Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli

Abstract

Basic ideas about the constancy and randomness of mutagenesis that drives evolution were challenged by the discovery of mutation pathways activated by stress responses. These pathways could promote evolution specifically when cells are maladapted to their environment (i.e., are stressed). However, the clearest example-a general stress-response-controlled switch to errorprone DNA break (double-strand break, DSB) repair-was suggested to be peculiar to an Escherichia coli F′ conjugative plasmid, not generally significant, and to occur by an alternative stress-independent mechanism. Moreover, mechanisms of spontaneous mutation in E. coli remain obscure. First, we demonstrate that this same mechanism occurs in chromosomes of starving F − E. coli. I-SceI endonuclease-induced chromosomal DSBs increase mutation 50-fold, dependent upon general/starvation-and DNA-damage-stress responses, DinB error-prone DNA polymerase, and DSB-repair proteins. Second, DSB repair is also mutagenic if the RpoS generalstress-response activator is expressed in unstressed cells, illustrating a stress-response-controlled switch to mutagenic repair. Third, DSB survival is not improved by RpoS or DinB, indicating that mutagenesis is not an inescapable byproduct of repair. Importantly, fourth, fully half of spontaneous frame-shift and base-substitution mutation during starvation also requires the same stress-response, DSB-repair, and DinB proteins. These data indicate that DSB-repairdependent stress-induced mutation, driven by spontaneous DNA breaks, is a pathway that cells usually use and a major source of spontaneous mutation. These data also rule out major alternative models for the mechanism. Mechanisms that couple mutagenesis to stress responses can allow cells to evolve rapidly and responsively to their environment.antibiotic resistance | cancer | genome evolution | rapid evolution | stressinduced mutagenesis H ow, when, and where mutations form underpins understanding pathogen-host interactions, antibiotic resistance, aging, cancer progression and therapy resistance, and evolution generally. Initial models of mutagenesis that drives evolution imagined random stochastic processes, roughly constant with time, and blind to selective environments (1). In contrast, bacterial, yeast, and human cells appear to possess mechanisms that induce mutation pathways specifically during stress, under the control of stress responses (2) (stress-induced mutagenesis or SIM). These pathways suggest mechanisms by which genetic diversity could be generated preferentially when cells are maladapted to their environment (i.e., are stressed), potentially accelerating evolution responsively to environments, a major departure from classic views (1). However, the significance of such mechanisms has been debated, as have the mechanisms themselves.First, mutagenesis associated with the DNA-damage response has been argued to be an unavoidable consequence of induced DNA repair (3, 4), not an evolutionary engine (5, 6). Second, the strongest support for the idea of increas...

Mitochondrial Genome Maintenance: Roles for Nuclear Nonhomologous End-Joining Proteins inSaccharomyces cerevisiae

“…These data demonstrate the relatively modest effect of MRX and Ku70/80 on nuclear mutation avoidance, while supporting a hypothesis in which these complexes contribute directly to mitochondrial mutagenesis, possibly via error-prone joining of DSBs. DSB repair-dependent mutagenesis has been observed in organisms, including Escherichia coli, yeast, and humans (Strathern et al 1995;Bentley et al 2004;Yang et al 2008b;Shee et al 2011). In E. coli the same mechanisms have been found to be responsible for mutagenesis at the sites of DSBs as well as spontaneous mutations (Shee et al 2011).…”

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in Starving Escherichia coli

“…RpoE promotes MBR at some genomic sites by promoting formation of DSBs by an as yet undetermined mechanism . RpoS licenses the use of DinB and other error-prone DNA polymerases in break repair by an unknown mechanism (Ponder et al 2005;Frisch et al 2010;Shee et al 2011). The SOS DNA-damage response is required for SNV formation (McKenzie et al 2000) and promotes MBR by its induction of the DinB error-prone DNA polymerase (McKenzie et al 2001;Galhardo et al 2009).…”

“…Repair of DNA double-stranded breaks (DSBs) in E. coli is switched from high fidelity to a mutagenic mode during starvation stress under control of the RpoS general/starvation stress response (Ponder et al 2005;Shee et al 2011;Rosenberg et al 2012). DSB repair switches either to a mutagenic homologous recombination (HR)-mediated repair pathway, using errorprone translesion DNA polymerases IV (DinB or Pol IV) (Ponder et al 2005), Pol V (Petrosino et al 2009;Shee et al 2011), or Pol II (Frisch et al 2010), which creates base substitution and indel mutations [single-nucleotide variations (SNVs)], or to a "micro-homologous" pathway that causes genome rearrangement [gross chromosomal rearrangements (GCRs)] using DNA Pol I [reviewed in Rosenberg et al (2012) and Rogers et al (2015)]. Both SNV and GCR pathways require RecA, RuvC, and RecBC HR proteins.…”

Epigenetic psychiatry: potential of the pre-emptive adaptation

“…Coupling of inducible mutagenesis pathways to a general stress response as RpoS causes that epigenetic diversity is generated responsively to different stressors and environments. Stress-induced mutagenesis and phenotypic diversification also contribute to climate/heat stress-induced increased expression of epigenetic variation causing rapid evolution [1,4].…”