Stationary phase-induction of G-->T mutations in Escherichia coli

Culture volume and vessel affect long-term survival, mutation frequency, and oxidative stress of Escherichia coli

Bacteria such as Escherichia coli are frequently studied during exponential- and stationary-phase growth. However, many strains can survive in long-term stationary phase (LTSP), without the addition of nutrients, from days to several years. During LTSP, cells experience a variety of stressors, including reactive oxidative species, nutrient depletion, and metabolic toxin buildup, that lead to physiological responses and changes in genetic stability. In this study, we monitored survival during LTSP, as well as reporters of genetic and physiological change, to determine how the physical environment affects E. coli during long-term batch culture. We demonstrate differences in yield during LTSP in cells incubated in LB medium in test tubes versus Erlenmeyer flasks, as well as growth in different volumes of medium. We determined that these differences are only partially due to differences in oxygen levels by incubating the cells in different volumes of media under anaerobic conditions. Since we hypothesized that differences in long-term survival are the result of changes in physiological outputs during the late log and early stationary phases, we monitored alkalization, mutation frequency, oxidative stress response, and glycation. Although initial cell yields are essentially equivalent under each condition tested, physiological responses vary greatly in response to culture environment. Incubation in lower-volume cultures leads to higher oxyR expression but lower mutation frequency and glycation levels, whereas incubation in high-volume cultures has the opposite effect. We show here that even under commonly used experimental conditions that are frequently treated as equivalent, the stresses experienced by cells can differ greatly, suggesting that culture vessel and incubation conditions should be carefully considered in the planning or analysis of experiments.

Antimutagenic specificities of two plant glycosylases, oxoguanine glycosylase and formamidopyrimidine glycosylase, assayed in vivo

The base-excision repair process protects genomes by removing and replacing altered bases in DNA. Two analogous glycosylases, oxoguanine glycosylase (OGG) and formamidopyrimidine glycosylase (FPG), can start the process by removing oxidized guanine, the most common modification that leads to misreading of DNA. Plants possess genes for both types of glycosylases. We have tested the hypothesis that the two enzymes in plants have diverged in their specificities by inserting the genes for each enzyme from Arabidopsis thaliana L. into Escherichia coli strains designed to indicate the frequencies of the six possible single-base changes. Both enzymes retain the ability to reduce the rate of GC-->TA transversion mutations. Both enzymes also reduce the frequency of two other base-change mutations, GC-->AT and AT-->TA. We do not find a divergence in the repair capabilities of the two enzymes, as measured in E. coli, although surprisingly FPG appears to increase the rate of mutations in one particular strain.