Ancient transcriptional regulators can easily evolve new pair-wise cooperativity

Area of Science:

• Evolutionary biology
• Molecular biology
• Genetics

Background:

• Cells use transcription regulators binding cis-regulatory DNA for gene expression control.
• Pair-wise cooperativity between regulators enables complex gene regulation and network evolution.
• Understanding the origin of cooperative interactions between regulators is crucial for evolutionary insights.

Purpose of the Study:

• To investigate the evolutionary emergence of a specific protein-protein interaction between Matα2 and Mcm1.
• To uncover the structural rules and constraints governing the evolution of transcriptional regulator cooperativity.

Main Methods:

• Deep mutational scanning combined with functional selection for cooperative gene expression.
• Testing millions of alternative evolutionary solutions for the Matα2-Mcm1 interaction interface.
• Analyzing functional variants to identify emergent structural and epistatic rules.

Main Results:

• Approximately 45% of random sequences functioned as well as or better than the natural Matα2-Mcm1 interaction.
• Functional solutions were highly degenerate, allowing diverse amino acid chemistries.
• Widespread epistasis was observed, limiting evolutionary success despite degeneracy.

Conclusions:

• Emergence of cooperativity between transcriptional regulators is not strictly contingent on historical pathways.
• Structural rules and epistatic constraints govern the evolution of protein-protein interactions in gene regulation.
• This work provides mechanistic insights into transcription network plasticity and the evolution of novel interactions.