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Meiosis-Specific Recombinase Dmc1 Is a Potent Inhibitor of the Srs2 Antirecombinase

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Meiosis-Specific Recombinase Dmc1 Is a Potent Inhibitor of the Srs2 Antirecombinase Meiosis-specific recombinase Dmc1 is a potent inhibitor of the Srs2 antirecombinase J. Brooks Crickarda, Kyle Kanieckib, Youngho Kwonc, Patrick Sungc, and Eric C. Greenea,1 aDepartment of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032; bDepartment of Genetics and Development, Columbia University, New York, NY 10032; and cDepartment of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520 Edited by Michael Lichten, National Cancer Institute, Bethesda, MD, and accepted by Editorial Board Member Kiyoshi Mizuuchi September 7, 2018 (received for review June 18, 2018) Cross-over recombination products are a hallmark of meiosis Srs2 is an ATP-dependent 3′→5′ ssDNA motor protein that because they are necessary for accurate chromosome segregation plays a central role in minimizing cross-overs during mitosis (2, and they also allow for increased genetic diversity during sexual 10–17). Srs2 functions by dismantling Rad51-ssDNA and D-loop reproduction. However, cross-overs can also cause gross chromo- intermediates, thereby channeling HR intermediates through somal rearrangements and are therefore normally down-regulated the synthesis-dependent strand annealing (SDSA) pathway, during mitotic growth. The mechanisms that enhance cross-over which exclusively yields non–cross-over recombination products product formation upon entry into meiosis remain poorly under- (Fig. 1A) (2, 10–16). Consequently, srs2Δ mutants have a mitotic stood. In Saccharomyces cerevisiae, the Superfamily 1 (Sf1) helicase hyperrecombination phenotype characterized by frequent cross- Srs2, which is an ATP hydrolysis-dependent motor protein that ac- overs and gross chromosomal rearrangements (15, 16, 18–20). tively dismantles recombination intermediates, promotes synthesis- Srs2 antirecombinase activity is counterbalanced by the Rad51 dependent strand annealing, the result of which is a reduction in paralog complex Rad55/57, the Shu complex (composed of the cross-over recombination products. Here, we show that the meiosis- Rad51 paralogs Psy3 and Csm2 and the SWIM-domain proteins specific recombinase Dmc1 is a potent inhibitor of Srs2. Biochemical Shu1 and Shu2), and Rad52, all of which enhance assembly or and single-molecule assays demonstrate that Dmc1 acts by inhibit- stability of early HR intermediates (Fig. 1A) (21–24). The role of ing Srs2 ATP hydrolysis activity, which prevents the motor protein Srs2 in helping to minimize cross-overs during mitosis is well from undergoing ATP hydrolysis-dependent translocation on Dmc1- established, but its functions during meiosis remain poorly un- BIOCHEMISTRY bound recombination intermediates. We propose a model in which derstood (15). Srs2 expression is up-regulated during meiosis Dmc1 helps contribute to cross-over formation during meiosis by (25), but srs2Δ mutants have relatively mild meiotic phenotypes antagonizing the antirecombinase activity of Srs2. (15, 26). However, mechanistic interpretation of the molecular defects underlying srs2Δ phenotypes are complicated by the fact Srs2 | Rad51 | Dmc1 | meiosis | homologous recombination that Srs2 also participates in HR-independent processes related to genome integrity (reviewed in refs. 16 and 27), in particular omologous recombination (HR) is necessary for maintain- with respect to replication through DNA secondary structure – Hing genome integrity across all domains of life, and HR is (28 30), replication checkpoint activation (31, 32), preventing also required to repair programmed double strand breaks ssDNA gaps present at stalled replication forks from being used (DSBs) during meiosis (1–5). Meiosis is a broadly conserved to initiate recombination (33, 34), and Top1-mediated removal eukaryotic cellular program that yields haploid progeny from of misincorporated ribonucleotides (35). Interestingly, Srs2 overexpression in meiosis results in the diploid precursors and is essential for sexual reproduction (4, 6, disruption of Rad51 repair foci, but does not disrupt Dmc1 re- 7). HR plays a central role in meiosis, and, in most organisms, pair foci (36), leading to the suggestion that Srs2 may not play the chromosomal changes that take place during meiosis are a major role in regulating HR in meiosis (15). However, the dependent on recombination (4, 6, 7). Importantly, the transition activities of Srs2 on meiotic HR intermediates have not been from mitotic repair to meiotic repair is denoted by a marked – difference in cross-over vs. non cross-over HR outcomes. Cross- Significance overs are considered less desirable in mitotic cells because they can lead to loss of heterozygosity and other chromosomal rear- Here, we demonstrate that the antirecombinase Srs2 is unable to rangements (5, 8). In contrast, cross-overs are favored during dismantle recombination intermediates containing the meiosis- meiosis because they are essential for chromosome segregation specific recombinase Dmc1. Our work defines a function of and they also help enhance genetic diversity among progeny (4, Dmc1 as an inhibitor of the prototypical antirecombinase 6, 7). The molecular basis for the differential regulation of cross- Srs2. Based on these findings, we propose that the presence overs during mitosis and meiosis remains poorly understood. of Dmc1 may help to prevent Srs2 from disruption of early The DNA transactions that take place during HR are cata- meiotic recombination intermediates, which may in turn be an- lyzed by the broadly conserved Rad51/RecA family of recombi- ticipated to favor the formation of cross-over recombination nases, which are ATP-dependent DNA-binding proteins that products. form extended helical filaments on ssDNA (2, 3). Most eukary- otes require two recombinases, Rad51, which catalyzes DNA Author contributions: J.B.C. and E.C.G. designed research; J.B.C. and K.K. performed re- search; Y.K. and P.S. contributed new reagents/analytic tools; J.B.C. and E.C.G. analyzed strand exchange during mitosis, and Dmc1, which catalyzes data; and J.B.C., Y.K., P.S., and E.C.G. wrote the paper. strand exchange during meiosis (1, 3, 4). Rad51 and Dmc1 are ∼ The authors declare no conflict of interest. 46% identical and arose from a gene-duplication event early This article is a PNAS Direct Submission. M.L. is a guest editor invited by the in eukaryotic evolution coinciding with the emergence of mei- Editorial Board. osis (1, 3, 4, 9). However, it remains unknown why eukaryotes Published under the PNAS license. require a specialized recombinase for meiosis, and the re- 1To whom correspondence should be addressed. Email: [email protected]. lationship between recombinase identity and the regulation of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. cross-over vs. non–cross-over recombination outcomes remains 1073/pnas.1810457115/-/DCSupplemental. unknown (1–5). www.pnas.org/cgi/doi/10.1073/pnas.1810457115 PNAS Latest Articles | 1of8 Downloaded by guest on October 2, 2021 explored in vitro, and it remains unknown whether this differ- Dmc1 acts by inhibiting the ATP hydrolysis by Srs2, which in turn ential response of Rad51 and Dmc1 foci to Srs2 overexpression prevents Srs2 from undergoing ATP-dependent translocation on is caused by an inherent difference between the two recombi- ssDNA. Our results are consistent with a model in which direct nases, or whether it might reflect the effects of another protein physical contact with the 3′ ends of the Dmc1 filaments halts component of the meiotic presynaptic complex (reviewed in Srs2 motor activity, suggesting the possibility that this inhibition ref. 3), such as the Dmc1-specific mediator protein complex occurs through an allosteric regulatory mechanism. We propose Mei5/Sae3 (37), the Dmc1 accessory factors Hop2/Mnd1 (38, 39) a model in which meiotic recombination intermediates contain- or Rdh54 (40), or perhaps the ZMM proteins (including, Zip1, ing Dmc1 are protected from disruption by the antirecombinase Zip2, Zip3, Zip4/Spo22, Mer3, Msh4, and Msh5), which help to activity of Srs2, and therefore the ability of Dmc1 to inhibit coordinate recombination with synaptonemal complex formation Srs2 may help to promote cross-over recombination outcomes and have also been implicated as inhibitors of Sgs1 (41). during meiosis. To gain insights into the molecular mechanisms governing cross-over regulation during meiosis, here, we investigated the Results ability of a central regulator of mitotic cross-over formation, the Dmc1 Is a Potent Inhibitor of Srs2 ATP Hydrolysis Activity. To ex- Srs2 antirecombinase, to act upon meiotic recombination inter- amine potential functions for Srs2 regulation during meiosis, we mediates. By using a combination of biochemical and single- sought to determine whether Srs2 could dismantle Dmc1-ssDNA molecule imaging assays, we show that the meiosis-specific filaments. Srs2 uses ATP-dependent translocation to remove recombinase Dmc1 is a highly potent inhibitor of Srs2 activity. Rad51 from ssDNA; therefore ATP hydrolysis activity is a good Fig. 1. Srs2 cannot remove Dmc1 from ssDNA. (A) Model for mitotic HR highlighting the regulatory role of Srs2 in disruption of Rad51-containing inter- mediates. (B) Srs2 ATP hydrolysis assays with Rad51 or Dmc1. Data points represent the mean ± SD of three experiments. (C) Schematic of ssDNA curtain assay for Srs2. (D) Kymograph showing unlabeled Srs2 (500 pM) disruption of Rad51-ssDNA as revealed by RPA-GFP (100 pM) rebinding (shown in green). (E) Kymograph showing that
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