title: Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays.
abstract: WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the 'TTGACY' W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA-protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function.
authors: Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany and Department of Computer Science, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72076 Tübingen, Germany.
authors: Luise H
authors: LH
authors: Brand
authors: Nina M
authors: NM
authors: Fischer
authors: Klaus
authors: K
authors: Harter
authors: Oliver
authors: O
authors: Kohlbacher
authors: Dierk
authors: D
authors: Wanke
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D019143:Evolution, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein; D014157:Transcription Factors / Q000737:chemistry* / Q000145:classification / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D014157:Transcription Factors; C517320:WRKY11 protein, Arabidopsis; C557638:WRKY50 protein, Arabidopsis
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