W-box

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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References

  1. ↑ Rushton, Paul; Macdonald, H.; Huttly, A.K.; Lazarus, C.M.; Hooley, R (1995). "Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes". Plant Molecular Biology 29: 29: 691–702. doi:10.1007/bf00041160. PMID 8541496.
  2. 1 2 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.
  3. ↑ Rushton, Paul. "The Lab of Dr. Paul Rushton". wordpress.com. Retrieved 17 June 2013.
  4. ↑ 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.
  5. 1 2 Brand, Fischer, Harter, Kohlbacher and Wanke (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41(21). 9764-9778
  6. ↑ 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.

See also


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