The Effect of Mismatch Repair and Heteroduplex Formation on Sexual Isolation in Bacillus

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Jacek Majewski ◽  
Frederick M Cohan
Keyword(s):  
Mismatch Repair ◽  
Wild Type Strain ◽  
Resistance Mechanism ◽  
Sequence Divergence ◽  
Sexual Isolation ◽  
Wild Type ◽  
Exponential Relationship ◽  
Dna Strands ◽  
The Relationship ◽  
Heteroduplex Formation

AbstractIn Bacillus transformation, sexual isolation is known to be an exponential function of the sequence divergence between donor and recipient. Here, we have investigated the mechanism under which sequence divergence results in sexual isolation. We tested the effect of mismatch repair by comparing a wild-type strain and an isogenic mismatch-repair mutant for the relationship between sexual isolation and sequence divergence. Mismatch repair was shown to contribute to sexual isolation but was responsible for only a small fraction of the sexual isolation observed. Another possible mechanism of sexual isolation is that more divergent recipient and donor DNA strands have greater difficulty forming a heteroduplex because a region of perfect identity between donor and recipient is required for initiation of the heteroduplex. A mathematical model showed that this heteroduplex-resistance mechanism yields an exponential relationship between sexual isolation and sequence divergence. Moreover, this model yields an estimate of the size of the region of perfect identity that is comparable to independent estimates for Escherichia coli. For these reasons, and because all other mechanisms of sexual isolation may be ruled out, we conclude that resistance to heteroduplex formation is predominantly responsible for the exponential relationship between sexual isolation and sequence divergence in Bacillus transformation.

scholarly journals The Role of the Mismatch Repair Machinery in Regulating Mitotic and Meiotic Recombination Between Diverged Sequences in Yeast

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1299-1313 ◽  
Author(s):  
Wenliang Chen ◽  
Sue Jinks-Robertson
Keyword(s):  
Mismatch Repair ◽  
Meiotic Recombination ◽  
Type Strain ◽  
Wild Type Strain ◽  
Sequence Divergence ◽  
Rate Data ◽  
Wild Type ◽  
Recombination Rates ◽  
Sequence Identity

Abstract Nonidentical recombination substrates recombine less efficiently than do identical substrates in yeast, and much of this inhibition can be attributed to action of the mismatch repair (MMR) machinery. In this study an intron-based inverted repeat assay system has been used to directly compare the rates of mitotic and meiotic recombination between pairs of 350-bp substrates varying from 82% to 100% in sequence identity. The recombination rate data indicate that sequence divergence impacts mitotic and meiotic recombination similarly, although subtle differences are evident. In addition to assessing recombination rates as a function of sequence divergence, the endpoints of mitotic and meiotic recombination events involving 94%-identical substrates were determined by DNA sequencing. The endpoint analysis indicates that the extent of meiotic heteroduplex DNA formed in a MMR-defective strain is 65% longer than that formed in a wild-type strain. These data are consistent with a model in which the MMR machinery interferes with the formation and/or extension of heteroduplex intermediates during recombination.

scholarly journals Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation

2000 ◽  
Vol 182 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Jacek Majewski ◽  
Piotr Zawadzki ◽  
Paul Pickerill ◽  
Frederick M. Cohan ◽  
Christopher G. Dowson
Keyword(s):  
Streptococcus Pneumoniae ◽  
Mismatch Repair ◽  
Bacterial Species ◽  
Sequence Divergence ◽  
Sexual Isolation ◽  
Genetic Exchange ◽  
Repair System ◽  
Exponential Relationship ◽  
Rapid Acquisition ◽  
Mismatch Repair System

ABSTRACT Interspecies genetic exchange is an important evolutionary mechanism in bacteria. It allows rapid acquisition of novel functions by transmission of adaptive genes between related species. However, the frequency of homologous recombination between bacterial species decreases sharply with the extent of DNA sequence divergence between the donor and the recipient. In Bacillus andEscherichia, this sexual isolation has been shown to be an exponential function of sequence divergence. Here we demonstrate that sexual isolation in transformation between Streptococcus pneumoniae recipient strains and donor DNA from related strains and species follows the described exponential relationship. We show that the Hex mismatch repair system poses a significant barrier to recombination over the entire range of sequence divergence (0.6 to 27%) investigated. Although mismatch repair becomes partially saturated, it is responsible for 34% of the observed sexual isolation. This is greater than the role of mismatch repair inBacillus but less than that in Escherichia. The remaining non-Hex-mediated barrier to recombination can be provided by a variety of mechanisms. We discuss the possible additional mechanisms of sexual isolation, in view of earlier findings fromBacillus, Escherichia, andStreptococcus.

scholarly journals Highly Mismatched Molecules Resembling Recombination Intermediates Efficiently Transform Mismatch Repair Proficient Escherichia coli

Genetics ◽  
1997 ◽  
Vol 145 (1) ◽  
pp. 29-38
Author(s):  
James Westmoreland ◽  
Gregory Porter ◽  
Miroslav Radman ◽  
Michael A Resnick
Keyword(s):  
Mismatch Repair ◽  
Sequence Divergence ◽  
Strand Exchange ◽  
Wild Type ◽  
E Coli ◽  
Key Factor ◽  
Homeologous Recombination ◽  
Related Dnas ◽  
Heteroduplex Formation

The ability of related DNAs to undergo recombination decreases with increased sequence divergence. Mismatch repair has been proposed to be a key factor in preventing homeologous recombination; however, the contribution of mismatch repair is not universal. Although mismatch repair has been proposed to act by preventing strand exchange and/or inactivating multiply mismatched heteroduplexes, there has been no systematic study to determine at what step(s) in recombination mismatch repair acts in vivo. Since heteroduplex is a commonly proposed intermediate in many models of recombination, we have investigated the consequences of mismatch repair on plasmids that are multiply mismatched in heteroduplex structures that are similar to those that might arise during recombination. Plasmids containing multiply mismatched regions were transformed into wild-type and Mut–  Eschericia coli mutants. There was only a 30–40% reduction in transformation of Mut+ as compared to mutS and mutL strains for DNAs containing an 18% mismatched heteroduplex. The products obtained from mutS hosts differed from those obtained from Mut+ hosts in that there were many more colonies containing mixtures of two plasmids, due to survival of both strands of the heteroduplex. There were nearly 10 times more recombinants obtained from the mutS as compared to the wild-type host. Based on these results and those from other studies with E. coli and yeast, we propose that the prevention of recombination between highly diverged DNAs may be at a step earlier than heteroduplex formation.

scholarly journals Mismatch Repair Proteins Regulate Heteroduplex Formation during Mitotic Recombination in Yeast

1998 ◽  
Vol 18 (11) ◽  
pp. 6525-6537 ◽  
Author(s):  
Wenliang Chen ◽  
Sue Jinks-Robertson
Keyword(s):  
Gene Conversion ◽  
Mismatch Repair ◽  
Sister Chromatid ◽  
Type Strain ◽  
Wild Type Strain ◽  
Sequence Data ◽  
Mitotic Recombination ◽  
Assay System ◽  
Wild Type ◽  
Mmr Proteins

Mismatch repair (MMR) proteins actively inhibit recombination between diverged sequences in both prokaryotes and eukaryotes. Although the molecular basis of the antirecombination activity exerted by MMR proteins is unclear, it presumably involves the recognition of mismatches present in heteroduplex recombination intermediates. This recognition could be exerted during the initial stage of strand exchange, during the extension of heteroduplex DNA, or during the resolution of recombination intermediates. We previously used an assay system based on 350-bp inverted-repeat substrates to demonstrate that MMR proteins strongly inhibit mitotic recombination between diverged sequences inSaccharomyces cerevisiae. The assay system detects only those events that reverse the orientation of the region between the recombination substrates, which can occur as a result of either intrachromatid crossover or sister chromatid conversion. In the present study we sequenced the products of mitotic recombination between 94%-identical substrates in order to map gene conversion tracts in wild-type versus MMR-defective yeast strains. The sequence data indicate that (i) most recombination occurs via sister chromatid conversion and (ii) gene conversion tracts in an MMR-defective strain are significantly longer than those in an isogenic wild-type strain. The shortening of conversion tracts observed in a wild-type strain relative to an MMR-defective strain suggests that at least part of the antirecombination activity of MMR proteins derives from the blockage of heteroduplex extension in the presence of mismatches.

scholarly journals Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins.

1997 ◽  
Vol 17 (5) ◽  
pp. 2844-2850 ◽  
Author(s):  
C N Greene ◽  
S Jinks-Robertson
Keyword(s):  
Mismatch Repair ◽  
Wild Type Strain ◽  
Frameshift Mutation ◽  
Protein A ◽  
Repair System ◽  
Wild Type ◽  
Base Pairs ◽  
Replication Errors ◽  
Mismatch Repair System ◽  
Mismatch Repair Proteins

A change in the number of base pairs within a coding sequence can result in a frameshift mutation, which almost invariably eliminates the function of the encoded protein. A frameshift reversion assay with Saccharomyces cerevisiae that can be used to examine the types of insertions and deletions that are generated during DNA replication, as well as the editing functions that remove such replication errors, has been developed. Reversion spectra have been obtained in a wild-type strain and in strains defective for defined components of the postreplicative mismatch repair system (msh2, msh3, msh6, msh3 msh6, pms1, and mih1 mutants). Comparison of the spectra reveals that yeast mismatch repair proteins preferentially remove frameshift intermediates that arise in homopolymer tracts and indicates that some of the proteins have distinct substrate or context specificities.

scholarly journals Involvement of CO2 generated by urease in multiplication of Helicobacter pylori

2021 ◽  
Vol 7 (3) ◽  
pp. 045-053
Author(s):  
Masaaki Minami ◽  
Shin-nosuke Hashikawa ◽  
Takafumi Ando ◽  
Hiroshi Kobayashi ◽  
Hidemi Goto ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Mutant Strain ◽  
Type Strain ◽  
Wild Type Strain ◽  
Neutral Medium ◽  
Wild Type ◽  
In The Wild ◽  
H Pylori ◽  
Carbon Dioxide Co2 ◽  
The Relationship

Helicobacter pylori (H. pylori) urease generates both ammonia (NH3) and carbon dioxide (CO2) from urea. NH3 helps H. pylori to survive in the stomach in part by neutralizing gastric acid. However, the relationship between CO2 and H. pylori is not completed cleared. We examined the effect of CO2 generated by urease on multiplication of H. pylori by using isogenic ureB mutant and ureB complemented strain from H. pylori strain JP26. Wild-type strain survived in the medium supplement with 1mM urea in room air, however, the urease negative strain did not. To discern whether CO2 was incorporated into H. pylori, 14C in bacillus was counted after 6 hours incubation with 14C urea in both acidic and neutral medium. Significant more 14C uptake was detected in wild-type strain compared to ureB mutant strain and this uptake in the wild-type strain was more under acidic condition compared to under neutral condition, but no difference was identified in the mutant strain. These results suggest that CO2 generated by urease plays a role in multiplication of H. pylori.

scholarly journals Human mismatch repair system corrects errors produced during lagging strand replication more effectively

2016 ◽  
Author(s):  
Maria Andrianova ◽  
Georgii A Bazykin ◽  
Sergey Nikolaev ◽  
Vladimir Seplyarskiy
Keyword(s):  
Mismatch Repair ◽  
Mutation Rates ◽  
Repair System ◽  
Wild Type ◽  
Strand Asymmetry ◽  
Exonuclease Domain ◽  
Mismatch Repair System ◽  
Dna Strands ◽  
Leading Strand ◽  
Lagging Strand

Mismatch repair (MMR) is one of the main systems maintaining fidelity of replication. Different effectiveness in correction of errors produced during replication of the leading and the lagging DNA strands was reported in yeast, but this effect is poorly studied in humans. Here, we use MMR-deficient (MSI) and MMR-proficient (MSS) cancer samples to investigate properties of the human MMR. MSI, but not MSS, cancers demonstrate unequal mutation rates between the leading and the lagging strands. The direction of strand asymmetry in MSI cancers matches that observed in cancers with mutated exonuclease domain of polymerase δ, indicating that polymerase δ contributes more mutations than its leading-strand counterpart, polymerase ε. As polymerase δ primarily synthesizes DNA during the lagging strand replication, this implies that mutations produced in wild type cells during lagging strand replication are repaired by the MMR ~3 times more effectively, compared to those produced on the leading strand.

scholarly journals Efficacy of Humanized Carbapenem and Ceftazidime Regimens against Enterobacteriaceae Producing OXA-48 Carbapenemase in a Murine Infection Model

2013 ◽  
Vol 58 (3) ◽  
pp. 1678-1683 ◽  
Author(s):  
Dora E. Wiskirchen ◽  
Patrice Nordmann ◽  
Jared L. Crandon ◽  
David P. Nicolau
Keyword(s):  
Wild Type Strain ◽  
Treatment Options ◽  
Infection Model ◽  
Wild Type ◽  
Content Type ◽  
Phenotypic Profile ◽  
Infection Models ◽  
The Relationship ◽  
Growth Controls

ABSTRACTEnterobacteriaceaeproducing the OXA-48 carbapenemase are emerging worldwide, leaving few treatment options. Efficacy has been demonstratedin vivowith ceftazidime against a ceftazidime-susceptible OXA-48 isolate but not with imipenem despite maintaining susceptibility. The relationship between phenotype andin vivoefficacy was assessed for OXA-48 producers using humanized regimens of 2 g doripenem every 8 h (q8h; 4 h infusion), 1 g ertapenem q24h, 2 g ceftazidime q8h (2 h inf), and 500 mg levofloxacin q24h. Each regimen was evaluated over 24 h against an isogenic pair (wild-type and OXA-48Klebsiella pneumoniaestrains) and six clinical OXA-48 isolates with and without other extended-spectrum β-lactamases in immunocompetent and neutropenic murine thigh infection models. Efficacy was determined using the change in bacterial density versus 24-h growth controls in immunocompetent studies and 0-h controls in neutropenic studies. Bacterial reductions of ≥1 log CFU were observed with all agents for the wild-type strain. Consistent with low MICs, ceftazidime and levofloxacin exhibited efficacy against the isogenic OXA-48 strain, whereas doripenem did not, despite having a susceptible MIC; no activity was observed with ertapenem, consistent with a resistant MIC. Similar trends were observed for the clinical isolates evaluated. Ceftazidime, levofloxacin, and ertapenem efficacy against isogenic and clinical OXA-48-producing strains correlated well with phenotypic profiles and pharmacodynamic targets, whereas efficacy with doripenem was variable over the MIC range studied. These data suggest that carbapenems may not be a reliable treatment for treating OXA-48 producers and add to previous observations with KPC and NDM-1 suggesting that genotype may better predict activity of the carbapenems than the phenotypic profile.

Spontaneous Frameshift Mutations in Saccharomyces cerevisiae: Accumulation During DNA Replication and Removal by Proofreading and Mismatch Repair Activities

Genetics ◽  
2001 ◽  
Vol 159 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Christopher N Greene ◽  
Sue Jinks-Robertson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Wild Type Strain ◽  
Dna Polymerases ◽  
Wild Type ◽  
Triple Mutant ◽  
Repair Capacity ◽  
Frameshift Mutations ◽  
Dna Polymerization ◽  
In The Wild

Abstract The accumulation of frameshift mutations during DNA synthesis is determined by the rate at which frameshift intermediates are generated during DNA polymerization and the efficiency with which frameshift intermediates are removed by DNA polymerase-associated exonucleolytic proofreading activity and/or the postreplicative mismatch repair machinery. To examine the relative contributions of these factors to replication fidelity in Saccharomyces cerevisiae, we determined the reversion rates and spectra of the lys2ΔBgl +1 frameshift allele. Wild-type and homozygous mutant diploid strains with all possible combinations of defects in the exonuclease activities of DNA polymerases δ and ε (conferred by the pol3-01 and pol2-4 alleles, respectively) and in mismatch repair (deletion of MSH2) were analyzed. Although there was no direct correlation between homopolymer run length and frameshift accumulation in the wild-type strain, such a correlation was evident in the triple mutant strain lacking all repair capacity. Furthermore, examination of strains defective in one or two repair activities revealed distinct biases in the removal of the corresponding frameshift intermediates by exonucleolytic proofreading and/or mismatch repair. Finally, these analyses suggest that the mismatch repair machinery may be important for generating some classes of frameshift mutations in yeast.

scholarly journals DNA Sequence Similarity Requirements for Interspecific Recombination in Bacillus

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1525-1533 ◽  
Author(s):  
Jacek Majewski ◽  
Frederick M Cohan
Keyword(s):  
Dna Sequence ◽  
Sequence Similarity ◽  
Genetic Material ◽  
Sequence Divergence ◽  
Antibiotic Resistance Genes ◽  
Sexual Isolation ◽  
Repair System ◽  
Exponential Relationship ◽  
Dna Strand ◽  
Major Factors

Abstract Gene transfer in bacteria is notoriously promiscuous. Genetic material is known to be transferred between groups as distantly related as the Gram positives and Gram negatives. However, the frequency of homologous recombination decreases sharply with the level of relatedness between the donor and recipient. Several studies show that this sexual isolation is an exponential function of DNA sequence divergence between recombining substrates. The two major factors implicated in producing the recombinational barrier are the mismatch repair system and the requirement for a short region of sequence identity to initiate strand exchange. Here we demonstrate that sexual isolation in Bacillus transformation results almost exclusively from the need for regions of identity at both the 5′ and 3′ ends of the donor DNA strand. We show that, by providing the essential identity, we can effectively eliminate sexual isolation between highly divergent sequences. We also present evidence that the potential of a donor sequence to act as a recombinogenic, invasive end is determined by the stability (melting point) of the donor-recipient complex. These results explain the exponential relationship between sexual isolation and sequence divergence observed in bacteria. They also suggest a model for rapid spread of novel adaptations, such as antibiotic resistance genes, among related species.

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