Mismatch repair in Bacillus subtilis compensates for the correction bias of PolC exonuclease

Overview & Synopsis

The spontaneous mutation rate is a crucial parameter in molecular evolution. Three main factors determine it : (1) base selection, or the capacity of the DNA polymerase to incorporate the right nucleotide during DNA replication (2) proofreading, i.e. the capability that some polymerases have to correct misincorporations ; (3) mismatch repair (MMR). Here, we constructed Bacillus subtilis strains with a proofreading-deficient allele of the essential DNA polymerase PolC and/or a deficient allele of an MMR gene. Using mutation accumulations followed by whole-genome sequencing, we characterized the whole-genome mutation rate and spectrum of each of the strains. Our strongest hypermutator reached a mutation rate ~ 1,500 fold higher than that of the wild-type. Among eight factors thought to potentially influence the mutation spectra, only the reference pair, its orientation with regards to replication, and neighbouring nucleotides had a significant effect. We identified the frequency of different types of mutations depending on the activity (or lack thereof) of each system, and revealed that the mutation spectrum is the least uniform when PolC exonuclease is active and the MMR is not. Altogether these results indicate that the proofreading activity of PolC generates a mutation bias, which the MMR reduces.