Academic journal article Genetics

A Delicate Balance between Repair and Replication Factors Regulates Recombination between Divergent DNA Sequences in Saccharomyces Cerevisiae

Academic journal article Genetics

A Delicate Balance between Repair and Replication Factors Regulates Recombination between Divergent DNA Sequences in Saccharomyces Cerevisiae

Article excerpt

HOMOLOGOUS recombination between nonallelic, divergent sequences in the genome can lead to chromosomal rearrangements. Multiple cellular mechanisms contribute to suppressing such deleterious events. For example, the organization of the interphase nucleus helps to limit physical interactions between distant regions of the genome, and cell cycle regulation of homologous recombination factors suppresses recombination events at times when distant genomic regions and nonallelic sequences tend to be unprotected or closer to each other (reviewed in George and Alani 2012). Despite these lines of defense, physical interactions between nonallelic sequences can still frequently occur, and when damage or replication stalling occurs in the vicinity of these interactions, nonallelic homologous recombination (NAHR) can be initiated (reviewed in Liu et al. 2012). Several mechanisms have been proposed to understand how recombination events between divergent DNA sequences, known as homeologous recombination, are prevented. One such mechanism, heteroduplex rejection, requires helicase-mediated unwinding of recombination intermediates (Sugawara et al. 2004; Surtees et al. 2004).

The DNA mismatch repair (MMR) system acts to repair polymerase errors incurred during DNA replication. DNA mismatch repair factors also play critical roles in maintaining the fidelity of homologous recombination in both prokaryotes and eukaryotes by inhibiting recombination between divergent sequences, and this function is directly related to levels of sequence divergence (Rayssiguier et al. 1989; Shen and Huang 1989; Petit et al. 1991; de Wind et al. 1995; Selva et al. 1995; Chambers et al. 1996; Datta et al. 1996; Hunter et al. 1996; Porter et al. 1996; Elliott and Jasin 2001; Nicholson et al. 2000). In the yeast Saccharomyces cerevisiae, MMR is initiated by either the Msh2-Msh6 (MutSa)orMsh2-Msh3 (MutSb) heterodimer binding to DNA containing mismatches; Msh2-Msh6 shows high specificity for single base- base mismatches and single nucleotide insertions/deletions, whereas Msh2-Msh3 shows high specificity for insertion/ deletion loops up to 16 nucleotides in size (reviewed in Kunkel and Erie 2005). Msh2-Msh6 has been shown in baker's yeast to colocalize with the DNA replication machinery (Hombauer et al. 2011a). Mlh heterodimers (primarily Mlh1Pms1) then interact with Msh-mismatch complexes to recruit downstream factors that complete MMR through excision, resynthesis, and ligation steps. These downstream factors include the Exo1 exonuclease, the PCNA processivity clamp, replication factor C (RFC), DNA polymerases d and e, and RPA single-strand binding protein (reviewed in Kunkel and Erie 2005).

Antirecombination has been hypothesized to occur by regulation ofbranch migration ofrecombinationintermediates to limit heteroduplex extension, rejection of recombination intermediates through nucleolytic degradation, or by unwinding heteroduplex DNA intermediates (Sugawara et al. 2004; Surtees et al. 2004; Goldfarb and Alani 2005; Waldman 2008). The single-strand annealing (SSA) pathway provides a relatively simple system to study antirecombination mechanisms (Figure 1A). This Rad52-dependent pathway is a specialized type of homologous recombination that is initiated by a double-strand break (DSB) between closely spaced repeat sequences. Resection of single-strand DNA (ssDNA) at the break, followed by annealing of homologous sequences, tail clipping, DNA synthesis, and ligation, results in repair of the DSB involving a deletion between the repeat sequences (Lin and Sternberg 1984; Fishman-Lobell et al. 1992: Sugawara and Haber 1992). A critical step required to complete SSA is the removal of 39 nonhomologous tails, which occurs in steps requiring Msh2-Msh3 and the Rad1-Rad10 endonuclease (Fishman-Lobell et al. 1992; Sugawara et al. 1997).

SSA is thought to be the predominant form of DSB repair within highly repetitive regions of the genome, such as the ribosomal DNA (Kobayashi 2006; Li et al. …

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