DNA polymerases δ and λ cooperate in repairing double-strand breaks by microhomology-mediated end-joining in Saccharomyces cerevisiae

Abstract

Maintenance of genome stability is carried out by a suite of DNA repair pathways that ensure the repair of damaged DNA and faithful replication of the genome. Of particular importance are the repair pathways, which respond to DNA double-strand breaks (DSBs), and how the efficiency of repair is influenced by sequence homology. In this study, we developed a genetic assay in diploid Saccharomyces cerevisiae cells to analyze DSBs requiring microhomologies for repair, known as microhomology-mediated end-joining (MMEJ). MMEJ repair efficiency increased concomitant with microhomology length and decreased upon introduction of mismatches. The central proteins in homologous recombination (HR), Rad52 and Rad51, suppressed MMEJ in this system, suggesting a competition between HR and MMEJ for the repair of a DSB. Importantly, we found that DNA polymerase delta (Pol δ) is critical for MMEJ, independent of microhomology length and base-pairing continuity. MMEJ recombinants showed evidence that Pol δ proofreading function is active during MMEJ-mediated DSB repair. Furthermore, mutations in Pol δ and DNA polymerase 4 (Pol λ), the DNA polymerase previously implicated in MMEJ, cause a synergistic decrease in MMEJ repair. Pol λ showed faster kinetics associating with MMEJ substrates following DSB induction than Pol δ. The association of Pol δ depended on RAD1, which encodes the flap endonuclease needed to cleave MMEJ intermediates before DNA synthesis. Moreover, Pol δ recruitment was diminished in cells lacking Pol λ. These data suggest cooperative involvement of both polymerases in MMEJ.DNA repair | genome stability | translocation D NA double-strand breaks (DSBs) are toxic lesions that can be repaired by two major pathways in eukaryotes: nonhomologous end-joining (NHEJ) and homologous recombination (HR) (1). Although HR repairs DSBs in a template-dependent, high-fidelity manner, NHEJ functions to ligate DSB ends together using no or very short (1-4 bp) homology. Recently, a new pathway was identified in eukaryotes, which uses microhomologies (MHs) to repair a DSB and does not require the central proteins used in HR (Rad51, Rad52) or NHEJ (Ku70-Ku80) (2-5). In mammalian cells, this pathway of repair is known as alternative end-joining (Alt-EJ) and is often but not always associated with MHs, whereas in budding yeast, the commensurate pathway, MH-mediated end-joining (MMEJ), will typically use 5-25 bp of MH (6, 7). These pathways are associated with genomic rearrangements, and cancer genomes show evidence of MH-mediated rearrangements (8-12). In addition, eukaryotic genomes contain many dispersed repetitive elements that can lead to genome rearrangements when recombination occurs between them (13-16). Therefore, controlling DSB repair in the human genome, which features a variety of repeats, is especially important given the fact that recombination between repetitive elements has been implicated in genomic instability associated with disease (17-20).The original characterization of Alt-EJ in mammalian cells suggested it did not rep...

Eukaryotic DNA Polymerases in Homologous Recombination

“…DNA polymerase β is mainly involved in base-excision repair (109). DNA polymerases λ, μ, and TdT have been implicated in NHEJ, MMEJ/alt-EJ, and variable-diversity-joining [V(D)J] recombination, in addition to processes responsible for generating diversity in the immunoglobulin and T cell receptors during the early stages of B and T cell maturation, respectively (90, 109). The Y family comprises DNA polymerases η, ι, κ, and Rev1, which act primarily in lesion bypass (32, 109).…”

“…It is particularly adept at extending the 3′-OH end of the invading strand in the D-loop, performing first-end DNA synthesis in all HR pathways (Figure 1). Interestingly, Pol δ is also involved in MMEJ/alt-EJ-associated DNA synthesis in budding yeast (67, 90). …”

“…DNA polymerase lambda (λ) is a single-subunit enzyme lacking proofreading activity that has a major function in NHEJ and MMEJ/alt-EJ in budding yeast and mammals (7, 67, 90, 108, 110). Pol λ processivity and affinity for 3′-hydroxyl ends, but not its fidelity, are stimulated by RPA and PCNA (77).…”

“…For example, human Rev1 collaborates with polymerases η, ι, and κ, but not ζ, to replicate UV-damaged templates (163), whereas XP-variant cells lacking Pol η utilize pol ζ, ι, and κ in bypass of cyclobutane pyrimidine dimers (165). Recently, polymerases δ and λ were shown to work together to promote efficient MMEJ/alt-EJ repair of DSBs (90). …”

Noncanonical views of homology-directed DNA repair

“…Subsequent studies in S. cerevisiae identified the molecular machinery that drives MMEJ: (1) initiation of end resection by the MRX-Sae2; (2) if the microhomologous sequences are >2 kb away from the DSB ends, extensive bidirectional resection is performed by Sgs1-Dna2 and/or Exo1; (3) annealing of microhomologous sequences and removal of 3 ′ single-stranded flaps by Rad1-Rad10; (4) and filling of gaps by polymerases Pol λ (Pol 4) and Pol δ in conjunction with its nonessential subunit, Pol 32 (Ma et al 2003;Decottignies 2007;Garcia et al 2011;Symington and Gautier 2011;Villarreal et al 2012;Cannavo and Cejka 2014;Deng et al 2014;Meyer et al 2015). Rad51 filament formation is considered to be a critical feature in dictating GC versus MMEJ events.…”