1
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Trouillard O, Dupaigne P, Dunoyer M, Doulazmi M, Herlin MK, Frismand S, Riou A, Legros V, Chevreux G, Veaute X, Busso D, Fouquet C, Saint-Martin C, Méneret A, Trembleau A, Dusart I, Dubacq C, Roze E. Congenital mirror movements are associated with defective polymerisation of RAD51. J Med Genet 2023; 60:1116-1126. [PMID: 37308287 DOI: 10.1136/jmg-2023-109189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/21/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Mirror movements are involuntary movements of one hand that mirror intentional movements of the other hand. Congenital mirror movements (CMM) is a rare genetic disorder with autosomal dominant inheritance, in which mirror movements are the main neurological manifestation. CMM is associated with an abnormal decussation of the corticospinal tract, a major motor tract for voluntary movements. RAD51 is known to play a key role in homologous recombination with a critical function in DNA repair. While RAD51 haploinsufficiency was first proposed to explain CMM, other mechanisms could be involved. METHODS We performed Sanger sequencing of RAD51 in five newly identified CMM families to identify new pathogenic variants. We further investigated the expression of wild-type and mutant RAD51 in the patients' lymphoblasts at mRNA and protein levels. We then characterised the functions of RAD51 altered by non-truncating variants using biochemical approaches. RESULTS The level of wild-type RAD51 protein was lower in the cells of all patients with CMM compared with their non-carrier relatives. The reduction was less pronounced in asymptomatic carriers. In vitro, mutant RAD51 proteins showed loss-of-function for polymerisation, DNA binding and strand exchange activity. CONCLUSION Our study demonstrates that RAD51 haploinsufficiency, including loss-of-function of non-truncating variants, results in CMM. The incomplete penetrance likely results from post-transcriptional compensation. Changes in RAD51 levels and/or polymerisation properties could influence guidance of the corticospinal axons during development. Our findings open up new perspectives to understand the role of RAD51 in neurodevelopment.
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Affiliation(s)
- Oriane Trouillard
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Margaux Dunoyer
- Hôpital Pitié-Salpêtrière, Département de Neurologie, AP-HP, Paris, France
| | - Mohamed Doulazmi
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Biological Adaptation and Ageing, B2A, Sorbonne Université, F-75005 Paris, France
| | - Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Audrey Riou
- Service de génétique clinique & Service de neurologie, CHU Rennes, Rennes, France
| | - Véronique Legros
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Guillaume Chevreux
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Xavier Veaute
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, CIGEx/iRCM/IBFJ, Université Paris Cité, F-92260 Fontenay-aux-Roses, France
| | - Didier Busso
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, CIGEx/iRCM/IBFJ, Université Paris Cité, F-92260 Fontenay-aux-Roses, France
| | - Coralie Fouquet
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Cécile Saint-Martin
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique Médicale, Sorbonne Université, Paris, France
| | - Aurélie Méneret
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
- Hôpital Pitié-Salpêtrière, DMU Neuroscience 6, AP-HP, Paris, France
| | - Alain Trembleau
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Isabelle Dusart
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Caroline Dubacq
- INSERM, CNRS, Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Emmanuel Roze
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
- Hôpital Pitié-Salpêtrière, DMU Neuroscience 6, AP-HP, Paris, France
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2
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Greenhough LA, Liang CC, Belan O, Kunzelmann S, Maslen S, Rodrigo-Brenni MC, Anand R, Skehel M, Boulton SJ, West SC. Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor. Nature 2023; 619:650-657. [PMID: 37344587 PMCID: PMC7614784 DOI: 10.1038/s41586-023-06179-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023]
Abstract
Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers1-10 and the cancer-prone syndrome Fanconi anaemia11-13. The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects14,15, but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance.
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Affiliation(s)
| | | | - Ondrej Belan
- The Francis Crick Institute, London, UK
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
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3
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Appleby R, Bollschweiler D, Chirgadze DY, Joudeh L, Pellegrini L. A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly. iScience 2023; 26:106689. [PMID: 37216117 PMCID: PMC10192527 DOI: 10.1016/j.isci.2023.106689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
The RAD51 ATPase polymerizes on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the reaction of homologous recombination. ATP binding maintains the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, contributing to NPF disassembly.
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Affiliation(s)
- Robert Appleby
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | - Luay Joudeh
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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4
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Knadler C, Graham V W, Rolfsmeier M, Haseltine CA. Divalent metal cofactors differentially modulate RadA-mediated strand invasion and exchange in Saccharolobus solfataricus. Biosci Rep 2023; 43:BSR20221807. [PMID: 36601994 PMCID: PMC9950535 DOI: 10.1042/bsr20221807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Central to the universal process of recombination, RecA family proteins form nucleoprotein filaments to catalyze production of heteroduplex DNA between substrate ssDNAs and template dsDNAs. ATP binding assists the filament in assuming the necessary conformation for forming heteroduplex DNA, but hydrolysis is not required. ATP hydrolysis has two identified roles which are not universally conserved: promotion of filament dissociation and enhancing flexibility of the filament. In this work, we examine ATP utilization of the RecA family recombinase SsoRadA from Saccharolobus solfataricus to determine its function in recombinase-mediated heteroduplex DNA formation. Wild-type SsoRadA protein and two ATPase mutant proteins were evaluated for the effects of three divalent metal cofactors. We found that unlike other archaeal RadA proteins, SsoRadA-mediated strand exchange is not enhanced by Ca2+. Instead, the S. solfataricus recombinase can utilize Mn2+ to stimulate strand invasion and reduce ADP-binding stability. Additionally, reduction of SsoRadA ATPase activity by Walker Box mutation or cofactor alteration resulted in a loss of large, complete strand exchange products. Depletion of ADP was found to improve initial strand invasion but also led to a similar loss of large strand exchange events. Our results indicate that overall, SsoRadA is distinct in its use of divalent cofactors but its activity with Mn2+ shows similarity to human RAD51 protein with Ca2+.
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Affiliation(s)
- Corey J. Knadler
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - William J. Graham V
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Michael L. Rolfsmeier
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Cynthia A. Haseltine
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
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5
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Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW. Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination. Nucleic Acids Res 2021; 49:13135-13149. [PMID: 34871438 PMCID: PMC8682777 DOI: 10.1093/nar/gkab1141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/01/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022] Open
Abstract
Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51-DNA and Dmc1-DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
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Affiliation(s)
- Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Sijia Peng
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Rui Liang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Tian
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60615, USA
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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6
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Špírek M, Taylor MRG, Belan O, Boulton SJ, Krejci L. Nucleotide proofreading functions by nematode RAD51 paralogs facilitate optimal RAD51 filament function. Nat Commun 2021; 12:5545. [PMID: 34545070 PMCID: PMC8452638 DOI: 10.1038/s41467-021-25830-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Here, we define unappreciated mechanisms by which the RAD51 paralog complex RFS-1/RIP-1 limits the accumulation of RAD-51-ssDNA complexes with unfavorable nucleotide content. We find RAD51 paralogs promote the turnover of ADP-bound RAD-51 from ssDNA, in striking contrast to their ability to stabilize productive ATP-bound RAD-51 nucleoprotein filaments. In addition, RFS-1/RIP-1 inhibits binding of nucleotide-free RAD-51 to ssDNA. We propose that ‘nucleotide proofreading’ activities of RAD51 paralogs co-operate to ensure the enrichment of active, ATP-bound RAD-51 filaments on ssDNA to promote HR. A RAD51 paralog complex, RFS-1/RIP-1, is shown to control ssDNA binding and dissociation by RAD-51 differentially in the presence and absence of nucleotide cofactors. These nucleotide proofreading activities drive a preferential accumulation of RAD-51-ssDNA complexes with optimal nucleotide content.
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Affiliation(s)
- Mário Špírek
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500, Brno, Czech Republic.,Department of Biology Masaryk University, 62500, Brno, Czech Republic
| | | | - Ondrej Belan
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lumir Krejci
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500, Brno, Czech Republic. .,Department of Biology Masaryk University, 62500, Brno, Czech Republic. .,National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic.
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7
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Muraszko J, Kramarz K, Argunhan B, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H, Dziadkowiec D. Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res 2021; 49:6832-6848. [PMID: 34157114 PMCID: PMC8266636 DOI: 10.1093/nar/gkab511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Rad51 is the key protein in homologous recombination that plays important roles during DNA replication and repair. Auxiliary factors regulate Rad51 activity to facilitate productive recombination, and prevent inappropriate, untimely or excessive events, which could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in modulating Rad51 function, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 levels in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 function. Rrp1 affects Rad51 binding at centromeres. Additionally, we demonstrate in vivo and in vitro that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
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Affiliation(s)
| | - Karol Kramarz
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Bilge Argunhan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Kentaro Ito
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | | - Yumiko Kurokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
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8
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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9
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Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY. Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism. eLife 2018; 7:e37373. [PMID: 30526846 PMCID: PMC6310460 DOI: 10.7554/elife.37373] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/26/2018] [Indexed: 01/01/2023] Open
Abstract
The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
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Affiliation(s)
- Daria N Shalaeva
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscowRussia
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Andrey V Golovin
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Armen Y Mulkidjanian
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
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10
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Alligand B, Le Breton M, Marquis D, Vallette F, Fleury F. Functional effects of diphosphomimetic mutations at cAbl-mediated phosphorylation sites on Rad51 recombinase activity. Biochimie 2017; 139:115-124. [PMID: 28571978 DOI: 10.1016/j.biochi.2017.05.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/27/2017] [Indexed: 01/10/2023]
Abstract
Homologous Recombination enables faithful repair of the deleterious double strand breaks of DNA. This pathway relies on Rad51 to catalyze homologous DNA strand exchange. Rad51 is known to be phosphorylated in a sequential manner on Y315 and then on Y54, but the effect of such phosphorylation on Rad51 function remains poorly understood. We have developed a phosphomimetic model in order to study all the phosphorylation states. With the purified phosphomimetic proteins we performed in vitro assays to determine the activity of Rad51. Here we demonstrate the inhibitory effect of the double phosphomimetic mutant and suggest that it may be due to a defect in nucleofilament formation.
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Affiliation(s)
- Brendan Alligand
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France; Team 9 Apoptosis in Nervous Central System Tumours, CRCINA, INSERM U892, Nantes University, France
| | - Magali Le Breton
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France
| | - Damien Marquis
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France
| | - François Vallette
- Team 9 Apoptosis in Nervous Central System Tumours, CRCINA, INSERM U892, Nantes University, France
| | - Fabrice Fleury
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France.
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11
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Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW. Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange. Nat Struct Mol Biol 2016; 24:40-46. [PMID: 27941862 DOI: 10.1038/nsmb.3336] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/07/2016] [Indexed: 01/16/2023]
Abstract
The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) and generates a helical filament that is able to search for and invade homologous double-stranded DNA (dsDNA), thus leading to strand separation and formation of new base pairs between the initiating ssDNA and the complementary strand within the duplex. Here, we used cryo-EM to solve the structures of human RAD51 in complex with DNA molecules, in presynaptic and postsynaptic states, at near-atomic resolution. Our structures reveal both conserved and distinct structural features of the human RAD51-DNA complexes compared with their prokaryotic counterpart. Notably, we also captured the structure of an arrested synaptic complex. Our results provide new insight into the molecular mechanisms of the DNA homology search and strand-exchange processes.
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Affiliation(s)
- Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Xu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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12
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Senavirathne G, Mahto SK, Hanne J, O'Brian D, Fishel R. Dynamic unwrapping of nucleosomes by HsRAD51 that includes sliding and rotational motion of histone octamers. Nucleic Acids Res 2016; 45:685-698. [PMID: 27738136 PMCID: PMC5314800 DOI: 10.1093/nar/gkw920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/01/2016] [Accepted: 10/10/2016] [Indexed: 01/24/2023] Open
Abstract
Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine triphosphate (ATP) the human RAD51 (HsRAD51) recombinase can form a nucleoprotein filament (NPF) on double-stranded DNA (dsDNA) that is capable of unwrapping the nucleosomal DNA from the histone octamer (HO). Here, we have used single molecule Förster Resonance Energy Transfer (smFRET) to examine the real time nucleosome dynamics in the presence of the HsRAD51 NPF. We show that oligomerization of HsRAD51 leads to stepwise, but stochastic unwrapping of the DNA from the HO in the presence of ATP. The highly reversible dynamics observed in single-molecule trajectories suggests an antagonistic mechanism between HsRAD51 binding and rewrapping of the DNA around the HO. These stochastic dynamics were independent of the nucleosomal DNA sequence or the asymmetry created by the presence of a linker DNA. We also observed sliding and rotational oscillations of the HO with respect to the nucleosomal DNA. These studies underline the dynamic nature of even tightly associated protein-DNA complexes such as nucleosomes.
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Affiliation(s)
- Gayan Senavirathne
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Santosh K Mahto
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Jeungphill Hanne
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Daniel O'Brian
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA .,Physics Department, The Ohio State University, Columbus, OH 43210, USA
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13
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Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. Proc Natl Acad Sci U S A 2016; 113:E6045-E6054. [PMID: 27671650 DOI: 10.1073/pnas.1604807113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The DNA strand exchange protein RAD51 facilitates the central step in homologous recombination, a process fundamentally important for accurate repair of damaged chromosomes, restart of collapsed replication forks, and telomere maintenance. The active form of RAD51 is a nucleoprotein filament that assembles on single-stranded DNA (ssDNA) at the sites of DNA damage. The c-Abl tyrosine kinase and its oncogenic counterpart BCR-ABL fusion kinase phosphorylate human RAD51 on tyrosine residues 54 and 315. We combined biochemical reconstitutions of the DNA strand exchange reactions with total internal reflection fluorescence microscopy to determine how the two phosphorylation events affect the biochemical activities of human RAD51 and properties of the RAD51 nucleoprotein filament. By mimicking RAD51 tyrosine phosphorylation with a nonnatural amino acid, p-carboxymethyl-l-phenylalanine (pCMF), we demonstrated that Y54 phosphorylation enhances the RAD51 recombinase activity by at least two different mechanisms, modifies the RAD51 nucleoprotein filament formation, and allows RAD51 to compete efficiently with ssDNA binding protein RPA. In contrast, Y315 phosphorylation has little effect on the RAD51 activities. Based on our work and previous cellular studies, we propose a mechanism underlying RAD51 activation by c-Abl/BCR-ABL kinases.
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14
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Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. Dynamic binding of replication protein a is required for DNA repair. Nucleic Acids Res 2016; 44:5758-72. [PMID: 27131385 PMCID: PMC4937323 DOI: 10.1093/nar/gkw339] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/15/2016] [Indexed: 12/14/2022] Open
Abstract
Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA-DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions.
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Affiliation(s)
- Ran Chen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Shyamal Subramanyam
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adrian H Elcock
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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15
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Dynamic control of strand excision during human DNA mismatch repair. Proc Natl Acad Sci U S A 2016; 113:3281-6. [PMID: 26951673 DOI: 10.1073/pnas.1523748113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3'- or 5'-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5'-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5' → 3' exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5'-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5' MMR.
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16
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Schay G, Borka B, Kernya L, Bulyáki É, Kardos J, Fekete M, Fidy J. Without Binding ATP, Human Rad51 Does Not Form Helical Filaments on ssDNA. J Phys Chem B 2016; 120:2165-78. [PMID: 26890079 DOI: 10.1021/acs.jpcb.5b12220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Bálint Borka
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Linda Kernya
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Éva Bulyáki
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Melinda Fekete
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
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17
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Chang HY, Liao CY, Su GC, Lin SW, Wang HW, Chi P. Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1. J Biol Chem 2015; 290:19863-73. [PMID: 26088134 DOI: 10.1074/jbc.m115.666289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
DMC1 and RAD51 are conserved recombinases that catalyze homologous recombination. DMC1 and RAD51 share similar properties in DNA binding, DNA-stimulated ATP hydrolysis, and catalysis of homologous DNA strand exchange. A large body of evidence indicates that attenuation of ATP hydrolysis leads to stabilization of the RAD51-ssDNA presynaptic filament and enhancement of DNA strand exchange. However, the functional relationship of ATPase activity, presynaptic filament stability, and DMC1-mediated homologous DNA strand exchange has remained largely unexplored. To address this important question, we have constructed several mutant variants of human DMC1 and characterized them biochemically to gain mechanistic insights. Two mutations, K132R and D223N, that change key residues in the Walker A and B nucleotide-binding motifs ablate ATP binding and render DMC1 inactive. On the other hand, the nucleotide-binding cap D317K mutant binds ATP normally but shows significantly attenuated ATPase activity and, accordingly, forms a highly stable presynaptic filament. Surprisingly, unlike RAD51, presynaptic filament stabilization achieved via ATP hydrolysis attenuation does not lead to any enhancement of DMC1-catalyzed homologous DNA pairing and strand exchange. This conclusion is further supported by examining wild-type DMC1 with non-hydrolyzable ATP analogues. Thus, our results reveal an important mechanistic difference between RAD51 and DMC1.
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Affiliation(s)
- Hao-Yen Chang
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Chia-Yu Liao
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Guan-Chin Su
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Sheng-Wei Lin
- the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
| | - Hong-Wei Wang
- the Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter Chi
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan, the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
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18
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Bower BD, Griffith JD. TRF1 and TRF2 differentially modulate Rad51-mediated telomeric and nontelomeric displacement loop formation in vitro. Biochemistry 2014; 53:5485-95. [PMID: 25115914 PMCID: PMC4151696 DOI: 10.1021/bi5006249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A growing
body of literature suggests that the homologous recombination/repair
(HR) pathway cooperates with components of the shelterin complex to
promote both telomere maintenance and nontelomeric HR. This may be
due to the ability of both HR and shelterin proteins to promote strand
invasion, wherein a single-stranded DNA (ssDNA) substrate base pairs
with a homologous double-stranded DNA (dsDNA) template displacing
a loop of ssDNA (D-loop). Rad51 recombinase catalyzes D-loop formation
during HR, and telomere repeat binding factor 2 (TRF2) catalyzes the
formation of a telomeric D-loop that stabilizes a looped structure
in telomeric DNA (t-loop) that may facilitate telomere protection.
We have characterized this functional interaction in vitro using a fluorescent D-loop assay measuring the incorporation of
Cy3-labeled 90-nucleotide telomeric and nontelomeric substrates into
telomeric and nontelomeric plasmid templates. We report that preincubation
of a telomeric template with TRF2 inhibits the ability of Rad51 to
promote telomeric D-loop formation upon preincubation with a telomeric
substrate. This suggests Rad51 does not facilitate t-loop formation
and suggests a mechanism whereby TRF2 can inhibit HR at telomeres.
We also report a TRF2 mutant lacking the dsDNA binding domain promotes
Rad51-mediated nontelomeric D-loop formation, possibly explaining
how TRF2 promotes nontelomeric HR. Finally, we report telomere repeat
binding factor 1 (TRF1) promotes Rad51-mediated telomeric D-loop formation,
which may facilitate HR-mediated replication fork restart and explain
why TRF1 is required for efficient telomere replication.
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Affiliation(s)
- Brian D Bower
- Curriculum in Genetics and Molecular Biology, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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19
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Honda M, Okuno Y, Hengel SR, Martín-López JV, Cook CP, Amunugama R, Soukup RJ, Subramanyam S, Fishel R, Spies M. Mismatch repair protein hMSH2-hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate. Proc Natl Acad Sci U S A 2014; 111:E316-25. [PMID: 24395779 PMCID: PMC3903253 DOI: 10.1073/pnas.1312988111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High fidelity homologous DNA recombination depends on mismatch repair (MMR), which antagonizes recombination between divergent sequences by rejecting heteroduplex DNA containing excessive nucleotide mismatches. The hMSH2-hMSH6 heterodimer is the first responder in postreplicative MMR and also plays a prominent role in heteroduplex rejection. Whether a similar molecular mechanism underlies its function in these two processes remains enigmatic. We have determined that hMSH2-hMSH6 efficiently recognizes mismatches within a D-loop recombination initiation intermediate. Mismatch recognition by hMSH2-hMSH6 is not abrogated by human replication protein A (HsRPA) bound to the displaced single-stranded DNA (ssDNA) or by HsRAD51. In addition, ATP-bound hMSH2-hMSH6 sliding clamps that are essential for downstream MMR processes are formed and constrained within the heteroduplex region of the D-loop. Moreover, the hMSH2-hMSH6 sliding clamps are stabilized on the D-loop by HsRPA bound to the displaced ssDNA. Our findings reveal similarities and differences in hMSH2-hMSH6 mismatch recognition and sliding-clamp formation between a D-loop recombination intermediate and linear duplex DNA.
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Affiliation(s)
- Masayoshi Honda
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Yusuke Okuno
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sarah R. Hengel
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Juana V. Martín-López
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Christopher P. Cook
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Ravindra Amunugama
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Randal J. Soukup
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Shyamal Subramanyam
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Richard Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
- Human Genetics Institute, Ohio State University Medical Center, Columbus, OH 43210; and
- Physics Department, Ohio State University, Columbus, OH 43210
| | - Maria Spies
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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20
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Burkovics P, Sebesta M, Balogh D, Haracska L, Krejci L. Strand invasion by HLTF as a mechanism for template switch in fork rescue. Nucleic Acids Res 2013; 42:1711-20. [PMID: 24198246 PMCID: PMC3919600 DOI: 10.1093/nar/gkt1040] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Stalling of replication forks at unrepaired DNA lesions can result in discontinuities opposite the damage in the newly synthesized DNA strand. Translesion synthesis or facilitating the copy from the newly synthesized strand of the sister duplex by template switching can overcome such discontinuities. During template switch, a new primer–template junction has to be formed and two mechanisms, including replication fork reversal and D-loop formation have been suggested. Genetic evidence indicates a major role for yeast Rad5 in template switch and that both Rad5 and its human orthologue, Helicase-like transcription factor (HLTF), a potential tumour suppressor can facilitate replication fork reversal. This study demonstrates the ability of HLTF and Rad5 to form a D-loop without requiring ATP binding and/or hydrolysis. We also show that this strand-pairing activity is independent of RAD51 in vitro and is not mechanistically related to that of another member of the SWI/SNF family, RAD54. In addition, the 3′-end of the invading strand in the D-loop can serve as a primer and is extended by DNA polymerase. Our data indicate that HLTF is involved in a RAD51-independent D-loop branch of template switch pathway that can promote repair of gaps formed during replication of damaged DNA.
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Affiliation(s)
- Peter Burkovics
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, HU-6726 Szeged, Hungary, Department of Biology, Masaryk University, Brno, Czech Republic, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic and International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-62500 Brno, Czech Republic
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21
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Molecular modeling and molecular dynamics simulations of recombinase Rad51. Biophys J 2013; 104:1556-65. [PMID: 23561532 DOI: 10.1016/j.bpj.2013.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/29/2013] [Accepted: 02/07/2013] [Indexed: 11/24/2022] Open
Abstract
The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the γ-phosphate of ATP, K(+) ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K(+) ions was changed. The simulated structures suggested that K(+) ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K(+) ions function as glue between protomers.
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22
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The HsRAD51B-HsRAD51C stabilizes the HsRAD51 nucleoprotein filament. DNA Repair (Amst) 2013; 12:723-32. [PMID: 23810717 DOI: 10.1016/j.dnarep.2013.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/28/2013] [Accepted: 05/14/2013] [Indexed: 12/17/2022]
Abstract
There are six human RAD51 related proteins (HsRAD51 paralogs), HsRAD51B, HsRAD51C, HsRAD51D, HsXRCC2, HsXRCC3 and HsDMC1, that appear to enhance HsRAD51 mediated homologous recombinational (HR) repair of DNA double strand breaks (DSBs). Here we model the structures of HsRAD51, HsRAD51B and HsRAD51C and show similar domain orientations within a hypothetical nucleoprotein filament (NPF). We then demonstrate that HsRAD51B-HsRAD51C heterodimer forms stable complex on ssDNA and partially stabilizes the HsRAD51 NPF against the anti-recombinogenic activity of BLM. Moreover, HsRAD51B-HsRAD51C stimulates HsRAD51 mediated D-loop formation in the presence of RPA. However, HsRAD51B-HsRAD51C does not facilitate HsRAD51 nucleation on a RPA coated ssDNA. These results suggest that the HsRAD51B-HsRAD51C complex plays a role in stabilizing the HsRAD51 NPF during the presynaptic phase of HR, which appears downstream of BRCA2-mediated HsRAD51 NPF formation.
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23
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North JA, Amunugama R, Klajner M, Bruns AN, Poirier MG, Fishel R. ATP-dependent nucleosome unwrapping catalyzed by human RAD51. Nucleic Acids Res 2013; 41:7302-12. [PMID: 23757189 PMCID: PMC3753615 DOI: 10.1093/nar/gkt411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Double-strand breaks (DSB) occur in chromatin following replication fork collapse and chemical or physical damage [Symington and Gautier (Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011;45:247–271.)] and may be repaired by homologous recombination (HR) and non-homologous end-joining. Nucleosomes are the fundamental units of chromatin and must be remodeled during DSB repair by HR [Andrews and Luger (Nucleosome structure(s) and stability: variations on a theme. Annu. Rev. Biophys. 2011;40:99–117.)]. Physical initiation of HR requires RAD51, which forms a nucleoprotein filament (NPF) that catalyzes homologous pairing and strand exchange (recombinase) between DNAs that ultimately bridges the DSB gap [San Filippo, Sung and Klein. (Mechanism of eukaryotic HR. Annu. Rev. Biochem. 2008;77:229–257.)]. RAD51 forms an NPF on single-stranded DNA and double-stranded DNA (dsDNA). Although the single-stranded DNA NPF is essential for recombinase initiation, the role of the dsDNA NPF is less clear. Here, we demonstrate that the human RAD51 (HsRAD51) dsDNA NPF disassembles nucleosomes by unwrapping the DNA from the core histones. HsRAD51 that has been constitutively or biochemically activated for recombinase functions displays significantly reduced nucleosome disassembly activity. These results suggest that HsRAD51 can perform ATP hydrolysis-dependent nucleosome disassembly in addition to its recombinase functions.
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Affiliation(s)
- Justin A North
- Department of Physics, The Ohio State University, Columbus OH 43210, USA, Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210, USA, Chemistry and Biochemistry Department, The Ohio State University, Columbus OH 43210, USA and Human Cancer Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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24
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Du L, Luo Y. Structure of a filament of stacked octamers of human DMC1 recombinase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:382-6. [PMID: 23545642 PMCID: PMC3614161 DOI: 10.1107/s1744309113005678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/26/2013] [Indexed: 11/10/2022]
Abstract
Eukaryal DMC1 proteins play a central role in homologous recombination in meiosis by assembling at the sites of programmed DNA double-strand breaks and carrying out a search for allelic DNA sequences located on homologous chromatids. They are close homologs of eukaryal Rad51 and archaeal RadA proteins and are remote homologs of bacterial RecA proteins. These recombinases (also called DNA strand-exchange proteins) promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. An octameric form of a truncated human DMC1 devoid of its small N-terminal domain (residues 1-83) has been crystallized. The structure of the truncated DMC1 octamer is similar to that of the previously reported full-length DMC1 octamer, which has disordered N-terminal domains. In each protomer, only the ATP cap regions (Asp317-Glu323) show a noticeable conformational difference. The truncated DMC1 octamers further stack with alternate polarity into a filament. Similar filamentous assemblies of DMC1 have been observed to form on DNA by electron microscopy.
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Affiliation(s)
- Liqin Du
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
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