Evolution of a Eukaryotic Transcription Factor’s co-TF Dependence Involves Multiple Intrinsically Disordered Regions Affecting Activation and Autoinhibition
Combinatorial control by multiple transcription factors (TFs) allows for increased specificity and information integration. Despite its prevalence in eukaryotes and crucial roles in gene regulation, the reason why eukaryotic TFs often depend on one another, and whether and how such codependency evolves, are not well understood. We exploit natural variation in co-TF dependence in the phosphate starvation response between related yeasts to address this question. In Saccharomyces cerevisiae , a bHLH TF, Pho4, relies on the homeodomain co-TF Pho2 to regulate ~28 genes. By contrast, Pho4 in a related yeast pathogen, Candida glabrata , exhibits significantly reduced Pho2 dependence and an expanded target set of ~70 genes. Biochemical analyses showed C. glabrata Pho4 (CgPho4) binds to the same consensus motif with a 3-4 fold higher affinity than ScPho4. A machine-learning-based prediction and yeast two-hybrid assay identified two Intrinsically Disordered Regions (IDRs) in CgPho4 that can boos