Epistasis facilitates functional evolution in an ancient transcription factor.

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Genetics

Background:

• Protein function is determined by genetic architecture, but complex interactions were thought to constrain evolution.
• Previous studies often overlooked functional specificity and the evolution of new functions.

Purpose of the Study:

• To develop a novel method for characterizing the global genetic determinants of multiple protein functions.
• To investigate the genetic architecture and evolution of a transcription factor's DNA binding specificity.

Main Methods:

• Utilized ordinal logistic regression to analyze deep mutational scanning (DMS) data.
• Applied a combinatorial DMS approach to a steroid hormone receptor's DNA recognition.
• Examined the impact of genetic architecture on protein-DNA interactions and functional specificity.

Main Results:

• Identified dense main and pairwise effects in DNA recognition, with minimal higher-order epistasis.
• Demonstrated that pairwise interactions significantly influence DNA element specificity.
• Showed that pairwise epistasis expands functional sequence space and facilitates specificity switching.

Conclusions:

• The genetic architecture of DNA recognition is governed by extensive pairwise interactions.
• Pairwise epistasis plays a crucial role in protein functional specificity and the evolution of new functions.
• Contrary to prior assumptions, these interactions facilitate, rather than constrain, evolutionary trajectories.