1
|
Ma CJ, Kwon Y, Sung P, Greene EC. Human RAD52 interactions with replication protein A and the RAD51 presynaptic complex. J Biol Chem 2017; 292:11702-11713. [PMID: 28551686 PMCID: PMC5512066 DOI: 10.1074/jbc.m117.794545] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/24/2017] [Indexed: 11/06/2022] Open
Abstract
Rad52 is a highly conserved protein involved in the repair of DNA damage. Human RAD52 has been shown to mediate single-stranded DNA (ssDNA) and is synthetic lethal with mutations in other key recombination proteins. For this study, we used single-molecule imaging and ssDNA curtains to examine the binding interactions of human RAD52 with replication protein A (RPA)-coated ssDNA, and we monitored the fate of RAD52 during assembly of the presynaptic complex. We show that RAD52 binds tightly to the RPA-ssDNA complex and imparts an inhibitory effect on RPA turnover. We also found that during presynaptic complex assembly, most of the RPA and RAD52 was displaced from the ssDNA, but some RAD52-RPA-ssDNA complexes persisted as interspersed clusters surrounded by RAD51 filaments. Once assembled, the presence of RAD51 restricted formation of new RAD52-binding events, but additional RAD52 could bind once RAD51 dissociated from the ssDNA. Together, these results provide new insights into the behavior and dynamics of human RAD52 during presynaptic complex assembly and disassembly.
Collapse
Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032.
| |
Collapse
|
2
|
Nair A, Agarwal R, Chittela RK. Biochemical characterization of plant Rad52 protein from rice (Oryza sativa). Plant Physiol Biochem 2016; 106:108-117. [PMID: 27156135 DOI: 10.1016/j.plaphy.2016.04.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
DNA damage in living cells is repaired by two main pathways, homologous recombination (HR) and non-homologous end joining (NHEJ). Of all the genes promoting HR, Rad52 (Radiation sensitive 52) is an important gene which is found to be highly conserved across different species. It was believed that RAD52 is absent in plant systems until lately. However, recent genetic studies have shown the presence of RAD52 homologues in plants. Rad52 homologues in plant systems have not yet been characterized biochemically. In the current study, we bring out the biochemical properties of rice Rad52-2a protein. OsRad52-2a was over-expressed in Escherichia coli BL21 (DE3) cells and the protein was purified. The identity of purified OsRad52-2a protein was confirmed via peptide mass fingerprinting. Gel filtration and native PAGE analysis indicated that the OsRad52-2a protein in its native state probably formed an undecameric structure. Purified OsRad52-2a protein showed binding to single stranded DNA, double stranded DNA. Protein also mediated the renaturation of complementary single strands into duplex DNA in both agarose gel and FRET based assays. Put together, OsRad52-2a forms oligomeric structures and binds to ssDNA/dsDNA for mediating an important function like renaturation during homologous recombination. This study represents the first report on biochemical properties of OsRad52-2a protein from important crop like rice. This information will help in dissecting the recombination and repair machinery in plant systems.
Collapse
Affiliation(s)
- Anuradha Nair
- Bio-molecular Damage and Repair Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Rachna Agarwal
- Bio-molecular Damage and Repair Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Bio-molecular Damage and Repair Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India.
| |
Collapse
|
3
|
Silva S, Altmannova V, Eckert-Boulet N, Kolesar P, Gallina I, Hang L, Chung I, Arneric M, Zhao X, Buron LD, Mortensen UH, Krejci L, Lisby M. SUMOylation of Rad52-Rad59 synergistically change the outcome of mitotic recombination. DNA Repair (Amst) 2016; 42:11-25. [PMID: 27130983 DOI: 10.1016/j.dnarep.2016.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022]
Abstract
Homologous recombination (HR) is essential for maintenance of genome stability through double-strand break (DSB) repair, but at the same time HR can lead to loss of heterozygosity and uncontrolled recombination can be genotoxic. The post-translational modification by SUMO (small ubiquitin-like modifier) has been shown to modulate recombination, but the exact mechanism of this regulation remains unclear. Here we show that SUMOylation stabilizes the interaction between the recombination mediator Rad52 and its paralogue Rad59 in Saccharomyces cerevisiae. Although Rad59 SUMOylation is not required for survival after genotoxic stress, it affects the outcome of recombination to promote conservative DNA repair. In some genetic assays, Rad52 and Rad59 SUMOylation act synergistically. Collectively, our data indicate that the described SUMO modifications affect the balance between conservative and non-conservative mechanisms of HR.
Collapse
Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Nadine Eckert-Boulet
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Kolesar
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Irene Gallina
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Lisa Hang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Inn Chung
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Milica Arneric
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Line Due Buron
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| |
Collapse
|
4
|
Sullivan K, Cramer-Morales K, McElroy DL, Ostrov DA, Haas K, Childers W, Hromas R, Skorski T. Identification of a Small Molecule Inhibitor of RAD52 by Structure-Based Selection. PLoS One 2016; 11:e0147230. [PMID: 26784987 PMCID: PMC4718542 DOI: 10.1371/journal.pone.0147230] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022] Open
Abstract
It has been reported that inhibition of RAD52 either by specific shRNA or a small peptide aptamer induced synthetic lethality in tumor cell lines carrying BRCA1 and BRCA2 inactivating mutations. Molecular docking was used to screen two chemical libraries: 1) 1,217 FDA approved drugs, and 2) 139,735 drug-like compounds to identify candidates for interacting with DNA binding domain of human RAD52. Thirty six lead candidate compounds were identified that were predicted to interfere with RAD52 –DNA binding. Further biological testing confirmed that 9 of 36 candidate compounds were able to inhibit the binding of RAD52 to single-stranded DNA in vitro. Based on molecular binding combined with functional assays, we propose a model in which the active compounds bind to a critical “hotspot” in RAD52 DNA binding domain 1. In addition, one of the 9 active compounds, adenosine 5’-monophosphate (A5MP), and also its mimic 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) 5’ phosphate (ZMP) inhibited RAD52 activity in vivo and exerted synthetic lethality against BRCA1 and BRCA2–mutated carcinomas. These data suggest that active, inhibitory RAD52 binding compounds could be further refined for efficacy and safety to develop drugs inducing synthetic lethality in tumors displaying deficiencies in BRCA1/2-mediated homologous recombination.
Collapse
Affiliation(s)
- Katherine Sullivan
- Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States of America
| | - Kimberly Cramer-Morales
- Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States of America
| | - Daniel L. McElroy
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida & Shands, Gainesville, Florida 32610, United States of America
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida & Shands, Gainesville, Florida 32610, United States of America
| | - Kimberly Haas
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States of America
| | - Wayne Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States of America
| | - Robert Hromas
- Department of Medicine, College of Medicine, University of Florida & Shands, Gainesville, Florida 32610, United States of America
| | - Tomasz Skorski
- Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States of America
- * E-mail:
| |
Collapse
|
5
|
Plate I, Hallwyl SCL, Shi I, Krejci L, Müller C, Albertsen L, Sung P, Mortensen UH. Interaction with RPA is necessary for Rad52 repair center formation and for its mediator activity. J Biol Chem 2008; 283:29077-85. [PMID: 18703507 PMCID: PMC2570898 DOI: 10.1074/jbc.m804881200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/12/2008] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination (HR) is a major DNA repair pathway and therefore essential for maintaining the integrity of the genome. HR is catalyzed by proteins encoded by genes of the RAD52 epistasis group, including the recombinase Rad51 and its mediator Rad52. HR proteins fused with green fluorescent protein form foci at damaged DNA reflecting the assembly of repair centers that harbor a high concentration of repair proteins. Rad52 mediates the recruitment of Rad51 and other HR proteins to DNA damage. To understand the mechanism for the assembly of Rad52-dependent DNA repair centers, we used a mutational strategy to identify a Rad52 domain essential for its recruitment to DNA repair foci. We present evidence to implicate an acidic domain in Rad52 in DNA repair focus formation. Mutations in this domain confer marked DNA damage sensitivity and recombination deficiency. Importantly, these Rad52 mutants are specifically compromised for interaction with the single-stranded DNA-binding factor RPA. Based on these findings, we propose a model where Rad52 displaces RPA from single-stranded DNA using the acidic domain as a molecular lever.
Collapse
Affiliation(s)
- Iben Plate
- Center for Microbial Biotechnology, Technical University of Denmark, Lyng by 2800, Denmark
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Increasing genomic instability is associated with aging in eukaryotes, but the connection between genomic instability and natural variation in life span is unknown. We have quantified chronological life span and loss-of-heterozygosity (LOH) in 11 natural isolates of Saccharomyces cerevisiae. We show that genomic instability increases and mitotic asymmetry breaks down during chronological aging. The age-dependent increase of genomic instability generally lags behind the drop of viability and this delay accounts for approximately 50% of the observed natural variation of replicative life span in these yeast isolates. We conclude that the abilities of yeast strains to tolerate genomic instability co-vary with their replicative life spans. To the best of our knowledge, this is the first quantitative evidence that demonstrates a link between genomic instability and natural variation in life span.
Collapse
Affiliation(s)
- Hong Qin
- Center for Aging and Development Biology, Department of Biology, University of Rochester, Rochester, New York, United States of America.
| | | | | |
Collapse
|
7
|
Seong C, Sehorn MG, Plate I, Shi I, Song B, Chi P, Mortensen U, Sung P, Krejci L. Molecular anatomy of the recombination mediator function of Saccharomyces cerevisiae Rad52. J Biol Chem 2008; 283:12166-74. [PMID: 18310075 PMCID: PMC2335352 DOI: 10.1074/jbc.m800763200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Indexed: 11/06/2022] Open
Abstract
A helical filament of Rad51 on single-strand DNA (ssDNA), called the presynaptic filament, catalyzes DNA joint formation during homologous recombination. Rad52 facilitates presynaptic filament assembly, and this recombination mediator activity is thought to rely on the interactions of Rad52 with Rad51, the ssDNA-binding protein RPA, and ssDNA. The N-terminal region of Rad52, which has DNA binding activity and an oligomeric structure, is thought to be crucial for mediator activity and recombination. Unexpectedly, we find that the C-terminal region of Rad52 also harbors a DNA binding function. Importantly, the Rad52 C-terminal portion alone can promote Rad51 presynaptic filament assembly. The middle portion of Rad52 associates with DNA-bound RPA and contributes to the recombination mediator activity. Accordingly, expression of a protein species that harbors the middle and C-terminal regions of Rad52 in the rad52 Delta327 background enhances the association of Rad51 protein with a HO-made DNA double-strand break and partially complements the methylmethane sulfonate sensitivity of the mutant cells. Our results provide a mechanistic framework for rationalizing the multi-faceted role of Rad52 in recombination and DNA repair.
Collapse
Affiliation(s)
- Changhyun Seong
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Abstract
Homologous recombination (HR) is a ubiquitous cellular pathway that mediates transfer of genetic information between homologous or near homologous (homeologous) DNA sequences. During meiosis it ensures proper chromosome segregation in the first division. Moreover, HR is critical for the tolerance and repair of DNA damage, as well as in the recovery of stalled and broken replication forks. Together these functions preserve genomic stability and assure high fidelity transmission of the genetic material in the mitotic and meiotic cell divisions. This review will focus on the Rad54 protein, a member of the Snf2-family of SF2 helicases, which translocates on dsDNA but does not display strand displacement activity typical for a helicase. A wealth of genetic, cytological, biochemical and structural data suggests that Rad54 is a core factor of HR, possibly acting at multiple stages during HR in concert with the central homologous pairing protein Rad51.
Collapse
Affiliation(s)
- Wolf-Dietrich Heyer
- Sections of Microbiology, University of California Davis, CA 95616-8665, USA.
| | | | | | | |
Collapse
|
9
|
Thorpe PH, Marrero VA, Savitzky MH, Sunjevaric I, Freeman TC, Rothstein R. Cells expressing murine RAD52 splice variants favor sister chromatid repair. Mol Cell Biol 2006; 26:3752-63. [PMID: 16648471 PMCID: PMC1488992 DOI: 10.1128/mcb.26.10.3752-3763.2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RAD52 gene is essential for homologous recombination in the yeast Saccharomyces cerevisiae. RAD52 is the archetype in an epistasis group of genes essential for DNA damage repair. By catalyzing the replacement of replication protein A with Rad51 on single-stranded DNA, Rad52 likely promotes strand invasion of a double-stranded DNA molecule by single-stranded DNA. Although the sequence and in vitro functions of mammalian RAD52 are conserved with those of yeast, one difference is the presence of introns and consequent splicing of the mammalian RAD52 pre-mRNA. We identified two novel splice variants from the RAD52 gene that are expressed in adult mouse tissues. Expression of these splice variants in tissue culture cells elevates the frequency of recombination that uses a sister chromatid template. To characterize this dominant phenotype further, the RAD52 gene from the yeast Saccharomyces cerevisiae was truncated to model the mammalian splice variants. The same dominant sister chromatid recombination phenotype seen in mammalian cells was also observed in yeast. Furthermore, repair from a homologous chromatid is reduced in yeast, implying that the choice of alternative repair pathways may be controlled by these variants. In addition, a dominant DNA repair defect induced by one of the variants in yeast is suppressed by overexpression of RAD51, suggesting that the Rad51-Rad52 interaction is impaired.
Collapse
Affiliation(s)
- Peter H Thorpe
- Department of Genetics and Development, Columbia University Medical Center, HHSC 1608, 701 West 168th St., New York, New York 10032, USA
| | | | | | | | | | | |
Collapse
|
10
|
de Mayolo AA, Lisby M, Erdeniz N, Thybo T, Mortensen UH, Rothstein R. Multiple start codons and phosphorylation result in discrete Rad52 protein species. Nucleic Acids Res 2006; 34:2587-97. [PMID: 16707661 PMCID: PMC1463902 DOI: 10.1093/nar/gkl280] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52 protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks.
Collapse
Affiliation(s)
| | - Michael Lisby
- Department of Genetics, Institute of Molecular Biology and Physiology, University of CopenhagenØster Farimagsgade 2A, DK-1353 Copenhagen K, Denmark
| | - Naz Erdeniz
- Department of Molecular and Medical Genetics, Oregon Health Sciences University3181 SW Sam Jackson Park Road, Mail Code L103, Portland, OR 97201, USA
| | - Tanja Thybo
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of DenmarkBuilding 223, DK-2800 Lyngby, Denmark
| | - Uffe H. Mortensen
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of DenmarkBuilding 223, DK-2800 Lyngby, Denmark
| | - Rodney Rothstein
- To whom correspondence should be addressed. Tel: +1 212 305 1733; Fax: +1 212 923 2090;
| |
Collapse
|