Negative feedback as a facilitator of gene network evolution

Despite the examples of protein evolution via mutations in coding sequences, we have very limited understanding on gene network evolution via changes in cis-regulatory elements. Using the galactose network as a model, we studied how the regulatory promoters of the network contribute to the evolved network activity between two yeast species. In Saccharomyces cerevisiae, we combinatorially replaced all regulatory network promoters by their counterparts from Saccharomyces paradoxus, measured the resulting network inducibility profiles, and modeled the results. Lowering relative strength of GAL80-mediated negative feedback by replacing GAL80 promoter was necessary and sufficient to have high network inducibility levels as in S. paradoxus. This was achieved by increasing OFF-to-ON phenotypic switching rates. Competitions performed among strains with or without the GAL80 promoter replacement showed strong relationships between network inducibility and fitness. Our results support the hypothesis that gene network activity can evolve by optimizing the strength of negative-feedback regulation.