Transcriptome of Aged and Unaged E. coli populations

Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogenous environment. During this incubation, E. coli acquires mutations that are selected for in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogenous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10-days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified putative mutations in the regulatory gene sspA, as well as other genes, that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation, while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive. Analysis of 2 replicates of the transcriptome of E. coli in populations that are unaged (grown overnight) and aged (incubated for 10 days, then frozen and regrown).