scholarly journals Relevance of GC content to the conservation of DNA polymerase III/mismatch repair system in Gram-positive bacteria

2013 ◽  
Vol 4 ◽  
Author(s):  
Motohiro Akashi ◽  
Hirofumi Yoshikawa
Keyword(s):  
Mismatch Repair ◽  
Dna Polymerase ◽  
Gc Content ◽  
Repair System ◽  
Dna Polymerase Iii ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Polymerase Iii ◽  
Mismatch Repair System

scholarly journals Slipped Misalignment Mechanisms of Deletion Formation: In Vivo Susceptibility to Nucleases

1999 ◽  
Vol 181 (2) ◽  
pp. 477-482 ◽  
Author(s):  
Malgorzata Bzymek ◽  
Catherine J. Saveson ◽  
Vladimir V. Feschenko ◽  
Susan T. Lovett
Keyword(s):  
Mismatch Repair ◽  
Dna Polymerase ◽  
Repeated Sequences ◽  
Repair System ◽  
Dna Polymerase Iii ◽  
Exonuclease I ◽  
Polymerase Iii ◽  
Mismatch Repair System ◽  
Genetic Rearrangements

ABSTRACT Misalignment of repeated sequences during DNA replication can lead to deletions or duplications in genomic DNA. In Escherichia coli, such genetic rearrangements can occur at high frequencies, independent of the RecA-homologous recombination protein, and are sometimes associated with sister chromosome exchange (SCE). Two mechanisms for RecA-independent genetic rearrangements have been proposed: simple replication misalignment of the nascent strand and its template and SCE-associated misalignment involving both nascent strands. We examined the influence of the 3′ exonuclease of DNA polymerase III and exonuclease I on deletion via these mechanisms in vivo. Because mutations in these exonucleases stimulate tandem repeat deletion, we conclude that displaced 3′ ends are a common intermediate in both mechanisms of slipped misalignments. Our results also confirm the notion that two distinct mechanisms contribute to slipped misalignments: simple replication misalignment events are sensitive to DNA polymerase III exonuclease, whereas SCE-associated events are sensitive to exonuclease I. If heterologies are present between repeated sequences, the mismatch repair system dependent on MutS and MutH aborts potential deletion events via both mechanisms. Our results suggest that simple slipped misalignment and SCE-associated misalignment intermediates are similarly susceptible to destruction by the mismatch repair system.

scholarly journals In Vitro Antimicrobial Activities of Novel Anilinouracils Which Selectively Inhibit DNA Polymerase III of Gram-Positive Bacteria

2000 ◽  
Vol 44 (8) ◽  
pp. 2217-2221 ◽  
Author(s):  
Jennifer S. Daly ◽  
Theodore J. Giehl ◽  
Neal C. Brown ◽  
Chengxin Zhi ◽  
George E. Wright ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Antimicrobial Activities ◽  
Dna Polymerase Iii ◽  
Coagulase Negative Staphylococci ◽  
Gram Positive ◽  
New Agents ◽  
Gram Positive Bacteria ◽  
Polymerase Iii ◽  
Time Kill

ABSTRACT The 6-anilinouracils are novel dGTP analogs that selectively inhibit the replication-specific DNA polymerase III of gram-positive eubacteria. Two specific derivatives, IMAU (6-[3′-iodo-4′-methylanilino]uracil) and EMAU (6-[3′-ethyl-4′-methylanilino]uracil), were substituted with either a hydroxybutyl (HB) or a methoxybutyl (MB) group at their N3 positions to produce four agents: HB-EMAU, MB-EMAU, HB-IMAU, and MB-IMAU. These four new agents inhibited Staphylococcus aureus, coagulase-negative staphylococci, Enterococcus faecalis, and Enterococcus faecium. Time-kill assays and broth dilution testing confirmed bactericidal activity. These anilinouracil derivatives represent a novel class of antimicrobials with promising activities against gram-positive bacteria that are resistant to currently available agents, validating replication-specific DNA polymerase III as a new target for antimicrobial development.

The 3′–5′ exonuclease site of DNA polymerase III from Gram-positive bacteria: definition of a novel motif structure

Gene ◽  
1995 ◽  
Vol 165 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Marjorie H. Barnes ◽  
Peter Spacciapoli ◽  
Dong Hui Li ◽  
Neal C. Brown
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerase Iii ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Polymerase Iii ◽  
Definition Of

scholarly journals Inhibitors of DNA Polymerase III as Novel Antimicrobial Agents against Gram-Positive Eubacteria

1999 ◽  
Vol 43 (8) ◽  
pp. 1982-1987 ◽  
Author(s):  
Paul M. Tarantino ◽  
Chengxin Zhi ◽  
George E. Wright ◽  
Neal C. Brown
Keyword(s):  
Dna Polymerase ◽  
Antimicrobial Agents ◽  
Staphylococcal Infection ◽  
Dna Polymerase Iii ◽  
Chromosomal Dna ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Gram Positive Bacteria ◽  
Polymerase Iii

ABSTRACT 6-Anilinouracils are selective inhibitors of DNA polymerase III, the enzyme required for the replication of chromosomal DNA in gram-positive bacteria (N. C. Brown, L. W. Dudycz, and G. E. Wright, Drugs Exp. Clin. Res. 12:555–564, 1986). A new class of 6-anilinouracils based on N-3 alkyl substitution of the uracil ring was synthesized and analyzed for activity as inhibitors of the gram-positive bacterial DNA polymerase III and the growth of gram-positive bacterial pathogens. Favorable in vitro properties of N-3-alkyl derivatives prompted the synthesis of derivatives in which the R group at N-3 was replaced with more-hydrophilic methoxyalkyl and hydroxyalkyl groups. These hydroxyalkyl and methoxyalkyl derivatives displayed Ki values in the range from 0.4 to 2.8 μM against relevant gram-positive bacterial DNA polymerase IIIs and antimicrobial activity with MICs in the range from 0.5 to 15 μg/ml against a broad spectrum of gram-positive bacteria, including methicillin-resistant staphylococci and vancomycin-resistant enterococci. Two of these hydrophilic derivatives displayed protective activity in a simple mouse model of lethal staphylococcal infection.

scholarly journals DNA Polymerases of Low-GC Gram-Positive Eubacteria: Identification of the Replication-Specific Enzyme Encoded by dnaE

2002 ◽  
Vol 184 (14) ◽  
pp. 3834-3838 ◽  
Author(s):  
Marjorie H. Barnes ◽  
Shelley D. Miller ◽  
Neal C. Brown
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Polymerase Iii ◽  
Specific Enzyme ◽  
Gram Positive ◽  
Pol Ii ◽  
Gram Positive Bacteria ◽  
Polymerase Iii ◽  
Antigenic Properties ◽  
Pol Iii

ABSTRACT dnaE, the gene encoding one of the two replication-specific DNA polymerases (Pols) of low-GC-content gram-positive bacteria (E. Dervyn et al., Science 294:1716-1719, 2001; R. Inoue et al., Mol. Genet. Genomics 266:564-571, 2001), was cloned from Bacillus subtilis, a model low-GC gram-positive organism. The gene was overexpressed in Escherichia coli. The purified recombinant product displayed inhibitor responses and physical, catalytic, and antigenic properties indistinguishable from those of the low-GC gram-positive-organism-specific enzyme previously named DNA Pol II after the polB-encoded DNA Pol II of E. coli. Whereas a polB-like gene is absent from low-GC gram-positive genomes and whereas the low-GC gram-positive DNA Pol II strongly conserves a dnaE-like, Pol III primary structure, it is proposed that it be renamed DNA polymerase III E (Pol III E) to accurately reflect its replicative function and its origin from dnaE. It is also proposed that DNA Pol III, the other replication-specific Pol of low-GC gram-positive organisms, be renamed DNA polymerase III C (Pol III C) to denote its origin from polC. By this revised nomenclature, the DNA Pols that are expressed constitutively in low-GC gram-positive bacteria would include DNA Pol I, the dispensable repair enzyme encoded by polA, and the two essential, replication-specific enzymes Pol III C and Pol III E, encoded, respectively, by polC and dnaE.

scholarly journals The Polymerase η Translesion Synthesis DNA Polymerase Acts Independently of the Mismatch Repair System To Limit Mutagenesis Caused by 7,8-Dihydro-8-Oxoguanine in Yeast

2009 ◽  
Vol 29 (19) ◽  
pp. 5316-5326 ◽  
Author(s):  
Sarah V. Mudrak ◽  
Caroline Welz-Voegele ◽  
Sue Jinks-Robertson
Keyword(s):  
Dna Replication ◽  
Mismatch Repair ◽  
Dna Polymerase ◽  
Translesion Synthesis ◽  
Nuclear Antigen ◽  
Repair System ◽  
New Paradigm ◽  
Mismatch Repair System ◽  
Mutation Assay ◽  
Proliferating Cell

ABSTRACT Reactive oxygen species are ubiquitous mutagens that have been linked to both disease and aging. The most studied oxidative lesion is 7,8-dihydro-8-oxoguanine (GO), which is often miscoded during DNA replication, resulting specifically in GC → TA transversions. In yeast, the mismatch repair (MMR) system repairs GO·A mismatches generated during DNA replication, and the polymerase η (Polη) translesion synthesis DNA polymerase additionally promotes error-free bypass of GO lesions. It has been suggested that Polη limits GO-associated mutagenesis exclusively through its participation in the filling of MMR-generated gaps that contain GO lesions. In the experiments reported here, the SUP4-o forward-mutation assay was used to monitor GC → TA mutation rates in strains defective in MMR (Msh2 or Msh6) and/or in Polη activity. The results clearly demonstrate that Polη can function independently of the MMR system to prevent GO-associated mutations, presumably through preferential insertion of cytosine opposite replication-blocking GO lesions. Furthermore, the Polη-dependent bypass of GO lesions is more efficient on the lagging strand of replication and requires an interaction with proliferating cell nuclear antigen. These studies establish a new paradigm for the prevention of GO-associated mutagenesis in eukaryotes.

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