PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G14410.1
Common NameATWHY1, F14L17.18, PTAC1, WHY1
Organism
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
1Whirly228.74.4e-71862241139
       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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.109.7E-7976246IPR009044ssDNA-binding 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:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
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
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
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A1e-121742412169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B1e-121742412169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C1e-121742412169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D1e-121742412169Single-stranded DNA-binding protein WHY1, chloroplastic
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
GEO1453356940.0
Genevisible261493_at0.0
Expression AtlasAT1G14410-
AtGenExpressAT1G14410-
ATTED-IIAT1G14410-
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. [Whirly 1][AtWHY1]
    [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. [Whirly1] [WHY1]
    [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]
  7. 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]
  8. Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis
    [PMID: 29112140]
  9. 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
SourceLink
PlantRegMapAT1G14410.1
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
PlantRegMapRetrieve-
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_172893.10.0ssDNA-binding transcriptional regulator
SwissprotQ9M9S30.0WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A178WFQ80.0A0A178WFQ8_ARATH; WHY1
STRINGAT1G14410.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM50232752
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
    [PMID:14576160]
  2. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  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
    [PMID:14960277]
  4. 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]
  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
    [PMID:15967440]
  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
    [PMID:16326926]
  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
    [PMID:17217467]
  8. Zybailov B, et al.
    Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
    PLoS ONE, 2008. 3(4): p. e1994
    [PMID:18431481]
  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
    [PMID:19666500]
  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
    [PMID:19669906]
  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
    [PMID:20551348]
  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
    [PMID:21911368]
  13. Isemer R, et al.
    Recombinant Whirly1 translocates from transplastomic chloroplasts to the nucleus.
    FEBS Lett., 2012. 586(1): p. 85-8
    [PMID:22154598]
  14. 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]
  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
    [PMID:23922267]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]