Summary DNA recombination and repair pathways require structure-specific endonucleases to process DNA structures that include forks, flaps, and Holliday junctions. Previously, we determined that the Drosophila MEI-9-ERCC1 endonuclease interacts with the novel MUS312 protein to produce meiotic crossovers, and that MUS312 has a MEI-9-independent role in interstrand crosslink (ICL) repair. The importance of MUS312 to pathways crucial for maintaining genomic stability in Drosophila prompted us to search for orthologs in other organisms. Based on sequence, expression pattern, conserved protein-protein interactions, and ICL repair function, we determined that the mammalian ortholog of MUS312 is BTBD12. Orthology between these proteins and S. cerevisiae Slx4 helped identify a conserved interaction with a second structure-specific endonuclease, SLX1. Genetic and biochemical evidence described here and in related papers suggest that MUS312 and BTBD12 direct Holliday junction resolution by at least two distinct endonucleases in different recombination and repair contexts.

Generation of meiotic crossovers in many eukaryotes requires the elimination of anti-crossover activities by utilizing the Msh4–Msh5 heterodimer to block helicases. Msh4 and Msh5 have been lost from the flies Drosophila and Glossina but we identified a complex of mini-chromosome maintenance (MCM) proteins that functionally replace Msh4–Msh5. REC, an ortholog of MCM8 that evolved under strong positive selection in flies, interacts with MEI-217 and MEI-218, which arose from a previously undescribed metazoan-specific MCM protein. Meiotic crossovers are reduced in Drosophila rec, mei-217, and mei-218 mutants; however, removal of the Bloom syndrome helicase ortholog restores crossovers. Thus, MCMs were co-opted into a novel complex that replaces the meiotic pro-crossover function of Msh4–Msh5 in flies.

The evolution of sexual reproduction is often explained by Red Queen dynamics: Organisms must continually evolve to maintain fitness relative to interacting organisms, such as parasites. Recombination accompanies sexual reproduction and helps diversify an organism's offspring, so that parasites cannot exploit static host genotypes. Here we show that Drosophila melanogaster plastically increases the production of recombinant offspring after infection. The response is consistent across genetic backgrounds, developmental stages, and parasite types but is not induced after sterile wounding. Furthermore, the response appears to be driven by transmission distortion rather than increased recombination. Our study extends the Red Queen model to include the increased production of recombinant offspring and uncovers a remarkable ability of hosts to actively distort their recombination fraction in rapid response to environmental cues.

Meiotic crossovers facilitate the segregation of homologous chromosomes and increase genetic diversity. The formation of meiotic crossovers was previously posited to occur via two pathways, with the relative use of each pathway varying between organisms; however, this paradigm could not explain all crossovers, and many of the key proteins involved were unidentified. Recent studies that identify some of these proteins reinforce and expand the model of two meiotic crossover pathways. The results provide novel insights into the evolutionary origins of the pathways, suggesting that one is similar to a mitotic DNA repair pathway and the other evolved to incorporate special features unique to meiosis. MEIOSIS is essential to maintaining the proper complement of chromosomes in sexually reproducing organisms. By following one round of DNA replication with two rounds of cellular division, meiosis effectively halves the chromosome content of participating cells. Prior to the first meiotic division, homologous chromosomes pair and, in many organisms, undergo recombination. Both crossovers, characterized by the reciprocal exchange of flanking markers, and noncrossovers, in which flanking DNA remains unchanged, result from these recombination events. Crossovers can also occur in mitotically proliferating cells during repair of certain types of DNA damage, especially double-strand breaks. Meiotic crossovers likewise are initiated from double-strand breaks, and many of the proteins used in mitotic repair are also used in meiotic recombination. This has led to the suggestion that meiotic recombination evolved from mitotic recombination (Marcon and Moens 2005). However, several modifications were necessary to give rise to meiotic recombination in its current form (reviewed in Villeneuve and Hillers 2001). First, a mechanism of generating programmed double-strand breaks to initiate recombination was needed. This was achieved through the use of Spo11, a conserved protein that generates regulated meiotic double-strand breaks (Keeney et al. 1997). Second, whereas crossovers are avoided in mitotic cells to prevent loss of heterozygosity and chromosome rearrangement, crossover formation is emphasized in meiotic recombination to facilitate the segregation of homologous chromosomes and to increase genetic diversity. Third, the preferred repair template was changed from the sister chromatid in mitotic cells to the homologous chromosome in meiotic cells, since only crossovers between homologs give the aforementioned benefits. Finally, exquisite crossover control mechanisms arose to regulate the number and distribution of crossovers across the genome and relative to one another. In particular, every chromosome pair receives at least one crossover, sometimes called an obligate crossover (Jones 1984). Also, if additional crossovers occur, they tend not to be near one another, a phenomenon called crossover interference (reviewed in Berchowitz and Copenhaver 2010).A complication obscuring the relationship between the mitotic and meiot...

Summary In most sexually reproducing organisms, crossover formation between homologous chromosomes is necessary for proper chromosome disjunction during meiosis I. During meiotic recombination, a subset of programmed DNA double-strand breaks (DSBs) are repaired as crossovers, with the remainder becoming noncrossovers [1]. Whether a repair intermediate is designated to become a crossover is a highly-regulated decision that integrates several crossover patterning processes, both along chromosome arms (interference and the centromere effect) and between chromosomes (crossover assurance) [2]. Because the mechanisms that generate crossover patterning have remained elusive for over a century, it has been difficult to assess the relationship between crossover patterning and meiotic chromosome behavior. We show here that meiotic crossover patterning is lost in Drosophila melanogaster mutants that lack the Bloom syndrome helicase. In the absence of interference and the centromere effect, crossovers are distributed more uniformly along chromosomes. Crossovers even occur on the small chromosome 4, which normally never has meiotic crossovers [3]. Regulated distribution of crossovers between chromosome pairs is also lost, resulting in an elevated frequency of homologs that do not receive a crossover, which in turn leads to elevated nondisjunction.

Several helicases function during repair of double-strand breaks and handling of blocked or stalled replication forks to promote pathways that prevent formation of crossovers. Among these are the Bloom syndrome helicase BLM and the Fanconi anemia group M (FANCM) helicase. To better understand functions of these helicases, we compared phenotypes of Drosophila melanogaster Blm and Fancm mutants. As previously reported for BLM, FANCM has roles in responding to several types of DNA damage in preventing mitotic and meiotic crossovers and in promoting the synthesis-dependent strand annealing pathway for repair of a double-strand gap. In most assays, the phenotype of Fancm mutants is less severe than that of Blm mutants, and the phenotype of Blm Fancm double mutants is more severe than either single mutant, indicating both overlapping and unique functions. It is thought that mitotic crossovers arise when structure-selective nucleases cleave DNA intermediates that would normally be unwound or disassembled by these helicases. When BLM is absent, three nucleases believed to function as Holliday junction resolvases-MUS81-MMS4, MUS312-SLX1, and GEN-become essential. In contrast, no single resolvase is essential in mutants lacking FANCM, although simultaneous loss of GEN and either of the others is lethal in Fancm mutants. Since Fancm mutants can tolerate loss of a single resolvase, we were able to show that spontaneous mitotic crossovers that occur when FANCM is missing are dependent on MUS312 and either MUS81 or SLX1.

Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. Cyclical environmental conditions have also been shown to yield evolved increases in recombination frequency. Here, we use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate and/or increased recombination rate in response to temperature. In contrast to expectation, we find no evidence for either enhanced plasticity in recombination or increased rates of recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct.

The Bloom syndrome helicase, BLM, has numerous functions that prevent mitotic crossovers. We used unique features of Drosophila melanogaster to investigate origins and properties of mitotic crossovers that occur when BLM is absent. Induction of lesions that block replication forks increased crossover frequencies, consistent with functions for BLM in responding to fork blockage. In contrast, treatment with hydroxyurea, which stalls forks, did not elevate crossovers, even though mutants lacking BLM are sensitive to killing by this agent. To learn about sources of spontaneous recombination, we mapped mitotic crossovers in mutants lacking BLM. In the male germline, irradiation-induced crossovers were distributed randomly across the euchromatin, but spontaneous crossovers were nonrandom. We suggest that regions of the genome with a high frequency of mitotic crossovers may be analogous to common fragile sites in the human genome. Interestingly, in the male germline there is a paucity of crossovers in the interval that spans the pericentric heterochromatin, but in the female germline this interval is more prone to crossing over. Finally, our system allowed us to recover pairs of reciprocal crossover chromosomes. Sequencing of these revealed the existence of gene conversion tracts and did not provide any evidence for mutations associated with crossovers. These findings provide important new insights into sources and structures of mitotic crossovers and functions of BLM helicase. MEIOTIC recombination was discovered 100 years ago by T. H. Morgan and his students in classic studies of Drosophila genetics (Morgan 1911). Since that time, a great deal has been learned about the functions, molecular mechanisms, and regulation of meiotic recombination. This process is initiated through the introduction of programmed DNA doublestrand breaks (DSBs), which are then repaired through highly regulated homologous recombination (HR) pathways such that a substantial fraction of repair events produce reciprocal crossovers (reviewed in Kohl and Sekelsky 2013). The chiasmata that form at sites of crossovers help to ensure accurate segregation of homologous chromosomes. In addition, crossovers generate chromosomes with novel combinations of alleles at linked loci, leading to increased genetic diversity.A quarter century after the discovery of meiotic recombination, Curt Stern, also working with Drosophila, found that crossovers can occur in somatic cells (Stern 1936). This phenomenon is usually called "mitotic recombination," although most such events are thought to occur during interphase rather than in mitosis per se. Compared to meiotic recombination, little is known about mitotic recombination. Except in some specialized cases, like antibody gene rearrangement, mitotic recombination occurs in response to DNA damage (spontaneous or exogenously induced). Mitotic recombination, like meiotic recombination, can be initiated by DSBs, but it is unclear whether DSBs constitute a substantial fraction of the events that initiate spontan...