W-box refers to promoter elements with the sequence TTGACC or TTGACT.
The W box (TTGACC ⁄ T) is the binding site for the WRKY family of transcription factors transcription factor. Nearly twenty years of research have shown that the conservation of the WRKY domain in WRKY transcription factors is mirrored by a remarkable conservation of its cognate binding site, the W box (TTGACC ⁄ T). This conservation 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. It has also been shown that multiple W boxes have a synergistic effect on transcription.
Almost all WRKY TFs 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. We still cannot fully answer this question, but Ciolkowski et al. (2008) showed that although the W box core is required, adjacent sequences also play a role in determining binding-site preference. 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.
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. 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 axis. As predicted amino acids in the conserved WRKYGQK signature motif contact the W box DNA.
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- Rushton PJ, Somssich IE, Ringler P, Shen QJ (May 2010). "WRKY transcription factors". Trends Plant Sci. 15 (5): 247–58. doi:10.1016/j.tplants.2010.02.006. PMID 20304701.
- Ciolkowski, I.; Wanke D; Birkenbihl RP; Somssich IE. (2008). "Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function". Plant Mol Biol. 68: 81–92. doi:10.1007/s11103-008-9353-1. PMID 18523729.
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- Yamasaki, K.; Kigawa T; Watanabe S; Inoue M; Yamasaki T; Seki M; Shinozaki K; Yokoyama S. (2012). "Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor". J. Biol. Chem. 287: 7683–91. doi:10.1074/jbc.M111.279844. PMID 22219184.
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