Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G14410.1
Common NameATWHY1, F14L17.18, PTAC1, WHY1
Taxonomic ID
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
AT1G14410.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
       Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkveP 98 
                  7************************************************************************************************* PP

       Whirly  99 lpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                  **************************************996 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA: transcriptional regulator
SuperFamilySSF544473.37E-7980263IPR009044ssDNA-binding transcriptional regulator
PfamPF085367.6E-6187221IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0006952Biological Processdefense response
GO:0032211Biological Processnegative regulation of telomere maintenance via telomerase
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0045910Biological Processnegative regulation of DNA recombination
GO:0009507Cellular Componentchloroplast
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003697Molecular Functionsingle-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0042162Molecular Functiontelomeric DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007057developmental stageseed germination stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 263 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A1e-121742412169Single-stranded DNA-binding protein WHY1, chl
4koo_B1e-121742412169Single-stranded DNA-binding protein WHY1, chl
4koo_C1e-121742412169Single-stranded DNA-binding protein WHY1, chl
4koo_D1e-121742412169Single-stranded DNA-binding protein WHY1, chl
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.120430.0flower| inflorescence| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G14410-
Functional Description ? help Back to Top
Source Description
TAIREncodes a homolog of the potato p24 protein. Binds single strand telomeric repeats. Negatively regulates telomerase activity and telomere length.
UniProtSingle-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
  1. AtWHY1 is a new family of telomere end-binding proteins that plays a role in regulating telomere-length homeostasis in Arabidopsis.
    [PMID: 17217467]
  2. 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]
  3. AtWHY1 and AtWHY3, as two components of KBF1, can be recruited at the KPRE site to mediate the transcriptional repression of AtKP1.
    [PMID: 19669906]
  4. Whirly1 is translocated from the plastid to the nucleus where it affects expression of target genes such as PR1.
    [PMID: 22154598]
  5. WHY1 was an upstream regulator of WRKY53 during leaf senescence.
    [PMID: 23922267]
  6. The redox state of the photosynthetic electron transport chain triggers the movement of WHIRLY1 from the chloroplasts to the nucleus.
    [PMID: 24591713]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDsalicylic acid
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION 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 ExpressAT1G14410
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3324520.0AF332452.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBankAF3701560.0AF370156.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBankAY0590970.0AY059097.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_172893.10.0single-stranded DNA-binding protein WHY1
SwissprotQ9M9S30.0WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
STRINGAT1G14410.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP23161635
Publications ? help Back to Top
  1. 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
  2. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  3. 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
  4. Desveaux D,Maréchal A,Brisson N
    Whirly transcription factors: defense gene regulation and beyond.
    Trends Plant Sci., 2005. 10(2): p. 95-102
  5. 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
  6. 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
  7. 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
  8. Zybailov B, et al.
    Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
    PLoS ONE, 2008. 3(4): p. e1994
  9. 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
  10. 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
  11. 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
  12. 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
  13. Isemer R, et al.
    Recombinant Whirly1 translocates from transplastomic chloroplasts to the nucleus.
    FEBS Lett., 2012. 586(1): p. 85-8
  14. Isemer R, et al.
    Plastid Located WHIRLY1 Enhances the Responsiveness of Arabidopsis Seedlings Toward Abscisic Acid.
    Front Plant Sci, 2012. 3: p. 283
  15. 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
  16. 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
  17. 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