On the fidelity of DNA replication: herpes DNA potymerase and its associated exonuclease

Abbotts, John; Nishiyama, Yukihiro; Yoshida, Shonen; Loeb, Lawrence A.

doi:10.1093/nar/15.3.1185

Cited by 15 publications

(7 citation statements)

References 39 publications

(24 reference statements)

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“…It is unclear what influences the number of novel SNPs/INDELs in a given strain. The number of novel mutations that we detected is higher than that which may be expected, given that HSV-1 polymerase has a lower error rate than eukaryotic polymerases (45). Recombination studies in vaccinia virus found a small number of rare mutations, with a low estimated error rate of 1 ϫ 10 Ϫ8 mutation per nucleotide copied per cycle of replication (46).…”

Section: Resultsmentioning

confidence: 52%

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

Lee

Kolb

Sverchkov

et al. 2015

J Virol

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Herpes simplex virus 1 (HSV-1) causes recurrent mucocutaneous ulcers and is the leading cause of infectious blindness and sporadic encephalitis in the United States. HSV-1 has been shown to be highly recombinogenic; however, to date, there has been no genome-wide analysis of recombination. To address this, we generated 40 HSV-1 recombinants derived from two parental strains, OD4 and CJ994. The 40 OD4-CJ994 HSV-1 recombinants were sequenced using the Illumina sequencing system, and recombination breakpoints were determined for each of the recombinants using the Bootscan program. Breakpoints occurring in the terminal inverted repeats were excluded from analysis to prevent double counting, resulting in a total of 272 breakpoints in the data set. By placing windows around the 272 breakpoints followed by Monte Carlo analysis comparing actual data to simulated data, we identified a recombination bias toward both high GC content and intergenic regions. A Monte Carlo analysis also suggested that recombination did not appear to be responsible for the generation of the spontaneous nucleotide mutations detected following sequencing. Additionally, kernel density estimation analysis across the genome found that the large, inverted repeats comprise a recombination hot spot. IMPORTANCEHerpes simplex virus 1 (HSV-1) virus is the leading cause of sporadic encephalitis and blinding keratitis in developed countries. HSV-1 has been shown to be highly recombinogenic, and recombination itself appears to be a significant component of genome replication. To date, there has been no genome-wide analysis of recombination. Here we present the findings of the first genomewide study of recombination performed by generating and sequencing 40 HSV-1 recombinants derived from the OD4 and CJ994 parental strains, followed by bioinformatics analysis. Recombination breakpoints were determined, yielding 272 breakpoints in the full data set. Kernel density analysis determined that the large inverted repeats constitute a recombination hot spot. Additionally, Monte Carlo analyses found biases toward high GC content and intergenic and repetitive regions. Herpes simplex virus 1 (HSV-1) is a double-stranded DNA (dsDNA) virus in the Alphaherpesvirinae subfamily which causes recurrent, mucocutaneous lesions. HSV-1 is the leading cause of both sporadic encephalitis and infectious keratitis in the United States (1, 2). Animal studies have shown that disease severity is dependent on three factors: innate host resistance, the host immune response, and the viral strain (1, 3-16). Previous work of ours examining the role of the viral strain in virulence involved generating recombinant HSV-1 strains through mixed infections with two strains, OD4 and CJ994 (17). The advent of next-generation sequencing technologies has allowed multiple HSV-1 genomes to be sequenced (18,19), thus allowing the opportunity to sequence previously generated recombinants and examine genome-level recombination phenomena.The HSV-1 genome is approximately 152 kb in length and is arra...

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Section: Resultsmentioning

confidence: 52%

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

Lee

Kolb

Sverchkov

et al. 2015

J Virol

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“…For example, it was demonstrated that recombinants containing mutated Exo III Pol are extremely mutagenic and replicate the thymidine kinase (tk) gene at a mutation frequency approximately 300-to 800-fold higher than that of wild-type Pol (12). These recombinants, however, replicated with only a four-to fivefold increase in the mutation frequency of the supF gene in a plasmid-borne assay (13), supporting an earlier hypothesis that HSV-1-associated exonuclease activity has a negligible impact on DNA replication accuracy (1). However, the discrepancies between these results could be attributed to sequence context effects, including the sequence compositions of target genes, and the forms of replications.…”

supporting

confidence: 70%

Exonuclease-Deficient Polymerase Mutant of Herpes Simplex Virus Type 1 Induces Altered Spectra of Mutations

Hwang

2003

J Virol

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The effect of exonuclease activity of the herpes simplex virus DNA polymerase (Pol) on DNA replication fidelity was examined by using the supF mutagenesis assay. The recombinants with exonuclease-deficient Pol, containing an integrated supF gene in the thymidine kinase locus (tk), exhibited supF mutation frequencies ranging from 0.14 to 5.6%, consistent with the tk mutation frequencies reported previously (Y. T. Hwang, B.-Y. Liu, D. M. Coen, and C. B. C. Hwang, J. Virol. 71:7791-7798, 1997). The increased mutation frequencies were 10-to 500-fold higher than those observed for wild-type Pol recombinants. The increased mutation frequencies also were significantly higher than those of supF mutant replicated by exonuclease-deficient Pols in the plasmid-borne assay. Furthermore, characterization of supF mutants demonstrated that recombinants with a defective exonuclease induced types and distributions of supF mutations different from those induced by wild-type Pol recombinants. The types of supF mutations induced by exonuclease-deficient recombinants differed between the plasmid-and genome-based assays. The spectra of supF mutations also differed between the two assays. In addition, exonuclease-defective viruses also induced different spectra of supF and tk mutations. Therefore, both the assay methods and the target genes used for mutagenesis studies can affect the repication fidelity of herpes simplex virus type 1 Pol with defective exonuclease activity.

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“…However, because the EBV DNA polymerase possesses an intrinsic proofreading 3Ј to 5Ј exonuclease activity (34,61), fidelity of viral genome replication is thought to be high. Furthermore, the HSV DNA polymerase is more accurate than purified eukaryotic DNA polymerases (62). Thus, coupling of the MMR system with viral genome synthesis might function to increase viral genome integrity, rather than to activate cytotoxic responses.…”

Section: Discussionmentioning

confidence: 99%

Postreplicative Mismatch Repair Factors Are Recruited to Epstein-Barr Virus Replication Compartments

Daikoku

Kudoh

Sugaya

et al. 2006

Journal of Biological Chemistry

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The mismatch repair (MMR) system, highly conserved throughout evolution, corrects nucleotide mispairing that arise during cellular DNA replication. We report here that proliferating cell nuclear antigen (PCNA), the clamp loader complex (RF-C), and a series of MMR proteins like MSH-2, MSH-6, MLH1, and hPSM2 can be assembled to Epstein-Barr virus replication compartments, the sites of viral DNA synthesis. Levels of the DNA-bound form of PCNA increased with progression of viral productive replication. Bromodeoxyuridine-labeled chromatin immunodepletion analyses confirmed that PCNA is loaded onto newly synthesized viral DNA as well as BALF2 and BMRF1 viral proteins during lytic replication. Furthermore, the anti-PCNA, -MSH2, -MSH3, or -MSH6 antibodies could immunoprecipitate BMRF1 replication protein probably via the viral DNA genome. PCNA loading might trigger transfer of a series of host MMR proteins to the sites of viral DNA synthesis. The MMR factors might function for the repair of mismatches that arise during viral replication or act to inhibit recombination between moderately divergent (homologous) sequences. Mismatch repair (MMR)2 systems play a primary role in mutation avoidance by removing base-base and small insertion-deletion mismatches that arise during DNA replication (1). Prokaryotes and eukaryotes have evolved similar systems for repair (2) and in Escherichia coli MMR is initiated when MutS binds to mismatched DNA, possibly through its interaction with the ␤-clamp accessory protein that is required for processive DNA replication (3-6). MutL binds to MutS to form MutS-MutL-DNA complexes that stimulate MutH binding and cleavage of unmethylated DNA strands at GATC sequences, either 5Ј or 3Ј of recognized mismatches. Exonucleases then chew away at the DNA beyond the mismatch site so that highly accurate DNA polymerase III can correctly re-synthesize the strand.In eukaryotes, mismatch recognition is accomplished by MSH2 (MutS homolog 2) forming a heterodimer with either MSH3 or MSH6 to bind to distinct but overlapping spectra of mismatches (7). In both the yeast Saccharomyces cerevisiae and humans, the repair of base-base mismatches appears to be solely dependent on MSH2-MSH6, whereas both MSH2-MSH6 and MSH2-MSH3 can participate in the repair of small (1 to 12-nucleotide) loop insertions. Currently, it is thought that MSH heterodimer binding to a mismatch triggers ATP-dependent steps that allow interactions with MLH (MutL homolog) heterodimers composed of MLH1-Pms1 or MLH1-MLH3 (7,8). No MutH homolog, however, has been identified in eukaryotes, and the exact details of strand discrimination and error removal are not known, although in both yeast and humans a number of other proteins have been implicated in MMR, including proliferating cell nuclear antigen (PCNA), replication factor C (RF-C), and DNA polymerases ␦ and ⑀ (9 -16).PCNA was originally characterized as a DNA sliding clamp for replicative DNA polymerases, but subsequent studies have revealed its striking ability to interact with multiple partner...

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On the fidelity of DNA replication: herpes DNA potymerase and its associated exonuclease

Cited by 15 publications

References 39 publications

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

Exonuclease-Deficient Polymerase Mutant of Herpes Simplex Virus Type 1 Induces Altered Spectra of Mutations

Postreplicative Mismatch Repair Factors Are Recruited to Epstein-Barr Virus Replication Compartments

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