Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation

Escarceller, Mònica; Hicks, J. Kevin; Guðmundsson, Guðmundur A.; Trump, Gary N.; Touati, Danièle; Lovett, Susan; Foster, Patricia L.; McEntee, Kevin; Goodman, Myron F.

doi:10.1128/jb.176.20.6221-6228.1994

Cited by 86 publications

(68 citation statements)

References 56 publications

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“…Pol II, encoded by the polB gene, is an accurate DNA polymerase that is also induced as part of the SOS response (4). In a polB mutant strain adaptive mutation is increased 10-fold (15). As in a recG mutant strain, levels of Pol IV are elevated in polB mutant cells (44) and all of the extra mutations are due to Pol IV (22).…”

Section: Role Of Recgmentioning

confidence: 99%

Adaptive Mutation in Escherichia coli

Foster¹

2000

Cold Spring Harbor Symposia on Quantitative Biology

102

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In 1988 John Cairns, Julie Overbaugh, and Stephan Miller published a paper entitled "The origin of mutants," in which they suggested that bacteria could choose which mutations to make (11). Shortly thereafter, Cairns and I began collaborating on a National Science Foundation-funded project to investigate the genetic basis of what was popularly called "directed mutation" (although at the time we were calling it "selectiondependent mutation," which now seems as good a name as any). Our plan was to mutagenize an appropriate strain of Escherichia coli and identify and characterize variants defective in selection-dependent mutation. Cairns and coworkers had been investigating a strain called SM195, described in their original paper (11). However, the mechanisms of mutation in this strain had proved to be complicated, and we wanted a new experimental subject. We were setting up to investigate selection-induced activation of the cryptic bgl operon (36), when Jeffrey Miller gave us a Lac Ϫ strain, called ␣45, that he said had a high rate of reversion to Lac ϩ after plating on minimum lactose medium. The lac allele in this strain is a fusion of lacI to lacZ that eliminates the lac regulatory region as well as several residues of lacI and lacZ; transcription of the fusion is constitutive, initiating at the lacI promoter (7). ␣45 has a ϩ1 frameshift mutation, lacI33, in the lacI coding region (12). Miller and coworkers have used several similar strains to study various mutational mechanisms (52, 67). As in many of the strains that originated with Jacob and Monod, proAB and lac are deleted from the chromosome and carried on an episome, FЈ128. This arrangement greatly facilitates genetic manipulations and turned out to be important to adaptive mutation. We mated the episome from ␣45 into a ⌬(lac-pro) recipient that we had made rifampin resistant and named the new strain FC40 (Foster and Cairns #40).In our first paper (10), we showed that Lac ϩ revertants of FC40 accumulate at a constant rate for about a week after the cells are plated on minimal lactose plates. Two days after plating (the first day that Lac ϩ colonies appear), the numbers of mutants among cultures has a Luria-Delbrück distribution (meaning that the mutations occurred prior to plating), whereas on subsequent days the distribution becomes Poisson (meaning that the mutations occurred after plating). After 5 days on lactose plates, there are about 100 Lac ϩ colonies per 10 8 cells plated. We calculated that the normal preplating mutation rate was about 10 Ϫ9 Lac ϩ revertants per cell per generation, whereas the postplating mutation rate was about 10 Ϫ9 per cell per h; considering that the doubling time in minimal medium is about an hour, this means that per unit time, the two mutation rates are the same. We have never figured out if this similarity is informative or merely a coincidence.The high postplating reversion rate of FC40 allowed us to eliminate a number of artifactual explanations for the phenomenon. In our first paper (10) we ruled out the possibility ...

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Section: Role Of Recgmentioning

confidence: 99%

Adaptive Mutation in Escherichia coli

Foster¹

2000

Cold Spring Harbor Symposia on Quantitative Biology

102

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“…The oligodeoxynucleotide containing Ua was prepared by hydrolysis of the Oa-containing oligodeoxynucleotide (30). Each oligonucleotide was ligated into a singlestranded bacteriophage M13mp7L2 vector as described (39 (41). For the pol IV Ϫ strain, P1 transduction was used to transfer the ⌬dinBW2::cat allele (18) to E. coli AB1157.…”

Section: Methodsmentioning

confidence: 99%

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

Neeley

Delaney

Alekseyev

et al. 2007

Journal of Biological Chemistry

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Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.The genome is continually damaged by spontaneously generated and environmental chemical agents. Many of the lesions formed in DNA strongly inhibit replicative polymerases. If repair of these lesions fails or is not fast enough, cells can biochemically adapt to "tolerate" the toxic DNA lesions, as evidenced by replication of the damaged DNA (1). Human cells possess at least 15 DNA polymerases, including 5 that are referred to as translesion synthesis (TLS) 3 polymerases and are specifically involved in the replication of damaged DNA. Four of these enzymes, pol , pol , pol , and REV1, belong to the Y family of DNA polymerases, whereas pol belongs to the B family (2). Escherichia coli possess three polymerases, pol II, pol IV, and pol V, whose expression levels are up-regulated in response to DNA damage. Extensive research on the structure and function of these polymerases and their homologues suggests that these polymerases allow replication to progress in the presence of DNA lesions that are strongly inhibitory to the replicative polymerase, pol III (1). The presence of the three SOSinducible polymerases allows E. coli to be used as a model system for DNA replication past damage products.pol II (pol B) (3) is a B family DNA polymerase and has 3Ј 3 5Ј-exonuclease activity. Consequently, this enzyme replicates normal DNA with high fidelity and has an error rate less of than 10 Ϫ6 (4). pol II participates in error-free replication restart (5, 6) and can also carry out TLS past abasic sites (3, 7), 3,N 4 -ethenocytosine (8), and N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (9). pol IV (DinB) (10) and pol V (UmuD 2 ЈC) (11) are members of the Y family of DNA polymerases, which have less sterically restrictive active sites than normal replicative polymerases (12) and lack exonuclease activity (1). The error rates of these polymerases are much higher than the other E. coli polymerases and are on the order of 10 Ϫ4 to 10 Ϫ5 for pol IV (13) and 10 Ϫ3 to 10 Ϫ4...

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“…pol II was subsequently shown to be encoded by the DNA damage-inducible polB (dinA) gene (3)(4)(5). A ⌬polB strain shows no measurable UV sensitivity, and SOS-induced mutagenesis occurs at normal levels (6,7). However, a ⌬polB ⌬umuDC double mutant strain is more sensitive to killing by UV light than either of the single mutant strains, implying that the two SOS-induced polymerases might play compensatory roles in vivo (8).…”

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confidence: 99%

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli

Pham

Rangarajan

Woodgate

et al. 2001

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

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DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD 2 proteins, working in conjunction with RecA, single-stranded DNA (ssDNA)-binding protein (SSB), ␤ sliding clamp, and ␥ clamp loading complex, are responsible for most SOS lesion-targeted mutations in Escherichia coli, by catalyzing translesion synthesis (TLS). DNA polymerase II, the product of the damage-inducible polB (dinA ) gene plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Replication-restart takes place almost immediately after the DNA is damaged (Ϸ2 min post-UV irradiation), whereas TLS occurs after pol V is induced Ϸ50 min later. We discuss recent data for pol V-catalyzed TLS and pol II-catalyzed replicationrestart. Specific roles during TLS for pol V and each of its accessory factors have been recently determined. Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins.T wo seemingly unconnected questions arising during the early and mid 1970s were to decipher the biochemical basis of SOS mutagenesis in Escherichia coli, often referred to as SOS errorprone repair (1), and to determine a cellular role for E. coli DNA polymerase II. A tentative link between the two was established when it was determined that pol II was induced as part of the LexA-regulon (2). pol II was subsequently shown to be encoded by the DNA damage-inducible polB (dinA) gene (3-5). A ⌬polB strain shows no measurable UV sensitivity, and SOS-induced mutagenesis occurs at normal levels (6, 7). However, a ⌬polB ⌬umuDC double mutant strain is more sensitive to killing by UV light than either of the single mutant strains, implying that the two SOS-induced polymerases might play compensatory roles in vivo (8).The ability of pols II and V to complement each other does not mean that these activities are functionally redundant, and indeed they are not. pol V is able to copy UV-damaged DNA in a process referred to as error-prone translesion synthesis (TLS). TLS generates mutations targeted specifically to DNA template damage sites (9-12). In contrast, pol II copies chromosomal DNA during error-free replication-restart (8). Although both polymerases are induced by DNA damage, they appear to function on widely disparate time frames-pol II-catalyzed replication-restart occurs 2 min post-UV irradiation whereas pol V-catalyzed TLS begins roughly 50 min later (8). In this paper, we discuss current models for the roles of pol V in TLS and pol II in replication-restart.Coping with DNA Damage in E. coli There are over 40 genes induced on DNA damage in E. coli that have been identified recently by using microarray chip technology (13), of which at least 31 are known to be negatively regulated at the transcriptional level by the LexA protein (14). Many of these genes encode proteins required to repair DNA damage (15). The overriding importance of DNA repair is apparent from the ob...

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Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation

Cited by 86 publications

References 56 publications

Adaptive Mutation in Escherichia coli

Adaptive Mutation in Escherichia coli

DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli

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