Mutant Mut Research Articles

Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs.

Bacterial mutS and mutL mutations confer large increases in recombination between sequences that are divergent by several percent at the nucleotide level, an effect attributed to a role for products of these genes in control of recombination fidelity. Since MutS and MutL are proteins involved in the earliest steps of mismatch repair, including mismatch recognition by MutS, we have tested the possibility that they may affect strand exchange in response to occurrence of mispairs within the recombination heteroduplex. We show that MutS abolishes RecA-catalyzed strand transfer between fd and M13 bacteriophage DNAs, which vary by 3% at the nucleotide level, but is without effect on M13-M13 or fd-fd exchange. Although MutL alone has no effect on M13-fd heteroduplex formation, the protein dramatically enhances the inhibition of strand transfer mediated by MutS. Analysis of strand-transfer intermediates that accumulate in the presence of MutS and MutL indicates that the proteins block branch migration, presumably in response to occurrence of mispairs within newly formed heteroduplex.

Purification of the MutX protein of Streptococcus pneumoniae, a homologue of Escherichia coli MutT. Identification of a novel catalytic domain for nucleoside triphosphate pyrophosphohydrolase activity.

The mutX gene of Streptococcus pneumoniae, a homologue of the Escherichia coli mutT mutator gene (Méjean, V., Salles, C., Bullions, L. C., Bessman, M. J., and Claverys, J.-P. (1993) Mol. Microbiol. 11, 323-330) has been cloned into an expression vector, and its gene product, the MutX protein, has been purified to apparent homogeneity. Like MutT, the pure MutX protein hydrolyzes all of the canonical nucleoside triphosphates at different rates with a preference for dGTP, yielding nucleoside monophosphates and inorganic pyrophosphate. Despite this similarity in enzymatic activity, the two proteins have notably dissimilar primary and quaternary structures. They share only a small region of amino acid homology, and under the same conditions in which MutT exists as a monomer in solution, MutX behaves as a trimer. The small region of conserved amino acid sequence most likely identifies a protein domain responsible for the novel nucleoside triphosphate pyrophosphohydrolase activity shared by the two enzymes, and by another protein of unknown function, the product of the E. coli orf17 gene (Takahagi, M., Iwasaki, H., Nakata, A., and Shinegawa, H. (1991) J. Bacteriol. 173, 5747-5753).

Characterization of the mutX gene of Streptococcus pneumoniae as a homologue of Escherichia coli mutT, and tentative definition of a catalytic domain of the dGTP pyrophosphohydroiases

We show that deletion of a gene of Streptococcus pneumoniae, which we call mutX, confers a mutator phenotype to resistance to streptomycin. Analysis of the DNA sequence changes that occurred in several streptomycin-resistant mutants showed that mutations are unidirectional AT to CG transversions. The mutX gene is located immediately downstream of the previously identified ung gene and genetic evidence suggests that the two genes are co-ordinately regulated. Nucleotide sequence determination reveals that the mutX gene encodes a 17,870 Da protein (154 residues) which exhibits significant homology with the MutT protein of Escherichia coli, a nucleoside triphosphatase (dGTP pyrophosphohydrolase). The mutX gene complements the E. coli mutT mutator phenotype when introduced on a plasmid. Site-directed mutagenesis and analysis of nitrosoguanidine-induced mutT mutants suggest that a small region of high homology between the two proteins (61% identity over 23 residues) is part of the catalytic site of the nucleoside triphosphatase. Computer searching for sequence homology to MutX uncovered a second E. coli protein, the product of orf17, a gene of unknown function located near the ruvC gene. The region of high homology between MutX and MutT is also conserved in this protein, which raises the interesting possibility that the orf17 gene plays some role in determining mutation rates in E. coli. Finally, a small set of proteins, including a family of virus-encoded proteins and two evolutionarily conserved proteins encoded by an antisense transcript from the Xenopus laevis and human bFGF genes, were also found to harbour significant homology to this highly conserved region.

Analysis of the genetic requirements for viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants

RecBCD protein, necessary for Escherichia coli dam mutant viability, is directly required for DNA repair. Recombination genes recF+, recN+, recO+, and recQ+ are not essential for dam mutant viability; they are required for recBC sbcBC dam mutant survival. mutH, mutL, or mutS mutations do not suppress subinduction of SOS genes in dam mutants.

Mutations in the mutY gene of Escherichia coli enhance the frequency of targeted G:C-->T:a transversions induced by a single 8-oxoguanine residue in single-stranded DNA.

Oxidative damage to guanine in DNA results in the formation of 8-oxoguanine, which has been shown to induce G-->T transversions targeted to this site. The mutagenicity of this lesion was studied in several mutator strains of Escherichia coli, using single-stranded DNA containing a single 8-oxoguanine residue. The frequencies of targeted G-->T transversions increased markedly in mutY strains, while this mutagenic event was not affected in mutM or mutS strains. Introduction of a mutM mutation into a mutY strain caused a somewhat higher frequency of G-->T transversions than that in the mutY strain and the effect of a mutS mutation was marginal. We conclude that the mutY gene plays a crucial role in preventing targeted G-->T mutations derived from misreplication of the 8-oxoguanine-containing template DNA.

The interaction of the Escherichia coli mutD and mutT pathways in the prevention of A:T → C:G transversions

The Escherichia coli mutT mutator allele produces high frequencies of exclusively A:T → C:G transversions. This is thought to be caused by a failure to prevent or remove A:G mispairs during DNA replication. The mutD5 mutator allele maps to the dnaQ locus which encodes the epsilon subunit of the DNA polymerase III holoenzyme. This subunit provides 3′ → 5′ exonuclease, proofreading, activity for removing mispaired nucleotides at the 3′ end of the newly synthesized DNA strand. mutD5 has an altered epsilon resulting in reduced levels of proofreading and subsequent high mutation frequencies for all base-pair substitutions. We have analyzed the interaction between mutD5 and mutT-induced A:T → C:G transversions by measuring reversion frequencies in mutD5 and mutT single mutator strains and mutD5mutT double mutator strains using the well-characterized trpA58 and trpA88 alleles. We find that the double mutator strains produce more A:T → C:G substitutions than would be expected from simple additivity of the single mutator strains. We interpret this to mean that the two systems, at least in part, do act together to prevent the same mutational intermediate from producing A:T → C:G transversions. It is estimated that over 90% of the mutT-induced A:G mispairs are corrected by proofreading at the trpA58 site while only about 30% are corrected at trpA88. Reversion frequencies in the mutD5mutT double mutator strains indicate A:G misincorporations occur about 100 × more frequently at trpA58 than at the trpA88 site. Using these and other data we also provide estimations of the fidelity contributions for mutT editing, proofreading and methyl-directed mismatch repair at the two trpA sites for both transversions and the one transition that could be scored. In the case of A:T → C:G transversions, both mutT editing and proofreading make major contributions in error reduction with mismatch repair playing a small or no role at all. For the A:T → G:C transition, proofreading and mismatch repair were both important in preventing mutations while no contribution was observed for mutT editing.

Cairnsian mutagenesis inEscherichia coli: Genetic evidence for two pathways regulated bymutS andmutL genes

The phenomenon of Cairnsian mutagenesis was studied inEscherichia coli mutants bearing mutations inmutS,mutL,recA andlexA genes. It is shown that development of resistance to exogenous valine could be used as an example of Cairnsian response. Strains defective inmutS andmutL show a high frequency of Cairnsian mutagenesis to valine resistance. The response inmutS mutants is dependent upon cleavability of the LexA protein whereas that inmutL is not. The latter is independent ofrecA also. The need for LexA protein cleavage inmutS mutants can be bypassed by over-production of the RecA protein due to arecA operator constitutive mutation. Genetic evidence is presented to show that the products ofmutS andmutL genes negativelycontrol two pathways of Cairnsian mutagenesis. Cairnsian response is also elicited whenmutS ormutL strains are grown under conditions wherein a required nutrient is present in sub-optimal concentrations. Random, unselected mutagenic events are likely to occur during or after Cairnsian mutagenesis provided the cells are SOS inducible.

Involvement of RecB-mediated (but not RecF-mediated) repair of DNA double-strand breaks in the γ-radiation production of long deletions in Escherichia coli

Experiments were designed to determine the association between the repair of γ-radiation-induced DNA double-strand breaks (DSB) and the induction of 700–1000 bp long deletions (Lac − → Lac +), base substitutions ( leuB19 → Leu +), and frameshifts ( trpE9777 → Trp +) in Escherichia coli K-12. Over the range of 2.5–20 krad, deletions were induced with linear kinetics, as has been shown for the induction of DSB, while the induction kinetics of base substitutions and frameshifts were curvilinear. Like the repair of DSB, deletion induction showed an absolute requirement for an intact recB gene as well as a dependency on the type of preirradiation growth medium; these requirements were not seen for base substitutions or frameshifts. In addition, about 80% of the spontaneous deletions were absent in the recB21 strain. A recC1001 mutation, which confers a “hyper-Rec” phenotype, increased the rate of γ-radiation-induced deletions as well as the low-dose production of base substitutions and frameshifts. A recF143 mutation increased the yield of γ-radiation-induced deletions without increasing base substitutions or frameshifts. A mutS mutation markedly enhanced the γ-radiation induction of frameshifts, and had a slight effect on base substitutions, but did not affect the induction of deletions. Resistance to γ-irradiation and the capacity to repair DSB (albeit at about half the normal rate) were restored to the radiosensitive recB21 strain by the addition of the sbcB215 and sbcC201 mutations. However, the radioresistant recB sbcBC strain, which is recombination proficient via the RecF pathway, was still grossly deficient in the ability to produce deletions. A model for deletion induction as a by-product of the recB-dependent (Chi-dependent) repair of γ-radiation-induced DSB is discussed, as is the inability to detect deletions in cells that use only the recF-dependent (Chi-independent) mechanism to repair DSB.

Mismatch repair genes of Streptococcus pneumoniae: HexA confers a mutator phenotype in Escherichia coli by negative complementation

DNA repair systems able to correct base pair mismatches within newly replicated DNA or within heteroduplex molecules produced during recombination are widespread among living organisms. Evidence that such generalized mismatch repair systems evolved from a common ancestor is particularly strong for two of them, the Hex system of the gram-positive Streptococcus pneumoniae and the Mut system of the gram-negative Escherichia coli and Salmonella typhimurium. The homology existing between HexA and MutS and between HexB and MutL prompted us to investigate the effect of expressing hex genes in E. coli. Complementation of mutS or mutL mutations, which confer a mutator phenotype, was assayed by introducing on a multicopy plasmid the hexA and hexB genes, under the control of an inducible promoter, either individually or together in E. coli strains. No decrease in mutation rate was conferred by either hexA or hexB gene expression. However, a negative complementation effect was observed in wild-type E. coli cells: expression of hexA resulted in a typical Mut- mutator phenotype. hexB gene expression did not increase the mutation rate either individually or in conjunction with hexA. Since expression of hexA did not affect the mutation rate in mutS mutant cells and the hexA-induced mutator effect was recA independent, it is concluded that this effect results from inhibition of the Mut system. We suggest that HexA, like its homolog MutS, binds to mismatches resulting from replication errors, but in doing so it protects them from repair by the Mut system. In agreement with this hypothesis, an increase in mutS gene copy number abolished the hexA-induced mutator phenotype. HexA protein could prevent repair either by being unable to interact with Mut proteins or by producing nonfunctional repair complexes.

Interspecific recombination between Escherichia coli and Salmonella typhimurium occurs by the RecABCD pathway

Interspecific recombination in conjugation between Escherichia coli and Salmonella typhimurium is several orders of magnitude lower than intraspecies recombination and is dependent on the RecA function. This low efficiency is due to a 20% divergence in the DNA sequence. The methyl-directed ( mut H, L, S dependent) mismatch repair system appears to control the fidelity of homologous recombination; inactivating one of the Mut functions increases the interspecies recombination at least by 10 3-fold. The interspecific recombination in mutS or mutL mutant is only ≈ 10 3-fold lower than recombination in homospecific crosses as found after correction for the efficiency of mating and DNA transfer by zygotic induction experiments. The interspecific recombination is dependent on the RecABCD pathway: it was abolished in a recA mutant and decreased ≈ 10 3-fold in a recC mutant.

The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants

The requirement for DNA sequence homology in generalized genetic recombination is greatly relaxed in bacterial mutL, mutS and mutH mutants deficient in mismatch repair. In such mutants, intergeneric recombination occurs efficiently between Escherichia coli and Salmonella typhimurium, which are approximately 20% divergent in DNA sequence. This finding has implications for speciation, for regulating recombination between diverged repeated sequences, and for hitherto difficult interspecies hybridizations.

Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants.

The effect of mutations in known recombination genes (recA, recB, recC, recE, recF, recJ, recN, recO, recQ and ruv) on intramolecular recombination of plasmids was studied in recB recC sbcB and recB recC sbcA Escherichia coli mutants. The rate of recombination of circular dimer plasmids was at least 1000-fold higher in recB recC sbcB or recB recC sbcA mutants as compared to wild-type cells. The rate was decreased by mutations in recA, recF, recJ, recO, ruv or mutS in recB recC sbcB mutants, and by mutations in recE, recN, recO, recQ, ruv or mutS in recB recC sbcA mutants. In addition to measuring the recombination rate of circular dimer plasmids, the recombination-mediated transformation of linear dimer plasmids was also studied. Linear dimer plasmids transformed recB recC sbcB and recB recC sbcA mutants 20- to 40-fold more efficiently than wild-type cells. The transformation efficiency of linear dimer plasmids in recB recC sbcB mutants was decreased by mutations in recA, recF, recJ, recO, recQ or lexA (lexA3). In recB recC sbcA mutants the transformation efficiency of linear dimers was decreased only by a recE mutation. Physical analysis of linear dimer- or circular dimer-transformed recB recC sbcB mutants revealed that all transformants contained recombinant monomer genotypes. This suggests that recombination in recB recC sbcB cells is very efficient.

Cloning and characterization ofmutLandmutSgenes ofVibrio cholerae: nucleotide sequence of themutLgene

The mutL and mutS genes of Vibrio cholerae have been identified using interspecific complementation of Escherichia coli mutL and mutS mutants with plasmids containing the gene bank of V. cholerae. The recombinant plasmid pJT470, containing a 4.7 kb fragment of V. cholerae DNA codes for a protein of molecular weight 92,000. The product of this gene reduces the spontaneous mutation frequency of the E. coli mutS mutant. The plasmid, designated pJT250, containing a 2.5 kb DNA fragment of V. cholerae and coding for a protein of molecular weight 62,000, complements the mutL gene function of E. coli mutL mutants. These gene products are involved in the repair of mismatches in DNA. The complete nucleotide sequence of mutL gene of V. cholerae has been determined.

Escherichia coli mutT mutator effect during in vitro DNA synthesis. Enhanced A.G replicational errors.

The mechanism of the Escherichia coli mutT mutator effect was investigated using single-stranded phage as a mutational target. In vivo experiments showed that two M13mp2 lacZ alpha nonsense mutants reverted at a higher rate on a mutT1 host than on the wild-type host. The specificity of this mutator effect was identical to that observed for E. coli genes: A.T----C.G transversions. The mutT effect was subsequently demonstrated in vitro during DNA replication of M13mp2 DNA in cell-free extracts of E. coli. Replication (the single-stranded----replicative form conversion) in mutT1 extracts proceeded with a higher error rate than in wild-type extracts, and DNA sequence analysis of the in vitro revertants revealed the specific induction of A.T----C.G transversions. On the basis of the template specificity of the mutT effect in vitro, we conclude that the mutT effect involves the aberrant processing of A.G rather than T.C mispairs.

Molecular cloning and nucleotide sequence of the mutT mutator of Escherichia coli that causes A:T to C:G transversion.

The Escherichia coli mutator gene mutT, which causes A:T----C:G transversion, was cloned in pBR 322. mutT+ plasmids carry a 0.9 kb PvuII DNA fragment derived from the E. coli chromosome. Specific labelling of plasmid-encoded proteins by the maxicell method revealed that mutT codes for a polypeptide of about 15,000 daltons. The protein was overproduced when the mutT gene was placed under the control of the lac regulatory region on a multicopy runaway plasmid. The nucleotide sequence of the mutT gene was determined by the dideoxy method.

Inviability of dam recA and dam recB cells of Escherichia coli is correlated with their inability to repair DNA double-strand breaks produced by mismatch repair.

The molecular basis for the inviability of dam-3 recA200(Ts) and dam-3 recB270(Ts) cells was studied. The dam-3 recA200(Ts) cells were inviable in yeast extract-nutrient broth or in minimal medium at 42 degrees C. Although the dam-3 recB270(Ts) cells were inviable in yeast extract-nutrient broth at 42 degrees C, they were viable at 42 degrees C in minimal medium, in which the high salt content suppresses the mutant phenotype caused by the recB270(Ts) mutation at 42 degrees C. Under the growth conditions rendering dam rec cells inviable, the cells accumulated double-strand breaks in their DNA. Introduction of a mutL or mutS mutation restored the viability of dam-3 recB270(Ts) cells grown in yeast extract-nutrient broth at 42 degrees C and eliminated the formation of DNA double-strand breaks in these cells. We conclude that the inability to repair DNA double-strand breaks produced by the mismatch repair process accounts for the inviability of the dam recA and dam recB cells.

Handicapped individua in evolutionary processes.

Usually, when considering an evolutionary development, the fittest individua and their successful mutations receive most attention. The less fit ones, existing due to selection-mutation equilibria, are regarded, as an inevitable waste. It appears that these handicapped individua play an important role in evolution, as they make escapes from evolutionary traps possible. It is concluded that crucial improvements come from mutations of mutants. The implications seem to account to some extent for the observed speed and mode of evolution. An appropriate stochastic model is introduced, numerical experiments reported and results discussed.

Competition between the dam mutator and the isogenic wild-type of Escherichia coli

Previous studies have shown that the mutT, mutH, mutL and mutS mutators of Escherichia coli confer a marked selective advantage on their respective hosts in competition with otherwise isogenic wild-type strains. We have conducted competition experiments between dam − and dam + strains of Escherichia coli and have found that dam mutator strains are negatively selected. Although dam − is the first mutator to have a lower fitness than wild-type under chemostat conditions our result does not contradict the hypothesis that increased mutation rates are of evolutionary advantage under environmental stress conditions. Only in the special case of dam − does the advantage of higher mutation rates not outweigh the disadvantage due to the dam − -caused heavy pleiotropic effects.

The specificity of base-pair substitution induced by the mutL and mutS mutators in E. coli

The Escherichia coli mutator alleles, mutL and mutS, produced transversion as well as transition basepair substitutions with the trpA reversion system. Transversion, however, were generally mutator-induced at a lower level than transitions and the specific type of transversion and its nucleotide position appeared to strongly affect its level of enhancement. These results are interpreted to mean that mutL- and mutS-dependent mismatch correction is generally more effective at correcting transition mispairings than transversion mispairings. Correction of transversion mispairings is probably dependent upon site of occurrence and type of mismatch.

Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli.

The efficiency of methyl-directed DNA mismatch-repair of E. coli acting in vivo on heteroduplex genomes of phage M13 was found to be strongly dependent on the nature of the base/base mismatch to be corrected. Three efficiency classes were characterized:high (T/G, C/A and G/G); intermediate (A/A); and low (G/A, A/G, T/T, C/C, C/T and T/C). Methyl-directed DNA mismatch repair was lost completely for any type of mismatch in strains carrying either mutL or mutS mutations. Data obtained with a mutH mutant suggest that this locus is involved in methyl-dependent DNA strand discrimination. A functional correlation is suggested between the differential repair efficiencies and the frequencies of the corresponding replication errors.