Transcriptome of E. coli during Long-Term Stationary Phase

Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we begin to unravel the cells' responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program, and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold-shock. By competing cells missing these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment, and lead to identification of novel functions of proteins. Overall design: Analysis of 3 replicates of the transcriptome of E. coli at 6 time points throughout the life cycle. Post inoculation: 4 hours (log phase), 8 hours (late-log phase), 24 hours (stationary phase), 72 hours (death phase), 144 hours (long-term stationary phase), 192 hours (long-term stationary phase)