Anaerobically grown Escherichia coli has an enhanced mutation rate and and distinct mutational spectra

For organisms that are exposed to different environments, the rates and types of spontaneous mutations that arise in each environment can vary, and potentially impact the direction of evolution as a whole. Oxidative stress is a major cause of mutation, but the effect of oxygen availability on the mutation rates and mutation molecular spectrum of organisms grown in aerobic as compared to anaerobic environments is not well understood at the whole genome level. We directly measured the spontaneous mutation rates and spectra of a model facultative anaerobe, Escherichia coli strain REL4536, grown aerobically and anaerobically in long-term mutation accumulation experiments. Whole genome analyses revealed that the spontaneous mutation rate of the anaerobically grown cultures, 4.14 × 10-10 mutations per nucleotide per generation, was greater than that of the aerobically grown cultures, at 2.50 × 10-10 mutations per nucleotide per generation. Different base pair substitutions (BPSs) biases under aerobic and anaerobic growth conditions were observed. In particular, G  T transversions, commonly associated with oxidative DNA damage, were more abundant on the clockwise replichore in aerobically grown cells, while C  T mutations and A  C mutations were more prevalent on the clockwise and counter-clockwise replichores, respectively, of anaerobically grown cells. Structural variations (SVs) were over two-fold more abundant in anaerobically grown cells as compared to aerobically grown cells, where IS150 transposition occurred almost 10 times more frequently. The frequency and spectrum of spontaneous mutations during anaerobic growth provides valuable insights into factors affecting mutations during anaerobic metabolism in facultative anaerobes.