Slipped misalignment mechanisms of deletion formation: In vivo susceptibility to nucleases

Misalignment of repeated sequences during DNA replication can lead to delet ions or duplications in genomic DNA, In Escherichia coli, such genetic rear rangements can occur at high frequencies, independent of the RecA-homologou s recombination protein, and are sometimes associated with sister chromosom e exchange (SCE). Two mechanisms for RecA-independent genetic rearrangement s have been proposed: simple replication misalignment of the nascent strand and its template and SCE-associated misalignment involving both nascent st rands. We examined the influence of the 3' exonuclease of DNA polymerase In and exonuclease I on deletion via these mechanisms in vivo. Because mutati ons in these exonucleases stimulate tandem repeat deletion, we conclude tha t displaced 3' ends are a common intermediate in both mechanisms of slipped misalignments, Our results also confirm the notion that two distinct mecha nisms contribute to slipped misalignments: simple replication misalignment events are sensitive to DNA polymerase III exonuclease, whereas SCE-associa ted events are sensitive to exonuclease I. If heterologies are present betw een repeated sequences, the mismatch repair system dependent on MutS and Mu tH aborts potential deletion events via both mechanisms. Our results sugges t that simple slipped misalignment and SCE-associated misalignment intermed iates are similarly susceptible to destruction by the mismatch repair syste m.