Opposing effects of population density and stress on Escherichia coli mutation rate

Abstract

Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis -SIM) and decrease at high population density (density-associated mutation-rate plasticity -DAMP). We hypothesised that these two forms of mutation rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli bacteria in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on errorprone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM result in a mutation rate minimum at intermediate nutrient levels ( ). These findings demonstrate a strikingly close and nuanced relationship of ecological factors -stress and population density -with mutation, the fuel of all evolution.

An extreme mutational hotspot innlpDdepends on transcriptional induction ofrpoS

“…This 3 was enhanced by the activity of the promoter and orientation of the gene, leading to the suggestion that stalled RNA polymerase can allow deamidation of nucleotides on template strands. Such specific mutagenic processes can interact with regional mutational biases, such as genomic strandedness and location, to enhance mutation rates (Horton, Flanagan, Jackson, Priest, & Taylor, 2021;Shepherd, Horton, & Taylor, 2022), but also any process that biases the spectrum of mutations in the genome (Gifford et al, 2024;Krasovec et al, 2018;Sane, Diwan, Bhat, Wahl, & Agashe, 2023). The multitude of mechanistic causes of hotspots has a singular consequence: they increase the production of variants presented to selection (McCandlish & Stoltzfus, 2014), often explaining instances of parallel evolution (Lind, Libby, Herzog, & Rainey, 2019).…”