Competition of Escherichia coli DNA Polymerases I, II and III with DNA Pol IV in Stressed Cells

Hastings, P. J.; Hersh, Megan N.; Thornton, P. C.; Fonville, Natalie C.; Slack, Andrew; Frisch, Ryan L.; Ray, Mellanie P.; Harris, Reuben S.; Leal, Suzanne M.; Rosenberg, Susan M.

doi:10.1371/journal.pone.0010862

Cited by 50 publications

(58 citation statements)

References 67 publications

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“…In addition, as with F′ Lac + reversion (e.g., ref. 35), Pol II appears to compete with DinB/Pol IV such that Pol II − cells show increased DSB-dependent SIM that is DinB-dependent (Fig. 3B).…”

Section: Rpos Activates Dsb-dependent Mutation In Unstressed Growingmentioning

confidence: 97%

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

Shee

Gibson

Darrow

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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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...

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Section: Rpos Activates Dsb-dependent Mutation In Unstressed Growingmentioning

confidence: 97%

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

Shee

Gibson

Darrow

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

125

259

View full text Add to dashboard Cite

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“…25 To gain mechanistic insight into such competition, we modeled SOS-induced conditions in vitro by reconstituting RDR using relative concentrations of these polymerases in stressed cells. We found that pol IV, which is the most abundant polymerase during stress, outcompetes other DNA polymerases at D-loops, including the multi-subunit pol III replisome.…”

Section: Pol IV Preferentially Extends D-loops During Stressmentioning

confidence: 99%

“…The mechanism of RDR in stressed E. coli cells, however, appears to be very different. For example, since genetic studies indicate that competition exists between DNA polymerases at D-loops in growth-limited E. coli, 25 RDR is likely to be non-processive during stress. Thus, this particular mode of replication may not utilize the replicative DnaB helicase.…”

Section: Perspectives On Error-prone Rdrmentioning

confidence: 99%

DNA polymerases are error-prone at RecA-mediated recombination intermediates

2013

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G enetic studies have suggested thatY-family translesion DNA polymerase IV (DinB) performs error-prone recombination-directed replication (RDR) under conditions of stress due to its ability to promote mutations during double-strand break (DSB) repair in growth-limited E. coli cells. In recent studies we have demonstrated that pol IV is preferentially recruited to D-loop recombination intermediates at stressinduced concentrations and is highly mutagenic during RDR in vitro. These findings verify longstanding genetic data that have implicated pol IV in promoting stress-induced mutagenesis at D-loops. In this Extra View, we demonstrate the surprising finding that A-family pol I, which normally exhibits high-fidelity DNA synthesis, is highly error-prone at D-loops like pol IV. These findings indicate that DNA polymerases are intrinsically error-prone at RecA-mediated D-loops and suggest that auxiliary factors are necessary for suppressing mutations during RDR in non-stressed proliferating cells.

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“…The genetic system is composed of strains with both an antimutator dnaE allele (dnaE915) (21), encoding a variant of the replicative DNA polymerase active subunit, Pol III␣(915), and the wild-type dinB (dinB ϩ ) or the catalytically inactive dinB(D103N) allele. Pol III␣(915) is an antimutator either because it synthesizes DNA slower than the native replicative DNA polymerase active subunit, DNA Pol III␣ (21,22), or because it might inhibit low-fidelity DNA synthesis by TLS DNA polymerases, specifically DinB (23). Its antimutator activity is also dependent upon another TLS DNA polymerase, DNA Pol II, which likely prevents mutagenesis generated by DinB (24).…”

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confidence: 99%

Selection of dinB Alleles Suppressing Survival Loss upon dinB Overexpression in Escherichia coli

et al. 2014

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Escherichia coli strains overproducing DinB undergo survival loss; however, the mechanisms regulating this phenotype are poorly understood. Here we report a genetic selection revealing DinB residues essential to effect this loss-of-survival phenotype. The selection uses strains carrying both an antimutator allele of DNA polymerase III (Pol III) ␣-subunit (dnaE915) and either chromosomal or plasmid-borne dinB alleles. We hypothesized that dnaE915 cells would respond to DinB overproduction differently from dnaE ؉ cells because the dnaE915 allele is known to have an altered genetic interaction with dinB ؉ compared to its interaction with dnaE ؉ . Notably, we observe a loss-of-survival phenotype in dnaE915 strains with either a chromosomal catalytically inactive dinB(D103N) allele or a low-copy-number plasmid-borne dinB ؉ upon DNA damage treatment. Furthermore, we find that the loss-of-survival phenotype occurs independently of DNA damage treatment in a dnaE915 strain expressing the catalytically inactive dinB(D103N) allele from a low-copy-number plasmid. The selective pressure imposed resulted in suppressor mutations that eliminated growth defects. The dinB intragenic mutations examined were either base pair substitutions or those that we inferred to be loss of function (i.e., deletions and insertions). Further analyses of selected novel dinB alleles, generated by single-base-pair substitutions in the dnaE915 strain, indicated that these no longer effect loss of survival upon overproduction in dnaE ؉ strains. These mutations are mapped to specific areas of DinB; this permits us to gain insights into the mechanisms underlying the DinB-mediated overproduction loss-of-survival phenotype.A ll cells accumulate DNA damage that, if left unrepaired, will stall DNA replication due to the inability of high-fidelity DNA polymerases (Pol) to use lesion-containing DNA as templates, a potentially lethal event (1). To ensure survival, Escherichia coli responds to replication fork stalling by upregulating the expression of the SOS-regulated genes (1-3), among which are specialized low-fidelity DNA polymerase genes. These polymerases can perform translesion synthesis (TLS), consisting of both insertion opposite to and elongation from DNA lesions on the template strand (4). TLS can result in elevated mutagenesis. In fact, data suggest that mutations responsible for resistance to several classes of antibiotics require TLS DNA polymerases (5-8). Moreover, these DNA polymerases appear to play a role in the development of disorders such as cancer in metazoans (9-12).E. coli strains lacking the dinB gene (⌬dinB), encoding DinB (DNA Pol IV), one of the TLS DNA polymerases, are sensitive to nitrofurazone (NFZ) and 4-nitroquinoline-1-oxide (4-NQO) (13-15), reagents that generate persistent DNA lesions on the N 2 group of deoxyguanine (N 2 -dG), as well as alkylating agents such as methyl methanesulfonate (MMS) (14,16). Moreover, strains overproducing DinB undergo survival loss. It has been proposed that this is the result of lethal double-s...

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Competition of Escherichia coli DNA Polymerases I, II and III with DNA Pol IV in Stressed Cells

Cited by 50 publications

References 67 publications

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

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

DNA polymerases are error-prone at RecA-mediated recombination intermediates

Selection of dinB Alleles Suppressing Survival Loss upon dinB Overexpression in Escherichia coli

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