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Halder S, Sanchez A, Ranjha L, Reginato G, Ceppi I, Acharya A, Anand R, Cejka P. Double-stranded DNA binding function of RAD51 in DNA protection and its regulation by BRCA2. Mol Cell 2022; 82:3553-3565.e5. [PMID: 36070766 DOI: 10.1016/j.molcel.2022.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
RAD51 and the breast cancer suppressor BRCA2 have critical functions in DNA double-strand (dsDNA) break repair by homologous recombination and the protection of newly replicated DNA from nucleolytic degradation. The recombination function of RAD51 requires its binding to single-stranded DNA (ssDNA), whereas binding to dsDNA is inhibitory. Using reconstituted MRE11-, EXO1-, and DNA2-dependent nuclease reactions, we show that the protective function of RAD51 unexpectedly depends on its binding to dsDNA. The BRC4 repeat of BRCA2 abrogates RAD51 binding to dsDNA and accordingly impairs the function of RAD51 in protection. The BRCA2 C-terminal RAD51-binding segment (TR2) acts in a dominant manner to overcome the effect of BRC4. Mechanistically, TR2 stabilizes RAD51 binding to dsDNA, even in the presence of BRC4, promoting DNA protection. Our data suggest that RAD51's dsDNA-binding capacity may have evolved together with its function in replication fork protection and provide a mechanistic basis for the DNA-protection function of BRCA2.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland.
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2
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Halder S, Ranjha L, Taglialatela A, Ciccia A, Cejka P. Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex. Nucleic Acids Res 2022; 50:8008-8022. [PMID: 35801922 PMCID: PMC9371921 DOI: 10.1093/nar/gkac583] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
SMARCAL1, ZRANB3 and HLTF are required for the remodeling of replication forks upon stress to promote genome stability. RAD51, along with the RAD51 paralog complex, were also found to have recombination-independent functions in fork reversal, yet the underlying mechanisms remained unclear. Using reconstituted reactions, we build upon previous data to show that SMARCAL1, ZRANB3 and HLTF have unequal biochemical capacities, explaining why they have non-redundant functions. SMARCAL1 uniquely anneals RPA-coated ssDNA, which depends on its direct interaction with RPA, but not on ATP. SMARCAL1, along with ZRANB3, but not HLTF efficiently employ ATPase driven translocase activity to rezip RPA-covered bubbled DNA, which was proposed to mimic elements of fork reversal. In contrast, ZRANB3 and HLTF but not SMARCAL1 are efficient in branch migration that occurs downstream in fork remodeling. We also show that low concentrations of RAD51 and the RAD51 paralog complex, RAD51B–RAD51C–RAD51D–XRCC2 (BCDX2), directly stimulate the motor-driven activities of SMARCAL1 and ZRANB3 but not HLTF, and the interplay is underpinned by physical interactions. Our data provide a possible mechanism explaining previous cellular experiments implicating RAD51 and BCDX2 in fork reversal.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
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3
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Vernekar DV, Reginato G, Adam C, Ranjha L, Dingli F, Marsolier MC, Loew D, Guérois R, Llorente B, Cejka P, Borde V. The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length. Nucleic Acids Res 2021; 49:4522-4533. [PMID: 33823531 PMCID: PMC8096244 DOI: 10.1093/nar/gkab232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Meiotic recombination ensures proper chromosome segregation to form viable gametes and results in gene conversions events between homologs. Conversion tracts are shorter in meiosis than in mitotically dividing cells. This results at least in part from the binding of a complex, containing the Mer3 helicase and the MutLβ heterodimer, to meiotic recombination intermediates. The molecular actors inhibited by this complex are elusive. The Pif1 DNA helicase is known to stimulate DNA polymerase delta (Pol δ) -mediated DNA synthesis from D-loops, allowing long synthesis required for break-induced replication. We show that Pif1 is also recruited genome wide to meiotic DNA double-strand break (DSB) sites. We further show that Pif1, through its interaction with PCNA, is required for the long gene conversions observed in the absence of MutLβ recruitment to recombination sites. In vivo, Mer3 interacts with the PCNA clamp loader RFC, and in vitro, Mer3-MutLβ ensemble inhibits Pif1-stimulated D-loop extension by Pol δ and RFC-PCNA. Mechanistically, our results suggest that Mer3-MutLβ may compete with Pif1 for binding to RFC-PCNA. Taken together, our data show that Pif1's activity that promotes meiotic DNA repair synthesis is restrained by the Mer3-MutLβ ensemble which in turn prevents long gene conversion tracts and possibly associated mutagenesis.
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Affiliation(s)
- Dipti Vinayak Vernekar
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Céline Adam
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Marie-Claude Marsolier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Unité Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS UMR7206, Université de Paris, Paris, France
| | - Damarys Loew
- Institut Curie, Université PSL, LSMP, Paris, France
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Bertrand Llorente
- CRCM, Inserm, U1068, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105; CNRS, UMR7258, Marseille, France
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Valérie Borde
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
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Grigaitis R, Ranjha L, Wild P, Kasaciunaite K, Ceppi I, Kissling V, Henggeler A, Susperregui A, Peter M, Seidel R, Cejka P, Matos J. Phosphorylation of the RecQ Helicase Sgs1/BLM Controls Its DNA Unwinding Activity during Meiosis and Mitosis. Dev Cell 2020; 53:706-723.e5. [DOI: 10.1016/j.devcel.2020.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/18/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022]
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He W, Rao HBDP, Tang S, Bhagwat N, Kulkarni DS, Ma Y, Chang MAW, Hall C, Bragg JW, Manasca HS, Baker C, Verhees GF, Ranjha L, Chen X, Hollingsworth NM, Cejka P, Hunter N. Regulated Proteolysis of MutSγ Controls Meiotic Crossing Over. Mol Cell 2020; 78:168-183.e5. [PMID: 32130890 DOI: 10.1016/j.molcel.2020.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/03/2020] [Accepted: 01/31/2020] [Indexed: 01/04/2023]
Abstract
Crossover recombination is essential for accurate chromosome segregation during meiosis. The MutSγ complex, Msh4-Msh5, facilitates crossing over by binding and stabilizing nascent recombination intermediates. We show that these activities are governed by regulated proteolysis. MutSγ is initially inactive for crossing over due to an N-terminal degron on Msh4 that renders it unstable by directly targeting proteasomal degradation. Activation of MutSγ requires the Dbf4-dependent kinase Cdc7 (DDK), which directly phosphorylates and thereby neutralizes the Msh4 degron. Genetic requirements for Msh4 phosphorylation indicate that DDK targets MutSγ only after it has bound to nascent joint molecules (JMs) in the context of synapsing chromosomes. Overexpression studies confirm that the steady-state level of Msh4, not phosphorylation per se, is the critical determinant for crossing over. At the DNA level, Msh4 phosphorylation enables the formation and crossover-biased resolution of double-Holliday Junction intermediates. Our study establishes regulated protein degradation as a fundamental mechanism underlying meiotic crossing over.
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Affiliation(s)
- Wei He
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - H B D Prasada Rao
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Shangming Tang
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Nikhil Bhagwat
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Dhananjaya S Kulkarni
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Yunmei Ma
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Maria A W Chang
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Christie Hall
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Junxi Wang Bragg
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Harrison S Manasca
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Christa Baker
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Gerrik F Verhees
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Xiangyu Chen
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Nancy M Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, USA; Department of Molecular & Cellular Biology, University of California, Davis, Davis, California, USA; Department of Cell Biology & Human Anatomy, University of California, Davis, Davis, California, USA.
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6
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Ranjha L, Levikova M, Altmannova V, Krejci L, Cejka P. Sumoylation regulates the stability and nuclease activity of Saccharomyces cerevisiae Dna2. Commun Biol 2019; 2:174. [PMID: 31098407 PMCID: PMC6506525 DOI: 10.1038/s42003-019-0428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023] Open
Abstract
Dna2 is an essential nuclease-helicase that acts in several distinct DNA metabolic pathways including DNA replication and recombination. To balance these functions and prevent unscheduled DNA degradation, Dna2 activities must be regulated. Here we show that Saccharomyces cerevisiae Dna2 function is controlled by sumoylation. We map the sumoylation sites to the N-terminal regulatory domain of Dna2 and show that in vitro sumoylation of recombinant Dna2 impairs its nuclease but not helicase activity. In cells, the total levels of the non-sumoylatable Dna2 variant are elevated. However, non-sumoylatable Dna2 shows impaired nuclear localization and reduced recruitment to foci upon DNA damage. Non-sumoylatable Dna2 reduces the rate of DNA end resection, as well as impedes cell growth and cell cycle progression through S phase. Taken together, these findings show that in addition to Dna2 phosphorylation described previously, Dna2 sumoylation is required for the homeostasis of the Dna2 protein function to promote genome stability.
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Affiliation(s)
- Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Maryna Levikova
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
- National Center for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
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7
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Anand R, Jasrotia A, Bundschuh D, Howard SM, Ranjha L, Stucki M, Cejka P. NBS1 promotes the endonuclease activity of the MRE11-RAD50 complex by sensing CtIP phosphorylation. EMBO J 2019; 38:e101005. [PMID: 30787182 PMCID: PMC6443204 DOI: 10.15252/embj.2018101005] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/08/2019] [Accepted: 02/01/2019] [Indexed: 11/09/2022] Open
Abstract
DNA end resection initiates DNA double-strand break repair by homologous recombination. MRE11-RAD50-NBS1 and phosphorylated CtIP perform the first resection step via MRE11-catalyzed endonucleolytic DNA cleavage. Human NBS1, more than its homologue Xrs2 in Saccharomyces cerevisiae, is crucial for this process, highlighting complex mechanisms that regulate the MRE11 nuclease in higher eukaryotes. Using a reconstituted system, we show here that NBS1, through its FHA and BRCT domains, functions as a sensor of CtIP phosphorylation. NBS1 then activates the MRE11-RAD50 nuclease through direct physical interactions with MRE11. In the absence of NBS1, MRE11-RAD50 exhibits a weaker nuclease activity, which requires CtIP but not strictly its phosphorylation. This identifies at least two mechanisms by which CtIP augments MRE11: a phosphorylation-dependent mode through NBS1 and a phosphorylation-independent mode without NBS1. In support, we show that limited DNA end resection occurs in vivo in the absence of the FHA and BRCT domains of NBS1. Collectively, our data suggest that NBS1 restricts the MRE11-RAD50 nuclease to S-G2 phase when CtIP is extensively phosphorylated. This defines mechanisms that regulate the MRE11 nuclease in DNA metabolism.
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Affiliation(s)
- Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Arti Jasrotia
- Department of Gynecology, University of Zurich, Schlieren, Switzerland
| | - Diana Bundschuh
- Department of Gynecology, University of Zurich, Schlieren, Switzerland
| | - Sean Michael Howard
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Schlieren, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
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8
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De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V. A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation. Genes Dev 2018; 32:283-296. [PMID: 29440262 PMCID: PMC5859969 DOI: 10.1101/gad.308510.117] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/24/2018] [Indexed: 11/24/2022]
Abstract
De Muyt et al. identified the ZZS (Zip2–Zip4–Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2–Zip4–Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF–ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals.
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Affiliation(s)
- Arnaud De Muyt
- UMR3244, Centre Nationnal de la Recherche Scientifique (CNRS), Institut Curie, PSL (Paris Sciences and Letters) Research University, 75005 Paris, France.,Université Pierre et Marie Curie (UPMC), 75005 Paris, France
| | - Alexandra Pyatnitskaya
- UMR3244, Centre Nationnal de la Recherche Scientifique (CNRS), Institut Curie, PSL (Paris Sciences and Letters) Research University, 75005 Paris, France.,Université Pierre et Marie Curie (UPMC), 75005 Paris, France
| | - Jessica Andréani
- Institut de Biologie Intégrative de la Cellule (I2BC), Institut de biologie et de technologies de Saclay (iBiTec-S), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), UMR9198, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France.,Université Paris Sud, 91400 Orsay, France
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Claire Ramus
- University of Grenoble Alpes, CEA, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et Biotechnologies de Grenoble (BIG-BGE), 38000 Grenoble, France
| | - Raphaëlle Laureau
- UMR3244, Centre Nationnal de la Recherche Scientifique (CNRS), Institut Curie, PSL (Paris Sciences and Letters) Research University, 75005 Paris, France.,Université Pierre et Marie Curie (UPMC), 75005 Paris, France
| | - Ambra Fernandez-Vega
- UMR3244, Centre Nationnal de la Recherche Scientifique (CNRS), Institut Curie, PSL (Paris Sciences and Letters) Research University, 75005 Paris, France.,Université Pierre et Marie Curie (UPMC), 75005 Paris, France
| | - Daniel Holoch
- Université Pierre et Marie Curie (UPMC), 75005 Paris, France.,Institut Curie, PSL Research University, UMR934, CNRS, 75005 Paris, France
| | - Elodie Girard
- Institut Curie, PSL Research University, Mines ParisTech, U900, INSERM, 75005 Paris, France
| | - Jérome Govin
- University of Grenoble Alpes, CEA, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et Biotechnologies de Grenoble (BIG-BGE), 38000 Grenoble, France
| | - Raphaël Margueron
- Université Pierre et Marie Curie (UPMC), 75005 Paris, France.,Institut Curie, PSL Research University, UMR934, CNRS, 75005 Paris, France
| | - Yohann Couté
- University of Grenoble Alpes, CEA, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et Biotechnologies de Grenoble (BIG-BGE), 38000 Grenoble, France
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland
| | - Raphaël Guérois
- Institut de Biologie Intégrative de la Cellule (I2BC), Institut de biologie et de technologies de Saclay (iBiTec-S), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), UMR9198, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France.,Université Paris Sud, 91400 Orsay, France
| | - Valérie Borde
- UMR3244, Centre Nationnal de la Recherche Scientifique (CNRS), Institut Curie, PSL (Paris Sciences and Letters) Research University, 75005 Paris, France.,Université Pierre et Marie Curie (UPMC), 75005 Paris, France
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9
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Ranjha L, Howard SM, Cejka P. Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes. Chromosoma 2018; 127:187-214. [PMID: 29327130 DOI: 10.1007/s00412-017-0658-1] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/16/2022]
Abstract
DNA double-strand breaks arise accidentally upon exposure of DNA to radiation and chemicals or result from faulty DNA metabolic processes. DNA breaks can also be introduced in a programmed manner, such as during the maturation of the immune system, meiosis, or cancer chemo- or radiotherapy. Cells have developed a variety of repair pathways, which are fine-tuned to the specific needs of a cell. Accordingly, vegetative cells employ mechanisms that restore the integrity of broken DNA with the highest efficiency at the lowest cost of mutagenesis. In contrast, meiotic cells or developing lymphocytes exploit DNA breakage to generate diversity. Here, we review the main pathways of eukaryotic DNA double-strand break repair with the focus on homologous recombination and its various subpathways. We highlight the differences between homologous recombination and end-joining mechanisms including non-homologous end-joining and microhomology-mediated end-joining and offer insights into how these pathways are regulated. Finally, we introduce noncanonical functions of the recombination proteins, in particular during DNA replication stress.
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Affiliation(s)
- Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sean M Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
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10
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Taglialatela A, Alvarez S, Leuzzi G, Sannino V, Ranjha L, Huang JW, Madubata C, Anand R, Levy B, Rabadan R, Cejka P, Costanzo V, Ciccia A. Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers. Mol Cell 2017; 68:414-430.e8. [PMID: 29053959 DOI: 10.1016/j.molcel.2017.09.036] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/17/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022]
Abstract
To ensure the completion of DNA replication and maintenance of genome integrity, DNA repair factors protect stalled replication forks upon replication stress. Previous studies have identified a critical role for the tumor suppressors BRCA1 and BRCA2 in preventing the degradation of nascent DNA by the MRE11 nuclease after replication stress. Here we show that depletion of SMARCAL1, a SNF2-family DNA translocase that remodels stalled forks, restores replication fork stability and reduces the formation of replication stress-induced DNA breaks and chromosomal aberrations in BRCA1/2-deficient cells. In addition to SMARCAL1, other SNF2-family fork remodelers, including ZRANB3 and HLTF, cause nascent DNA degradation and genomic instability in BRCA1/2-deficient cells upon replication stress. Our observations indicate that nascent DNA degradation in BRCA1/2-deficient cells occurs as a consequence of MRE11-dependent nucleolytic processing of reversed forks generated by fork remodelers. These studies provide mechanistic insights into the processes that cause genome instability in BRCA1/2-deficient cells.
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Affiliation(s)
- Angelo Taglialatela
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Silvia Alvarez
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Chioma Madubata
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.
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11
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Duroc Y, Kumar R, Ranjha L, Adam C, Guérois R, Md Muntaz K, Marsolier-Kergoat MC, Dingli F, Laureau R, Loew D, Llorente B, Charbonnier JB, Cejka P, Borde V. Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion. eLife 2017; 6. [PMID: 28051769 PMCID: PMC5215242 DOI: 10.7554/elife.21900] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI:http://dx.doi.org/10.7554/eLife.21900.001
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Affiliation(s)
- Yann Duroc
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Rajeev Kumar
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Lepakshi Ranjha
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Céline Adam
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Raphaël Guérois
- I2BC, iBiTec-S, CEA, CNRS UMR 9198, Université Paris-Sud, Gif-sur-Yvette, France.,Université Paris Sud, Orsay, France
| | - Khan Md Muntaz
- CRCM, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, CNRS UMR7258, Marseille, France
| | - Marie-Claude Marsolier-Kergoat
- I2BC, iBiTec-S, CEA, CNRS UMR 9198, Université Paris-Sud, Gif-sur-Yvette, France.,Université Paris Sud, Orsay, France.,Musée de l'Homme, CNRS UMR 7206, Paris, France
| | - Florent Dingli
- Institut Curie, Centre de Recherche, PSL Research University, LSMP, Paris, France
| | - Raphaëlle Laureau
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, LSMP, Paris, France
| | - Bertrand Llorente
- CRCM, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, CNRS UMR7258, Marseille, France
| | - Jean-Baptiste Charbonnier
- I2BC, iBiTec-S, CEA, CNRS UMR 9198, Université Paris-Sud, Gif-sur-Yvette, France.,Université Paris Sud, Orsay, France
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Valérie Borde
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Université Pierre et Marie Curie, Paris, France
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12
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Anand R, Ranjha L, Cannavo E, Cejka P. Phosphorylated CtIP Functions as a Co-factor of the MRE11-RAD50-NBS1 Endonuclease in DNA End Resection. Mol Cell 2016; 64:940-950. [PMID: 27889449 DOI: 10.1016/j.molcel.2016.10.017] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/26/2016] [Accepted: 10/13/2016] [Indexed: 12/26/2022]
Abstract
To repair a DNA double-strand break (DSB) by homologous recombination (HR), the 5'-terminated strand of the DSB must be resected. The human MRE11-RAD50-NBS1 (MRN) and CtIP proteins were implicated in the initiation of DNA end resection, but the underlying mechanism remained undefined. Here, we show that CtIP is a co-factor of the MRE11 endonuclease activity within the MRN complex. This function is absolutely dependent on CtIP phosphorylation that includes the key cyclin-dependent kinase target motif at Thr-847. Unlike in yeast, where the Xrs2/NBS1 subunit is dispensable in vitro, NBS1 is absolutely required in the human system. The MRE11 endonuclease in conjunction with RAD50, NBS1, and phosphorylated CtIP preferentially cleaves 5'-terminated DNA strands near DSBs. Our results define the initial step of HR that is particularly relevant for the processing of DSBs bearing protein blocks.
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Affiliation(s)
- Roopesh Anand
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lepakshi Ranjha
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Elda Cannavo
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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13
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Singleton BK, Ahmed M, Green CA, Heimpel H, Woźniak MJ, Ranjha L, Seeney F, Bomford A, Mehta P, Guest A, Mushens R, King MJ. CD44 as a Potential Screening Marker for Preliminary Differentiation Between Congenital Dyserythropoietic Anemia Type II and Hereditary Spherocytosis. Cytometry 2016; 94:312-326. [DOI: 10.1002/cyto.b.21488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 11/07/2022]
Affiliation(s)
- B. K. Singleton
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant; Bristol UK
| | - M. Ahmed
- Department of Haematology; University College London Cancer Institute; London UK
| | - C. A. Green
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant; Bristol UK
| | - H. Heimpel
- German Registry on Congenital Dyserythropoietic Anaemias, Medizinishe; Universitätsklinik III; Ulm Germany
| | - M. J. Woźniak
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant; Bristol UK
| | - L. Ranjha
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant; Bristol UK
| | - F. Seeney
- Statistics and Clinical Studies; NHS Blood and Transplant; Bristol UK
| | - A. Bomford
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust; London UK
| | - P. Mehta
- Department of Haematology; Bristol Royal Infirmary, North Bristol NHS Trust; UK
| | - A. Guest
- International Blood Group Reference Laboratory; NHS Blood and Transplant; Bristol UK
| | - R. Mushens
- International Blood Group Reference Laboratory; NHS Blood and Transplant; Bristol UK
| | - M.-J. King
- International Blood Group Reference Laboratory; NHS Blood and Transplant; Bristol UK
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14
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Piwko W, Mlejnkova LJ, Mutreja K, Ranjha L, Stafa D, Smirnov A, Brodersen MM, Zellweger R, Sturzenegger A, Janscak P, Lopes M, Peter M, Cejka P. The MMS22L-TONSL heterodimer directly promotes RAD51-dependent recombination upon replication stress. EMBO J 2016; 35:2584-2601. [PMID: 27797818 DOI: 10.15252/embj.201593132] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/02/2016] [Accepted: 10/06/2016] [Indexed: 11/09/2022] Open
Abstract
Homologous recombination (HR) is a key pathway that repairs DNA double-strand breaks (DSBs) and helps to restart stalled or collapsed replication forks. How HR supports replication upon genotoxic stress is not understood. Using in vivo and in vitro approaches, we show that the MMS22L-TONSL heterodimer localizes to replication forks under unperturbed conditions and its recruitment is increased during replication stress in human cells. MMS22L-TONSL associates with replication protein A (RPA)-coated ssDNA, and the MMS22L subunit directly interacts with the strand exchange protein RAD51. MMS22L is required for proper RAD51 assembly at DNA damage sites in vivo, and HR-mediated repair of stalled forks is abrogated in cells expressing a MMS22L mutant deficient in RAD51 interaction. Similar to the recombination mediator BRCA2, recombinant MMS22L-TONSL limits the assembly of RAD51 on dsDNA, which stimulates RAD51-ssDNA nucleoprotein filament formation and RAD51-dependent strand exchange activity in vitro Thus, by specifically regulating RAD51 activity at uncoupled replication forks, MMS22L-TONSL stabilizes perturbed replication forks by promoting replication fork reversal and stimulating their HR-mediated restart in vivo.
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Affiliation(s)
- Wojciech Piwko
- Department of Biology, Institute of Biochemistry ETH Zurich, Zurich, Switzerland
| | - Lucie J Mlejnkova
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Karun Mutreja
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Lepakshi Ranjha
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Diana Stafa
- Department of Biology, Institute of Biochemistry ETH Zurich, Zurich, Switzerland
| | - Alexander Smirnov
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Mia Ml Brodersen
- Department of Biology, Institute of Biochemistry ETH Zurich, Zurich, Switzerland
| | - Ralph Zellweger
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Andreas Sturzenegger
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry ETH Zurich, Zurich, Switzerland
| | - Petr Cejka
- Institute of Molecular Cancer Research University of Zurich, Zurich, Switzerland
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15
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Ranjha L, Anand R, Cejka P. The Saccharomyces cerevisiae Mlh1-Mlh3 heterodimer is an endonuclease that preferentially binds to Holliday junctions. J Biol Chem 2014; 289:5674-86. [PMID: 24443562 DOI: 10.1074/jbc.m113.533810] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis.
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Affiliation(s)
- Lepakshi Ranjha
- From the Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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