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At least 577 records · Page 32Linked to original sources
PubMed1998

PCR-based DNA amplification and presumptive detection of Escherichia coli O157:H7 with an internal fluorogenic probe and the 5' nuclease (TaqMan) assay.

Presumptive identification of Escherichia coli O157:H7 is possible in an individual, nonmultiplexed PCR if the reaction targets the enterohemorrhagic E. coli (EHEC) eaeA gene. In this report, we describe the development and evaluation of the sensitivity and specificity of a PCR-based 5' nuclease assay for presumptively detecting E. coli O157:H7 DNA. The specificity of the eaeA-based 5' nuclease assay system was sufficient to correctly identify all E. coli O157:H7 strains evaluated, mirroring the previously described specificity of the PCR primers. The SZ-primed, eaeA-targeted 5' nuclease detection assay was capable of rapid, semiautomated, presumptive detection of E. coli O157:H7 when >/=10(3) CFU/ml was present in modified tryptic soy broth (mTSB) or modified E. coli broth and when >/=10(4) CFU/ml was present in ground beef-mTSB mixtures. Incorporating an immunomagnetic separation (IMS) step, followed by a secondary enrichment culturing step and DNA recovery with a QIAamp tissue kit (Qiagen), improved the detection threshold to >/=10(2) CFU/ml. Surprisingly, immediately after IMS, the sensitivity of culturing on sorbitol MacConkey agar containing cefeximine and tellurite (CT-SMAC) was such that identifiable colonies were demonstrated only when >/=10(4) CFU/ml was present in the sample. Several factors that might be involved in creating these false-negative CT-SMAC culture results are discussed. The SZ-primed, eaeA-targeted 5' nuclease detection system demonstrated that it can be integrated readily into standard culturing procedures and that the assay can be useful as a rapid, automatable process for the presumptive identification of E. coli O157:H7 in ground beef and potentially in other food and environmental samples.

Adhesins, Bacterial↗
PubMed2001

Rapid evolution of novel traits in microorganisms.

The use of natural microorganisms in biotransformations is frequently constrained by their limited tolerance to the high concentrations of metabolites and solvents required for effective industrial production. In many cases, more robust strains have to be generated by random mutagenesis and selection. This process of directed evolution can be accelerated in mutator strains, which carry defects in one or more of their DNA repair genes. However, in order to use mutator strains, it is essential to restore the normal low mutation rate of the selected organisms immediately after selection to prevent the accumulation of undesirable spontaneous mutations. To enable this process, we constructed temperature-sensitive plasmids that temporarily increase the mutation frequency of their hosts by 20- to 4,000-fold. Under appropriate selection pressure, microorganisms transformed with mutator plasmids can be quickly evolved to exhibit new, complex traits. By using this approach, we were able to increase the tolerance of three bacterial strains to dimethylformamide by 10 to 20 g/liter during only two subsequent transfers. Subsequently, the evolved strains were returned to their normal low mutation rate by curing the cells of the mutator plasmids. Our results demonstrate a new and efficient method for rapid strain improvement based on in vivo mutagenesis.

Dimethylformamide↗
PubMed1999

Effect of mutS and recD mutations on Salmonella virulence.

Hybrid derivatives of closely related bacteria may be used to dissect strain-specific functions that contribute to virulence within a host. However, mismatches between DNA sequences are a potent barrier to recombination. Recipients with mutS and recD mutations overcome this barrier, allowing construction of genetic hybrids. To determine whether Salmonella hybrids constructed in a mutS recD host can be used to study virulence, we assayed the effect of mutS and recD mutations on the virulence of Salmonella typhimurium 14028s in mice. Mutants defective in either mutS or recD do not affect the time course or the 50% lethal dose (LD(50)) of the infection. In contrast, the inactivation of both mutS and recD results in a synthetic phenotype which substantially increases the time required to cause a lethal infection without changing the LD(50). This phenotype results from an inability of mutS recD double mutants to rapidly adapt to purine-limiting conditions present within macrophages. Although the disease progression is slower, S. typhimurium mutS recD mutants retain the ability to cause lethal infections, and, thus, hybrids constructed in mutS recD hosts may permit the analysis of virulence factors in a surrogate animal model.

Adenosine Triphosphatases↗
PubMed2002

Phenotypes of a naturally defective recB allele in Neisseria meningitidis clinical isolates.

Neisseria meningitidis strains belonging to the hypervirulent lineage ET-37 and several unrelated strains are extremely UV sensitive. The phenotype is consequent to the presence of a nonfunctional recB(ET-37) allele carrying multiple missense mutations. Phenotypic analysis has been performed with congenic meningococcal strains harboring either the wild-type recB allele or the recB(ET-37) allele. Congenic recB(ET-37) meningococci, in addition to being sensitive to UV, were defective both in repair of DNA lesions induced by UV treatment and, partially, in recombination-mediated transformation. Consistently, the wild-type, but not the recB(ET-37), allele was able to complement the Escherichia coli recB21 mutation to UV resistance and proficiency in recombination. recB(ET-37) meningococci did not exhibit higher frequencies of spontaneous mutation to rifampin resistance than recB-proficient strains. However, mutation rates were enhanced following UV treatment, a phenomenon not observed in the recB-proficient counterpart. Interestingly, the results of PCR-based assays demonstrated that the presence of the recB(ET-37) allele considerably increased the frequency of recombination at the pilin loci. The main conclusion that can be drawn is that the presence of the defective recB(ET-37) allele in N. meningitidis isolates causes an increase in genetic diversity, due to an ineffective RecBCD-dependent DNA repair and recombination pathway, and an increase in pilin antigenic variation.

Alleles↗
PubMed2006

Neisseria gonorrhoeae DNA recombination and repair enzymes protect against oxidative damage caused by hydrogen peroxide.

The strict human pathogen Neisseria gonorrhoeae is exposed to oxidative damage during infection. N. gonorrhoeae has many defenses that have been demonstrated to counteract oxidative damage. However, recN is the only DNA repair and recombination gene upregulated in response to hydrogen peroxide (H(2)O(2)) by microarray analysis and subsequently shown to be important for oxidative damage protection. We therefore tested the importance of RecA and DNA recombination and repair enzymes in conferring resistance to H(2)O(2) damage. recA mutants, as well as RecBCD (recB, recC, and recD) and RecF-like pathway mutants (recJ, recO, and recQ), all showed decreased resistance to H(2)O(2). Holliday junction processing mutants (ruvA, ruvC, and recG) showed decreased resistance to H(2)O(2) resistance as well. Finally, we show that RecA protein levels did not increase as a result of H(2)O(2) treatment. We propose that RecA, recombinational DNA repair, and branch migration are all important for H(2)O(2) resistance in N. gonorrhoeae but that constitutive levels of these enzymes are sufficient for providing protection against oxidative damage by H(2)O(2).

Anti-Bacterial Agents↗
PubMed1983

Escherichia coli RecBC pseudorevertants lacking chi recombinational hotspot activity.

Pseudorevertants of an Escherichia coli exonuclease V (RecBC enzyme)-negative mutant have been isolated after ethyl methane sulfonate mutagenesis of a recC73 (presumed missense) mutant. The remedial mutations in each of the four pseudorevertants studied in detail map and complement as recC mutations. By several criteria, such as recombination proficiency, support of phage growth, RecBC nuclease activity, and cell viability, the pseudorevertants appear to have regained partially or completely various aspects of RecBC activity. However, chi recombinational hotspots, which stimulate exclusively the RecBC pathway of recombination, have no detectable activity in lambda vegetative crosses in the pseudorevertants. The properties of these mutants, in which the RecBC pathway of recombination is active yet in which chi is not active, are consistent with the hypothesis that wild-type RecBC enzyme directly interacts with chi sites; alternatively, the mutants may block or bypass the productive interaction of another recombinational enzyme with chi.

Coliphages↗
PubMed1983

Anaerobic cultures of Salmonella typhimurium do not exhibit inducible proteolytic function of the recA gene and recBC function.

In a strict anaerobic environment, lack of expression of bacterial recBC function and recA regulatory functions for the SOS repair system is demonstrated by the use of the carcinogenesis-mutagenesis assay and Salmonella phage P22 mutants requiring these host functions for replication. Therefore, we suggest that error-prone repair (SOS repair) is confined to aerobic environments in facultative anaerobes.

Aerobiosis↗
PubMed1983

In vitro coupled transcription-translation of linear DNA fragments in a lysate derived from a recB rna pnp strain of Escherichia coli.

A recB21 derivative (CLB7) of an Escherichia coli rna-19 pnp-7 strain (PR7) was constructed for use in examining the in vitro coupled transcription-translation of linear DNA. The expression of linearized DNAs in CLB7 (recB21 rna-19 pnp-7) lysates was enhanced significantly when compared with expression of the same DNAs in lysates prepared from the PR7 or the original recB21 (CF300) strains. In addition, the endogenous incorporation of [35S]methionine into protein was considerably reduced in CLB7 lysates relative to lysates derived from the original recB21 strain.

Bacterial Proteins↗
PubMed1984

Exonucleases I, III, and V are required for stability of ColE1-related plasmids in Escherichia coli.

The stability of two ColE1-related plasmids (pRSF2124 and pMB9) was examined in strains of Escherichia coli multiply deficient in exonucleases I (sbcB), III (xthA), or V (recB recC). Any combination of exonuclease I, III, and V deficiency resulted in dramatically decreased stability of both pRSF2124 and pMB9. Inactivation of the RecF pathway by introducing either recF or recJ mutations to the recB recC subcB background resulted in nearly wild-type levels of stability for both plasmids. In contrast, the introduction of uvrD3 uvr-257, uvrE100, or recL152 into the recB21 recC22 sbcB15 strain did not affect plasmid stability. Furthermore, the amount of plasmid DNA recovered from pRSF2124 or pMB9 transformants of a xthA1 sbcB15 strain was strikingly reduced relative to that of a wild-type control. Taken together, these results suggest that some aspect of DNA repair is required for stable maintenance of ColE1-related plasmids in E. coli.

Bacteriocin Plasmids↗
PubMed1984

Escherichia coli recBC deletion mutants.

Mutants of Escherichia coli with deletions of the recB and recC genes were obtained by two methods using transposable DNA elements. The phenotypes of these mutants are similar to those of mutants with recBC point mutations. These results indicate that the RecBC gene products, exonuclease V, is not essential for the growth of E. coli but is important for DNA repair and recombination.

Chromosome Deletion↗
PubMed1985

General recombination in Escherichia coli K-12: in vivo role of RecBC enzyme.

Heterozygous lacZ- merodiploids of Escherichia coli K-12 have been used to study the role of the RecBC enzyme in general recombination. The transcribable intermediate assay detects the product of early steps in recombination without requiring the formation of viable recombinant colonies. Recombination is initiated by infection with lambda precA+. We have found that transcribable intermediate formation in crosses between F42 lac and chromosomal lac is dependent on F fertility functions and an active RecBC enzyme. Thus, the products of the recB and recC genes are required in early steps of recombination between these two substrates. Introduction of the F42 lac donor DNA by conjugation immediately after infection with lambda precA+ abolishes the requirement for an active RecBC enzyme.

Conjugation, Genetic↗
PubMed1985

Mutation-dependent suppression of recB21 recC22 by a region cloned from the Rac prophage of Escherichia coli K-12.

Using pBR322 as a vector, we cloned a 5.95-kilobase fragment of the Rac prophage together with 1.70 kilobases of a flanking Escherichia coli chromosome sequence. The resulting plasmid (pRAC1) was unable to suppress the mitomycin and UV sensitivity and recombination deficiency of a recB21 recC22 strain. Five spontaneous mitomycin-resistant derivatives contained deletion mutant plasmids. These plasmids also suppressed the UV sensitivity and recombination deficiency of their recB21 recC22 hosts. All five deletions were contained within a 2.45-kilobase EcoRI-to-HindIII segment of the plasmid. By substituting the corresponding 2.45-kilobase EcoRI-toHindIII fragments of Rac prophage isolated from sbcA+, sbcA6, and sbcA23 strains for the shortened segment of one of the deletion mutant plasmids, we were able to show that sbcA mutations map in this region. Also in this region is the site (or closely linked sites) at which previous studies had shown that insertion of Tn5 and IS50 leads to suppression of recB21 recC22. The sequence in this region that must be altered or circumvented to allow suppression is discussed. Also presented are data correlating the expression of nuclease activity with the degree of suppression.

Bacteriophage lambda↗
PubMed1985

Spontaneous induction of colicin E1 in Escherichia coli strains deficient in both exonucleases I and V.

Colicin E1 synthesis is spontaneously induced in pRSF2124-carrying strains of Escherichia coli deficient in exonucleases I (sbcB) and V (recB recC). In contrast, the specific activity of beta-lactamase, which is also encoded by pRSF2124, is not affected by the absence of these enzymes. These results suggest that colicin E1 induction is specific and does not result either from a significant change in overall plasmid transcription or copy number. Furthermore, the level of spontaneous induction was similar to that obtained with mitomycin C.

Colicins↗
PubMed1986

Synthesis of linear plasmid multimers in Escherichia coli K-12.

Linear plasmid multimers were identified in extracts of recB21 recC22 strains containing derivatives of the ColE1-type plasmids pACYC184 and pBR322. A mutation in sbcB increases the proportion of plasmid DNA as linear multimers. A model to explain this is based on proposed roles of RecBC enzyme and SbcB enzyme (DNA exonuclease I) in preventing two types of rolling-circle DNA synthesis. Support for this hypothesis was obtained by derepressing synthesis of an inhibitor of RecBC enzyme and observing a difference in control of linear multimer synthesis and monomer circle replication. Reinitiation of rolling-circle DNA synthesis was proposed to occur by recA+-dependent and recA+-independent recombination events involving linear multimers. The presence of linear plasmid multimers in recB and recC mutants sheds new light on plasmid recombination frequencies in various mutant strains.

DNA, Bacterial↗
PubMed1986

Identification and characterization of recD, a gene affecting plasmid maintenance and recombination in Escherichia coli.

We isolated mutations that reduce plasmid stability in dividing cell populations and mapped these mutations to a previously undescribed gene, recD, that affects recombination frequency and consequently the formation of plasmid concatemers. Insertions of the transposable element Tn10 into recD resulted in increased concatemerization and loss of pSC101 and ColE1-like replicons during nonselective growth. Both concatemer formation and plasmid instability in recD mutants require a functional recA gene. Mutations in recD are recessive to recD+ and map to a small region of the Escherichia coli chromosome located between recB and argA. Although the recD locus is distinct from loci encoding the two previously identified subunits of the RecBC enzyme, mutations in recD appear to affect the exonuclease activity of this enzyme.

Chromosome Mapping↗
PubMed1987

Rec dependence of mu transposition from P22-transduced fragments.

Derivatives of bacteriophage Mu carrying a lac operon and a selectable drug resistance element (Mu d phages) are frequently used tools of bacterial genetics. Mu d prophages used in this way can be treated as transposons, in that the inserted material can be transduced from one strain to another by general transducing phages, such as P1 and P22. When a Mu d prophage is transduced into a new recipient by P1 or P22, the Mu d element can transpose from the transduced fragment into the bacterial chromosome. Transposition of the Mu d element from a P22-transduced fragment shows several striking differences from transposition of a Mu d genome injected by a Mu virion. First, the frequency of transposition from a transduced fragment is greatly enhanced by a P22 helper genome. Second, transposition requires the host recA, B, and C functions. Transposition of Mu following injection by a Mu virion is rec independent. While the basis of these observations is not understood, we suggest that the Mu X protein, a 65-kilodalton protein injected by a Mu virion and required for Mu transposition, may not be packaged by P22. We suggest that the effects seen reflect the behavior of a Mu genome in the absence of the X protein.

Bacteriophage mu↗
PubMed1988

Cloning and characterization of a Bacillus subtilis transcription unit involved in ATP-dependent DNase synthesis.

By insertional mutagenesis, 36 transformation-deficient, mitomycin C-sensitive Bacillus subtilis mutants were isolated, 16 of which were ATP-dependent DNase (ADD) deficient. PBS1 transduction showed that the mutations were closely linked to the metD marker and weakly linked to the glyB marker. With the aid of one of the mutants, a transcription unit involved in ADD synthesis was cloned. The chromosomal location of the transcription unit was established at the restriction site level by determining the presence or absence of ADD in transformants of wild-type cells obtained with various DNA fragments inserted in pUC derivatives. The transcription unit complemented a mutant in which the add transcription unit had been deleted.

Bacillus subtilis↗