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M Radman

Publications and source records attributed to M Radman.

At least 73 records · Page 4Linked to original sources
PubMed1989

Mismatch repair and the fidelity of genetic recombination.

Two modes of mismatch repair are known to operate in bacteria: long-patch mismatch repair and very short patch mismatch repair. Very short patch mismatch repair systems act on a specific mismatch by conserving only one base pair. Therefore, when very short patch mismatch repair acts on heteroduplex recombination intermediates, it hyper-recombines specific markers by creating patchwork sequences, i.e., apparent multiple exchange events, on the repaired strand. Long-patch mismatch repair is antirecombinagenic, apparently by decomposing heteroduplex DNA or aborting its formation whenever well-recognized mismatches are formed by strand exchange between nonidentical parental sequences. It is postulated here that mismatch-stimulated antirecombination by long-patch mismatch repair is a "proofreading" system assuring high fidelity of homologous recombination. This accounts for chromosomal stability in eucaryotes (i.e., the rare occurrence of chromosomal aberrations and mitotic recombination versus the high frequency of precise sister chromatid exchange), suggests a role for diverged repetitive and other noncoding sequences as chromosomal antirecombination elements, and provides a molecular mechanism for speciation without the necessity of geographical separation.

Biological Evolution↗
PubMed1988

Purification and characterization of an inducible Escherichia coli DNA polymerase capable of insertion and bypass at abasic lesions in DNA.

We have investigated the ability of DNA polymerases from SOS-induced and uninduced Escherichia coli to incorporate nucleotides at a well-defined abasic (apurinic/apyrimidinic) DNA template site and to extend these chains from this unpaired 3' terminus. A DNA polymerase activity has been purified from E. coli, deleted for DNA polymerase I, that appears to be induced 7-fold in cells following treatment with nalidixic acid. Induction of this polymerase (designated DNA polymerase X) appears to be part of the SOS response of E. coli since it cannot be induced in strains containing a noncleavable form of the LexA repressor (Ind-). The enzyme is able to incorporate nucleotides efficiently opposite the abasic template lesion and to continue DNA synthesis. Although we observe an approximate 2-fold induction of DNA polymerase III in cells treated with nalidixic acid, several lines of evidence argue that DNA polymerase X is unrelated to DNA polymerase III (pol III). In contrast to pol X, pol III shows almost no detectable ability to incorporate at or extend beyond the abasic site; incorporation efficiency at the abasic lesion is at least 100-fold larger for pol X compared to pol III holoenzyme, pol III core, or pol III* (the polymerase III holoenzyme subassembly lacking the beta subunit). Pol X does not cross-react with polyclonal antibody directed against pol III holoenzyme complex or with monoclonal antibody prepared to the alpha subunit of pol III. Despite these structural and biochemical differences, pol X appears to interact specifically with the beta subunit of the pol III holoenzyme in the presence of single-stranded binding protein. Pol X has a molecular mass of 84 kDa. Our results indicate that this novel activity is likely to be identical to DNA polymerase II of E. coli.

Base Sequence↗
PubMed1987

Mismatch repair and recombination in E. coli.

The involvement of the E. coli methyl-directed and very short patch (vsp) mismatch repair systems in bacteriophage lambda recombination has been studied. Genetic crosses and heteroduplex transfection experiments were performed using lambda phages with sequenced mutations in the cl gene. The results indicate that methyl-directed repair does operate during bacteriophage lambda recombination but generally does not contribute to the formation of recombinants involving close markers. Vsp repair apparently acts during bacteriophage lambda recombination to produce recombinants involving close markers because its action does not involve extensive excision tracts. Marker-specific hyperrecombination and the apparent clustering of genetic exchanges in bacteriophage lambda recombination can be accounted for by the action of the vsp repair system.

Bacteriophage lambda↗
PubMed1987

Mismatch repair of deaminated 5-methyl-cytosine.

Deamination of 5-methyl-cytosine in double-stranded DNA produces a G-T mismatch. Heteroduplexes of bacteriophage lambda DNA containing a G-T mismatch at the site of a G-5-meC base-pair in one of the parental phages were constructed and used to transfect Escherichia coli cells. Genetic analysis of the progeny phages derived from such heteroduplexes suggests that, in E. coli, mismatches resulting from the deamination of 5-methyl-cytosine are repaired by a system requiring the E. coli dcm methylase and some, but not all, of the functions of the E. coli methyl-directed mismatch repair system. The repair appears to act only on the G-T mismatch and acts specifically to restore the cytosine methylation sequence.

5-Methylcytosine↗
PubMed1987

GATC sequences, DNA nicks and the MutH function in Escherichia coli mismatch repair.

Circular heteroduplex DNAs of bacteriophage phi X174 have been constructed carrying either a G:T (Eam+/Eam3) or a G:A (Bam+/Bam16) mismatch and containing either two, one or no GATC sequences. Mismatches were efficiently repaired in wild-type Escherichia coli transfected with phi X174 heteroduplexes only when two unmethylated GATC sequences were present in phi X174 DNA. The requirements for GATC sequences in substrate DNA and for the E. coli MutH function in E. coli mismatch repair can be alleviated by the presence of a persistent nick (transfection with nicked heteroduplex DNA in ligase temperature-sensitive mutant at 40 degrees C). A persistent nick in the GATC sequence is as effective in stimulating mutL- and mutS-dependent mismatch repair as a nick distant from the GATC sequence and from the mismatch. These observations suggest that the MutH protein participates in methyl-directed mismatch repair by recognizing unmethylated DNA GATC sequences and/or stimulating the nicking of unmethylated strands.

Bacteriophage phi X 174↗
PubMed1987

Large non-homology in heteroduplex DNA is processed differently than single base pair mismatches.

Unmethylated DNA heteroduplexes with a large single stranded loop in one strand have been prepared from separated strands of DNA from two different strains of bacteriophage lambda, one of which has a approximately 800 base pair IS1 insertion in the cI gene. The results of transfections with these heteroduplexes into wild-type and mismatch repair deficient bacteria indicate that such large non-homologies are not repaired by the Escherichia coli mismatch repair system. However, the results do suggest that some process can act to repair such large non-homologies in heteroduplex DNA. Transfections of a series of recombination and excision repair deficient mutants suggest that known excision or recombination repair systems of E. coli are not responsible for the repair. Repair of large non-homologies may play a role in gene conversion involving large insertion or deletion mutations.

Base Composition↗
PubMed1987

Carcinogenic potency in rodents versus genotoxic potency in E. coli: a correlation analysis for bifunctional alkylating agents.

The mutagenic (M), recombinagenic (R) and SOS inducing (I) potencies of 6 bifunctional directly acting alkylating agents (mitomycin C, thiotepa, chlorambucil, nitrogen mustard, bis(2-chloroethyl)ether and bis(2-chloroethyl)nitrosourea) were measured in an E. coli test system (E. coli multitest) as the integral under the yield-dose curve obtained for each event. This potency corresponds to the cumulative yield of the affected cell population over the entire effective dose range of the chemical treatment. A weak mutagenic activity was detected only for mitomycin C and thiotepa. Except for bis(2-chloroethyl)ether, all agents were recombinagenic and SOS inducing. When the 3 genotoxic potencies (M, R and I) of these bifunctional alkylating agents were correlated, separately or in combination, with the respective carcinogenic potencies in rodents, a highly significant correlation was obtained with both the recombinagenic and SOS inducing potencies.

Alkylating Agents↗
PubMed1987

Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence.

Heteroduplexes with single base pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. A series of transition (G:T and A:C) and transversion (G:A and C:T) mismatches located throughout most of the bacteriophage lambda cI gene has been examined. The results suggest that the transition mismatches are generally better repaired than the transversion mismatches and that, at least for the transversion mismatches studied, repair efficiency increases with increasing G:C content in the neighboring nucleotide sequence. This specificity of the E. coli mismatch repair system can account, in part, for the similar frequencies of base substitution mutations throughout the E. coli genome.

Bacteriophage lambda↗
PubMed1986

Structures of mismatched base pairs in DNA and their recognition by the Escherichia coli mismatch repair system.

The Escherichia coli mismatch repair system does not recognize and/or repair all mismatched base pairs with equal efficiency: whereas transition mismatches (G X T and A X C) are well repaired, the repair of some transversion mismatches (e.g. A X G or C X T) appears to depend on their position in heteroduplex DNA of phage lambda. Undecamers were synthesized and annealed to form heteroduplexes with a single base-pair mismatch in the centre and with the five base pairs flanking each side corresponding to either repaired or unrepaired heteroduplexes of lambda DNA. Nuclear magnetic resonance (n.m.r.) studies show that a G X A mismatch gives rise to an equilibrium between fully helical and a looped-out structure. In the unrepaired G X A mismatch duplex the latter predominates, while the helical structure is predominant in the case of repaired G X A and G X T mismatches. It appears that the E. coli mismatch repair enzymes recognize and repair intrahelical mismatched bases, but not the extrahelical bases in the looped-out structures.

Bacteriophage lambda↗
PubMed1986

Evidence for an intermediate in DNA synthesis involving pyrophosphate exchange. A possible role in fidelity.

The incorporation of exogenous deoxyribonucleotide monophates (dNMP) was measured under conditions of ongoing DNA synthesis, providing arguments for the existence of a [DNAn X dNMP X PPi] intermediate in the nucleotide incorporation step of DNA synthesis: (formula; see text). The existence of such an intermediate is suggested by an apparent exchange of both dNMP and pyrophosphate (PPi) moieties of the deoxyribonucleotide triphosphate (dNTP) substrate with exogenous molecules. Such exchange and the incorporation of exogenous dNMP into DNA, strictly require ongoing DNA synthesis, suggesting that the energy for exchange reactions is provided by the cleavage of dNTP substrate. We propose that nucleotide selection during ongoing DNA synthesis results largely from the different relative rates of forward (beta) and backward (-alpha) reactions involving the [DNAn X dNMP X PPi] intermediate: the forward (incorporation) reaction is expected to predominate for the correct nucleotide, whereas the backward (abortive) reaction is expected to predominate for incorrect nucleotides.

Animals↗
PubMed1986

GATC sequence and mismatch repair in Escherichia coli.

The Escherichia coli mismatch repair system greatly improves DNA replication fidelity by repairing single mispaired and unpaired bases in newly synthesized DNA strands. Transient undermethylation of the GATC sequences makes the newly synthesized strands susceptible to mismatch repair enzymes. The role of unmethylated GATC sequences in mismatch repair was tested in transfection experiments with heteroduplex DNA of phage phi 174 without any GATC sequence or with two GATC sequences, containing in addition either a G:T mismatch (Eam+/Eam3) or a G:A mismatch (Bam+/Bam16). It appears that only DNA containing GATC sequences is subject to efficient mismatch repair dependent on E. coli mutH, mutL, mutS and mutU genes; however, also in the absence of GATC sequence some mut-dependent mismatch repair can be observed. These observations suggest that the mismatch repair enzymes recognize both the mismatch and the unmethylated GATC sequence in DNA over long distances. The presence of GATC sequence(s) in the substrate appears to be required for full mismatch repair activity and not only for its strand specificity according to the GATC methylation state.

Bacteriophage phi X 174↗
PubMed1986

Methyl-directed repair of frameshift mutations in heteroduplex DNA.

DNA heteroduplexes with single unpaired bases of the four different kinds were prepared by annealing separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. Genetic analysis of the progeny phages obtained from transfected bacteria indicates that the E. coli mismatch repair system can recognize and repair heteroduplexes with single unpaired bases--i.e., frameshift/wild-type heteroduplexes. The repair of a particular strand of the heteroduplex is inhibited by full methylation of the adenines in the GATC sequences of that strand. Thus, it appears that the E. coli mismatch repair system can act on newly synthesized DNA strands to remove replication errors involving the insertion or deletion of a single base.

Bacteriophage lambda↗
PubMed1986

Mismatch-stimulated killing.

DNA duplexes with or without mismatches and with or without adenine-methylated GATC sequences were prepared from separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. Unmethylated heteroduplexes containing one or more repairable mismatches transfect cells with a functioning mismatch repair system less efficiently than they transfect cells deficient in mismatch repair. No difference is observed when the duplexes contain no mismatch or a poorly repaired mismatch or when the heteroduplexes are fully or hemimethylated. These results and the phenotypes of E. coli dam mutants suggest that the E. coli mismatch repair system may introduce double-strand breaks in unmethylated DNA at or near repairable mismatches.

Adenine↗
PubMed1985

A system for detection of genetic and epigenetic alterations in Escherichia coli induced by DNA-damaging agents.

In order to compare the genetic and epigenetic effects of genotoxic agents, we have constructed Escherichia coli K12 strains that allow the detection of mutagenesis, SOS induction (epigenetic effect) and genetic recombination in the same genetic background. The epigenetic effect was detected in a similar way to any genetic alteration, i.e. by counting altered clones (colonies), using a gene fusion system that responds to a temporary epigenetic effect by a stable, heritable switch. The gene fusion consists of the E. coli gal operon and a partially deleted prophage lambda, resulting in the gal operon coming under the control of the cI and cro genes. It allows the detection of SOS induction and forward mutagenesis in the cI gene. Even a temporary inactivation of the CI repressor in this particular system leads to a stable epigenetic switch transmitted to the cellular progeny, which can be detected as Gal+ (red) colonies. The genetic (mutational inactivation of gene cI) and epigenetic (proteolytic inactivation of the product of gene cI) mechanisms leading to gal expression can be distinguished. Genetic recombination between two heteroallelic lacZ genes, one located in the bacterial chromosome, the other on an F'lac plasmid, can be detected as Lac+ colonies. Radiation and several chemical mutagens show very different capacities in generating mutants, inductants and recombinants; therefore, a dose range of any physical or chemical agent generates a set of relative values for the generation of mutants, inductants and recombinants that are characteristic of the agent.

Aflatoxin B1↗
PubMed1985

Involvement of DNA polymerase III in UV-induced mutagenesis of bacteriophage lambda.

It has been proposed that the mutation fixation processes stimulated by SOS induction result from an induced infidelity of DNA replication (Radman 1974). The aim of this study was to determine if mutator mutations in the E. coli DNA polymerase III might affect UV-induced mutagenesis. Using a phage lambda mutation assay which can discriminate between targeted and untargeted mutations, we show that the polC74 mutator mutation (Sevastopoulos and Glaser 1977) primarily affects untargeted mutagenesis, which occurs in a recA1 genetic background and is amplified in the recA+ genetic background. The polC74 mutation also increases the UV-induced mutagenesis of the bacterial chromosome. These results suggest that DNA polymerase III is involved in the process of UV-induced mutagenesis in E. coli.

Bacteriophage lambda↗