of Jasmonate-Induced Leaf Senescence by Antagonism between bHLH Subgroup IIIe and IIId Factors in Arabidopsis. Plant Cell, 2015. 27(6): p. 1634-49 [PMID:26071420] Zhang F, et al. Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling. Nature, 2015. 525(7568): p. 269-73 [PMID:26258305] de Torres Zabala M, et al. Novel JAZ co-operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection. New Phytol., 2016. 209(3): p. 1120-34 [PMID:26428397] Yu J, et al. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. J. Exp. Bot., 2016. 67(3): p. 751-62 [PMID:26547795] Chen X,Huang H,Qi T,Liu B,Song S New perspective of the bHLH-MYB complex in jasmonate-regulated plant fertility in arabidopsis. Plant Signal Behav, 2016. 11(2): p. e1135280 [PMID:26829586] Schmiesing A,Emonet A,Gouhier-Darimont C,Reymond P Arabidopsis MYC Transcription Factors Are the Target of Hormonal Salicylic Acid/Jasmonic Acid Cross Talk in Response to Pieris brassicae Egg Extract. Plant Physiol., 2016. 170(4): p. 2432-43 [PMID:26884488] Thatcher LF, et al. Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum. J. Exp. Bot., 2016. 67(8): p. 2367-86 [PMID:26896849] Gao C, et al. MYC2, MYC3, and MYC4 function redundantly in seed storage protein accumulation in Arabidopsis. Plant Physiol. Biochem., 2016. 108: p. 63-70 [PMID:27415132] Gimenez-Ibanez S, et al. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol., 2017. 213(3): p. 1378-1392 [PMID:28005270] Zhang F, et al. Structural insights into alternative splicing-mediated desensitization of jasmonate signaling. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(7): p. 1720-1725 [PMID:28137867] Lian TF,Xu YP,Li LF,Su XD Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep, 2017. 19(7): p. 1334-1342 [PMID:28514654] Wang H, et al. The bHLH Transcription Factors MYC2, MYC3, and MYC4 Are Required for Jasmonate-Mediated Inhibition of Flowering in Arabidopsis. Mol Plant, 2017. 10(11): p. 1461-1464 [PMID:28827172] Song S, et al. MYC5 is Involved in Jasmonate-Regulated Plant Growth, Leaf Senescence and Defense Responses. Plant Cell Physiol., 2017. 58(10): p. 1752-1763 [PMID:29017003] Li B, et al. Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. Plant Cell, 2018. 30(1): p. 178-195 [PMID:29317470] Han X, et al. Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons. Plant Physiol., 2018. 176(4): p. 2871-2885 [PMID:29496884]