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

AT3G44750.2

Common Name

ATHD2A, HD2A, HDA3, HDT1

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

C2H2

Protein Properties

Length: 242aa MW: 25984.9 Da PI: 5.1327

Description

histone deacetylase 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G44750.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.9	0.00016	216	238	2	23
EETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 2 kCpdCgksFsrksnLkrHirt.H 23 +C+ C+k+F++ L++H + H AT3G44750.2 216 SCGSCKKTFNSGNALESHNKAkH 238 6*****************88766 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03066	6.5E-7	3	164	No hit	No description
PROSITE profile	PS50157	10.429	215	242	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	217	238	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009294	Biological Process	DNA mediated transformation
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010162	Biological Process	seed dormancy process
GO:0016569	Biological Process	covalent chromatin modification
GO:0005730	Cellular Component	nucleolus
GO:0003676	Molecular Function	nucleic acid binding
GO:0004407	Molecular Function	histone deacetylase activity
GO:0008270	Molecular Function	zinc ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
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: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: 242 aa Download sequence Send to blast
MEFWGIEVKS GKPVTVTPEE GILIHVSQAS LGECKNKKGE FVPLHVKVGN QNLVLGTLST 60 ENIPQLFCDL VFDKEFELSH TWGKGSVYFV GYKTPNIEPQ GYSEEEEEEV PAGNAAKAVA 120 KPKAKPAEVK PAVDDEEDES DSDGMDEDDS DGEDSEEEEP TPKKPASSKK RANETTPKAP 180 VSAKKAKVAV TPQKTDEKKK GGKAANQSPK SASQVSCGSC KKTFNSGNAL ESHNKAKHAA 240 AK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.20950	0.0	flower\| root

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	252625_at	0.0
Expression Atlas	AT3G44750	-
AtGenExpress	AT3G44750	-
ATTED-II	AT3G44750	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in leaves, roots, stems, young plantlets, flowers and siliques. Highest levels in ovules, embryos, shoot apical meristems and first leaves. Also expressed in somatic embryos. {ECO:0000269\|PubMed:10792817, ECO:0000269\|PubMed:15144374}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a histone deacetylase. Controls the development of adaxial/abaxial leaf polarity. Two lines with RNAi-directed against this gene show reduced Agrobacterium-mediated DNA transformation of the roots.
UniProt	Probably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Required for histone H3 'Lys-9' deacetylation. Involved in rRNA gene silencing in nucleolar dominance. Seems to be implicated in the regulation of genes involved in seeds development. {ECO:0000269\|PubMed:10792817, ECO:0000269\|PubMed:12694598, ECO:0000269\|PubMed:14992728, ECO:0000269\|PubMed:15144374}.

Function -- GeneRIF ? help Back to Top
HD2A and HD2C may have different and opposing functions in germination with the glucose/HD2A pathway acting to restrain germination and the HD2C pathway acting to enhance germination. [PMID: 21739146] These results suggest that by repressing the expression of GA2ox2, HDT1/2 likely fine-tune gibberellin metabolism. [PMID: 28855334]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G44750.2

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	AT5G17430 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G34710(A), AT2G45190(A), AT4G37870(R)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G44750

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF195545	0.0	AF195545.1 Arabidopsis thaliana putative histone deacetylase (HD2A) mRNA, complete cds.
GenBank	AY065396	0.0	AY065396.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.
GenBank	AY096729	0.0	AY096729.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001190012.1	1e-175	histone deacetylase 3
Swissprot	Q9FVE6	1e-138	HDT1_ARATH; Histone deacetylase HDT1
TrEMBL	F4J378	1e-174	F4J378_ARATH; Histone deacetylase 3
STRING	AT3G44750.1	1e-136	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT3G44750.2
Entrez Gene	823605
iHOP	AT3G44750
wikigenes	AT3G44750

Publications ? help Back to Top
Wu K,Tian L,Malik K,Brown D,Miki B Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J., 2000. 22(1): p. 19-27 [PMID:10792817] Pandey R, et al. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res., 2002. 30(23): p. 5036-55 [PMID:12466527] Zhou C, et al. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J., 2004. 38(5): p. 715-24 [PMID:15144374] Pendle AF, et al. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol. Biol. Cell, 2005. 16(1): p. 260-9 [PMID:15496452] Ueno Y, et al. Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis. Plant Cell, 2007. 19(2): p. 445-57 [PMID:17293570] Crane YM,Gelvin SB RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation. Proc. Natl. Acad. Sci. U.S.A., 2007. 104(38): p. 15156-61 [PMID:17827277] Pontes O, et al. Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance. PLoS ONE, 2007. 2(11): p. e1157 [PMID:17987131] Song Y,Wu K,Dhaubhadel S,An L,Tian L Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity. Biochem. Biophys. Res. Commun., 2010. 396(2): p. 187-92 [PMID:20331964] Zhang J,Henagan TM,Gao Z,Ye J Inhibition of glyceroneogenesis by histone deacetylase 3 contributes to lipodystrophy in mice with adipose tissue inflammation. Endocrinology, 2011. 152(5): p. 1829-38 [PMID:21406501] Colville A, et al. Role of HD2 genes in seed germination and early seedling growth in Arabidopsis. Plant Cell Rep., 2011. 30(10): p. 1969-79 [PMID:21739146] Bienvenut WV, et al. Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Mol. Cell Proteomics, 2012. 11(6): p. M111.015131 [PMID:22223895] Luo M, et al. HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis. J. Exp. Bot., 2012. 63(8): p. 3297-306 [PMID:22368268] Luo M,Wang YY,Liu X,Yang S,Wu K HD2 proteins interact with RPD3-type histone deacetylases. Plant Signal Behav, 2012. 7(6): p. 608-10 [PMID:22580696] Yano R,Takebayashi Y,Nambara E,Kamiya Y,Seo M Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. Plant J., 2013. 74(5): p. 815-28 [PMID:23464703] Waidmann S,Kusenda B,Mayerhofer J,Mechtler K,Jonak C A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. Plant Cell, 2014. 26(11): p. 4328-44 [PMID:25387881] 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] Lee K,Park OS,Jung SJ,Seo PJ Histone deacetylation-mediated cellular dedifferentiation in Arabidopsis. J. Plant Physiol., 2016. 191: p. 95-100 [PMID:26724747] Han Z, et al. AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana. Front Plant Sci, 2016. 7: p. 310 [PMID:27066015] Li H, et al. Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number. Plant Cell, 2017. 29(9): p. 2183-2196 [PMID:28855334]