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Guh CL, Lei KH, Chen YA, Jiang YZ, Chang HY, Liaw H, Li HW, Yen HY, Chi P. RAD51 paralogs synergize with RAD51 to protect reversed forks from cellular nucleases. Nucleic Acids Res 2023; 51:11717-11731. [PMID: 37843130 PMCID: PMC10681713 DOI: 10.1093/nar/gkad856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/17/2023] Open
Abstract
Fork reversal is a conserved mechanism to prevent stalled replication forks from collapsing. Formation and protection of reversed forks are two crucial steps in ensuring fork integrity and stability. Five RAD51 paralogs, namely, RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3, which share sequence and structural similarity to the recombinase RAD51, play poorly defined mechanistic roles in these processes. Here, using purified BCDX2 (RAD51BCD-XRCC2) and CX3 (RAD51C-XRCC3) complexes and in vitro reconstituted biochemical systems, we mechanistically dissect their functions in forming and protecting reversed forks. We show that both RAD51 paralog complexes lack fork reversal activities. Whereas CX3 exhibits modest fork protection activity, BCDX2 significantly synergizes with RAD51 to protect DNA against attack by the nucleases MRE11 and EXO1. DNA protection is contingent upon the ability of RAD51 to form a functional nucleoprotein filament on DNA. Collectively, our results provide evidence for a hitherto unknown function of RAD51 paralogs in synergizing with RAD51 nucleoprotein filament to prevent degradation of stressed replication forks.
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Affiliation(s)
- Chia-Lun Guh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yi-An Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yung Yen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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2
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Meaza I, Williams AR, Lu H, Kouokam JC, Toyoda JH, Croom-Perez TJ, Wise SS, Aboueissa AEM, Wise JP. Prolonged particulate hexavalent chromium exposure induces RAD51 foci inhibition and cytoplasmic accumulation in immortalized and primary human lung bronchial epithelial cells. Toxicol Appl Pharmacol 2023; 479:116711. [PMID: 37805091 PMCID: PMC10841504 DOI: 10.1016/j.taap.2023.116711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a human lung carcinogen with widespread exposure risks. Cr(VI) causes DNA double strand breaks that if unrepaired, progress into chromosomal instability (CIN), a key driving outcome in Cr(VI)-induced tumors. The ability of Cr(VI) to cause DNA breaks and inhibit repair is poorly understood in human lung epithelial cells, which are extremely relevant since pathology data show Cr(VI)-induced tumors originate from bronchial epithelial cells. In the present study, we considered immortalized and primary human bronchial epithelial cells. Cells were treated with zinc chromate at concentrations ranging 0.05 to 0.4μg/cm2 for acute (24 h) and prolonged (120 h) exposures. DNA double strand breaks (DSBs) were measured by neutral comet assay and the status of homologous recombination repair, the main pathway to fix Cr(VI)-induced DSBs, was measured by RAD51 foci formation with immunofluorescence, RAD51 localization with confocal microscopy and sister chromatid exchanges. We found acute and prolonged Cr(VI) exposure induced DSBs. Acute exposure induced homologous recombination repair, but prolonged exposure inhibited it resulting in chromosome instability in immortalized and primary human bronchial epithelial cells.
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Affiliation(s)
- Idoia Meaza
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | - Aggie R Williams
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | - Haiyan Lu
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | - J Calvin Kouokam
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | - Jennifer H Toyoda
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | - Tayler J Croom-Perez
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 6900 Lake Nona Blvd., Orlando, FL 32827, United States of America
| | - Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America
| | | | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, 500 S Preston Street, Building 55A, Room 1422, Louisville, KY 40292, United States of America.
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3
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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4
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Argunhan B, Iwasaki H, Tsubouchi H. Post-translational modification of factors involved in homologous recombination. DNA Repair (Amst) 2021; 104:103114. [PMID: 34111757 DOI: 10.1016/j.dnarep.2021.103114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/04/2023]
Abstract
DNA is the molecule that stores the chemical instructions necessary for life and its stability is therefore of the utmost importance. Despite this, DNA is damaged by both exogenous and endogenous factors at an alarming frequency. The most severe type of DNA damage is a double-strand break (DSB), in which a scission occurs in both strands of the double helix, effectively dividing a single normal chromosome into two pathological chromosomes. Homologous recombination (HR) is a universal DSB repair mechanism that solves this problem by identifying another region of the genome that shares high sequence similarity with the DSB site and using it as a template for repair. Rad51 possess the enzymatic activity that is essential for this repair but several auxiliary factors are required for Rad51 to fulfil its function. It is becoming increasingly clear that many HR factors are subjected to post-translational modification. Here, we review what is known about how these modifications affect HR. We first focus on cases where there is experimental evidence to support a function for the modification, then discuss speculative cases where a function can be inferred. Finally, we contemplate why such modifications might be necessary.
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Affiliation(s)
- Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hideo Tsubouchi
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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5
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Tye S, Ronson GE, Morris JR. A fork in the road: Where homologous recombination and stalled replication fork protection part ways. Semin Cell Dev Biol 2021; 113:14-26. [PMID: 32653304 PMCID: PMC8082280 DOI: 10.1016/j.semcdb.2020.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
In response to replication hindrances, DNA replication forks frequently stall and are remodelled into a four-way junction. In such a structure the annealed nascent strand is thought to resemble a DNA double-strand break and remodelled forks are vulnerable to nuclease attack by MRE11 and DNA2. Proteins that promote the recruitment, loading and stabilisation of RAD51 onto single-stranded DNA for homology search and strand exchange in homologous recombination (HR) repair and inter-strand cross-link repair also act to set up RAD51-mediated protection of nascent DNA at stalled replication forks. However, despite the similarities of these pathways, several lines of evidence indicate that fork protection is not simply analogous to the RAD51 loading step of HR. Protection of stalled forks not only requires separate functions of a number of recombination proteins, but also utilises nucleases important for the resection steps of HR in alternative ways. Here we discuss how fork protection arises and how its differences with HR give insights into the differing contexts of these two pathways.
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Affiliation(s)
- Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - George E Ronson
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
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6
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Garcin EB, Gon S, Sullivan MR, Brunette GJ, Cian AD, Concordet JP, Giovannangeli C, Dirks WG, Eberth S, Bernstein KA, Prakash R, Jasin M, Modesti M. Differential Requirements for the RAD51 Paralogs in Genome Repair and Maintenance in Human Cells. PLoS Genet 2019; 15:e1008355. [PMID: 31584931 PMCID: PMC6795472 DOI: 10.1371/journal.pgen.1008355] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/16/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A cells. Underlining their importance for genomic stability, mutant cell lines display variable growth defects, impaired sister chromatid recombination, reduced levels of stable RAD51 nuclear foci, and hyper-sensitivity to mitomycin C and olaparib, with the weakest phenotypes observed in RAD51B-deficient cells. Altogether these observations underscore the contributions of RAD51 paralogs in diverse DNA repair processes, and demonstrate essential differences in different cell types. Finally, this study will provide useful reagents to analyze patient-derived mutations and to investigate mechanisms of chemotherapeutic resistance deployed by cancers.
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Affiliation(s)
- Edwige B. Garcin
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Stéphanie Gon
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Meghan R. Sullivan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Gregory J. Brunette
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Anne De Cian
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Jean-Paul Concordet
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Carine Giovannangeli
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Wilhelm G. Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kara A. Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mauro Modesti
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
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7
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Abstract
Homologous recombination (HR) is a universally conserved mechanism used to maintain genomic integrity. In eukaryotes, HR is used to repair the spontaneous double strand breaks (DSBs) that arise during mitotic growth, and the programmed DSBs that form during meiosis. The mechanisms that govern mitotic and meiotic HR share many similarities, however, there are also several key differences, which reflect the unique attributes of each process. For instance, even though many of the proteins involved in mitotic and meiotic HR are the same, DNA target specificity is not: mitotic DSBs are repaired primarily using the sister chromatid as a template, whereas meiotic DBSs are repaired primarily through targeting of the homologous chromosome. These changes in template specificity are induced by expression of meiosis-specific HR proteins, down-regulation of mitotic HR proteins, and the formation of meiosis-specific chromosomal structures. Here, we compare and contrast the biochemical properties of key recombination intermediates formed during the pre-synapsis phase of mitotic and meiotic HR. Throughout, we try to highlight unanswered questions that will shape our understanding of how homologous recombination contributes to human cancer biology and sexual reproduction.
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8
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Jacquinet A, Brown L, Sawkins J, Liu P, Pugash D, Van Allen MI, Patel MS. Expanding the FANCO/RAD51C associated phenotype: Cleft lip and palate and lobar holoprosencephaly, two rare findings in Fanconi anemia. Eur J Med Genet 2017; 61:257-261. [PMID: 29278735 DOI: 10.1016/j.ejmg.2017.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/06/2017] [Accepted: 12/20/2017] [Indexed: 10/18/2022]
Abstract
Fanconi anemia is a rare chromosome instability disorder with a highly variable phenotype. In the antenatal and neonatal periods, the diagnosis is usually suggested by the presence of typical congenital abnormalities such as intrauterine growth retardation, microcephaly and radial ray defects. We report a newborn female with a prenatal diagnosis of Fanconi anemia, complementation group O (FANCO). Antenatal ultrasounds identified symmetrical intrauterine growth retardation, complex heart defect as well as brain anomalies, overlapping fingers and cleft lip and palate. Imperforate anus was detected after birth. Compound heterozygous RAD51C variants c. [571+5G > A]; [c.935G > A] were detected by prenatal whole exome sequencing and cellular hypersensitivity to DNA interstrand crosslinking agents (DEB, MMC) was confirmed after birth. With only one previously described homozygous RAD51C variant to date, our findings expand the phenotypic spectrum of FANCO and suggest it should be part of the antenatal differential diagnosis for trisomy 13 and 18, due to the presence of atypical findings such as cleft lip and palate, holoprosencephaly, growth restriction and overlapping fingers.
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Affiliation(s)
- Adeline Jacquinet
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Center for Human Genetics, Centre Hospitalier Universitaire and University of Liège, Liège, Belgium.
| | - Lindsay Brown
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jessica Sawkins
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Denise Pugash
- Department of Radiology, University of British Columbia, Vancouver, Canada
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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9
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Remodeling and Control of Homologous Recombination by DNA Helicases and Translocases that Target Recombinases and Synapsis. Genes (Basel) 2016; 7:genes7080052. [PMID: 27548227 PMCID: PMC4999840 DOI: 10.3390/genes7080052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/24/2016] [Accepted: 08/12/2016] [Indexed: 11/16/2022] Open
Abstract
Recombinase enzymes catalyse invasion of single-stranded DNA (ssDNA) into homologous duplex DNA forming "Displacement loops" (D-loops), a process called synapsis. This triggers homologous recombination (HR), which can follow several possible paths to underpin DNA repair and restart of blocked and collapsed DNA replication forks. Therefore, synapsis can be a checkpoint for controlling whether or not, how far, and by which pathway, HR proceeds to overcome an obstacle or break in a replication fork. Synapsis can be antagonized by limiting access of a recombinase to ssDNA and by dissociation of D-loops or heteroduplex formed by synapsis. Antagonists include DNA helicases and translocases that are identifiable in eukaryotes, bacteria and archaea, and which target synaptic and pre-synaptic DNA structures thereby controlling HR at early stages. Here we survey these events with emphasis on enabling DNA replication to be resumed from sites of blockage or collapse. We also note how knowledge of anti-recombination activities could be useful to improve efficiency of CRISPR-based genome editing.
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10
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Browning CL, Qin Q, Kelly DF, Prakash R, Vanoli F, Jasin M, Wise JP. Prolonged Particulate Hexavalent Chromium Exposure Suppresses Homologous Recombination Repair in Human Lung Cells. Toxicol Sci 2016; 153:70-8. [PMID: 27449664 DOI: 10.1093/toxsci/kfw103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genomic instability is one of the primary models of carcinogenesis and a feature of almost all cancers. Homologous recombination (HR) repair protects against genomic instability by maintaining high genomic fidelity during the repair of DNA double strand breaks. The defining step of HR repair is the formation of the Rad51 nucleofilament, which facilitates the search for a homologous sequence and invasion of the template DNA strand. Particulate hexavalent chromium (Cr(VI)), a human lung carcinogen, induces DNA double strand breaks and chromosome instability. Since the loss of HR repair increases Cr(VI)-induced chromosome instability, we investigated the effect of extended Cr(VI) exposure on HR repair. We show acute (24 h) Cr(VI) exposure induces a normal HR repair response. In contrast, prolonged (120 h) exposure to particulate Cr(VI) inhibited HR repair and Rad51 nucleofilament formation. Prolonged Cr(VI) exposure had a profound effect on Rad51, evidenced by reduced protein levels and Rad51 mislocalization to the cytoplasm. The response of proteins involved in Rad51 nuclear import and nucleofilament formation displayed varying responses to prolonged Cr(VI) exposure. BRCA2 formed nuclear foci after prolonged Cr(VI) exposure, while Rad51C foci formation was suppressed. These results suggest that particulate Cr(VI), a major chemical carcinogen, inhibits HR repair by targeting Rad51, causing DNA double strand breaks to be repaired by a low fidelity, Rad51-independent repair pathway. These results further enhance our understanding of the underlying mechanism of Cr(VI)-induced chromosome instability and thus, carcinogenesis.
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Affiliation(s)
- Cynthia L Browning
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| | - Qin Qin
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Rohit Prakash
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Fabio Vanoli
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Maria Jasin
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - John Pierce Wise
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
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11
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Higgs MR, Reynolds JJ, Winczura A, Blackford AN, Borel V, Miller ES, Zlatanou A, Nieminuszczy J, Ryan EL, Davies NJ, Stankovic T, Boulton SJ, Niedzwiedz W, Stewart GS. BOD1L Is Required to Suppress Deleterious Resection of Stressed Replication Forks. Mol Cell 2015; 59:462-77. [PMID: 26166705 DOI: 10.1016/j.molcel.2015.06.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/15/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Recognition and repair of damaged replication forks are essential to maintain genome stability and are coordinated by the combined action of the Fanconi anemia and homologous recombination pathways. These pathways are vital to protect stalled replication forks from uncontrolled nucleolytic activity, which otherwise causes irreparable genomic damage. Here, we identify BOD1L as a component of this fork protection pathway, which safeguards genome stability after replication stress. Loss of BOD1L confers exquisite cellular sensitivity to replication stress and uncontrolled resection of damaged replication forks, due to a failure to stabilize RAD51 at these forks. Blocking DNA2-dependent resection, or downregulation of the helicases BLM and FBH1, suppresses both catastrophic fork processing and the accumulation of chromosomal damage in BOD1L-deficient cells. Thus, our work implicates BOD1L as a critical regulator of genome integrity that restrains nucleolytic degradation of damaged replication forks.
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Affiliation(s)
- Martin R Higgs
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - John J Reynolds
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Alicja Winczura
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Valérie Borel
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
| | - Edward S Miller
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Anastasia Zlatanou
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jadwiga Nieminuszczy
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ellis L Ryan
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicholas J Davies
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tatjana Stankovic
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Simon J Boulton
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
| | - Wojciech Niedzwiedz
- The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Grant S Stewart
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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12
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Prakash R, Zhang Y, Feng W, Jasin M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol 2015; 7:a016600. [PMID: 25833843 DOI: 10.1101/cshperspect.a016600] [Citation(s) in RCA: 549] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks in mammalian cells, the defining step of which is homologous strand exchange directed by the RAD51 protein. The physiological importance of HR is underscored by the observation of genomic instability in HR-deficient cells and, importantly, the association of cancer predisposition and developmental defects with mutations in HR genes. The tumor suppressors BRCA1 and BRCA2, key players at different stages of HR, are frequently mutated in familial breast and ovarian cancers. Other HR proteins, including PALB2 and RAD51 paralogs, have also been identified as tumor suppressors. This review summarizes recent findings on BRCA1, BRCA2, and associated proteins involved in human disease with an emphasis on their molecular roles and interactions.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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13
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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14
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Ceccaldi R, Liu JC, Amunugama R, Hajdu I, Primack B, Petalcorin MIR, O'Connor KW, Konstantinopoulos PA, Elledge SJ, Boulton SJ, Yusufzai T, D'Andrea AD. Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair. Nature 2015; 518:258-62. [PMID: 25642963 PMCID: PMC4415602 DOI: 10.1038/nature14184] [Citation(s) in RCA: 592] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022]
Abstract
Large-scale genomic studies have shown that half of epithelial ovarian cancers (EOCs) have alterations in genes regulating homologous recombination (HR) repair. Loss of HR accounts for the genomic instability of EOCs and for their cellular hyper-dependence on alternative poly-ADP ribose polymerase (PARP)-mediated DNA repair mechanisms. Previous studies have implicated the DNA polymerase θ (Polθ also known as POLQ, encoded by POLQ) in a pathway required for the repair of DNA double-strand breaks, referred to as the error-prone microhomology-mediated end-joining (MMEJ) pathway. Whether Polθ interacts with canonical DNA repair pathways to prevent genomic instability remains unknown. Here we report an inverse correlation between HR activity and Polθ expression in EOCs. Knockdown of Polθ in HR-proficient cells upregulates HR activity and RAD51 nucleofilament assembly, while knockdown of Polθ in HR-deficient EOCs enhances cell death. Consistent with these results, genetic inactivation of an HR gene (Fancd2) and Polq in mice results in embryonic lethality. Moreover, Polθ contains RAD51 binding motifs and it blocks RAD51-mediated recombination. Our results reveal a synthetic lethal relationship between the HR pathway and Polθ-mediated repair in EOCs, and identify Polθ as a novel druggable target for cancer therapy.
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Affiliation(s)
- Raphael Ceccaldi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jessica C Liu
- 1] Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA [2] Department of Biological Chemistry &Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA [3] Department of Molecular &Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ravindra Amunugama
- Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ildiko Hajdu
- Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Benjamin Primack
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Mark I R Petalcorin
- DNA Damage Response Laboratory, Cancer Research UK, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Kevin W O'Connor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Simon J Boulton
- DNA Damage Response Laboratory, Cancer Research UK, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Timur Yusufzai
- 1] Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA [2] Department of Biological Chemistry &Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
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15
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Lorenz A, Mehats A, Osman F, Whitby MC. Rad51/Dmc1 paralogs and mediators oppose DNA helicases to limit hybrid DNA formation and promote crossovers during meiotic recombination. Nucleic Acids Res 2014; 42:13723-35. [PMID: 25414342 PMCID: PMC4267644 DOI: 10.1093/nar/gku1219] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 10/17/2014] [Accepted: 11/06/2014] [Indexed: 11/30/2022] Open
Abstract
During meiosis programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination using the sister chromatid or the homologous chromosome (homolog) as a template. This repair results in crossover (CO) and non-crossover (NCO) recombinants. Only CO formation between homologs provides the physical linkages guiding correct chromosome segregation, which are essential to produce healthy gametes. The factors that determine the CO/NCO decision are still poorly understood. Using Schizosaccharomyces pombe as a model we show that the Rad51/Dmc1-paralog complexes Rad55-Rad57 and Rdl1-Rlp1-Sws1 together with Swi5-Sfr1 play a major role in antagonizing both the FANCM-family DNA helicase/translocase Fml1 and the RecQ-type DNA helicase Rqh1 to limit hybrid DNA formation and promote Mus81-Eme1-dependent COs. A common attribute of these protein complexes is an ability to stabilize the Rad51/Dmc1 nucleoprotein filament, and we propose that it is this property that imposes constraints on which enzymes gain access to the recombination intermediate, thereby controlling the manner in which it is processed and resolved.
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Affiliation(s)
- Alexander Lorenz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alizée Mehats
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Fekret Osman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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16
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Charlot F, Chelysheva L, Kamisugi Y, Vrielynck N, Guyon A, Epert A, Le Guin S, Schaefer DG, Cuming AC, Grelon M, Nogué F. RAD51B plays an essential role during somatic and meiotic recombination in Physcomitrella. Nucleic Acids Res 2014; 42:11965-78. [PMID: 25260587 PMCID: PMC4231755 DOI: 10.1093/nar/gku890] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic RecA homologue Rad51 is a key factor in homologous recombination and recombinational repair. Rad51-like proteins have been identified in yeast (Rad55, Rad57 and Dmc1), plants and vertebrates (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3 and DMC1). RAD51 and DMC1 are the strand-exchange proteins forming a nucleofilament for strand invasion, however, the function of the paralogues in the process of homologous recombination is less clear. In yeast the two Rad51 paralogues, Rad55 and Rad57, have been shown to be involved in somatic and meiotic HR and they are essential to the formation of the Rad51/DNA nucleofilament counterbalancing the anti-recombinase activity of the SRS2 helicase. Here, we examined the role of RAD51B in the model bryophyte Physcomitrella patens. Mutant analysis shows that RAD51B is essential for the maintenance of genome integrity, for resistance to DNA damaging agents and for gene targeting. Furthermore, we set up methods to investigate meiosis in Physcomitrella and we demonstrate that the RAD51B protein is essential for meiotic homologous recombination. Finally, we show that all these functions are independent of the SRS2 anti-recombinase protein, which is in striking contrast to what is found in budding yeast where the RAD51 paralogues are fully dependent on the SRS2 anti-recombinase function.
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Affiliation(s)
- Florence Charlot
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Liudmila Chelysheva
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
| | - Nathalie Vrielynck
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Anouchka Guyon
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Aline Epert
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Sylvia Le Guin
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Didier G Schaefer
- Laboratoire de Biologie Moleculaire et Cellulaire, Institut de Biologie, Universite de Neuchatel, rue Emile-Argand 11, CH-2007 Neuchatel, Switzerland
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
| | - Mathilde Grelon
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
| | - Fabien Nogué
- INRA, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin UMR1318, Saclay Plant Sciences, Versailles, France
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17
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Liu J, Berger CL, Morrical SW. Kinetics of presynaptic filament assembly in the presence of single-stranded DNA binding protein and recombination mediator protein. Biochemistry 2013; 52:7878-89. [PMID: 24124995 DOI: 10.1021/bi401060p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Enzymes of the RecA/Rad51 family catalyze DNA strand exchange reactions that are important for homologous recombination and for the accurate repair of DNA double-strand breaks. RecA/Rad51 recombinases are activated by their assembly into presynaptic filaments on single-stranded DNA (ssDNA), a process that is regulated by ssDNA binding protein (SSB) and mediator proteins. Mediator proteins stimulate strand exchange by accelerating the rate-limiting displacement of SSB from ssDNA by the incoming recombinase. The use of mediators is a highly conserved strategy in recombination, but the precise mechanism of mediator activity is unknown. In this study, the well-defined bacteriophage T4 recombination system (UvsX recombinase, Gp32 SSB, and UvsY mediator) is used to examine the kinetics of presynaptic filament assembly on native ssDNA in vitro. Results indicate that the ATP-dependent assembly of UvsX presynaptic filaments on Gp32-covered ssDNA is limited by a salt-sensitive nucleation step in the absence of mediator. Filament nucleation is selectively enhanced and rendered salt-resistant by mediator protein UvsY, which appears to stabilize a prenucleation complex. This mechanism potentially explains how UvsY promotes presynaptic filament assembly at physiologically relevant ionic strengths and Gp32 concentrations. Other data suggest that presynaptic filament assembly involves multiple nucleation events, resulting in many short UvsX-ssDNA filaments or clusters, which may be the relevant form for recombination in vivo. Together, these findings provide the first detailed kinetic model for presynaptic filament assembly involving all three major protein components (recombinase, mediator, and SSB) on native ssDNA.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry and ‡Department of Molecular Physiology and Biophysics, University of Vermont College of Medicine , Burlington, Vermont 05405, United States
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