Genomic analysis of laboratory-evolved, heat-adapted Escherichia coli strains

Adaptive laboratory evolution to high incubation temperatures represents a complex evolutionary problem, and each study to date performed in Escherichia coli has resulted in a different set of mutations. We performed adaptive laboratory evolution of E. coli to heat by passaging a culture at elevated temperatures for 150 days. Throughout the adaptive evolution we expressed a set of genes that induce hyper-mutagenesis. These growth conditions yielded a strain with a maximum growth temperature approximately 2 °C above that of the parental strain. We preserved evolved isolates weekly and obtained and analyzed whole-genome sequencing data for three isolates from different time points. We identified hundreds of mutations, including mutations in components of the RNA polymerase (RpoB, RpoC and RpoD), Rho, and the heat shock proteins GroES, GroEL, DnaK, ClpB, IbpA and HslU. We compared the proteomes of the starting strain and final strain grown at 37 °C and 42.5 °C and identified changes in abundance between samples for GroESL, HslVU, DnaK, ClpB and other important proteins. This study details a distinct evolutionary route towards enhanced thermotolerance, contributes to our understanding of adaptation to heat in Escherichia coli and may provide insights into heat adaptation in other organisms.