Patterns of fitness and gene expression epistasis generated by beneficial mutations in the rho and rpoB genes of Escherichia coli during high-temperature adaptation.

Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Escherichia coli. The two genes encode essential functions for transcription, and the mutations in each gene were chosen because they were beneficial for adaptation to thermal stress (42.2°C). The double mutants exhibited patterns of fitness epistasis that included diminishing-returns epistasis at 42.2°C, stronger diminishing-returns between mutations with larger beneficial effects, and both negative and positive (sign) epistasis across environments (20.0°C and 37.0°C). By assessing gene expression between single and double mutants, we detected hundreds of genes with gene expression epistasis. Previous work postulated that highly-connected hub genes in co-expression networks have low epistasis, but we found the opposite: hub genes had high epistasis values in both co-expression and protein-interaction networks. We hypothesized that elevated epistasis in hub genes reflected that they were enriched for targets of Rho termination, but that was not the case. Altogether, gene expression and co-expression analyses revealed that thermal adaptation occurred in modules, through modulation of ribonucleotide biosynthetic processes and ribosome assembly, the attenuation of expression in genes related to heat shock and stress responses, and with an overall trend toward restoring gene expression towards the unstressed state.