Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.
PLoS Biol 2018;
16:e2005056. [PMID:
29750784 PMCID:
PMC5966242 DOI:
10.1371/journal.pbio.2005056]
[Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/23/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
The stress-induced mutagenesis hypothesis postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to better withstand the stress. This has implications for antibiotic treatment: exposure to subinhibitory doses of antibiotics has been reported to increase bacterial mutation rates and thus probably the rate at which resistance mutations appear and lead to treatment failure. More generally, the hypothesis posits that stress increases evolvability (the ability of a population to generate adaptive genetic diversity) and thus accelerates evolution. Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet subinhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus providing more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress. We developed a system based on plasmid segregation that allows us to measure death and division rates simultaneously in bacterial populations. Using this system, we found that a substantial death rate occurs at the tested subinhibitory concentrations previously reported to increase mutation rate. Taking this death rate into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover, even when antibiotics increase mutation rate, we show that subinhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics. We conclude that antibiotic-induced mutagenesis is overestimated because of death and that understanding evolvability under stress requires accounting for the effects of stress on population dynamics as much as on mutation rate. Our goal here is dual: we show that population dynamics and, in particular, the numbers of cell divisions are crucial but neglected parameters in the evolvability of a population, and we provide experimental and computational tools and methods to study evolvability under stress, leading to a reassessment of the magnitude and significance of the stress-induced mutagenesis paradigm.
The effect of environmental stress on bacterial mutagenesis has been a paradigm-shift discovery. Recent developments include evidence that various antibiotics increase mutation rates in bacteria when used at subinhibitory concentrations. It is therefore suggested that such treatments promote resistance evolution because they increase the generation of genetic variation on which natural selection can act. However, existing methods to compute mutation rate neglect the effect of stress on death and population dynamics. Developing new experimental and computational tools, we find that taking death into account significantly lowers the signal for stress-induced mutagenesis. Moreover, we show that treatments that increase mutation rate do not always lead to increased genetic diversity, which questions the standard paradigm of increased evolvability under stress.
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