Homologous recombination is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage including DNA double-stranded breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for active recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accumulation of toxic recombination intermediates. Evidently, homologous recombination must be carefully regulated to match specific cellular needs. Here we review the mechanistic stages and proteins in recombination that are subject to regulation and suggest that recombination achieves flexibility and robustness by proceeding through meta-stable, reversible intermediates.

The DNA structure-selective endonuclease Mus81-Mms4/Eme1 is a context-specific recombination factor that supports DNA replication, but is not essential for DSB repair in Saccharomyces cerevisiae. We overexpressed Mus81-Mms4 in S. cerevisiae, purified the heterodimer to apparent homogeneity, and performed a classical enzymological characterization. Kinetic analysis (kcat, KM) demonstrated that Mus81-Mms4 is catalytically active and identified three substrate classes in vitro. Class I substrates reflect low KM (3–7 nM) and high kcat (∼1 min−1) and include the nicked Holliday junction, 3′-flapped and replication fork-like structures. Class II substrates share low KM (1–6 nM) but low kcat (≤0.3 min−1) relative to Class I substrates and include the D-loop and partial Holliday junction. The splayed Y junction defines a class III substrate having high KM (∼30 nM) and low kcat (0.26 min−1). Holliday junctions assembled from oligonucleotides with or without a branch migratable core were negligibly cut in vitro. We found that Mus81 and Mms4 are phosphorylated constitutively and in the presence of the genotoxin MMS. The endogenous complex purified in either modification state is negligibly active on Holliday junctions. Hence, Holliday junction incision activity in vitro cannot be attributed to the Mus81-Mms4 heterodimer in isolation.

No abstract

Homologous Recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments—helical filaments of a recombinase enzyme bound to single-stranded DNA. Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we review the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments: some intrinsic such as recombinase ATP binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examine dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examine the biochemical properties of recombination proteins from four model systems (T4 phage, E. coli, S. cerevisiae, and H. sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We propose that the presynaptic filament has evolved to rely on multiple external factors for increased multi-level regulation of HR processes in genomes with greater structural and sequence complexity.

cMost spontaneous DNA double-strand breaks (DSBs) arise during replication and are repaired by homologous recombination (HR) with the sister chromatid. Many proteins participate in HR, but it is often difficult to determine their in vivo functions due to the existence of alternative pathways. Here we take advantage of an in vivo assay to assess repair of a specific replication-born DSB by sister chromatid recombination (SCR). We analyzed the functional relevance of four structure-selective endonucleases (SSEs), Yen1, Mus81-Mms4, Slx1-Slx4, and Rad1, on SCR in Saccharomyces cerevisiae. Physical and genetic analyses showed that ablation of any of these SSEs leads to a specific SCR decrease that is not observed in general HR. Our work suggests that Yen1, Mus81-Mms4, Slx4, and Rad1, but not Slx1, function independently in the cleavage of intercrossed DNA structures to reconstitute broken replication forks via HR with the sister chromatid. These unique effects, which have not been detected in other studies unless double mutant combinations were used, indicate the formation of distinct alternatives for the repair of replicationborn DSBs that require specific SSEs. D ouble-strand breaks (DSBs) are among the most harmful DNA lesions. Failure to repair DSBs is often associated with apoptosis, aging, and cancer in metazoans and can lead to different types of genome instability in all organisms, including high mutation frequency, chromosome rearrangements, or chromosome loss. As a consequence, cells have developed a variety of specialized and complex mechanisms for DSB repair, defined as nonhomologous end joining (NHEJ) and homologous recombination (HR). In contrast to NHEJ, which works preferentially in nondividing cells at the G 1 stage of the cell cycle, HR is the major DSB repair mechanism occurring at the S/G2 phase. In particular, HR is responsible for the repair of breaks that are associated with DNA replication (1). Understanding the mechanisms of HR and the proteins that catalyze these reactions is therefore central to our understanding of cell proliferation and associated pathological states and diseases.A key step in HR is the resolution of crossed-stranded DNA structures formed during DNA strand exchange (28,41,53). Dloops formed by Rad51-mediated DNA strand exchange may lead to the formation of double Holliday junctions (HJs), which can be resolved in two ways (17, 28): (i) by dissolution catalyzed by the Sgs1/BLM-Top3 helicase-topoisomerase complex (54); (ii) by endonucleolytic cleavage mediated by structure-selective endonucleases (SSEs) (28,32,35,38). Four conserved SSEs, Mus81-Mms4, Slx1-Slx4, Yen1, and Rad1-Rad10, have been identified in Saccharomyces cerevisiae, and their biochemical activities have been studied extensively (15,20,21,31). The in vivo roles of Mus81-Mms4, Slx1-Slx4, and Yen1, however, remain to be determined. One complication has been their apparent functional overlap and the presence of alternative pathways by which recombination intermediates can be resolved.Mus81-Mms4 (Mus81-Eme1 in Sc...