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

AT5G12870.1

Common Name

ATMYB46, MYB46, T24H18.40

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

MYB

Protein Properties

Length: 280aa MW: 31541.3 Da PI: 6.0373

Description

myb domain protein 46

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G12870.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	44.4	4e-14	20	67	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g W++eEd +l ++ G g+W+ +a+ g+ R++k+c++rw +yl AT5G12870.1 20 KGLWSPEEDSKLMQYMLSNGQGCWSDVAKNAGLQRCGKSCRLRWINYL 67 678*******************************************97 PP
2	Myb_DNA-binding	48.9	1.5e-15	73	116	1	46
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 rg+++++E++l+++ + lG++ W+ Ia++++ gRt++++k++w++ AT5G12870.1 73 RGAFSPQEEDLIIRFHSILGNR-WSQIAARLP-GRTDNEIKNFWNS 116 89******************.*****.*********97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	14.842	15	67	IPR017930	Myb domain
SuperFamily	SSF46689	9.77E-28	18	114	IPR009057	Homeodomain-like
SMART	SM00717	2.0E-10	19	69	IPR001005	SANT/Myb domain
Pfam	PF00249	2.1E-13	20	67	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	1.2E-22	21	74	IPR009057	Homeodomain-like
CDD	cd00167	1.75E-8	23	67	No hit	No description
PROSITE profile	PS51294	24.449	68	122	IPR017930	Myb domain
SMART	SM00717	2.3E-15	72	120	IPR001005	SANT/Myb domain
Pfam	PF00249	1.7E-14	73	116	IPR001005	SANT/Myb domain
CDD	cd00167	1.11E-10	75	115	No hit	No description
Gene3D	G3DSA:1.10.10.60	2.5E-25	75	123	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006357	Biological Process	regulation of transcription from RNA polymerase II promoter
GO:0009751	Biological Process	response to salicylic acid
GO:0030154	Biological Process	cell differentiation
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0050832	Biological Process	defense response to fungus
GO:1901348	Biological Process	positive regulation of secondary cell wall biogenesis
GO:0005634	Cellular Component	nucleus
GO:0000981	Molecular Function	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135	Molecular Function	transcription factor activity, RNA polymerase II transcription factor recruiting
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000230	anatomy	inflorescence meristem
PO:0000272	anatomy	protoxylem
PO:0000293	anatomy	guard cell
PO:0000372	anatomy	metaxylem
PO:0003015	anatomy	primary root differentiation zone
PO:0006202	anatomy	interfascicular region
PO:0009005	anatomy	root
PO:0009029	anatomy	stamen
PO:0009046	anatomy	flower
PO:0009053	anatomy	peduncle
PO:0009062	anatomy	gynoecium
PO:0020100	anatomy	hypocotyl
PO:0025022	anatomy	collective leaf structure
PO:0025257	anatomy	primary root elongation zone
PO:0007611	developmental stage	petal differentiation and expansion stage

Sequence ? help Back to Top
Protein Sequence Length: 280 aa Download sequence Send to blast
MRKPEVAIAA STHQVKKMKK GLWSPEEDSK LMQYMLSNGQ GCWSDVAKNA GLQRCGKSCR 60 LRWINYLRPD LKRGAFSPQE EDLIIRFHSI LGNRWSQIAA RLPGRTDNEI KNFWNSTIKK 120 RLKKMSDTSN LINNSSSSPN TASDSSSNSA SSLDIKDIIG SFMSLQEQGF VNPSLTHIQT 180 NNPFPTGNMI SHPCNDDFTP YVDGIYGVNA GVQGELYFPP LECEEGDWYN ANINNHLDEL 240 NTNGSGNAPE GMRPVEEFWD LDQLMNTEVP SFYFNFKQSI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1a5j_A	8e-28	20	122	7	108	B-MYB
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.5283	0.0	inflorescence

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30684156	0.0
Genevisible	250322_at	0.0
Expression Atlas	AT5G12870	-
AtGenExpress	AT5G12870	-
ATTED-II	AT5G12870	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed at low levels in stems and siliques, specifically in xylem. {ECO:0000269\|PubMed:16581911, ECO:0000269\|PubMed:17890373, ECO:0000269\|PubMed:9839469}.

Functional Description ? help Back to Top
Source	Description
TAIR	Member of the R2R3 factor gene family.
UniProt	Transcription activator. Involved in the regulation of secondary wall biosynthesis in fibers and vessels (PubMed:17890373). Transcription activator of the mannan synthase CSLA9 that recognizes and binds to the DNA consensus sequence 5'-[AG][GT]T[AT]GGT[GA]-3' cis-regulatory element of CSLA9 promoter (PubMed:24243147). Transcription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1. Functions redundantly with MYB83 in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels (PubMed:19808805). Transcription activator that binds to the DNA consensus sequence 5'-ACC[AT]A[AC][TC]-3', designated as the secondary wall MYB-responsive element (SMRE). Regulates directly numerous transcription factors and a number of genes involved in secondary wall biosynthesis that contain SMRE elements in their promoters (PubMed:22197883). Is an obligate component of the transcriptional regulatory complex toward the commitment of secondary wall cellulose synthesis. Is required for functional expression of the three secondary wall CESA genes, CESA4, CESA7 and CESA8 (PubMed:23726771). {ECO:0000269\|PubMed:17890373, ECO:0000269\|PubMed:19808805, ECO:0000269\|PubMed:22197883, ECO:0000269\|PubMed:23726771, ECO:0000269\|PubMed:24243147}.

Function -- GeneRIF ? help Back to Top
These results demonstrate that MYB46 is a direct target of SND1 and is another key player in the transcriptional network involved in the regulation of secondary wall biosynthesis in Arabidopsis. [PMID: 17890373] MYB46 activates the expression of selected transcription factors and genes involved in the biosynthesis of secondary wall components. [PMID: 19674407] MYB83 and MYB46, both of which are SND1 direct targets, function redundantly in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels. [PMID: 19808805] MYB46 gene expression does not change following interaction with pathogens. myb46 mutants have enhanced disease resistance to B. cinerea. [PMID: 21282403] The observed coordinated down-regulation of CesA genes is more pronounced, and occurs earlier, in myb46 mutant plants. [PMID: 21617373] MYB46 activates the secondary wall MYB-responsive element sites in the promoters of MYB46 direct targets. MYB46 and MYB83 directly activate a set of downstream transcription factors. [PMID: 22197883] MYB46 recognizes a cis-acting regulatory motif M46RE [PMID: 22271306] MYB46 mediated the transcriptional regulation of secondary wall biosynthesis. [PMID: 22914575] Data conclude that MYB46 is an obligate component of the transcriptional regulatory complex toward the commitment of secondary wall cellulose synthesis in Arabidopsis. [PMID: 23726771] Data indicate that transcription factors ANAC041, bZIP1 and MYB46 directly regulate the expression of CSLA9. [PMID: 24243147] MYB46 functions as a central and direct regulator of the genes involved in the biosynthesis of all three major secondary wall components. [PMID: 24879533] MYB46 is a unique transcription factor in that it directly regulates the biosynthesis genes for all of the three major components of the secondary wall as well as the transcription factors in the biosynthesis pathway. [PMID: 24984711] directly regulates all three secondary wall-associated cellulose synthase genes [PMID: 26011122]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00599	PBM	24477691	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G12870.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Slightly induced by salicylic acid (SA). Positively regulated by SND1 and homolog proteins. {ECO:0000269\|PubMed:16463103, ECO:0000269\|PubMed:17890373}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G32770 (A), AT1G71930 (A), AT2G46770 (A), AT3G61910 (A), AT5G62380 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G16490(A), AT1G62990(A), AT1G79180(A), AT4G22680(A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	salicylic acid

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G12870

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY519621	0.0	AY519621.1 Arabidopsis thaliana MYB transcription factor (At5g12870) mRNA, complete cds.
GenBank	BT000455	0.0	BT000455.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.
GenBank	BT002549	0.0	BT002549.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_196791.1	0.0	myb domain protein 46
Swissprot	Q9LXV2	0.0	MYB46_ARATH; Transcription factor MYB46
TrEMBL	A0A178UMY0	0.0	A0A178UMY0_ARATH; MYB46
STRING	AT5G12870.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6115	23	47
Representative plant	OGRP5	17	1784

Link Out ? help Back to Top
Phytozome	AT5G12870.1
Entrez Gene	831127
iHOP	AT5G12870
wikigenes	AT5G12870

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] Stracke R,Werber M,Weisshaar B The R2R3-MYB gene family in Arabidopsis thaliana. Curr. Opin. Plant Biol., 2001. 4(5): p. 447-56 [PMID:11597504] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Zhao C,Craig JC,Petzold HE,Dickerman AW,Beers EP The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiol., 2005. 138(2): p. 803-18 [PMID:15923329] Yanhui C, et al. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol. Biol., 2006. 60(1): p. 107-24 [PMID:16463103] Lee JY, et al. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2006. 103(15): p. 6055-60 [PMID:16581911] Mace DL, et al. Quantification of transcription factor expression from Arabidopsis images. Bioinformatics, 2006. 22(14): p. e323-31 [PMID:16873489] Zhong R,Richardson EA,Ye ZH The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell, 2007. 19(9): p. 2776-92 [PMID:17890373] Zhong R,Lee C,Zhou J,McCarthy RL,Ye ZH A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell, 2008. 20(10): p. 2763-82 [PMID:18952777] Zhou J,Lee C,Zhong R,Ye ZH MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. Plant Cell, 2009. 21(1): p. 248-66 [PMID:19122102] Cheng H, et al. Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis. PLoS Genet., 2009. 5(3): p. e1000440 [PMID:19325888] Ko JH,Kim WC,Han KH Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis. Plant J., 2009. 60(4): p. 649-65 [PMID:19674407] McCarthy RL,Zhong R,Ye ZH MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell Physiol., 2009. 50(11): p. 1950-64 [PMID:19808805] Zhong R,Ye ZH Transcriptional regulation of lignin biosynthesis. Plant Signal Behav, 2009. 4(11): p. 1028-34 [PMID:19838072] Winzell A,Aspeborg H,Wang Y,Ezcurra I Conserved CA-rich motifs in gene promoters of Pt x tMYB021-responsive secondary cell wall carbohydrate-active enzymes in Populus. Biochem. Biophys. Res. Commun., 2010. 394(3): p. 848-53 [PMID:20307500] McCarthy RL, et al. The poplar MYB transcription factors, PtrMYB3 and PtrMYB20, are involved in the regulation of secondary wall biosynthesis. Plant Cell Physiol., 2010. 51(6): p. 1084-90 [PMID:20427511] Ram MYB46 modulates disease susceptibility to Botrytis cinerea in Arabidopsis. Plant Physiol., 2011. 155(4): p. 1920-35 [PMID:21282403] Ram Enhanced disease resistance to Botrytis cinerea in myb46 Arabidopsis plants is associated to an early down-regulation of CesA genes. Plant Signal Behav, 2011. 6(6): p. 911-3 [PMID:21617373] Zhong R, et al. Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors. Plant Cell Physiol., 2011. 52(10): p. 1856-71 [PMID:21908441] Zhong R,Ye ZH MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol., 2012. 53(2): p. 368-80 [PMID:22197883] Kim WC,Ko JH,Han KH Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis. Plant Mol. Biol., 2012. 78(4-5): p. 489-501 [PMID:22271306] Ko JH,Kim WC,Kim JY,Ahn SJ,Han KH MYB46-mediated transcriptional regulation of secondary wall biosynthesis. Mol Plant, 2012. 5(5): p. 961-3 [PMID:22914575] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Yan L, et al. The heterologous expression in Arabidopsis thaliana of sorghum transcription factor SbbHLH1 downregulates lignin synthesis. J. Exp. Bot., 2013. 64(10): p. 3021-32 [PMID:23698629] Kim WC,Kim JY,Ko JH,Kim J,Han KH Transcription factor MYB46 is an obligate component of the transcriptional regulatory complex for functional expression of secondary wall-associated cellulose synthases in Arabidopsis thaliana. J. Plant Physiol., 2013. 170(15): p. 1374-8 [PMID:23726771] Kim WC, et al. Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana. Plant Mol. Biol., 2014. 84(4-5): p. 577-87 [PMID:24243147] Kim WC,Kim JY,Ko JH,Kang H,Han KH Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis. Plant Mol. Biol., 2014. 85(6): p. 589-99 [PMID:24879533] Ko JH,Jeon HW,Kim WC,Kim JY,Han KH The MYB46/MYB83-mediated transcriptional regulatory programme is a gatekeeper of secondary wall biosynthesis. Ann. Bot., 2014. 114(6): p. 1099-107 [PMID:24984711] Zhao Q, et al. Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry, 2015. 112: p. 170-8 [PMID:25107662] Sakamoto S,Mitsuda N Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant. Plant Cell Physiol., 2015. 56(2): p. 299-310 [PMID:25535195] 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 [PMID:25750178] Kim WC, et al. MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis. Plant J., 2013. 73(1): p. 26-36 [PMID:26011122] Vargas L, et al. Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants. Biotechnol Biofuels, 2016. 9: p. 139 [PMID:27390589] Takeuchi M,Kegasa T,Watanabe A,Tamura M,Tsutsumi Y Expression analysis of transporter genes for screening candidate monolignol transporters using Arabidopsis thaliana cell suspensions during tracheary element differentiation. J. Plant Res., 2018. 131(2): p. 297-305 [PMID:28921082] Kranz HD, et al. Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J., 1998. 16(2): p. 263-76 [PMID:9839469]