A single residue determines yAP-1 DNA-binding motif specificity. (A) Alignment and phylogeny of AP-1 DNA-binding domain basic regions (residues 6 to 20 are shown). Residue 12 (red star) is predictive of preference for overlapping (YRE-O) or adjacent (YRE-A) DNA-binding motifs (left). Note that Yap8 possesses an Asp at residue 12 and binds a 2-bp overlapping YRE-O (Harbison et al. 2004). Positions affecting Gcn4 half-site spacing preference (Kim and Struhl 1995) are shown (gray stars). (B) Recognition of the yAP-1 half-site (Fujii et al. 2000). Residue 12 (red star) is in close proximity to residues conferring AP-1 sequence specificity. (C,D) ScYap1.R79K and ScYap4.K252R mutants have altered half-site spacing preference as evidenced by ChIP-chip (Methods). P-values refer to differences in binding to genes with either YRE-O or YRE-A sites as assessed by Fisher's exact test. (E,F) ScYap1.R79K and ScYap4.K252R mutations cause mRNA expression changes among genes with YRE-O and YRE-A sites among the top 50 most differentially expressed genes. P-values denote the significance of YRE-A and YRE-O motifs among gene promoters compared with the genomic background.
