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 AT2G02740.2
Common NameATWHY3, PTAC11, T20F6.12, WHY3
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: 267aa    MW: 29640.8 Da    PI: 10.1011
Description ssDNA-binding transcriptional regulator
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G02740.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly220.31.7e-68902281139
       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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.102.0E-7879250IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.71E-8182267IPR009044ssDNA-binding transcriptional regulator
PfamPF085362.5E-5991225IPR013742Plant 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:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
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: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: 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
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A1e-120782452169Single-stranded DNA-binding protein WHY3, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.414600.0flower| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible267474_at1e-168
Expression AtlasAT2G02740-
AtGenExpressAT2G02740-
ATTED-IIAT2G02740-
Functional Description ? help Back to Top
Source Description
TAIREncodes 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.
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 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
  1. 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]
  2. 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
SourceLink
PlantRegMapAT2G02740.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salicylic acid (SA). {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. {ECO:0000269|PubMed:19666500}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G02740
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0153360.0BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.
GenBankBT0156410.0BT015641.1 Arabidopsis thaliana At2g02740 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_178377.20.0ssDNA-binding transcriptional regulator
SwissprotQ66GR60.0WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLA0A178VLN30.0A0A178VLN3_ARATH; WHY3
STRINGAT2G02740.10.0(Arabidopsis thaliana)
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. 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]
  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. 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]
  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. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]