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

AT5G03740.1

Common Name

F17C15_160, HD2C, HDT3, MED24.1

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: 294aa MW: 31830.4 Da PI: 4.5108

Description

histone deacetylase 2C

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G03740.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.1	6.6e-05	267	290	1	23
EEETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirt.H 23 + C+ C+++F++ + L++H + H AT5G03740.1 267 FGCKSCTRTFTSEMGLQSHTKAkH 290 56*****************99877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50157	10.492	267	294	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	269	290	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0007275	Biological Process	multicellular organism development
GO:0009414	Biological Process	response to water deprivation
GO:0009651	Biological Process	response to salt stress
GO:0009737	Biological Process	response to abscisic acid
GO:0016569	Biological Process	covalent chromatin modification
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
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:0000003	anatomy	whole plant
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
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:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
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: 294 aa Download sequence Send to blast
MEFWGVEVKN GKPLHLDPGL DRLVHISQVA LGESKNNVTE PIQLYVTVGS DKLLIGTLSH 60 EKFPQLSTEI VLERNFALSH TWKNGSVFFS GYKVDASDPE PEDLIDDQLE AAGFKAAPKS 120 AAKQVNFQLP NEDVKAKQDD DADGSEEDSS DDDDSENSGD EEEEKVTAES DSEEDDSSDD 180 EEDDSSEEET PKKPEEPKKR SAEPNSSKNP ASNKKAKFVT PQKTDSKKPH VHVATPHPSK 240 QAGKNSGGGS TGETSKQQQT PKSAGAFGCK SCTRTFTSEM GLQSHTKAKH SAAA

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.4771	0.0	flower\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	250912_at	0.0
Expression Atlas	AT5G03740	-
AtGenExpress	AT5G03740	-
ATTED-II	AT5G03740	-

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:15144374, ECO:0000269\|PubMed:16553900}.

Functional Description ? help Back to Top
Source	Description
TAIR	HD2-type histone deacetylase HDAC. Involved in the ABA and stress responses. Mediates transcriptional repression
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. Involved in the modulation of abscisic acid and stress-responsive genes. {ECO:0000269\|PubMed:12694598, ECO:0000269\|PubMed:16553900}.

Function -- GeneRIF ? help Back to Top
AtHD2C can modulate abscisic acid and stress responses. [PMID: 16553900] 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] HD2C functionally associates with HDA6 and regulates gene expression through histone modifications. [PMID: 22368268] HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response. [PMID: 27083783] this study reveals a multifaceted role of HD2C in ribosome biogenesis. [PMID: 29343504]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G03740.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by abscisic acid. {ECO:0000269\|PubMed:16553900}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT5G17430 (A)

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9LZR5

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G03740

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF255712	0.0	AF255712.1 Arabidopsis thaliana putative histone deacetylase HD2c mRNA, complete cds.
GenBank	AF372889	0.0	AF372889.1 Arabidopsis thaliana AT5g03740/F17C15_160 mRNA, complete cds.
GenBank	AF510168	0.0	AF510168.1 Arabidopsis thaliana HDT3 mRNA, complete cds.
GenBank	AY142039	0.0	AY142039.1 Arabidopsis thaliana At5g03740/F17C15_160 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_195994.3	0.0	histone deacetylase 2C
Swissprot	Q9LZR5	0.0	HDT3_ARATH; Histone deacetylase HDT3
TrEMBL	A0A178UP12	0.0	A0A178UP12_ARATH; HDT3
STRING	AT5G03740.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2027	26	67
Representative plant	OGRP1053	11	29

Link Out ? help Back to Top
Phytozome	AT5G03740.1
Entrez Gene	831733
iHOP	AT5G03740
wikigenes	AT5G03740

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] Dangl M,Brosch G,Haas H,Loidl P,Lusser A Comparative analysis of HD2 type histone deacetylases in higher plants. Planta, 2001. 213(2): p. 280-5 [PMID:11469594] 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] Wu K,Tian L,Zhou C,Brown D,Miki B Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J., 2003. 34(2): p. 241-7 [PMID:12694598] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] Stangeland B, et al. Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes. J. Exp. Bot., 2005. 56(419): p. 2495-505 [PMID:16014362] Pischke MS,Huttlin EL,Hegeman AD,Sussman MR A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol., 2006. 140(4): p. 1255-78 [PMID:16489130] Sridha S,Wu K Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis. Plant J., 2006. 46(1): p. 124-33 [PMID:16553900] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] 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] Van Leene J, et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol., 2010. 6: p. 397 [PMID:20706207] Tamura K,Fukao Y,Iwamoto M,Haraguchi T,Hara-Nishimura I Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell, 2010. 22(12): p. 4084-97 [PMID:21189294] 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] Khan A, et al. The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing. Plant J., 2014. 79(1): p. 28-43 [PMID:24724701] Zhong X, et al. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell, 2014. 157(5): p. 1050-60 [PMID:24855943] 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] 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] Buszewicz D, et al. HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. Plant Cell Environ., 2016. 39(10): p. 2108-22 [PMID:27083783] Chen X, et al. Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell, 2018. 30(1): p. 134-152 [PMID:29343504] Huang KC,Lin WC,Cheng WH Salt hypersensitive mutant 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with the ABA signaling pathway in Arabidopsis. BMC Plant Biol., 2018. 18(1): p. 40 [PMID:29490615]