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

AT2G02740.2

Common Name

ATWHY3, PTAC11, T20F6.12, WHY3

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

Whirly

Protein Properties

Length: 267aa MW: 29640.8 Da PI: 10.1011

Description

ssDNA-binding transcriptional regulator

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G02740.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	220.3	1.7e-68	90	228	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkveP 98 s+yk+kaal++++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++lv+l+++esceffhdp++++++eGkvrk+lkveP AT2G02740.2 90 SIYKGKAALTIEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPFKGKGDEGKVRKVLKVEP 187 7*********************************************************************************************** PP Whirly 99 lpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 lpdGsG f+nlsv+n+l++++es+++P++kaefavl+s+++ AT2G02740.2 188 LPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLISAFN 228 ************************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	2.0E-78	79	250	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	4.71E-81	82	267	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	2.5E-59	91	225	IPR013742	Plant transcription factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006281	Biological Process	DNA repair
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0006952	Biological Process	defense response
GO:0009508	Cellular Component	plastid chromosome
GO:0009570	Cellular Component	chloroplast stroma
GO:0003677	Molecular Function	DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
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: 267 aa Download sequence Send to blast
MSQLLSSPPM AVFSKTFINH KFSDARFLSS HSILTSGGFA GKIIPLKPTA RLKLTVKSRQ 60 SDYFEKQRFG DSSSSQNAEV SSPRFYVGHS IYKGKAALTI EPRAPEFVAL ESGAFKLTKE 120 GFLLLQFAPA AGVRQYDWSR KQVFSLSVTE IGNLVSLGPR ESCEFFHDPF KGKGDEGKVR 180 KVLKVEPLPD GSGRFFNLSV QNKLLNVDES VYIPITKAEF AVLISAFNFV LPHLIGWSAF 240 ANSIKPEDSN RLNNASPKYG GDYEWSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koq_A	1e-120	78	245	2	169	Single-stranded DNA-binding protein WHY3, chloroplastic
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.41460	0.0	flower\| root

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	267474_at	1e-168
Expression Atlas	AT2G02740	-
AtGenExpress	AT2G02740	-
ATTED-II	AT2G02740	-

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a homolog of the potato p24 protein. It shares the conserved KGKAAL domain, a putative DNA-binding domain, with potato p24 and is localized to the plastid and not the nucleus.
UniProt	Single-stranded DNA-binding protein that functions in both chloroplasts and nucleus. In chloroplasts, maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. In the nucleus, is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Can bind double-stranded DNA in vivo. {ECO:0000269\|PubMed:19666500, ECO:0000269\|PubMed:19669906, ECO:0000269\|PubMed:20551348, ECO:0000269\|PubMed:21911368}.

Function -- GeneRIF ? help Back to Top
Data show that a double KO of the genes AtWhy1 and AtWhy3 leads to the appearance of plants with variegated green/white/yellow leaves, symptomatic of nonfunctional chloroplasts. [PMID: 19666500] AtWHY1 and AtWHY3, as two components of KBF1, can be recruited at the KPRE site to mediate the transcriptional repression of AtKP1. [PMID: 19669906]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G02740.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By salicylic acid (SA). {ECO:0000269\|PubMed:19669906}.

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

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

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: No visible phenotype under normal growth conditions. {ECO:0000269\|PubMed:19666500}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G02740

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT015336	0.0	BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.
GenBank	BT015641	0.0	BT015641.1 Arabidopsis thaliana At2g02740 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_178377.2	0.0	ssDNA-binding transcriptional regulator
Swissprot	Q66GR6	0.0	WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBL	A0A178VLN3	0.0	A0A178VLN3_ARATH; WHY3
STRING	AT2G02740.1	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT2G02740.2
Entrez Gene	814803
iHOP	AT2G02740
wikigenes	AT2G02740

Publications ? help Back to Top
Vermel M, et al. A family of RRM-type RNA-binding proteins specific to plant mitochondria. Proc. Natl. Acad. Sci. U.S.A., 2002. 99(9): p. 5866-71 [PMID:11972043] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] Desveaux D, et al. A "Whirly" transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis. Dev. Cell, 2004. 6(2): p. 229-40 [PMID:14960277] Desveaux D,Maréchal A,Brisson N Whirly transcription factors: defense gene regulation and beyond. Trends Plant Sci., 2005. 10(2): p. 95-102 [PMID:15708347] Krause K, et al. DNA-binding proteins of the Whirly family in Arabidopsis thaliana are targeted to the organelles. FEBS Lett., 2005. 579(17): p. 3707-12 [PMID:15967440] Pfalz J,Liere K,Kandlbinder A,Dietz KJ,Oelmüller R pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell, 2006. 18(1): p. 176-97 [PMID:16326926] Rajagopalan R,Vaucheret H,Trejo J,Bartel DP A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev., 2006. 20(24): p. 3407-25 [PMID:17182867] Zybailov B, et al. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE, 2008. 3(4): p. e1994 [PMID:18431481] Maréchal A, et al. Whirly proteins maintain plastid genome stability in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(34): p. 14693-8 [PMID:19666500] Xiong JY, et al. Recruitment of AtWHY1 and AtWHY3 by a distal element upstream of the kinesin gene AtKP1 to mediate transcriptional repression. Plant Mol. Biol., 2009. 71(4-5): p. 437-49 [PMID:19669906] Cappadocia L, et al. Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell, 2010. 22(6): p. 1849-67 [PMID:20551348] Cappadocia L, et al. A conserved lysine residue of plant Whirly proteins is necessary for higher order protein assembly and protection against DNA damage. Nucleic Acids Res., 2012. 40(1): p. 258-69 [PMID:21911368] Miao Y,Jiang J,Ren Y,Zhao Z The single-stranded DNA-binding protein WHIRLY1 represses WRKY53 expression and delays leaf senescence in a developmental stage-dependent manner in Arabidopsis. Plant Physiol., 2013. 163(2): p. 746-56 [PMID:23922267] Lepage É,Zampini É,Brisson N Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signaling in Arabidopsis. Plant Physiol., 2013. 163(2): p. 867-81 [PMID:23969600] Cappadocia L,Parent JS,Sygusch J,Brisson N A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 2013. 69(Pt 11): p. 1207-11 [PMID:24192350] Zampini É,Lepage É,Tremblay-Belzile S,Truche S,Brisson N Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans. Genome Res., 2015. 25(5): p. 645-54 [PMID:25800675] Karpinska B,Alomrani SO,Foyer CH Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2018. [PMID:28808105]