Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria

Abstract

Living cells have multiple mechanisms for avoiding undesirable mutations in their DNA as a result of mistakes in replication or of subsequent damage. Reduction in error frequencies by a factor of 10-7 to 10-6 can be attributed to the adding and editing functions of the replicative polymerase. A further reduction of 10-2 to 10-3, in such diverse species as S. pneumoniae and E. coli, is attributable to heteroduplex base mismatch correction of newly synthesized DNA. Ancillary editing or correcting functions may affect those mispairs not recognized by the major repair systems or those that occur away from the replication fork. These mechanisms bring the spontaneous mutation frequency in bacteria to a level of <10-9 per nucleotide per generation. The Hex and Mut systems, which are the major heteroduplex repair systems of S. pneumoniae and E. coli, respectively, are remarkably similar. The evidence for both systems suggests that they recognize and eliminate lengthy tracts of the nascent strand in which a mismatch occurs. Inasmuch as both systems recognize mismatches without strand polarity, if they are to prevent mutations, they must have a way of identifying the newly synthesized strand to be corrected. The Hex system depends on the presence of single-strand breaks in that strand to identify it. The Mut system depends on the presence of unmethylated GATC sites for the identification, although it, too, may use strand breaks as an ultimate signal. The reason for the removal of lengthy tracts in both systems is probably the natural spacing of these identifying signals. The strand breaks or unmethylated sites bracketing the mismatch, therefore, may serve both to identify the strand to be corrected and to delimit the portion of it to be excised and resynthesized. The spectrum of mismatch recognition is virtually identical for the Hex and Mut systems. They both efficiently act on transition mispairs, some transversion mispairs, and frameshift but not longer deletion/insertions. Although the molecular basis of mismatch recognition has not been determined, mispairs that cause small deviations from the normal DNA helical structure appear to be recognized, but those that cause gross deviations are not. Several genes implicated in mismatch repair in each system have been cloned, and their protein products are currently under investigation. The hexA, hexB, mutL, and mutS genes presumably encode proteins able to recognize mismatches and excise DNA strand segments. The mutU gene encodes a helicase, but its function in the system is unknown; the ssb product was essential in an in vitro correction assay. One major difference between the Hex and Mut systems is the role in the latter of DNA methylation in strand targeting. The dam gene encodes the GATC methylase; the mutH gene may encode a protein that recognizes an unmethylated GATC site. The methylation dependence, which appears to reduce mutation rated by an additional factor of 10-1, may have arisen as an overlay on a simpler ancestral system such as Hex. Its protein components could have evolved from a restriction enzyme system. Although the main biological function of mismatch repair may be mutation avoidance, the repair systems also have important effects on genetic recombination. The Hex system reduces transformation frequencies in S. pneumoniae. The Mut system increases recombination frequencies in E. coli, and it appears to be responsible in part for multiple recombinatory switching known as high negative interference, although the most notable instances of such recombinatory behavior may be due to sequence-specific, short-patch repair, which has been observed in both E. coli and S. pneumoniae. These recombination events are not reciprocal and correspond, rather, to gene conversion. Analogous systems could be responsible for both homogenization and deversification of gene families in higher organisms. We have come full circle. Mismatch repair was postulated originally to account for gene conversion in fungi and yeasts. Subsequently, the Hex and Mut systems for mismatch repair were discovered in bacteria. Recent reports indicate an analogous system in yeasts responsible for gene conversion, with a spectrum of mismatch recognition similar to Hex and Mut (306). Transfection experiments with simian virus 40 heteroduplex DNA indicate that strand recognition for mismatch repair in mammalian cells also depends on nicks and hypomethylation, of C residues in this case (109). Mutations in the genes governing the yeast system give elevated spontaneous mutation rates (310). Such systems may be universal. Inasmuch as they appear to act subsequent to replication and, hence, are dispensable, their loss and regain by mutation allow a rapid shift between modes of high and low spontaneous mutation frequency. These shifts may be important in the evolution of species.