Coevolution of gene expression among interacting proteins.

Area of Science:

• Evolutionary biology
• Systems biology
• Bioinformatics

Background:

• Physically interacting proteins are expected to coevolve to maintain function.
• Coevolution at the amino acid sequence level is established and used for predicting interactions.
• Coexpression of interacting proteins is observed, likely for stoichiometric balance.

Purpose of the Study:

• To investigate if gene expression levels of physically interacting proteins coevolve.
• To determine if expression coevolution is a viable predictor of protein-protein interactions.
• To explore the evolutionary significance of maintaining coexpression.

Main Methods:

• Estimating average gene expression levels using the codon adaptation index (CAI) in four Saccharomyces species.
• Analyzing coordinated changes in expression levels of known interacting proteins across these species.
• Comparing the predictive power of expression coevolution versus sequence coevolution for protein interactions.

Main Results:

• Physically interacting proteins exhibit coordinated changes in their average expression levels across different species.
• Expression coevolution is a more powerful predictor of physical protein interactions than amino acid sequence coevolution.
• The study demonstrates that gene expression levels can indeed coevolve.

Conclusions:

• Gene expression levels coevolve, adding a new dimension to the study of protein interaction evolution.
• Maintaining coexpression of interacting proteins is evolutionarily important.
• Expression coevolution can be utilized for computational prediction of protein-protein interactions.