Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions

Area of Science:

• Molecular Biology
• Genetics
• Evolutionary Biology

Background:

• Combinatorial control by multiple transcription factors (TFs) is essential for eukaryotic gene regulation, enhancing specificity and information integration.
• The mechanisms and evolutionary basis of TF co-dependence remain poorly understood.
• The phosphate starvation (PHO) response in yeast provides a model to study natural variation in TF co-dependence.

Purpose of the Study:

• To investigate the molecular mechanisms and evolutionary drivers of co-transcription factor (co-TF) dependence.
• To understand how changes in co-TF dependence can lead to rewiring of gene regulatory networks.
• To compare co-TF dependence in the PHO response between *Saccharomyces cerevisiae* and *Candida glabrata*.

Main Methods:

• Comparative analysis of TF dependence in yeast species (*Saccharomyces cerevisiae* and *Candida glabrata*).
• Biochemical assays to determine DNA binding affinity.
• Machine-learning prediction and yeast one-hybrid assays to identify functional regions.
• Analysis of intrinsically disordered regions (IDRs) and their impact on TF activity.

Main Results:

• *Candida glabrata* Pho4 (CgPho4) exhibits reduced dependence on its co-TF Pho2 and regulates a larger gene set compared to *Saccharomyces cerevisiae* Pho4 (ScPho4).
• CgPho4 binds DNA with higher affinity, and its activity is boosted by two IDRs that enhance the main activation domain.
• An IDR in ScPho4 acts as a double-edged sword, mediating autoinhibition without Pho2 and enhanced activity with Pho2.

Conclusions:

• Evolutionary divergence of IDRs is a key driver of changes in co-TF dependence.
• Altered co-TF dependence, mediated by IDR evolution, can significantly rewire gene regulatory networks.
• This study provides molecular insights into the evolution of gene regulation and TF interdependence.