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The W box is a deoxyribonucleic acid (DNA) cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of WRKY transcription factors.[1][2]
Functionality and conservation of the W-box element across plant species has been shown by gel shift experiments, random binding site selection, yeast one-hybrid screens and co-transfection assays performed with many different WRKY proteins. In silico-based studies together with functional studies of plant promoters have identified clusters of W-boxes in stress-inducible promoters. The binding of WRKY proteins to W-boxes is a feature of both biotic and abiotic stress responses, together with other plant processes such as germination.[3] It has also been shown that multiple W-boxes have a synergistic effect on transcription.
Almost all WRKY transcription factors bind preferentially to W-boxes, and since their discovery, this has raised the question as to how they show specificity for the promoters of their target genes.[2] Ciolkowski et al. (2008) showed that although the W-box core is required, adjacent sequences also play a role in determining binding-site preference.[4] Recent evidence suggests that the TGAC core is more degenerate, composed of a guanine adenine cytosine (GAC) core, and the upstream thymine and downstream pyrimidine flanking sequences help dictate recognition by specific WRKY factors.[5] Basic residues of the WRKY protein domain also are believed to recognize the phosphate backbone of the cis-element.[5]
Recently, Yamasaki et al. have determined the solution structure of the C-terminal WRKY domain of Arabidopsis WRKY4 in complex with the W-box DNA by NMR.[6] They found that a four-stranded β-sheet enters the major groove of DNA in a structure they called the β-wedge, where the sheet is nearly perpendicular to the DNA helical ais. As predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA.
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