An Enhanced, in Vivo Assay for DNA Mismatch Repair Reveals Different Repair Mechanisms of Lagging Strand Mismatches

Abstract

In E. coli, a DNA mismatch repair (MMR) pathway corrects errors that occur during replication, such as the mis-pairing of nucleotides, by coordinating the excision and re-synthesis of a long tract of DNA between an epigenetic signal on the newly-replicated strand and the replication error after the error is identified by protein MutS. Recent evidence is suggestive that this “long-patch repair” between these sites is coordinated in the same direction of replication by the replisome. Using a novel replication-coupled assay to quantify the nucleotide-dependence, strand-dependence, and directionality of MMR on genomic mismatches in vivo, we find that repair of lagging strand mismatches occurs bidirectionally, and that directional bias in the origin of strand excision and effect of mutations to the MMR proteins is dependent on the molecular species of the mismatch.