Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

Abstract

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 began 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 lacking 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. IMPORTANCE Experimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study, we began to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more-natural conditions.

Molecular Evolutionary Dynamics of Energy Limited Microorganisms

“…These altered dynamics are likely partially due to the effects of stress in energy-depleted environments on the mutation spectrum, which has been noted in prior studies ( Saumaa et al 2002 ; Maharjan and Ferenci 2015 , 2017 , 2018 ; Chib et al 2017 ; Shoemaker and Lennon 2018 ). This recurring pattern of populations in 10- and 100-day treatments being more similar to one another than either were to the 1-day treatment suggests that the main effect of energy limitation on molecular evolution occurred shortly after the populations exited their exponential phase of growth, an observation consistent with recent findings documenting the physiological and cellular changes that microorganisms incur after energy depletion and may be relevant to clinical contexts ( Kram et al 2020 ).…”

Molecular evolutionary dynamics of energy limited microorganisms

“…A similar pattern was also found in our analyses of the direction of molecular evolution at the gene-level, where the degree of divergent evolution was at its lowest for comparisons made between 10 and 100-day regimes across taxa. This recurring pattern suggests that the main effect of energy limitation on molecular evolution occurred shortly after the populations exited their exponential phase of growth, an observation consistent with recent findings documenting the physiological and cellular changes that microorganisms incur after energy depletion 41 .…”

The role of sigma factor competition in bacterial adaptation under prolonged starvation

“…The role of external factors in the evolutionary dynamics in this phase is being increasingly recognized. Although the idea of sustained cultivation of microbes is not new, systematic observation of genomic and transcriptomic changes [106,122,123] in this survival phase has only begun in the last 30 years. From estimating competitive fitness in 10-day-old E. coli cultures [112], we have come a long way to the systemic tracking of E. coli populations over 1200 days under LTSP [8] (Fig.…”