1
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Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC. Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Nature 2024; 629:697-703. [PMID: 38658755 PMCID: PMC11096129 DOI: 10.1038/s41586-024-07347-7] [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: 06/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
RAD52 is important for the repair of DNA double-stranded breaks1,2, mitotic DNA synthesis3-5 and alternative telomere length maintenance6,7. Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA)8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair10. Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal11,12, and aberrant expression of RAD52 is associated with poor cancer prognosis13,14. As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers15-17. Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously18-20, RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52-ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52-RPA complex.
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Affiliation(s)
| | | | | | | | | | - Marcel Tuppi
- The Francis Crick Institute, London, UK
- Abcam, Cambridge Biomedical Campus, Cambridge, UK
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2
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Kinoshita C, Takizawa Y, Saotome M, Ogino S, Kurumizaka H, Kagawa W. The cryo-EM structure of full-length RAD52 protein contains an undecameric ring. FEBS Open Bio 2023; 13:408-418. [PMID: 36707939 PMCID: PMC9989933 DOI: 10.1002/2211-5463.13565] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/29/2022] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
The human RAD52 protein, which forms an oligomeric ring structure, is involved in DNA double-strand break repair. The N-terminal half of RAD52 is primarily responsible for self-oligomerisation and DNA binding. Crystallographic studies have revealed the detailed structure of the N-terminal half. However, only low-resolution structures have been reported for the full-length protein, and thus the structural role of the C-terminal half in self-oligomerisation has remained elusive. In this study, we determined the solution structure of the human RAD52 protein by cryo-electron microscopy (cryo-EM), at an average resolution of 3.5 Å. The structure revealed an undecameric ring that is nearly identical to the crystal structures of the N-terminal half. The cryo-EM map for the C-terminal half was poorly defined, indicating that the region is intrinsically disordered. The present cryo-EM structure provides important insights into the mechanistic roles played by the N-terminal and C-terminal halves of RAD52 during DNA double-strand break repair.
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Affiliation(s)
- Chiaki Kinoshita
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Japan
| | - Mika Saotome
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Shun Ogino
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Japan
| | - Wataru Kagawa
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Tokyo, Japan
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3
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Sharma AB, Erasimus H, Pinto L, Caron MC, Gopaul D, Peterlini T, Neumann K, Nazarov PV, Fritah S, Klink B, Herold-Mende CC, Niclou SP, Pasero P, Calsou P, Masson JY, Britton S, Van Dyck E. XAB2 promotes Ku eviction from single-ended DNA double-strand breaks independently of the ATM kinase. Nucleic Acids Res 2021; 49:9906-9925. [PMID: 34500463 PMCID: PMC8464071 DOI: 10.1093/nar/gkab785] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
Replication-associated single-ended DNA double-strand breaks (seDSBs) are repaired predominantly through RAD51-mediated homologous recombination (HR). Removal of the non-homologous end-joining (NHEJ) factor Ku from resected seDSB ends is crucial for HR. The coordinated actions of MRE11-CtIP nuclease activities orchestrated by ATM define one pathway for Ku eviction. Here, we identify the pre-mRNA splicing protein XAB2 as a factor required for resistance to seDSBs induced by the chemotherapeutic alkylator temozolomide. Moreover, we show that XAB2 prevents Ku retention and abortive HR at seDSBs induced by temozolomide and camptothecin, via a pathway that operates in parallel to the ATM-CtIP-MRE11 axis. Although XAB2 depletion preserved RAD51 focus formation, the resulting RAD51-ssDNA associations were unproductive, leading to increased NHEJ engagement in S/G2 and genetic instability. Overexpression of RAD51 or RAD52 rescued the XAB2 defects and XAB2 loss was synthetically lethal with RAD52 inhibition, providing potential perspectives in cancer therapy.
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Affiliation(s)
- Abhishek Bharadwaj Sharma
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Hélène Erasimus
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lia Pinto
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie-Christine Caron
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Diyavarshini Gopaul
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Thibaut Peterlini
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Katrin Neumann
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Multiomics Data Science Group, LIH, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, LIH, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg.,Functional Tumour Genetics Group, Department of Oncology, LIH, Luxembourg
| | | | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, LIH, Luxembourg.,Department of Biomedicine, University of Bergen, Norway
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France, Equipe Labellisée Ligue Nationale Contre le Cancer 2018
| | - Jean-Yves Masson
- CHU de Québec Research Center, Oncology Division, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France, Equipe Labellisée Ligue Nationale Contre le Cancer 2018
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
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4
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Al-Mugotir M, Lovelace JJ, George J, Bessho M, Pal D, Struble L, Kolar C, Rana S, Natarajan A, Bessho T, Borgstahl GEO. Selective killing of homologous recombination-deficient cancer cell lines by inhibitors of the RPA:RAD52 protein-protein interaction. PLoS One 2021; 16:e0248941. [PMID: 33784323 DOI: 10.1371/journal.pone.0248941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/09/2021] [Indexed: 12/29/2022] Open
Abstract
Synthetic lethality is a successful strategy employed to develop selective chemotherapeutics against cancer cells. Inactivation of RAD52 is synthetically lethal to homologous recombination (HR) deficient cancer cell lines. Replication protein A (RPA) recruits RAD52 to repair sites, and the formation of this protein-protein complex is critical for RAD52 activity. To discover small molecules that inhibit the RPA:RAD52 protein-protein interaction (PPI), we screened chemical libraries with our newly developed Fluorescence-based protein-protein Interaction Assay (FluorIA). Eleven compounds were identified, including FDA-approved drugs (quinacrine, mitoxantrone, and doxorubicin). The FluorIA was used to rank the compounds by their ability to inhibit the RPA:RAD52 PPI and showed mitoxantrone and doxorubicin to be the most effective. Initial studies using the three FDA-approved drugs showed selective killing of BRCA1-mutated breast cancer cells (HCC1937), BRCA2-mutated ovarian cancer cells (PE01), and BRCA1-mutated ovarian cancer cells (UWB1.289). It was noteworthy that selective killing was seen in cells known to be resistant to PARP inhibitors (HCC1937 and UWB1 SYr13). A cell-based double-strand break (DSB) repair assay indicated that mitoxantrone significantly suppressed RAD52-dependent single-strand annealing (SSA) and mitoxantrone treatment disrupted the RPA:RAD52 PPI in cells. Furthermore, mitoxantrone reduced radiation-induced foci-formation of RAD52 with no significant activity against RAD51 foci formation. The results indicate that the RPA:RAD52 PPI could be a therapeutic target for HR-deficient cancers. These data also suggest that RAD52 is one of the targets of mitoxantrone and related compounds.
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Affiliation(s)
- Mona Al-Mugotir
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Joseph George
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mika Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dhananjaya Pal
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lucas Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Carol Kolar
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sandeep Rana
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amarnath Natarajan
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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5
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Wdr70 regulates histone modification and genomic maintenance in fission yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118665. [PMID: 32007529 DOI: 10.1016/j.bbamcr.2020.118665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 11/20/2022]
Abstract
Eukaryotic genomes are packaged into highly condensed chromatin and this repressive chromatin barrier can be overcome by altering the chromatin structure via histone modification enzymes. Here, we report Wdr70 in Schizosaccharomyces pombe (spWdr70) plays important roles in multiple cellular processes including cell cycle progression, chromatin structure and DNA repair. Depletion of Wdr70 gene causes cell cycle delay, hypersensitivity to DNA damage reagents and quick phenotypic changes. Moreover, we observed strong genetic interaction between Wdr70 and genes regulating checkpoint and homologous recombination (HR), pinpointing the function of Wdr70 to DNA end resection. Finally, we show that the function of Wdr70 could be attributed to monoubiquitination of histone H2B (uH2B) in the vicinity of DNA double strand breaks (DSBs). Taken together, our data reveal that Wdr70 and H2B monoubiquitination-dependent chromatin modulation is required for chromatin homeostasis and genetic stability.
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6
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Nogueira A, Fernandes M, Catarino R, Medeiros R. RAD52 Functions in Homologous Recombination and Its Importance on Genomic Integrity Maintenance and Cancer Therapy. Cancers (Basel) 2019; 11:E1622. [PMID: 31652722 PMCID: PMC6893724 DOI: 10.3390/cancers11111622] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 01/27/2023] Open
Abstract
Genomes are continually subjected to DNA damage whether they are induced from intrinsic physiological processes or extrinsic agents. Double-stranded breaks (DSBs) are the most injurious type of DNA damage, being induced by ionizing radiation (IR) and cytotoxic agents used in cancer treatment. The failure to repair DSBs can result in aberrant chromosomal abnormalities which lead to cancer development. An intricate network of DNA damage signaling pathways is usually activated to eliminate these damages and to restore genomic stability. These signaling pathways include the activation of cell cycle checkpoints, DNA repair mechanisms, and apoptosis induction, also known as DNA damage response (DDR)-mechanisms. Remarkably, the homologous recombination (HR) is the major DSBs repairing pathway, in which RAD52 gene has a crucial repairing role by promoting the annealing of complementary single-stranded DNA and by stimulating RAD51 recombinase activity. Evidence suggests that variations in RAD52 expression can influence HR activity and, subsequently, influence the predisposition and treatment efficacy of cancer. In this review, we present several reports in which the down or upregulation of RAD52 seems to be associated with different carcinogenic processes. In addition, we discuss RAD52 inhibition in DDR-defective cancers as a possible target to improve cancer therapy efficacy.
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Affiliation(s)
- Augusto Nogueira
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal.
- Faculty of Medicine of University of Porto (FMUP), 4200-319 Porto, Portugal.
| | - Mara Fernandes
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal.
- Faculty of Medicine of University of Porto (FMUP), 4200-319 Porto, Portugal.
| | - Raquel Catarino
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal.
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal.
- Faculty of Medicine of University of Porto (FMUP), 4200-319 Porto, Portugal.
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University, 4249-004 Porto, Portugal.
- Research Department, Portuguese League against Cancer (NRNorte), 4200-172 Porto, Portugal.
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7
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Jalan M, Olsen KS, Powell SN. Emerging Roles of RAD52 in Genome Maintenance. Cancers (Basel) 2019; 11:E1038. [PMID: 31340507 PMCID: PMC6679097 DOI: 10.3390/cancers11071038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The maintenance of genome integrity is critical for cell survival. Homologous recombination (HR) is considered the major error-free repair pathway in combatting endogenously generated double-stranded lesions in DNA. Nevertheless, a number of alternative repair pathways have been described as protectors of genome stability, especially in HR-deficient cells. One of the factors that appears to have a role in many of these pathways is human RAD52, a DNA repair protein that was previously considered to be dispensable due to a lack of an observable phenotype in knock-out mice. In later studies, RAD52 deficiency has been shown to be synthetically lethal with defects in BRCA genes, making RAD52 an attractive therapeutic target, particularly in the context of BRCA-deficient tumors.
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Affiliation(s)
- Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Olsen
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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8
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Lee K, Ji JH, Yoon K, Che J, Seol JH, Lee SE, Shim EY. Microhomology Selection for Microhomology Mediated End Joining in Saccharomyces cerevisiae. Genes (Basel) 2019; 10:genes10040284. [PMID: 30965655 PMCID: PMC6523938 DOI: 10.3390/genes10040284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/03/2022] Open
Abstract
Microhomology-mediated end joining (MMEJ) anneals short, imperfect microhomologies flanking DNA breaks, producing repair products with deletions in a Ku- and RAD52-independent fashion. Puzzlingly, MMEJ preferentially selects certain microhomologies over others, even when multiple microhomologies are available. To define rules and parameters for microhomology selection, we altered the length, the position, and the level of mismatches to the microhomologies flanking homothallic switching (HO) endonuclease-induced breaks and assessed their effect on MMEJ frequency and the types of repair product formation. We found that microhomology of eight to 20 base pairs carrying no more than 20% mismatches efficiently induced MMEJ. Deletion of MSH6 did not impact MMEJ frequency. MMEJ preferentially chose a microhomology pair that was more proximal from the break. Interestingly, MMEJ events preferentially retained the centromere proximal side of the HO break, while the sequences proximal to the telomere were frequently deleted. The asymmetry in the deletional profile among MMEJ products was reduced when HO was induced on the circular chromosome. The results provide insight into how cells search and select microhomologies for MMEJ in budding yeast.
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Affiliation(s)
- Kihoon Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine. 164, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea.
| | - Kihoon Yoon
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
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9
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Caldwell BJ, Bell CE. Structure and mechanism of the Red recombination system of bacteriophage λ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:33-46. [PMID: 30904699 DOI: 10.1016/j.pbiomolbio.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA; Department of Chemistry and Biochemistry, 484 West 12th Avenue, 1060 Carmack Road, Columbus, OH, 43210, USA.
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10
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Structural Basis of Homology-Directed DNA Repair Mediated by RAD52. iScience 2018; 3:50-62. [PMID: 30428330 PMCID: PMC6137706 DOI: 10.1016/j.isci.2018.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
RAD52 mediates homologous recombination by annealing cDNA strands. However, the detailed mechanism of DNA annealing promoted by RAD52 has remained elusive. Here we report two crystal structures of human RAD52 single-stranded DNA (ssDNA) complexes that probably represent key reaction intermediates of RAD52-mediated DNA annealing. The first structure revealed a "wrapped" conformation of ssDNA around the homo-oligomeric RAD52 ring, in which the edges of the bases involved in base pairing are exposed to the solvent. The ssDNA conformation is close to B-form and appears capable of engaging in Watson-Crick base pairing with the cDNA strand. The second structure revealed a "trapped" conformation of ssDNA between two RAD52 rings. This conformation is stabilized by a different RAD52 DNA binding site, which promotes the accumulation of multiple RAD52 rings on ssDNA and the aggregation of ssDNA. These structures provide a structural framework for understanding the mechanism of RAD52-mediated DNA annealing.
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11
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TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats. Cell Rep 2018; 22:2146-2159. [DOI: 10.1016/j.celrep.2018.01.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 12/19/2017] [Accepted: 01/25/2018] [Indexed: 11/19/2022] Open
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12
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Cao J, Luo C, Peng R, Guo Q, Wang K, Wang P, Ye H, Song C. MiRNA-binding site functional polymorphisms in DNA repair genes RAD51, RAD52, and XRCC2 and breast cancer risk in Chinese population. Tumour Biol 2016; 37:10.1007/s13277-016-5459-2. [PMID: 27726100 DOI: 10.1007/s13277-016-5459-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/23/2016] [Indexed: 01/14/2023] Open
Abstract
RAD51, RAD52, and XRCC2 are all involved in DNA homologous recombinational repair, and there are interactions among those genes. Polymorphisms in 3'-UTR of DNA repair genes may change DNA repair capacity by regulating gene expression. However, potential regulatory variants affecting their expression remain largely unexplored. Five miRNA-binding site SNPs (rs7180135 and rs45549040 in RAD51, rs1051669 and rs7963551 in RAD52 and rs3218550 in XRCC2) selected by bioinformatics method were genotyped in 498 breast cancer (BC) patients and 498 matched controls in Chinese population. Association between SNPs and BC risk was analyzed by adjusted odds ratios (ORs) and 95 % confidence intervals (CIs) in unconditional logistic regression model. Quantitative real-time (qRT) PCR and Western Blot assays were used to calculate the relative expression of RAD52 in recombinant plasmid-pGenesil-1-let-7b group and let-7b-inhibitor group. Gene-reproductive factors interactions were evaluated by multifactor dimensionality reduction (MDR) method. We found that individuals with AC (OR 0.684, 95%CI 0.492-0.951) and CC (OR 0.317, 95%CI 0.200-0.503) genotypes of rs7963551 had a significantly lower risk of breast cancer and qRT-PCR and Western Blot revealed that let-7b might downregulate the expression of RAD52 in MCF-7 and SKBR-3 cells. A significant interaction between the number of pregnancy (≥2) and rs7963551 (Ars7963551) was found to increase breast cancer risk by 2.63-fold (OR 2.63; 95%CI 2.03-3.42). In summary, the miRNA-binding SNPs in DNA repair genes RAD51, RAD52, and XRCC2 and their interaction with reproductive factors might play important roles in the development of BC, and let-7b might downregulate RAD52 expression in MCF-7 and SKBR-3 cells.
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Affiliation(s)
- Jingjing Cao
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Chenglin Luo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Rui Peng
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Qiaoyun Guo
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Kaijuan Wang
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, 450001, Henan, People's Republic of China
| | - Peng Wang
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, 450001, Henan, People's Republic of China
| | - Hua Ye
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, 450001, Henan, People's Republic of China
| | - Chunhua Song
- Department of Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, 450001, Henan, People's Republic of China.
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13
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Reappearance from Obscurity: Mammalian Rad52 in Homologous Recombination. Genes (Basel) 2016; 7:genes7090063. [PMID: 27649245 PMCID: PMC5042393 DOI: 10.3390/genes7090063] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 01/28/2023] Open
Abstract
Homologous recombination (HR) plays an important role in maintaining genomic integrity. It is responsible for repair of the most harmful DNA lesions, DNA double-strand breaks and inter-strand DNA cross-links. HR function is also essential for proper segregation of homologous chromosomes in meiosis, maintenance of telomeres, and resolving stalled replication forks. Defects in HR often lead to genetic diseases and cancer. Rad52 is one of the key HR proteins, which is evolutionarily conserved from yeast to humans. In yeast, Rad52 is important for most HR events; Rad52 mutations disrupt repair of DNA double-strand breaks and targeted DNA integration. Surprisingly, in mammals, Rad52 knockouts showed no significant DNA repair or recombination phenotype. However, recent work demonstrated that mutations in human RAD52 are synthetically lethal with mutations in several other HR proteins including BRCA1 and BRCA2. These new findings indicate an important backup role for Rad52, which complements the main HR mechanism in mammals. In this review, we focus on the Rad52 activities and functions in HR and the possibility of using human RAD52 as therapeutic target in BRCA1 and BRCA2-deficient familial breast cancer and ovarian cancer.
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14
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Saotome M, Saito K, Onodera K, Kurumizaka H, Kagawa W. Structure of the human DNA-repair protein RAD52 containing surface mutations. Acta Crystallogr F Struct Biol Commun 2016; 72:598-603. [PMID: 27487923 PMCID: PMC4973300 DOI: 10.1107/s2053230x1601027x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 06/24/2016] [Indexed: 11/10/2022] Open
Abstract
The Rad52 protein is a eukaryotic single-strand DNA-annealing protein that is involved in the homologous recombinational repair of DNA double-strand breaks. The isolated N-terminal half of the human RAD52 protein (RAD52(1-212)) forms an undecameric ring structure with a surface that is mostly positively charged. In the present study, it was found that RAD52(1-212) containing alanine mutations of the charged surface residues (Lys102, Lys133 and Glu202) is highly amenable to crystallization. The structure of the mutant RAD52(1-212) was solved at 2.4 Å resolution. The structure revealed an association between the symmetry-related RAD52(1-212) rings, in which a partially unfolded, C-terminal region of RAD52 extended into the DNA-binding groove of the neighbouring ring in the crystal. The alanine mutations probably reduced the surface entropy of the RAD52(1-212) ring and stabilized the ring-ring association observed in the crystal.
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Affiliation(s)
- Mika Saotome
- Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan
| | - Kengo Saito
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Keiichi Onodera
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Wataru Kagawa
- Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan
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15
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Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB. Proc Natl Acad Sci U S A 2016; 113:4308-13. [PMID: 27044084 DOI: 10.1073/pnas.1520847113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand complementarity. DdrB promotes high-fidelity annealing by constraining specific bases from unauthorized association and only releases annealed duplex when bound strands are fully complementary. To our knowledge, this mechanism provides the first understanding for how cells achieve accurate, protein-assisted strand annealing under biological conditions that would otherwise favor misannealing.
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16
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Durisova K, Salovska B, Pejchal J, Tichy A. Chemical inhibition of DNA repair kinases as a promising tool in oncology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2016; 160:11-9. [DOI: 10.5507/bp.2015.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 09/10/2015] [Indexed: 11/23/2022] Open
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17
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Smith CE, Bell CE. Domain Structure of the Redβ Single-Strand Annealing Protein: the C-terminal Domain is Required for Fine-Tuning DNA-binding Properties, Interaction with the Exonuclease Partner, and Recombination in vivo. J Mol Biol 2016; 428:561-578. [PMID: 26780547 DOI: 10.1016/j.jmb.2016.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/19/2015] [Accepted: 01/12/2016] [Indexed: 11/28/2022]
Abstract
Redβ is a component of the Red recombination system of bacteriophage λ that promotes a single strand annealing (SSA) reaction to generate end-to-end concatemers of the phage genome for packaging. Redβ interacts with λ exonuclease (λexo), the other component of the Red system, to form a "synaptosome" complex that somehow integrates the end resection and annealing steps of the reaction. Previous work using limited proteolysis and chemical modification revealed that Redβ consists of an N-terminal DNA binding domain, residues 1-177, and a flexible C-terminal "tail", residues 178-261. Here, we quantitatively compare the binding of the full-length protein (Redβ(FL)) and the N-terminal domain (Redβ(177)) to different lengths of ssDNA substrate and annealed duplex product. We find that in general, Redβ(FL) binds more tightly to annealed duplex product than to ssDNA substrate, while Redβ(177) binds more tightly to ssDNA. In addition, the C-terminal region of Redβ corresponding to residues 182-261 was purified and found to fold into an α-helical domain that is required for the interaction with λexo to form the synaptosome complex. Deletion analysis of Redβ revealed that removal of just eleven residues from the C-terminus disrupts the interaction with λexo as well as ssDNA and dsDNA recombination in vivo. By contrast, the determinants for self-oligomerization of Redβ appear to reside solely within the N-terminal domain. The subtle but significant differences in the relative binding of Redβ(FL) and Redβ(177) to ssDNA substrate and annealed duplex product may be important for Redβ to function as a SSA protein in vivo.
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Affiliation(s)
- Christopher E Smith
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210.
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18
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Rajavel M, Mullins MR, Taylor DJ. Multiple facets of TPP1 in telomere maintenance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1550-9. [PMID: 24780581 DOI: 10.1016/j.bbapap.2014.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/01/2014] [Accepted: 04/18/2014] [Indexed: 11/30/2022]
Abstract
Telomeres are nucleoprotein complexes that cap the ends of all linear chromosomes and function to prevent aberrant repair and end-to-end chromosome fusions. In somatic cells, telomere shortening is a natural part of the aging process as it occurs with each round of cell division. In germ and stem cells, however, the enzyme telomerase synthesizes telomere DNA to counter-balance telomere shortening and help maintain cellular proliferation. Of the primary telomere end-binding proteins, TPP1 has recently emerged as a primary contributor in protecting telomere DNA and in recruiting telomerase to the telomere ends. In this review, we summarize the current knowledge regarding the role of TPP1 in telomere maintenance.
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Affiliation(s)
- Malligarjunan Rajavel
- Department of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland OH 44106, USA
| | - Michael R Mullins
- Department of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland OH 44106, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland OH 44106, USA; Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland OH 44106, USA.
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19
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Azad GK, Singh V, Tomar RS. Assessment of the biological pathways targeted by isocyanate using N-succinimidyl N-methylcarbamate in budding yeast Saccharomyces cerevisiae. PLoS One 2014; 9:e92993. [PMID: 24664350 PMCID: PMC3963962 DOI: 10.1371/journal.pone.0092993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/27/2014] [Indexed: 02/05/2023] Open
Abstract
Isocyanates, a group of low molecular weight aromatic and aliphatic compounds possesses the functional isocyanate group. They are highly toxic in nature hence; we used N-succinimidyl N-methylcarbamate (NSNM), a surrogate chemical containing a functional isocyanate group to understand the mode of action of this class of compounds. We employed budding yeast Saccharomyces cerevisiae as a model organism to study the pathways targeted by NSNM. Our screening with yeast mutants revealed that it affects chromatin, DNA damage response, protein-ubiquitylation and chaperones, oxidative stress, TOR pathway and DNA repair processes. We also show that NSNM acts as an epigenetic modifier as its treatment causes reduction in global histone acetylation and formation of histone adducts. Cells treated with NSNM exhibited increase in mitochondrial membrane potential as well as intracellular ROS levels and the effects were rescued by addition of reduced glutathione to the medium. We also report that deletion of SOD1 and SOD2, the superoxide dismutase in Saccharomyces cerevisiae displayed hypersensitivity to NSNM. Furthermore, NSNM treatment causes rapid depletion of total glutathione and reduced glutathione. We also demonstrated that NSNM induces degradation of Sml1, a ribonucleotide reductase inhibitor involved in regulating dNTPs production. In summary, we define the various biological pathways targeted by isocyanates.
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Affiliation(s)
- Gajendra Kumar Azad
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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20
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Anti-cancer drug KP1019 modulates epigenetics and induces DNA damage response inSaccharomyces cerevisiae. FEBS Lett 2014; 588:1044-52. [DOI: 10.1016/j.febslet.2014.02.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 01/28/2014] [Accepted: 02/05/2014] [Indexed: 12/11/2022]
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21
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Ruff P, Koh KD, Keskin H, Pai RB, Storici F. Aptamer-guided gene targeting in yeast and human cells. Nucleic Acids Res 2014; 42:e61. [PMID: 24500205 PMCID: PMC3985672 DOI: 10.1093/nar/gku101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Gene targeting is a genetic technique to modify an endogenous DNA sequence in its genomic location via homologous recombination (HR) and is useful both for functional analysis and gene therapy applications. HR is inefficient in most organisms and cell types, including mammalian cells, often limiting the effectiveness of gene targeting. Therefore, increasing HR efficiency remains a major challenge to DNA editing. Here, we present a new concept for gene correction based on the development of DNA aptamers capable of binding to a site-specific DNA binding protein to facilitate the exchange of homologous genetic information between a donor molecule and the desired target locus (aptamer-guided gene targeting). We selected DNA aptamers to the I-SceI endonuclease. Bifunctional oligonucleotides containing an I-SceI aptamer sequence were designed as part of a longer single-stranded DNA molecule that contained a region with homology to repair an I-SceI generated double-strand break and correct a disrupted gene. The I-SceI aptamer-containing oligonucleotides stimulated gene targeting up to 32-fold in yeast Saccharomyces cerevisiae and up to 16-fold in human cells. This work provides a novel concept and research direction to increase gene targeting efficiency and lays the groundwork for future studies using aptamers for gene targeting.
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Affiliation(s)
- Patrick Ruff
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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22
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Amunugama R, Fishel R. Homologous Recombination in Eukaryotes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:155-206. [DOI: 10.1016/b978-0-12-387665-2.00007-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Scaltriti E, Launay H, Genois MM, Bron P, Rivetti C, Grolli S, Ploquin M, Campanacci V, Tegoni M, Cambillau C, Moineau S, Masson JY. Lactococcal phage p2 ORF35-Sak3 is an ATPase involved in DNA recombination and AbiK mechanism. Mol Microbiol 2011; 80:102-16. [PMID: 21276096 DOI: 10.1111/j.1365-2958.2011.07561.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Virulent phages of the Siphoviridae family are responsible for milk fermentation failures worldwide. Here, we report the characterization of the product of the early expressed gene orf35 from Lactococcus lactis phage p2 (936 group). ORF35(p2), also named Sak3, is involved in the sensitivity of phage p2 to the antiviral abortive infection mechanism AbiK. The localization of its gene upstream of a gene coding for a single-strand binding protein as well as its membership to a superfamily of single-strand annealing proteins (SSAPs) suggested a possible role in homologous recombination. Electron microscopy showed that purified ORF35(p2) form a hexameric ring-like structure that is often found in proteins with a conserved RecA nucleotide-binding core. Gel shift assays and surface plasmon resonance data demonstrated that ORF35(p2) interacts preferentially with single-stranded DNA with nanomolar affinity. Atomic force microscopy showed also that it preferentially binds to sticky DNA substrates over blunt ends. In addition, in vitro assays demonstrated that ORF35(p2) is able to anneal complementary strands. Sak3 also stimulates Escherichia coli RecA-mediated homologous recombination. Remarkably, Sak3 was shown to possess an ATPase activity that is required for RecA stimulation. Collectively, our results demonstrate that ORF35(p2) is a novel SSAP stimulating homologous recombination.
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Affiliation(s)
- Erika Scaltriti
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, case 932, 13288 Marseille cedex 09, France
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24
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Grimme JM, Spies M. FRET-based assays to monitor DNA binding and annealing by Rad52 recombination mediator protein. Methods Mol Biol 2011; 745:463-483. [PMID: 21660711 DOI: 10.1007/978-1-61779-129-1_27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
During homologous recombination and homology-directed repair of broken chromosomes, proteins that mediate and oppose recombination form dynamic complexes on damaged DNA. Quantitative analysis of these nucleoprotein assemblies requires a robust signal, which reports on the association of a recombination mediator with its substrate and on the state of substrate DNA within the complex. Eukaryotic Rad52 protein mediates recombination, repair, and restart of collapsed replication forks by facilitating replacement of ssDNA binding protein replication protein A (RPA) with Rad51 recombinase and by mediating annealing of two complementary DNA strands protected by RPA. The characteristic binding mode whereby ssDNA is wrapped around the Rad52 ring allowed us to develop robust and sensitive FRET-based assays for monitoring Rad52 interactions with protein-free DNA and ssDNA-RPA complexes. By reporting on the configuration of ssDNA dually labeled with Cy3 and Cy5 fluorescent dyes, solution-based FRET is used to analyze Rad52-RPA-DNA interactions under equilibrium binding conditions. Finally, FRET between Cy3 and Cy5 dyes incorporated into two homologous ssDNA molecules can be used to analyze interplay between Rad52-mediated DNA strand annealing and duplex DNA destabilization by RPA.
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Affiliation(s)
- Jill M Grimme
- US Army Engineer Research Development Center, Construction Engineering Research Laboratory, Champaign, IL 61822, USA.
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25
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Altmannova V, Eckert-Boulet N, Arneric M, Kolesar P, Chaloupkova R, Damborsky J, Sung P, Zhao X, Lisby M, Krejci L. Rad52 SUMOylation affects the efficiency of the DNA repair. Nucleic Acids Res 2010; 38:4708-21. [PMID: 20371517 PMCID: PMC2919706 DOI: 10.1093/nar/gkq195] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Homologous recombination (HR) plays a vital role in DNA metabolic processes including meiosis, DNA repair, DNA replication and rDNA homeostasis. HR defects can lead to pathological outcomes, including genetic diseases and cancer. Recent studies suggest that the post-translational modification by the small ubiquitin-like modifier (SUMO) protein plays an important role in mitotic and meiotic recombination. However, the precise role of SUMOylation during recombination is still unclear. Here, we characterize the effect of SUMOylation on the biochemical properties of the Saccharomyces cerevisiae recombination mediator protein Rad52. Interestingly, Rad52 SUMOylation is enhanced by single-stranded DNA, and we show that SUMOylation of Rad52 also inhibits its DNA binding and annealing activities. The biochemical effects of SUMO modification in vitro are accompanied by a shorter duration of spontaneous Rad52 foci in vivo and a shift in spontaneous mitotic recombination from single-strand annealing to gene conversion events in the SUMO-deficient Rad52 mutants. Taken together, our results highlight the importance of Rad52 SUMOylation as part of a 'quality control' mechanism regulating the efficiency of recombination and DNA repair.
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Affiliation(s)
- Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nadine Eckert-Boulet
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Milica Arneric
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter Kolesar
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Radka Chaloupkova
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiri Damborsky
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaolan Zhao
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael Lisby
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, 625 00 Brno, National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark, Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Loschmidt Laboratories, Institute of Experimental Biology, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA,*To whom correspondence should be addressed. Tel: +420 549493767; Fax: +420 549492556;
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26
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Grimme JM, Honda M, Wright R, Okuno Y, Rothenberg E, Mazin AV, Ha T, Spies M. Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes. Nucleic Acids Res 2010; 38:2917-30. [PMID: 20081207 PMCID: PMC2875008 DOI: 10.1093/nar/gkp1249] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Rad52 promotes the annealing of complementary strands of DNA bound by replication protein A (RPA) during discrete repair pathways. Here, we used a fluorescence resonance energy transfer (FRET) between two fluorescent dyes incorporated into DNA substrates to probe the mechanism by which human Rad52 (hRad52) interacts with and mediates annealing of ssDNA–hRPA complexes. Human Rad52 bound ssDNA or ssDNA–hRPA complex in two, concentration-dependent modes. At low hRad52 concentrations, ssDNA was wrapped around the circumference of the protein ring, while at higher protein concentrations, ssDNA was stretched between multiple hRad52 rings. Annealing by hRad52 occurred most efficiently when each complementary DNA strand or each ssDNA–hRPA complex was bound by hRad52 in a wrapped configuration, suggesting homology search and annealing occur via two hRad52–ssDNA complexes. In contrast to the wild type protein, hRad52RQK/AAA and hRad521–212 mutants with impaired ability to bind hRPA protein competed with hRPA for binding to ssDNA and failed to counteract hRPA-mediated duplex destabilization highlighting the importance of hRad52-hRPA interactions in promoting efficient DNA annealing.
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Affiliation(s)
- Jill M Grimme
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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27
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Deng X, Prakash A, Dhar K, Baia GS, Kolar C, Oakley GG, Borgstahl GEO. Human replication protein A-Rad52-single-stranded DNA complex: stoichiometry and evidence for strand transfer regulation by phosphorylation. Biochemistry 2009; 48:6633-43. [PMID: 19530647 PMCID: PMC2710861 DOI: 10.1021/bi900564k] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The eukaryotic single-stranded DNA-binding protein, replication protein A (RPA), is essential in DNA metabolism and is phosphorylated in response to DNA-damaging agents. Rad52 and RPA participate in the repair of double-stranded DNA breaks (DSBs). It is known that human RPA and Rad52 form a complex, but the molecular mass, stoichiometry, and exact role of this complex in DSB repair are unclear. In this study, absolute molecular masses of individual proteins and complexes were measured in solution using analytical size-exclusion chromatography coupled with multiangle light scattering, the protein species present in each purified fraction were verified via sodium dodecyl sulfate−polyacrylamide gel electrophoresis (SDS−PAGE)/Western analyses, and the presence of biotinylated ssDNA in the complexes was verified by chemiluminescence detection. Then, employing UV cross-linking, the protein partner holding the ssDNA was identified. These data show that phosphorylated RPA promoted formation of a complex with monomeric Rad52 and caused the transfer of ssDNA from RPA to Rad52. This suggests that RPA phosphorylation may regulate the first steps of DSB repair and is necessary for the mediator function of Rad52.
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Affiliation(s)
- Xiaoyi Deng
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA
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28
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Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes. Proc Natl Acad Sci U S A 2008; 105:20274-9. [PMID: 19074292 DOI: 10.1073/pnas.0810317106] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The Rad52 protein has critical functions in distinct pathways of the homology-directed DNA repair, one of which is to promote the annealing of complementary strands of DNA. Both yeast and human Rad52 proteins organize into ring-shaped oligomers with the predominant form being a heptamer. Despite the wealth of information obtained in previous investigations, how Rad52 mediates homology search and annealing remains unclear. Here, we developed single-molecule fluorescence resonance energy transfer approaches to probe hRad52-mediated DNA annealing events in real time. We found that annealing proceeds in successive steps involving rearrangements of the ssDNA-hRad52 complex. Moreover, after initial pairing, further search for extended homology occurs without dissociation. This search process is driven by an interaction between 2 overlapping nucleoprotein complexes. In light of these observations we propose a model for hRad52-mediated DNA annealing where ssDNA release and dsDNA zippering are coordinated through successive rearrangement of overlapping nucleoprotein complexes.
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29
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Abstract
Homologous recombination (HR) serves to eliminate deleterious lesions, such as double-stranded breaks and interstrand crosslinks, from chromosomes. HR is also critical for the preservation of replication forks, for telomere maintenance, and chromosome segregation in meiosis I. As such, HR is indispensable for the maintenance of genome integrity and the avoidance of cancers in humans. The HR reaction is mediated by a conserved class of enzymes termed recombinases. Two recombinases, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cells via a filamentous intermediate on ssDNA called the presynaptic filament. The assembly of the presynaptic filament is a rate-limiting process that is enhanced by recombination mediators, such as the breast tumor suppressor BRCA2. HR accessory factors that facilitate other stages of the Rad51- and Dmc1-catalyzed homologous DNA pairing and strand exchange reaction have also been identified. Recent progress on elucidating the mechanisms of action of Rad51 and Dmc1 and their cohorts of ancillary factors is reviewed here.
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Affiliation(s)
- Joseph San Filippo
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
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30
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Ploquin M, Bransi A, Paquet ER, Stasiak AZ, Stasiak A, Yu X, Cieslinska AM, Egelman EH, Moineau S, Masson JY. Functional and structural basis for a bacteriophage homolog of human RAD52. Curr Biol 2008; 18:1142-6. [PMID: 18656357 DOI: 10.1016/j.cub.2008.06.071] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 06/24/2008] [Accepted: 06/26/2008] [Indexed: 10/21/2022]
Abstract
In eukaryotes, homologous recombination proteins such as RAD51 and RAD52 play crucial roles in DNA repair and genome stability. Human RAD52 is a member of a large single-strand annealing protein (SSAP) family [1] and stimulates Rad51-dependent recombination [2, 3]. In prokaryotes and phages, it has been difficult to establish the presence of RAD52 homologs with conserved sequences. Putative SSAPs were recently found in several phages that infect strains of Lactococcus lactis[4]. One of these SSAPs was identified as Sak and was found in the virulent L. lactis phage ul36, which belongs to the Siphoviridae family [4, 5]. In this study, we show that Sak is homologous to the N terminus of human RAD52. Purified Sak binds single-stranded DNA (ssDNA) preferentially over double-stranded DNA (dsDNA) and promotes the renaturation of long complementary ssDNAs. Sak also binds RecA and stimulates homologous recombination reactions. Mutations shown to modulate RAD52 DNA binding [6] affect Sak similarly. Remarkably, electron-microscopic reconstruction of Sak reveals an undecameric (11) subunit ring, similar to the crystal structure of the N-terminal fragment of human RAD52 [7, 8]. For the first time, we propose a viral homolog of RAD52 at the amino acid, phylogenic, functional, and structural levels.
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Affiliation(s)
- Mickaël Ploquin
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, 9 McMahon, Québec City G1R 2J6, Canada
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31
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Kagawa W, Kagawa A, Saito K, Ikawa S, Shibata T, Kurumizaka H, Yokoyama S. Identification of a second DNA binding site in the human Rad52 protein. J Biol Chem 2008; 283:24264-73. [PMID: 18593704 DOI: 10.1074/jbc.m802204200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rad52 plays essential roles in homology-dependent double-strand break repair. Various studies have established the functions of Rad52 in Rad51-dependent and Rad51-independent repair processes. However, the precise molecular mechanisms of Rad52 in these processes remain unknown. In the present study we have identified a novel DNA binding site within Rad52 by a structure-based alanine scan mutagenesis. This site is closely aligned with the putative single-stranded DNA binding site determined previously. Mutations in this site impaired the ability of the Rad52-single-stranded DNA complex to form a ternary complex with double-stranded DNA and subsequently catalyze the formation of D-loops. We found that Rad52 introduces positive supercoils into double-stranded DNA and that the second DNA binding site is essential for this activity. Our findings suggest that Rad52 aligns two recombining DNA molecules within the first and second DNA binding sites to stimulate the homology search and strand invasion processes.
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Affiliation(s)
- Wataru Kagawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Japan
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32
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McIlwraith MJ, West SC. DNA repair synthesis facilitates RAD52-mediated second-end capture during DSB repair. Mol Cell 2008; 29:510-6. [PMID: 18313388 DOI: 10.1016/j.molcel.2007.11.037] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 09/27/2007] [Accepted: 11/05/2007] [Indexed: 11/27/2022]
Abstract
Homologous recombination (HR) is essential for the repair of DNA double-strand breaks (DSBs) in mitotic and meiotic cells. HR occurs through a series of steps involving DSB resection, invasion of single-stranded DNA into homologous duplex DNA to form a D loop, repair synthesis, and second-end capture. We show that DNA repair synthesis, catalyzed by human DNA polymerase eta (poleta) acting upon the priming strand of a D loop, leads to capture and annealing of the second end of a resected DSB in reactions mediated by RAD52 protein. Second-end capture products were not detected when poleta was replaced by other polymerases such as poldelta or poliota. RAD52 could not be replaced by RAD51. We also found that the RAD52-dependent reaction was stimulated by the single-strand binding protein RPA, but not by E. coli SSB. Following repair synthesis and second-end capture, de novo DNA synthesis was observed from the captured second DNA end.
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Affiliation(s)
- Michael J McIlwraith
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
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33
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de Vries FAT, Zonneveld JBM, de Groot AJ, Koning RI, van Zeeland AA, Pastink A. Schizosaccharomyces pombe Rad22A and Rad22B have similar biochemical properties and form multimeric structures. Mutat Res 2006; 615:143-52. [PMID: 17208257 DOI: 10.1016/j.mrfmmm.2006.11.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 11/10/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
The Saccharomyces cerevisiae Rad52 protein has a crucial role in the repair of DNA double-strand breaks by homologous recombination. In vitro, Rad52 displays DNA binding and strand annealing activities and promotes Rad51-mediated strand exchange. Schizosaccharomyces pombe has two Rad52 homologues, Rad22A and Rad22B. Whereas rad22A deficient strains exhibit severe defects in repair and recombination, rad22B mutants have a much less severe phenotype. To better understand the role of Rad22A and Rad22B in double-strand break repair, both proteins were purified to near homogeneity. Using gel retardation and filter binding assays, binding of Rad22A and Rad22B to short single-stranded DNAs was demonstrated. Binding of Rad22A to double-stranded oligonucleotides or linearized plasmid molecules containing blunt ends or short single-stranded overhangs could not be detected. Rad22B also does not bind efficiently to short duplex oligonucleotides but binds readily to DNA fragments containing 3'-overhangs. Rad22A as well as Rad22B efficiently promote annealing of complementary single-stranded DNAs. In the presence of Rad22A annealing of complementary DNAs is almost 90%. Whereas in reactions containing Rad22B the maximum level of annealing is 60%, most likely due to inhibition of the reaction by duplex DNA. Gel-filtration experiments and electron microscopic analyses indicate self-association of Rad22A and Rad22B and the formation of multimeric structures as has been observed for Rad52 in yeast and man.
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Affiliation(s)
- Femke A T de Vries
- Department of Toxicogenetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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34
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Kantidze OL, Razin SV. Chemotherapy-related secondary leukemias: A role for DNA repair by error-prone non-homologous end joining in topoisomerase II - Induced chromosomal rearrangements. Gene 2006; 391:76-9. [PMID: 17234368 DOI: 10.1016/j.gene.2006.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 12/08/2006] [Accepted: 12/08/2006] [Indexed: 11/22/2022]
Abstract
Chromosome rearrangements are believed to cause the secondary leukemias which constitute frequent complications of antitumor chemotherapy with topoisomerase II-specific drugs. Here we show that inhibition of DNA topoisomerase II in cultured cells stimulates association of components of the non-homologous end joining system with a known breakpoint cluster region of the human AML1 gene, suggesting that errors of DNA repair during NHEJ may be the cause of illegitimate recombination in cells treated with topoisomerase II poisons.
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Affiliation(s)
- Omar L Kantidze
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, 34/5 Vavilov Street, 119334 Moscow, Russia
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35
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Hamimes S, Bourgeon D, Stasiak AZ, Stasiak A, Van Dyck E. Nucleic acid-binding properties of the RRM-containing protein RDM1. Biochem Biophys Res Commun 2006; 344:87-94. [PMID: 16630539 DOI: 10.1016/j.bbrc.2006.03.154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Accepted: 03/21/2006] [Indexed: 11/30/2022]
Abstract
RDM1 (RAD52 Motif 1) is a vertebrate protein involved in the cellular response to the anti-cancer drug cisplatin. In addition to an RNA recognition motif, RDM1 contains a small amino acid motif, named RD motif, which it shares with the recombination and repair protein, RAD52. RDM1 binds to single- and double-stranded DNA, and recognizes DNA distortions induced by cisplatin adducts in vitro. Here, we have performed an in-depth analysis of the nucleic acid-binding properties of RDM1 using gel-shift assays and electron microscopy. We show that RDM1 possesses acidic pH-dependent DNA-binding activity and that it binds RNA as well as DNA, and we present evidence from competition gel-shift experiments that RDM1 may be capable of discrimination between the two nucleic acids. Based on reported studies of RAD52, we have generated an RDM1 variant mutated in its RD motif. We find that the L119GF --> AAA mutation affects the mode of RDM1 binding to single-stranded DNA.
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Affiliation(s)
- Samia Hamimes
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon, France
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36
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Vagin DA, Bashkirov VI, Khasanov FK. Analysis of mutations in the mat1 region of Schizosaccharomyces pombe strain with the deletion of gene rhp55
+. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Hamimes S, Arakawa H, Stasiak AZ, Kierzek AM, Hirano S, Yang YG, Takata M, Stasiak A, Buerstedde JM, Van Dyck E. RDM1, a Novel RNA Recognition Motif (RRM)-containing Protein Involved in the Cell Response to Cisplatin in Vertebrates. J Biol Chem 2005; 280:9225-35. [PMID: 15611051 DOI: 10.1074/jbc.m412874200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A variety of cellular proteins has the ability to recognize DNA lesions induced by the anti-cancer drug cisplatin, with diverse consequences on their repair and on the therapeutic effectiveness of this drug. We report a novel gene involved in the cell response to cisplatin in vertebrates. The RDM1 gene (for RAD52 Motif 1) was identified while searching databases for sequences showing similarities to RAD52, a protein involved in homologous recombination and DNA double-strand break repair. Ablation of RDM1 in the chicken B cell line DT40 led to a more than 3-fold increase in sensitivity to cisplatin. However, RDM1-/- cells were not hypersensitive to DNA damages caused by ionizing radiation, UV irradiation, or the alkylating agent methylmethane sulfonate. The RDM1 protein displays a nucleic acid binding domain of the RNA recognition motif (RRM) type. By using gel-shift assays and electron microscopy, we show that purified, recombinant chicken RDM1 protein interacts with single-stranded DNA as well as double-stranded DNA, on which it assembles filament-like structures. Notably, RDM1 recognizes DNA distortions induced by cisplatin-DNA adducts in vitro. Finally, human RDM1 transcripts are abundant in the testis, suggesting a possible role during spermatogenesis.
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Affiliation(s)
- Samia Hamimes
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon, France
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38
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Lloyd JA, McGrew DA, Knight KL. Identification of Residues Important for DNA Binding in the Full-length Human Rad52 Protein. J Mol Biol 2005; 345:239-49. [PMID: 15571718 DOI: 10.1016/j.jmb.2004.10.065] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 10/21/2004] [Accepted: 10/21/2004] [Indexed: 01/08/2023]
Abstract
Human Rad52 (HsRad52) is a DNA-binding protein (418 residues) that promotes the catalysis of DNA double strand break repair by the Rad51 recombinase. HsRad52 self-associates to form ring-shaped oligomers as well as higher order complexes of these rings. Analysis of the structural and functional organization of protein domains suggests that many of the determinants of DNA binding lie within the N-terminal 85 residues. Crystal structures of two truncation mutants, HsRad52(1-212) and HsRad52(1-209) support the idea that this region makes up an important part of the DNA binding domain. Here, we report the results of saturating alanine scanning mutagenesis of the N-terminal domain of full-length HsRad52 in which we identify residues that are likely involved in direct contact with single-stranded DNA (ssDNA). Our results largely agree with the position of side-chains seen in the crystal structures but also suggest that certain DNA binding and cross-subunit interactions differ between the 11 subunit ring in the crystal structures of the truncation mutant proteins versus the seven subunit ring formed by full-length HsRad52.
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Affiliation(s)
- Janice A Lloyd
- Department of Biochemistry and Molecular Pharmacology, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA
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39
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Tsukamoto M, Yamashita K, Miyazaki T, Shinohara M, Shinohara A. The N-terminal DNA-binding domain of Rad52 promotes RAD51-independent recombination in Saccharomyces cerevisiae. Genetics 2004; 165:1703-15. [PMID: 14704160 PMCID: PMC1462901 DOI: 10.1093/genetics/165.4.1703] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In Saccharomyces cerevisiae, the Rad52 protein plays a role in both RAD51-dependent and RAD51-independent recombination pathways. We characterized a rad52 mutant, rad52-329, which lacks the C-terminal Rad51-interacting domain, and studied its role in RAD51-independent recombination. The rad52-329 mutant is completely defective in mating-type switching, but partially proficient in recombination between inverted repeats. We also analyzed the effect of the rad52-329 mutant on telomere recombination. Yeast cells lacking telomerase maintain telomere length by recombination. The rad52-329 mutant is deficient in RAD51-dependent telomere recombination, but is proficient in RAD51-independent telomere recombination. In addition, we examined the roles of other recombination genes in the telomere recombination. The RAD51-independent recombination in the rad52-329 mutant is promoted by a paralogue of Rad52, Rad59. All components of the Rad50-Mre11-Xrs2 complex are also important, but not essential, for RAD51-independent telomere recombination. Interestingly, RAD51 inhibits the RAD51-independent, RAD52-dependent telomere recombination. These findings indicate that Rad52 itself, and more precisely its N-terminal DNA-binding domain, promote an essential reaction in recombination in the absence of RAD51.
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Affiliation(s)
- Mariko Tsukamoto
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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40
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Kumar JK, Gupta RC. Strand exchange activity of human recombination protein Rad52. Proc Natl Acad Sci U S A 2004; 101:9562-7. [PMID: 15205484 PMCID: PMC470714 DOI: 10.1073/pnas.0403416101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Repair of double-strand breaks is essential for the maintenance of genome integrity and cell survival. In eukaryotes, double-strand-break repair by homologous recombination requires the Rad52 group of proteins. Human Rad52 protein (HsRad52)-mediated annealing of complementary strands has been studied in detail, but little has been reported on the recombinase activities of HsRad52. For this study, we purified HsRad52 from Escherichia coli. DNase I protection experiments indicated that HsRad52 binds preferentially to single-stranded DNA and protects it against digestion by DNase I. HsRad52 catalyzed D-loop formation in superhelical DNA, as well as strand exchange among oligonucleotide substrates. The formation of a stoichiometric complex between HsRad52 and single-stranded DNA was found to be critical for strand exchange activity, and the coating of both the single- and double-stranded oligonucleotides inhibited the exchange reaction.
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Affiliation(s)
- Jaspal K Kumar
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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41
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Navadgi VM, Dutta A, Rao BJ. Human Rad52 facilitates a three-stranded pairing that follows no strand exchange: a novel pairing function of the protein. Biochemistry 2004; 42:15237-51. [PMID: 14690434 DOI: 10.1021/bi0350452] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human Rad52 protein, by analogy with the genetics of yeast Rad52, is believed to mediate a pathway of homologous recombination even independent of Rad51. Current study is focused on unraveling the molecular properties of hRad52 that endow the protein such an ability. We show here that the hRad52 protein binds single-stranded DNA (ssDNA) as well as 3'- and 5'-tailed duplexes severalfold better than blunt-ended duplexes, altering the sensitivity of the bound DNA to the action of DNase I. Protein binding is sensitive to the length of the ssDNA: targets as short as a 33mer poorly bind the protein, whereas that of a 61mer and above bind the protein stably well. Such stable ssDNA-hRad52 complexes are highly competent in mediating not only the annealing of two complementary strands but also three-stranded pairing. The latter involves homologous recognition of linear duplex DNA by the ssDNA-hRad52 complex. We show that the hRad52 protein facilitates homologous recognition between ssDNA and duplex-DNA through a process that involves unwinding or transient unpairing of the interacting duplex via a novel three-stranded intermediate that does not lead to strand exchange. The results enable us to visualize a novel role for hRad52 that may model its function in a pathway requiring no hRad51.
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Affiliation(s)
- Vasundhara M Navadgi
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai- 400 005, India
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42
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Miyazaki T, Bressan DA, Shinohara M, Haber JE, Shinohara A. In vivo assembly and disassembly of Rad51 and Rad52 complexes during double-strand break repair. EMBO J 2004; 23:939-49. [PMID: 14765116 PMCID: PMC380999 DOI: 10.1038/sj.emboj.7600091] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 01/05/2004] [Indexed: 01/09/2023] Open
Abstract
Assembly and disassembly of Rad51 and Rad52 complexes were monitored by immunofluorescence during homologous recombination initiated by an HO endonuclease-induced double-strand break (DSB) at the MAT locus. DSB-induced Rad51 and Rad52 foci colocalize with a TetR-GFP focus at tetO sequences adjacent to MAT. In strains in which HO cleaves three sites on chromosome III, we observe three distinct foci that colocalize with adjacent GFP chromosome marks. We compared the kinetics of focus formation with recombination intermediates and products when HO-cleaved MATalpha recombines with the donor, MATa. Rad51 assembly occurs 1 h after HO cleavage. Rad51 disassembly occurs at the same time that new DNA synthesis is initiated after single-stranded (ss) MAT DNA invades MATa. We present evidence for three distinct roles for Rad52 in recombination: a presynaptic role necessary for Rad51 assembly, a synaptic role with Rad51 filaments, and a postsynaptic role after Rad51 dissociates. Additional biochemical studies suggest the presence of an ssDNA complex containing both Rad51 and Rad52.
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Affiliation(s)
- Toshiko Miyazaki
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | | | - Miki Shinohara
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - James E Haber
- Rosenstiel Center, Brandeis University, Waltham, MA, USA
| | - Akira Shinohara
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
- PRESTO, Japanese Science Technology Agency, Kawaguchi, Saitama, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. Tel.: +81 6879 8624; Fax: +81 6879 8626; E-mail:
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43
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Ristic D, Modesti M, Kanaar R, Wyman C. Rad52 and Ku bind to different DNA structures produced early in double-strand break repair. Nucleic Acids Res 2003; 31:5229-37. [PMID: 12954758 PMCID: PMC203314 DOI: 10.1093/nar/gkg729] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks are repaired by one of two main pathways, non-homologous end joining or homologous recombination. A competition for binding to DNA ends by Ku and Rad52, proteins required for non-homologous end joining and homologous recombination, respectively, has been proposed to determine the choice of repair pathway. In order to test this idea directly, we compared Ku and human Rad52 binding to different DNA substrates. How ever, we found no evidence that these proteins would compete for binding to the same broken DNA ends. Ku bound preferentially to DNA with free ends. Under the same conditions, Rad52 did not bind preferentially to DNA ends. Using a series of defined substrates we showed that it is single-stranded DNA and not DNA ends that were preferentially bound by Rad52. In addition, Rad52 aggregated DNA, bringing different single-stranded DNAs in close proximity. This activity was independent of the presence of DNA ends and of the ability of the single-stranded sequences to form extensive base pairs. Based on these DNA binding characteristics it is unlikely that Rad52 and Ku compete as 'gatekeepers' of different DNA double-strand break repair pathways. Rather, they interact with different DNA substrates produced early in DNA double-strand break repair.
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Affiliation(s)
- Dejan Ristic
- Department of Cell Biology and Genetics, Erasmus MC, The Netherlands
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44
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Sugawara N, Wang X, Haber JE. In vivo roles of Rad52, Rad54, and Rad55 proteins in Rad51-mediated recombination. Mol Cell 2003; 12:209-19. [PMID: 12887906 DOI: 10.1016/s1097-2765(03)00269-7] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Repairing a double-strand break by homologous recombination requires binding of the strand exchange protein Rad51p to ssDNA, followed by synapsis with a homologous donor. Here we used chromatin immunoprecipitation to monitor the in vivo association of Saccharomyces cerevisiae Rad51p with both the cleaved MATa locus and the HML alpha donor. Localization of Rad51p to MAT precedes its association with HML, providing evidence of the time needed for the Rad51 filament to search the genome for a homologous sequence. Rad51p binding to ssDNA requires Rad52p. The absence of Rad55p delays Rad51p binding to ssDNA and prevents strand invasion and localization of Rad51p to HML alpha. Lack of Rad54p does not significantly impair Rad51p recruitment to MAT or its initial association with HML alpha; however, Rad54p is required at or before the initiation of DNA synthesis after synapsis has occurred at the 3' end of the invading strand.
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Affiliation(s)
- Neal Sugawara
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA
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45
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Abstract
The efficient repair of double-strand breaks in DNA is critical for the maintenance of genome stability and cell survival. Homologous recombination provides an efficient and faithful pathway of repair, especially in replicating cells, in which it plays a major role in tumour avoidance. Many of the enzymes that are involved in recombination have been isolated, and the details of this pathway are now being unravelled at the molecular level.
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Affiliation(s)
- Stephen C West
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK.
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46
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Abstract
Cancer develops when cells no longer follow their normal pattern of controlled growth. In the absence or disregard of such regulation, resulting from changes in their genetic makeup, these errant cells acquire a growth advantage, expanding into precancerous clones. Over the past decade many studies have revealed the relevance of genomic mutation in this process, be it by misreplication, environmental damage, or a deficiency in repairing endogenous and exogenous damage. Here we discuss the possibility of homologous recombination as an errant DNA repair mechanism that can result in loss of heterozygosity or genetic rearrangements. Some of these genetic alterations may play a primary role in carcinogenesis, but they are more likely to be involved in secondary and subsequent steps of carcinogenesis by which recessive oncogenic mutations are revealed. Patients, whose cells display an increased frequency of recombination, also have an elevated frequency of cancer, further supporting the link between recombination and carcinogenesis.
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47
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Symington LS. Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair. Microbiol Mol Biol Rev 2002; 66:630-70, table of contents. [PMID: 12456786 PMCID: PMC134659 DOI: 10.1128/mmbr.66.4.630-670.2002] [Citation(s) in RCA: 790] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The process of homologous recombination is a major DNA repair pathway that operates on DNA double-strand breaks, and possibly other kinds of DNA lesions, to promote error-free repair. Central to the process of homologous recombination are the RAD52 group genes (RAD50, RAD51, RAD52, RAD54, RDH54/TID1, RAD55, RAD57, RAD59, MRE11, and XRS2), most of which were identified by their requirement for the repair of ionizing-radiation-induced DNA damage in Saccharomyces cerevisiae. The Rad52 group proteins are highly conserved among eukaryotes, and Rad51, Mre11, and Rad50 are also conserved in prokaryotes and archaea. Recent studies showing defects in homologous recombination and double-strand break repair in several human cancer-prone syndromes have emphasized the importance of this repair pathway in maintaining genome integrity. Although sensitivity to ionizing radiation is a universal feature of rad52 group mutants, the mutants show considerable heterogeneity in different assays for recombinational repair of double-strand breaks and spontaneous mitotic recombination. Herein, I provide an overview of recent biochemical and structural analyses of the Rad52 group proteins and discuss how this information can be incorporated into genetic studies of recombination.
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Affiliation(s)
- Lorraine S Symington
- Department of Microbiology and Institute of Cancer Research, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.
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48
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Singleton MR, Wentzell LM, Liu Y, West SC, Wigley DB. Structure of the single-strand annealing domain of human RAD52 protein. Proc Natl Acad Sci U S A 2002; 99:13492-7. [PMID: 12370410 PMCID: PMC129701 DOI: 10.1073/pnas.212449899] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2002] [Indexed: 11/18/2022] Open
Abstract
In eukaryotic cells, RAD52 protein plays a central role in genetic recombination and DNA repair by (i) promoting the annealing of complementary single-stranded DNA and (ii) stimulation of the RAD51 recombinase. The single-strand annealing domain resides in the N-terminal region of the protein and is highly conserved, whereas the nonconserved RAD51-interaction domain is located in the C-terminal region. An N-terminal fragment of human RAD52 (residues 1-209) has been purified to homogeneity and, similar to the full-size protein (residues 1-418), shown to promote single-strand annealing in vitro. We have determined the crystal structure of this single-strand annealing domain at 2.7 A. The structure reveals an undecameric (11) subunit ring with extensive subunit contacts. A large, positively charged groove runs along the surface of the ring, readily suggesting a mechanism by which RAD52 presents the single strand for reannealing with complementary single-stranded DNA.
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Affiliation(s)
- Martin R Singleton
- Cancer Research U.K., London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK
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49
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Abstract
The human RAD52 protein has been implicated in DNA homologous recombination. Four major functional domains have been identified: a DNA binding domain (amino acids 1-85), a self-association and UBC9-interacting domain (amino acids 85-159), an RPA-interacting domain (amino acids 221-280), and a RAD51-interacting domain (amino acids 287-330). However, it is uncertain about the functional roles of the C-terminal region of RAD52 protein. In this report, we demonstrate an association of a C-terminal domain of human RAD52 (amino acids 302-418) with the XPB and XPD subunits of transcription factor TFIIH and RNA polymerase II (RNAPII). Using a Gal-4 binding based transcription assay, we further show that this C-terminal domain activates transcription. However, the RAD52 self-association domain suppresses transcription, resulting in an overall activity of transcriptional suppression by the full-length RAD52 protein. These results suggest a novel activity of RAD52 in transcription regulation and may further imply a functional role of RAD52 in targeting DNA damage on transcription active loci to recombinational repair.
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Affiliation(s)
- Jingmei Liu
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
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50
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González-Barrera S, García-Rubio M, Aguilera A. Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae. Genetics 2002; 162:603-14. [PMID: 12399375 PMCID: PMC1462300 DOI: 10.1093/genetics/162.2.603] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have made a comparative analysis of double-strand-break (DSB)-induced recombination and spontaneous recombination under low- and high-transcription conditions in yeast. We constructed two different recombination substrates, one for the analysis of intermolecular gene conversions and the other for intramolecular gene conversions and inversions. Such substrates were based on the same leu2-HOr allele fused to the tet promoter and containing a 21-bp HO site. Gene conversions and inversions were differently affected by rad1, rad51, rad52, and rad59 single and double mutations, consistent with the actual view that such events occur by different recombination mechanisms. However, the effect of each mutation on each type of recombination event was the same, whether associated with transcription or induced by the HO-mediated DSB. Both the highly transcribed DNA and the HO-cut sequence acted as recipients of the gene conversion events. These results are consistent with the hypothesis that transcription promotes initiation of recombination along the DNA sequence being transcribed. The similarity between transcription-associated and DSB-induced recombination suggests that transcription promotes DNA breaks.
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