The effects of network neighbours on protein evolution

Interacting proteins may often experience similar selection pressures. Thus, we may expect that neighbouring proteins in biological interaction networks evolve at similar rates. This has been previously shown for protein-protein interaction networks. Similarly, we find correlated rates of evolution of neighbours in networks based on co-expression, metabolism, and synthetic lethal genetic interactions. While the correlations are statistically significant, their magnitude is small, with network effects explaining only between 2% and 7% of the variation. The strongest known predictor of the rate of protein evolution remains expression level. We confirmed the previous observation that similar expression levels of neighbours indeed explain their similar evolution rates in protein-protein networks, and showed that the same is true for metabolic networks. In co-expression and synthetic lethal genetic interaction networks, however, neighbouring genes still show somewhat similar evolutionary rates even after simultaneously controlling for expression level, gene essentiality and gene length. Thus, similar expression levels and related functions (as inferred from co-expression and synthetic lethal interactions) seem to explain correlated evolutionary rates of network neighbours across all currently available types of biological networks.