Figure 8. Divergence of zinc cluster transcription factor (TF) paralogs correlates with changes in motif preferences.

(A) Dimerization and changes in motif preferences may explain divergence of zinc cluster paralogs: Zinc cluster paralogs vary in sequence and localized at different variants of their characteristic motif. Shown on the left with pairwise amino acid (AA) sequence conservation shown as color-code, DNA-binding domain (DBD) position indicated as cyan box, and disorder tendency (Mészáros et al., 2018) shown as black line; motif symbols indicated on the bottom (see Figure 8—figure supplement 1 for motif sequences). For each pair, top-bound promoters were selected, and peak-proximal motifs defined. Shown, as indicated, are promoter-binding signal (pbs, z-score, columns correspond to individual repeats), percentage of total promoter signal 50 bases around the indicated motifs (columns correspond to individual repeats), and binding change upon paralog deletion (log2, mean; *: indicates loss of binding specificity after paralog deletion). Suggested models explaining divergence, and the signal on exemplary promoters (indicated by small gray and black dots next to the pbs panel) are also shown. (B–E) Upc2/Ecm22 diverge through DNA-binding competition: shown in (B) are the disorder tendency (Mészáros et al., 2018) and pairwise sequence conservation of Upc2-Ecm22 along the respective protein length and that of their K. lactis ortholog with Upc2 (Figure 6—figure supplement 1). Promoter-binding preferences in the indicated backgrounds are shown in (C–D). (C) Large dots indicate top 50 K. lactis targets, color-coded by binding signal. Distribution of these targets across the Upc2/Ecm22 binding preferences are shown as histograms (red, gray: all promoters). Note that Upc2 and Ecm22 bind comparably to strong K. lactis targets, while Ecm22 dominates on low-intermediate targets. (D) Large dots indicate Upc2 and Ecm22 top 20 targets (in wild-type background), colors indicate the number of occurrences of the known in vitro motif (TA(T/A)ACGA) and arrows show change in binding relative to the wild-type. (E) Suggested model: Ecm22 and Upc2 bind a common motif, but Upc2 outcompetes Ecm22 on Upc2’s share of ancestral targets.

Figure 8—figure supplement 1. Homo- and heterodimerization’s role in the binding preferences and divergence of dimer-forming transcription factor (TF) paralog pairs.

(A) Heterodimer formation explains asymmetric dependency in the Skn7/Hms2 paralog pair of the HSF DNA-binding domain (DBD) family: Shown are the amino acid (AA) sequence conservation in color-code, DBD indicated as cyan box, and disorder tendency shown as black line. Peak-proximal motif symbols indicated on the bottom. Also shown is the binding behavior to the top-bound target promoters (binding signal of both TFs and their Kluyveromyces lactis ortholog, percentage of total promoter signal 50 bases around the indicated motifs and log2 change after paralog deletion; columns correspond to individual repeats), and binding signal on representative promoters (compare Figure 8A). *: indicates loss of binding specificity after paralog deletion. (B) Competition shapes the binding profile of the Ecm22/Upc2 paralog pair: as in (A) (Figure 8B–E). (C) Identified motifs in the top promoters of each paralog pair: Shown are the schematic and sequences for the proposed TF motifs found in the respective target promoters.