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Ramirez-Otero MA, Costanzo V. "Bridging the DNA divide": Understanding the interplay between replication- gaps and homologous recombination proteins RAD51 and BRCA1/2. DNA Repair (Amst) 2024; 141:103738. [PMID: 39084178 DOI: 10.1016/j.dnarep.2024.103738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
A key but often neglected component of genomic instability is the emergence of single-stranded DNA (ssDNA) gaps during DNA replication in the absence of functional homologous recombination (HR) proteins, such as RAD51 and BRCA1/2. Research in prokaryotes has shed light on the dual role of RAD51's bacterial ortholog, RecA, in HR and the protection of replication forks, emphasizing its essential role in preventing the formation of ssDNA gaps, which is vital for cellular viability. This phenomenon was corroborated in eukaryotic cells deficient in HR, where the formation of ssDNA gaps within newly synthesized DNA and their subsequent processing by the MRE11 nuclease were observed. Without functional HR proteins, cells employ alternative ssDNA gap-filling mechanisms to ensure survival, though this compensatory response can compromise genomic stability. A notable example is the involvement of the translesion synthesis (TLS) polymerase POLζ, along with the repair protein POLθ, in the suppression of replicative ssDNA gaps. Persistent ssDNA gaps may result in replication fork collapse, chromosomal anomalies, and cell death, which contribute to cancer progression and resistance to therapy. Elucidating the processes that avert ssDNA gaps and safeguard replication forks is critical for enhancing cancer treatment approaches by exploiting the vulnerabilities of cancer cells in these pathways.
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Affiliation(s)
| | - Vincenzo Costanzo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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2
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Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V. RAD51 protects abasic sites to prevent replication fork breakage. Mol Cell 2024; 84:3026-3043.e11. [PMID: 39178838 DOI: 10.1016/j.molcel.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/03/2024] [Accepted: 07/08/2024] [Indexed: 08/26/2024]
Abstract
Abasic sites are DNA lesions repaired by base excision repair. Cleavage of unrepaired abasic sites in single-stranded DNA (ssDNA) can lead to chromosomal breakage during DNA replication. How rupture of abasic DNA is prevented remains poorly understood. Here, using cryoelectron microscopy (cryo-EM), Xenopus laevis egg extracts, and human cells, we show that RAD51 nucleofilaments specifically recognize and protect abasic sites, which increase RAD51 association rate to DNA. In the absence of BRCA2 or RAD51, abasic sites accumulate as a result of DNA base methylation, oxidation, and deamination, inducing abasic ssDNA gaps that make replicating DNA fibers sensitive to APE1. RAD51 assembled on abasic DNA prevents abasic site cleavage by the MRE11-RAD50 complex, suppressing replication fork breakage triggered by an excess of abasic sites or POLθ polymerase inhibition. Our study highlights the critical role of BRCA2 and RAD51 in safeguarding against unrepaired abasic sites in DNA templates stemming from base alterations, ensuring genomic stability.
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Affiliation(s)
| | | | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Anna De Antoni
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Luay Joudeh
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Salli Waked
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Viviana Barra
- Institute Curie, PSL Research University, CNRS, UMR 144, 26 Rue d'Ulm, 75005 Paris, France
| | - Daniele Fachinetti
- Institute Curie, PSL Research University, CNRS, UMR 144, 26 Rue d'Ulm, 75005 Paris, France
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Vincenzo Costanzo
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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Williams AB, Hetrick KM, Foster PL. Interplay of DNA repair, homologous recombination, and DNA polymerases in resistance to the DNA damaging agent 4-nitroquinoline-1-oxide in Escherichia coli. DNA Repair (Amst) 2010; 9:1090-7. [PMID: 20724226 DOI: 10.1016/j.dnarep.2010.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/09/2010] [Accepted: 07/13/2010] [Indexed: 11/18/2022]
Abstract
Escherichia coli has three DNA damage-inducible DNA polymerases: DNA polymerase II (Pol II), DNA polymerase IV (Pol IV), and DNA polymerase V (Pol V). While the in vivo function of Pol V is well understood, the precise roles of Pol IV and Pol II in DNA replication and repair are not as clear. Study of these polymerases has largely focused on their participation in the recovery of failed replication forks, translesion DNA synthesis, and origin-independent DNA replication. However, their roles in other repair and recombination pathways in E. coli have not been extensively examined. This study investigated how E. coli's inducible DNA polymerases and various DNA repair and recombination pathways function together to convey resistance to 4-nitroquinoline-1-oxide (NQO), a DNA damaging agent that produces replication blocking DNA base adducts. The data suggest that full resistance to this compound depends upon an intricate interplay among the activities of the inducible DNA polymerases and recombination. The data also suggest new relationships between the different pathways that process recombination intermediates.
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Affiliation(s)
- Ashley B Williams
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
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Donaldson JR, Courcelle CT, Courcelle J. RuvABC is required to resolve holliday junctions that accumulate following replication on damaged templates in Escherichia coli. J Biol Chem 2006; 281:28811-21. [PMID: 16895921 DOI: 10.1074/jbc.m603933200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RuvABC is a complex that promotes branch migration and resolution of Holliday junctions. Although ruv mutants are hypersensitive to UV irradiation, the molecular event(s) that necessitate RuvABC processing in vivo are not known. Here, we used a combination of two-dimensional gel analysis and electron microscopy to reveal that although ruvAB and ruvC mutants are able to resume replication following arrest at UV-induced lesions, molecules that replicate in the presence of DNA damage accumulate unresolved Holliday junctions. The failure to resolve the Holliday junctions on the fully replicated molecules correlates with a delayed loss of genomic integrity that is likely to account for the loss of viability in these cells. The strand exchange intermediates that accumulate in ruv mutants are distinct from those observed at arrested replication forks and are not subject to resolution by RecG. These results indicate that the Holliday junctions observed in ruv mutants are intermediates of a repair pathway that is distinct from that of the recovery of arrested replication forks. A model is proposed in which RuvABC is required to resolve junctions that arise during the repair of a subset of nonarresting lesions after replication has passed through the template.
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Affiliation(s)
- Janet R Donaldson
- Department of Biology, Portland State University, Portland, Oregon 97207, USA.
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5
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Ellis K. Water disinfection: A review with some consideration of the requirements of the third world. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/10643389109388405] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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McCarthy D, Griffin K, Setlow JK. Plasmid containing a DNA ligase gene from Haemophilus influenzae. J Bacteriol 1984; 158:730-2. [PMID: 6373728 PMCID: PMC215491 DOI: 10.1128/jb.158.2.730-732.1984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A ligase gene from Haemophilus influenzae was cloned into the shuttle vector pDM2 . Although the plasmid did not affect X-ray sensitivity, it caused an increase in UV sensitivity of the wild-type but not excision-defective H. influenzae and a decrease in UV sensitivity of the rec-1 mutant.
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Trgovçević Z, Petranović D, Petranović M, Salaj-Smic E. Degradation of Escherichia coli DNA synthesized after ultraviolet irradiation in the absence of repair. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1984; 45:193-6. [PMID: 6365817 DOI: 10.1080/09553008414550211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA degradation in Escherichia coli uvrA recA bacteria exposed to a low dose (0.07 J/m2) of ultraviolet radiation was studied. A considerable amount of the newly-synthesized DNA, which contains gaps opposite pyrimidine dimers, is broken down. In contrast, parental, dimer-containing DNA is resistant to radiation-induced degradation.
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Trgovcević Z, Petranović D, Salaj-Smic E, Petranović M, Trinajstić N, Jericević Z. DNA replication past pyrimidine dimers in the absence of repair. Mutat Res 1983; 112:17-22. [PMID: 6338353 DOI: 10.1016/0167-8817(83)90020-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Post-UV DNA synthesis in Escherichia coli uvrA recA cells was studied. A low dose of UV radiation (0.07 J/m2), which caused no degradation of the dimer-containing DNA, was used. This enabled us to make a direct comparison between DNA synthesis on the normal template and DNA synthesis on the UV-damaged template. There was no change in the post-UV DNA synthesis kinetics during the first 60 min of post-irradiation incubation. A reduced rate of DNA synthesis was observed at later post-UV times when the dimers are expected to have passed through the normal replication complex. This reduced rate of DNA synthesis was associated with loss of the biological activity of the DNA. We suggest that the gaps opposite dimers rather than dimers per se interfere with normal replication, thus leading to cell death of uvrA recA bacteria.
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O'Brien PA, Houghton JA. UV-INDUCED DNA DEGRADATION IN THE CYANOBACTERIUM SYNECHOCYSTIS PCC 6308. Photochem Photobiol 1982. [DOI: 10.1111/j.1751-1097.1982.tb04396.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Nozu K, Ohnishi T. Ultraviolet sensitivity of Vibrio parahaemolyticus, a causative bacterium of food poisoning. Photochem Photobiol 1977; 26:483-6. [PMID: 594178 DOI: 10.1111/j.1751-1097.1977.tb07518.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Hofemeister J. DNA repair in Proteus mirabilis. IV. Post-irradiation DNA degradation as influenced by a function inducible in rec+ cells. MOLECULAR & GENERAL GENETICS : MGG 1977; 154:35-41. [PMID: 331077 DOI: 10.1007/bf00265574] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Wilmore PJ, Parry JM. Division delay and DNA degradation after mutagen treatment of the yeast, Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1976; 145:287-91. [PMID: 181669 DOI: 10.1007/bf00325825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The treatment of the yeast mutant TMP1-1, which is capable of incorporating low levels of 3H-thymidine-5' - monophosphate with UV light and ethyl methane sulphonate resulted in division delay when cultures were reinnoculated into fresh medium. The initiation of cell division was accompanied by the degradation of up to 20% of the nuclear DNA fraction. The period of DNA degradation correlates closely with the time at which yeast cultures undergo mitotic recombination and appears to represent the degradation of DNA during a post-replication repair process.
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14
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Suzuki K. Cell division and DNA synthesis in uvrA recA double mutants of E. coli K12. MOLECULAR & GENERAL GENETICS : MGG 1974; 129:249-58. [PMID: 4601268 DOI: 10.1007/bf00267917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Hatzfeld J. Correlation between degradation, replication and repair of yeast DNA irradiated by ultraviolet or -rays. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 299:43-53. [PMID: 4573527 DOI: 10.1016/0005-2787(73)90396-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Tuveson RW. Genetic and enzymatic analysis of a gene controlling UV sensitivity in Neurospora crassa. Mutat Res 1972; 15:411-24. [PMID: 4261527 DOI: 10.1016/0027-5107(72)90005-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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Yonei S, Nozu K. Mechanism of post-irradiation degradation of deoxyribonucleic acid in a radiosensitive Escherichia coli (NG30) irradiated with ultraviolet light. J Mol Biol 1972; 65:213-25. [PMID: 4557191 DOI: 10.1016/0022-2836(72)90278-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Green MH, Gray WJ, Murden DJ, Bridges BA. Influence of growth phase on UV induced lethality and DNA breakdown in a Kornberg polymerase deficient resA strain of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1971; 112:110-6. [PMID: 4940110 DOI: 10.1007/bf00267489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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19
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Fornili SL, Cordone L, Radman M. Phenomenological theory of repair kinetics of ultraviolet irradiated Lambda phage. Virology 1971; 43:422-6. [PMID: 5543830 DOI: 10.1016/0042-6822(71)90314-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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20
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Mutagenic and Lethal Effects of Visible and Near-Ultraviolet Light on Bacterial Cells. ADVANCES IN GENETICS 1971. [DOI: 10.1016/s0065-2660(08)60358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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21
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Smith KC, Meun DH. Repair of radiation-induced damage in Escherichia coli. I. Effect of rec mutations on post-replication repair of damage due to ultraviolet radiation. J Mol Biol 1970; 51:459-72. [PMID: 4923857 DOI: 10.1016/0022-2836(70)90001-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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