Figure 3

bZIP and VHR TFs. (a) Phylogeny and PBM-derived motifs for the eight bZIP and two VHR proteins analyzed in this study. The evolutionary tree was built from a ClustalW2 [59] multiple sequence alignment of the DBDs of the ten proteins, as annotated in UniProt [60]. Green and magenta backgrounds correspond to TFs that bind primarily to overlapping or adjacent half-sites, respectively. TFs that bind Yap-like half-sites are shown in red. TFs that bind Gcn4-like half-sites are shown in blue. All motif logos were generated using EnoLOGOS [58], based on motifs generated from PBM data in this study and Zhu et al. [11] using the Seed-and-Wobble algorithm [8, 15]. The numbers next to the motif logos represent the E-scores of the 8-mer seeds used to construct the motifs [8]. For proteins that bind both overlapping and adjacent half-sites, the motif corresponding to the largest seed E-score (sometimes referred to as the primary motif) is shown in a black box. (b) ClustalW2 multiple sequence alignment of the basic regions of bZIP proteins against the DBDs of VHRs. The Vhr1 and Vhr2 regions shown are the ones that best align to the eight basic regions considered, and they correspond to the first putative VHR basic region (see (e)). The residues shown in red and blue are important for YAP-like versus Gcn4-like half-site specificity. The residues shown in green and magenta are important for overlapping versus adjacent half-site binding. (c) Recognition of Yap-like and Gcn4-like half-sites [30, 61]. (d) Heat map of the DNA-binding preferences of Yap1 (as a representative of the Yap subfamily), Cst6, Sko1, Gcn4, Vhr1, and Vhr2. The rows correspond to 8-mers with an E-score ≥0.35 for any of the six TFs; the columns correspond to the TFs. The E-score scale is shown at the bottom. Black boxes indicate the 8-mers that correspond to various motifs (shown on the right). (e) Alignment of the full DBDs of Vhr1 and Vhr2. Residues that fold into alpha-helices (according to PSIPRED [62]) are shown in bold. Black boxes show the two putative basic domains in VHR proteins. (f) Alignment of the second putative VHR basic region to basic regions of the eight bZIPs analyzed in this study.