PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G71260.1
Common NameATWHY2, F3I17.9, WHY2
Organism
Arabidopsis thaliana
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: 238aa    MW: 26295.1 Da    PI: 10.2945
Description WHIRLY 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G71260.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly234.47.6e-73591971139
       Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkveP 98 
                  s++k+kaal+v++v+p+f+++dsgnl+++r+G+l++++++a++erkydWekkq+fals+tev++l++++sk+s+effhdp++k+sn+G+vrk+l+v+P
  AT1G71260.1  59 SIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKP 156
                  79************************************************************************************************ PP

       Whirly  99 lpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                  ++dGsG+f++lsv+ns++k+n++f+vPv+kaefav++++++
  AT1G71260.1 157 HADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFS 197
                  **************************************995 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.9E-7548215IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544472.28E-7751238IPR009044ssDNA-binding transcriptional regulator
PfamPF085366.5E-6160194IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0006952Biological Processdefense response
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA 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:0025281anatomypollen
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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 238 aa     Download sequence    Send to blast
MMKQARSLLS RSLCDQSKSL FEASTLRGFA SWSNSSTPGR GFPGKDAAKP SGRLFAPYSI  60
FKGKAALSVE PVLPSFTEID SGNLRIDRRG SLMMTFMPAI GERKYDWEKK QKFALSPTEV  120
GSLISMGSKD SSEFFHDPSM KSSNAGQVRK SLSVKPHADG SGYFISLSVN NSILKTNDYF  180
VVPVTKAEFA VMKTAFSFAL PHIMGWNRLT GHVNTEALPS RNVSHLKTEP QLELEWDK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4kop_A1e-122452132170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_B1e-122452132170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_C1e-122452132170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_D1e-122452132170Single-stranded DNA-binding protein WHY2, mitochondrial
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.280090.0flower| root| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453374070.0
Genevisible259942_at0.0
Expression AtlasAT1G71260-
AtGenExpressAT1G71260-
ATTED-IIAT1G71260-
Functional Description ? help Back to Top
Source Description
TAIREncodes WHY2, 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 mitochondria and not the nucleus. WHY2 is a member of the Whirly family proteins present mainly in the plant kingdom performing various activities related to DNA metabolism. Crystal structure of Solanum tuberosum WHY2, a close homolog of Arabidopsis WHY2, reveal that Whirly proteins bind to single strand DNA to promote accurate repair of DNA double-strand breaks over an error-prone repair pathway.
UniProtSingle-stranded DNA-binding protein that associates with mitochondrial DNA and may play a role in the regulation of the gene expression machinery. Seems also to be required to prevent break-induced DNA rearrangements in the mitochondrial genome. Can bind to melt double-stranded DNA in vivo. {ECO:0000269|PubMed:18423020, ECO:0000269|PubMed:20551348, ECO:0000269|PubMed:22762281}.
Function -- GeneRIF ? help Back to Top
  1. AtWhy2 is associated with mtDNA and its overexpression results in the production of dysfunctional mitochondria.
    [PMID: 18423020]
  2. AtWHY2 affects mtDNA copy number in pollen and suggest that low mtDNA copy numbers might be the normal means by which plant cells maintain mitochondrial genetic information.[AtWHIRLY2]
    [PMID: 26195569]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G71260.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: No visible phenotype under normal growth conditions. {ECO:0000269|PubMed:18423020}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G71260
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0721100.0AY072110.1 Arabidopsis thaliana unknown protein (At1g71260) mRNA, complete cds.
GenBankAY1229610.0AY122961.1 Arabidopsis thaliana unknown protein (At1g71260) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_177282.21e-176WHIRLY 2
SwissprotQ8VYF71e-177WHY2_ARATH; Single-stranded DNA-binding protein WHY2, mitochondrial
TrEMBLA0A178W9L51e-173A0A178W9L5_ARATH; WHY2
STRINGAT1G71260.11e-176(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM123582731
Representative plantOGRP23161635
Publications ? help Back to Top
  1. 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]
  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. Maréchal A, et al.
    Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function.
    BMC Plant Biol., 2008. 8: p. 42
    [PMID:18423020]
  7. 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]
  8. 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]
  9. Klopffleisch K, et al.
    Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.
    Mol. Syst. Biol., 2011. 7: p. 532
    [PMID:21952135]
  10. Janicka S, et al.
    A RAD52-like single-stranded DNA binding protein affects mitochondrial DNA repair by recombination.
    Plant J., 2012. 72(3): p. 423-35
    [PMID:22762281]
  11. 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]
  12. 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]
  13. Cai Q,Guo L,Shen ZR,Wang DY,Zhang Q
    Elevation of Pollen Mitochondrial DNA Copy Number by WHIRLY2: Altered Respiration and Pollen Tube Growth in Arabidopsis.
    Plant Physiol., 2015. 169(1): p. 660-73
    [PMID:26195569]