Instability of repetitive DNA sequences: the role of replication in multiple mechanisms

Abstract

Rearrangements between tandem sequence homologies of various lengths are a major source of genomic change and can be deleterious to the organism. These rearrangements can result in either deletion or duplication of genetic material flanked by direct sequence repeats. Molecular genetic analysis of repetitive sequence instability in Escherichia coli has provided several clues to the underlying mechanisms of these rearrangements. We present evidence for three mechanisms of RecA-independent sequence rearrangements: simple replication slippage, sister-chromosome exchange-associated slippage, and single-strand annealing. We discuss the constraints of these mechanisms and contrast their properties with RecA-dependent homologous recombination. Replication plays a critical role in the two slipped misalignment mechanisms, and difficulties in replication appear to trigger rearrangements via all these mechanisms.

Figure 1

Replication misalignment (“slippage”) model for genetic rearrangements. A slipped alignment of the nascent strain with respect to template can generate deletion or expansion of a directly repeated sequence and any intervening DNA.

Figure 2

Unequal crossing-over between circular molecules. Unequal crossing-over between direct repeats borne on plasmids generates a circular dimer, with one triplicated and deleted allele.

Figure 3

Model for SCE associated with replication slipped misalignment, yielding deletion (18). (A) A stalled replication fork with direct repeat sequences shown in black. (B) Displacement of nascent strand 3′ ends. (C) Misalignment of nascent ends at repeat sequences. (D) Processing of crossed strand to yield Holliday-junction structure. The structure can be processed in two alternative ways. If no realignment of parental strands occurs: (E) repair replication. (F) Junction cleavage to form a reciprocal triplication/deletion dimeric product. If realignment of parental strands occurs: (E′) repair replication. (F′) Junction cleavage by RuvC or other resolving activity to form a nonreciprocal deletion/duplication dimeric product. For deletion, this outcome is favored over that shown in F. In ruvAB mutants, F′ is favored, yielding a higher level of reciprocal products.

Figure 4

Single-strand annealing model for deletion associated with palindromes. Palindromic DNA can adopt cruciform structure. SbcCD initiates cleavage of the cruciform. Resection followed by annealing at the flanking direct repeats generates a deletion.

Figure 5

Dissolution of homeologous deletion intermediates by mismatch repair. (A) Slipped misalignment model. MutH incision of the unmethylated strand removes the slipped strand, thereby aborting the deletion event. In the absence of Dam methylation, the ability to target excision to the slipped deletion strand is lost, resulting in the observed elevation of homeologous deletion rates (45). (B) Single-strand annealing model. Mismatch excision of either DNA strand destabilizes the intermediate. However, preexisting nicks should obviate the need for MutH. There is likewise no reason to explain the stabilization of the intermediate when Dam methylase is lacking.