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

AT1G32770.1

Common Name

ANAC012, F6N18.15, NAC012, NST3, SND1

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

NAC

Protein Properties

Length: 358aa MW: 41520.4 Da PI: 5.5812

Description

NAC domain containing protein 12

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G32770.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	164	5.4e-51	16	144	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk..kvka.eekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk 95 +ppGfrFhPt+eel+++yL+kkv+++k++l +vi+evd++k+ePwd+++ ++ + +++wyfFs++dkky+tg+r+nrat +g+Wkatg+dk ++s AT1G32770.1 16 VPPGFRFHPTEEELLHYYLRKKVNSQKIDL-DVIREVDLNKLEPWDIQEecRIGStPQNDWYFFSHKDKKYPTGTRTNRATVAGFWKATGRDKIICS- 111 69**************************.9***********963433332456******************************9999. PP NAM 96 kgelvglkktLvfykgrapkgektdWvmheyrl 128 + +gl+ktLvfykgrap+g+k+dW+mheyrl AT1G32770.1 112 CVRRIGLRKTLVFYKGRAPHGQKSDWIMHEYRL 144 9999*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	1.01E-55	12	177	IPR003441	NAC domain
PROSITE profile	PS51005	55.084	16	177	IPR003441	NAC domain
Pfam	PF02365	6.6E-27	17	144	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0007275	Biological Process	multicellular organism development
GO:0009809	Biological Process	lignin biosynthetic process
GO:0009834	Biological Process	plant-type secondary cell wall biogenesis
GO:0010047	Biological Process	fruit dehiscence
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000230	anatomy	inflorescence meristem
PO:0000372	anatomy	metaxylem
PO:0005352	anatomy	xylem
PO:0005848	anatomy	secondary xylem
PO:0006202	anatomy	interfascicular region
PO:0006307	anatomy	root procambium
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009053	anatomy	peduncle
PO:0007611	developmental stage	petal differentiation and expansion stage

Sequence ? help Back to Top
Protein Sequence Length: 358 aa Download sequence Send to blast
MADNKVNLSI NGQSKVPPGF RFHPTEEELL HYYLRKKVNS QKIDLDVIRE VDLNKLEPWD 60 IQEECRIGST PQNDWYFFSH KDKKYPTGTR TNRATVAGFW KATGRDKIIC SCVRRIGLRK 120 TLVFYKGRAP HGQKSDWIMH EYRLDDTPMS NGYADVVTED PMSYNEEGWV VCRVFRKKNY 180 QKIDDCPKIT LSSLPDDTEE EKGPTFHNTQ NVTGLDHVLL YMDRTGSNIC MPESQTTTQH 240 QDDVLFMQLP SLETPKSESP VDQSFLTPSK LDFSPVQEKI TERPVCSNWA SLDRLVAWQL 300 NNGHHNPCHR KSFDEEEENG DTMMQRWDLH WNNDDNVDLW SSFTESSSSL DPLLHLSV

Sequence ? help Back to Top

Protein Sequence Length: 358 aa Download sequence Send to blast

MADNKVNLSI NGQSKVPPGF RFHPTEEELL HYYLRKKVNS QKIDLDVIRE VDLNKLEPWD  60
IQEECRIGST PQNDWYFFSH KDKKYPTGTR TNRATVAGFW KATGRDKIIC SCVRRIGLRK  120
TLVFYKGRAP HGQKSDWIMH EYRLDDTPMS NGYADVVTED PMSYNEEGWV VCRVFRKKNY  180
QKIDDCPKIT LSSLPDDTEE EKGPTFHNTQ NVTGLDHVLL YMDRTGSNIC MPESQTTTQH  240
QDDVLFMQLP SLETPKSESP VDQSFLTPSK LDFSPVQEKI TERPVCSNWA SLDRLVAWQL  300
NNGHHNPCHR KSFDEEEENG DTMMQRWDLH WNNDDNVDLW SSFTESSSSL DPLLHLSV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3ulx_A	1e-47	16	179	15	170	Stress-induced transcription factor NAC1
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	18398583	0.0
Genevisible	261703_at	0.0
Expression Atlas	AT1G32770	-
AtGenExpress	AT1G32770	-
ATTED-II	AT1G32770	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Stems and roots, specifically in interfascicular fibers (sclerenchyma), cells differentiating into vascular vessels (cambium), and xylem. {ECO:0000269\|PubMed:15923329, ECO:0000269\|PubMed:17114348, ECO:0000269\|PubMed:17237351, ECO:0000269\|PubMed:17565617}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes SND1, a NAC Domain transcription factor involved in secondary wall biosynthesis in fibers. Expressed specifically in interfascicular fibers and xylary fibers in stems. Expressed in the procambium of stem inflorescences and root. May act as a negative regulator of secondary wall thickening in xylary fibers. Acts redundantly with NST1 to control development of secondary walls in siliques.
UniProt	Transcriptional activator of genes involved in biosynthesis of secondary walls. Together with NST1, required for the secondary cell wall thickening and lignification of sclerenchymatous fibers and secondary xylem vessels (tracheary elements). Seems to repress the secondary cell wall thickening of xylary fibers. May also regulate the secondary cell wall lignification of other tissues. Binds to and activates the promoter of MYB46. {ECO:0000269\|PubMed:17114348, ECO:0000269\|PubMed:17237351, ECO:0000269\|PubMed:17333250, ECO:0000269\|PubMed:17565617, ECO:0000269\|PubMed:17890373}.

Function -- GeneRIF ? help Back to Top
These results reveal that SND1 is a key transcriptional activator involved in secondary wall biosynthesis in fibers. [PMID: 17114348] NST1 and NST3 redundantly regulate the secondary wall thickenings in interfascicular fiber of inflorescence stems and secondary xylem of hypocotyls in Arabidopsis without affecting the formation of cells destined to be woody tissues. [NST3] [PMID: 17237351] First line evidence demonstrating that SND1 and NST1 function redundantly in the regulation of secondary wall synthesis in fibers is presented. [PMID: 17333250] ANAC012 may act as a negative regulator of secondary wall thickening in xylary fibers. [PMID: 17565617] 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] NST1 and NST3 regulate the formation of secondary walls in siliques which regulates pod shattering. [PMID: 18657234] SND1 directly activates MYB83. [PMID: 19808805] SND1 upregulated genes that catalyze lignin biosynthesis. [PMID: 20952636] NST3 induced uniform non-striated deposition while VND7 induced striated deposition of secondary walls of the fiber cells, indicating the role of nature of transcriptional factors in secondary wall depositions. [PMID: 21284754] These results demonstrate that NST2 together with SND1 and NST1 regulate secondary wall biosynthesis in fibers of stems. [PMID: 25751728]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00016	PBM	25378322	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G32770.1

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G16490(A), AT1G17950(A), AT1G28470(A), AT1G62990(A), AT1G66230(A), AT1G73410(A), AT1G79180(A), AT4G12350(A), AT4G22680(A), AT4G28500(A), AT4G33450(A), AT5G12870(A), AT5G16600(A), AT5G56110(A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G32770

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF101892	0.0	EF101892.1 Arabidopsis thaliana SND1 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_174554.1	0.0	NAC domain containing protein 12
Swissprot	Q9LPI7	0.0	NAC12_ARATH; NAC domain-containing protein 12
TrEMBL	A0A178W7E9	0.0	A0A178W7E9_ARATH; SND1
STRING	AT1G32770.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM778	28	124
Representative plant	OGRP17	15	800

Link Out ? help Back to Top
Phytozome	AT1G32770.1
Entrez Gene	840171
iHOP	AT1G32770
wikigenes	AT1G32770

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] Ooka H, et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res., 2003. 10(6): p. 239-47 [PMID:15029955] 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] Zhong R,Demura T,Ye ZH SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell, 2006. 18(11): p. 3158-70 [PMID:17114348] Mitsuda N, et al. NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell, 2007. 19(1): p. 270-80 [PMID:17237351] Zhong R,Richardson EA,Ye ZH Two NAC domain transcription factors, SND1 and NST1, function redundantly in regulation of secondary wall synthesis in fibers of Arabidopsis. Planta, 2007. 225(6): p. 1603-11 [PMID:17333250] Ko JH,Yang SH,Park AH,Lerouxel O,Han KH ANAC012, a member of the plant-specific NAC transcription factor family, negatively regulates xylary fiber development in Arabidopsis thaliana. Plant J., 2007. 50(6): p. 1035-48 [PMID:17565617] 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] Mitsuda N,Ohme-Takagi M NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity. Plant J., 2008. 56(5): p. 768-78 [PMID:18657234] 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] Iwase A,Hideno A,Watanabe K,Mitsuda N,Ohme-Takagi M A chimeric NST repressor has the potential to improve glucose productivity from plant cell walls. J. Biotechnol., 2009. 142(3-4): p. 279-84 [PMID:19497342] Koizumi K,Yokoyama R,Nishitani K Mechanical load induces upregulation of transcripts for a set of genes implicated in secondary wall formation in the supporting tissue of Arabidopsis thaliana. J. Plant Res., 2009. 122(6): p. 651-9 [PMID:19582540] 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] Zhao Q, et al. Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(32): p. 14496-501 [PMID:20660755] Zhong R,Lee C,Ye ZH Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis. Mol Plant, 2010. 3(6): p. 1087-103 [PMID:20935069] Ohashi-Ito K,Oda Y,Fukuda H Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation. Plant Cell, 2010. 22(10): p. 3461-73 [PMID:20952636] Oikawa A, et al. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS ONE, 2010. 5(11): p. e15481 [PMID:21124849] Yamaguchi M, et al. VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J., 2011. 66(4): p. 579-90 [PMID:21284754] Lee C,Teng Q,Zhong R,Ye ZH The four Arabidopsis reduced wall acetylation genes are expressed in secondary wall-containing cells and required for the acetylation of xylan. Plant Cell Physiol., 2011. 52(8): p. 1289-301 [PMID:21673009] McCarthy RL,Zhong R,Ye ZH Secondary wall NAC binding element (SNBE), a key cis-acting element required for target gene activation by secondary wall NAC master switches. Plant Signal Behav, 2011. 6(9): p. 1282-5 [PMID:21847026] Wang H,Zhao Q,Chen F,Wang M,Dixon RA NAC domain function and transcriptional control of a secondary cell wall master switch. Plant J., 2011. 68(6): p. 1104-14 [PMID:21883551] 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] Hussey SG, et al. SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus. BMC Plant Biol., 2011. 11: p. 173 [PMID:22133261] Li Q, et al. Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. Proc. Natl. Acad. Sci. U.S.A., 2012. 109(36): p. 14699-704 [PMID:22915581] MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems. Plant J., 2013. 73(1): p. 63-76 [PMID:22967312] Lee C, et al. Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-o-methylation of glucuronic acid on xylan. Plant Cell Physiol., 2012. 53(11): p. 1934-49 [PMID:23045523] Matschi S, et al. Function of calcium-dependent protein kinase CPK28 of Arabidopsis thaliana in plant stem elongation and vascular development. Plant J., 2013. 73(6): p. 883-96 [PMID:23252373] Yuan Y,Teng Q,Zhong R,Ye ZH The Arabidopsis DUF231 domain-containing protein ESK1 mediates 2-O- and 3-O-acetylation of xylosyl residues in xylan. Plant Cell Physiol., 2013. 54(7): p. 1186-99 [PMID:23659919] 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] Fernández-Pérez F,Vivar T,Pomar F,Pedreño MA,Novo-Uzal E Peroxidase 4 is involved in syringyl lignin formation in Arabidopsis thaliana. J. Plant Physiol., 2015. 175: p. 86-94 [PMID:25506770] 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] Zhong R,Ye ZH The Arabidopsis NAC transcription factor NST2 functions together with SND1 and NST1 to regulate secondary wall biosynthesis in fibers of inflorescence stems. Plant Signal Behav, 2015. 10(2): p. e989746 [PMID:25751728] Yuan Y,Teng Q,Zhong R,Ye ZH TBL3 and TBL31, Two Arabidopsis DUF231 Domain Proteins, are Required for 3-O-Monoacetylation of Xylan. Plant Cell Physiol., 2016. 57(1): p. 35-45 [PMID:26556650] Huang J,Chen F,Wu S,Li J,Xu W Cotton GhMYB7 is predominantly expressed in developing fibers and regulates secondary cell wall biosynthesis in transgenic Arabidopsis. Sci China Life Sci, 2016. 59(2): p. 194-205 [PMID:26803299] Pascual MB, et al. PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine. Plant Biotechnol. J., 2018. 16(5): p. 1094-1104 [PMID:29055073]