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

AT1G14410.1

Common Name

ATWHY1, F14L17.18, PTAC1, WHY1

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: 263aa MW: 29058.1 Da PI: 9.8818

Description

ssDNA-binding transcriptional regulator

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G14410.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	228.7	4.4e-71	86	224	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkveP 98 s+yk+kaal+v++++p+f+aldsg++kl+++G+lll++a+++++r+ydW+kkq+f+ls+te+++lv+l+++esceffhdp++++s+eGkvrk+lkveP AT1G14410.1 86 SIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEP 183 7*********************************************************************************************** PP Whirly 99 lpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 lpdGsG+f+nlsv+n+lv+++es+++P+++aefavl+s+++ AT1G14410.1 184 LPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFAVLISAFN 224 ************************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	9.7E-79	76	246	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	3.37E-79	80	263	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	7.6E-61	87	221	IPR013742	Plant transcription factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006281	Biological Process	DNA repair
GO:0006952	Biological Process	defense response
GO:0032211	Biological Process	negative regulation of telomere maintenance via telomerase
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0045910	Biological Process	negative regulation of DNA recombination
GO:0009507	Cellular Component	chloroplast
GO:0009508	Cellular Component	plastid chromosome
GO:0009570	Cellular Component	chloroplast stroma
GO:0003697	Molecular Function	single-stranded DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0003723	Molecular Function	RNA binding
GO:0042162	Molecular Function	telomeric 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: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:0007057	developmental stage	seed germination 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:0007131	developmental stage	seedling development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 263 aa Download sequence Send to blast
MSQLLSTPLM AVNSNPRFLS SSSVLVTGGF AVKRHGFALK PTTKTVKLFS VKSRQTDYFE 60 KQRFGDSSSS PSPAEGLPAR FYVGHSIYKG KAALTVDPRA PEFVALDSGA FKLSKDGFLL 120 LQFAPSAGVR QYDWSKKQVF SLSVTEIGTL VSLGPRESCE FFHDPFKGKS DEGKVRKVLK 180 VEPLPDGSGH FFNLSVQNKL VNVDESIYIP ITRAEFAVLI SAFNFVLPYL IGWHAFANSI 240 KPEETSRVNN ASPNYGGDYE WNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koo_A	1e-121	74	241	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	1e-121	74	241	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	1e-121	74	241	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	1e-121	74	241	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.12043	0.0	flower\| inflorescence\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145335694	0.0
Genevisible	261493_at	0.0
Expression Atlas	AT1G14410	-
AtGenExpress	AT1G14410	-
ATTED-II	AT1G14410	-

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a homolog of the potato p24 protein. Binds single strand telomeric repeats. Negatively regulates telomerase activity and telomere length.
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 nucleus, modulates telomere length homeostasis by inhibiting the action of the telomerase at the extreme termini of chromosomes. Is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Is required for full salicylic acid-dependent plant disease resistance responses. Can bind double-stranded DNA in vivo. {ECO:0000269\|PubMed:14960277, ECO:0000269\|PubMed:17217467, ECO:0000269\|PubMed:19666500, ECO:0000269\|PubMed:19669906, ECO:0000269\|PubMed:20551348, ECO:0000269\|PubMed:21911368}.

Function -- GeneRIF ? help Back to Top
AtWHY1 is a new family of telomere end-binding proteins that plays a role in regulating telomere-length homeostasis in Arabidopsis. [Whirly 1][AtWHY1] [PMID: 17217467] 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] Whirly1 is translocated from the plastid to the nucleus where it affects expression of target genes such as PR1. [Whirly1] [WHY1] [PMID: 22154598] WHY1 was an upstream regulator of WRKY53 during leaf senescence. [PMID: 23922267] The redox state of the photosynthetic electron transport chain triggers the movement of WHIRLY1 from the chloroplasts to the nucleus. [PMID: 24591713] results demonstrate that CIPK14 regulates the phosphorylation and organellar distributions of WHY1 and pinpoint that CIPK14 may function as a cellular switch between leaf senescence and plastid development for coordinating the intercellular signaling in Arabidopsis [PMID: 28412544] Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis [PMID: 29112140] Study concludes that the CIPK14 phosphorylation-mediated WHY1 deficiency in plastids is related to the impairment of protein metabolism, leading to chloroplast dysfunction [PMID: 30065159]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G14410.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By salicylic acid (SA) and infection by H.parasitica. {ECO:0000269\|PubMed:14960277, 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, but mutant plants present a progressive lengthening of telomeric repeats. {ECO:0000269\|PubMed:17217467, ECO:0000269\|PubMed:19666500}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G14410

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF332452	0.0	AF332452.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AF370156	0.0	AF370156.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AY059097	0.0	AY059097.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_172893.1	0.0	ssDNA-binding transcriptional regulator
Swissprot	Q9M9S3	0.0	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A178WFQ8	0.0	A0A178WFQ8_ARATH; WHY1
STRING	AT1G14410.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5023	27	52
Representative plant	OGRP2316	16	35

Link Out ? help Back to Top
Phytozome	AT1G14410.1
Entrez Gene	838003
iHOP	AT1G14410
wikigenes	AT1G14410

Publications ? help Back to Top
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] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] Yoo HH,Kwon C,Lee MM,Chung IK Single-stranded DNA binding factor AtWHY1 modulates telomere length homeostasis in Arabidopsis. Plant J., 2007. 49(3): p. 442-51 [PMID:17217467] 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] Isemer R, et al. Recombinant Whirly1 translocates from transplastomic chloroplasts to the nucleus. FEBS Lett., 2012. 586(1): p. 85-8 [PMID:22154598] Isemer R, et al. Plastid Located WHIRLY1 Enhances the Responsiveness of Arabidopsis Seedlings Toward Abscisic Acid. Front Plant Sci, 2012. 3: p. 283 [PMID:23269926] 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] Foyer CH,Karpinska B,Krupinska K The functions of WHIRLY1 and REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 in cross tolerance responses in plants: a hypothesis. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2014. 369(1640): p. 20130226 [PMID:24591713] Carella P,Wilson DC,Cameron RK Some things get better with age: differences in salicylic acid accumulation and defense signaling in young and mature Arabidopsis. Front Plant Sci, 2014. 5: p. 775 [PMID:25620972] 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] Ren Y,Li Y,Jiang Y,Wu B,Miao Y Phosphorylation of WHIRLY1 by CIPK14 Shifts Its Localization and Dual Functions in Arabidopsis. Mol Plant, 2017. 10(5): p. 749-763 [PMID:28412544] 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] Huang D,Lin W,Deng B,Ren Y,Miao Y Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis. Int J Mol Sci, 2018. [PMID:29112140] Guan Z,Wang W,Yu X,Lin W,Miao Y Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis. Int J Mol Sci, 2018. [PMID:30065159]