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Kharlamova MA, Kushwah MS, Jachowski TJ, Subramaniam S, Schiff V, Stewart AF, Kukura P, Schäffer E. Monomers and short oligomers of human RAD52 promote single-strand annealing. Proc Natl Acad Sci U S A 2025; 122:e2420771122. [PMID: 40184180 PMCID: PMC12002259 DOI: 10.1073/pnas.2420771122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 02/25/2025] [Indexed: 04/05/2025] Open
Abstract
Genome maintenance and stability rely on the repair of DNA double-strand breaks. Breaks can be repaired via the single-strand-annealing pathway mediated by the protein RAD52. RAD52 oligomerizes to rings that are thought to promote annealing. However, rings have only been observed at micromolar concentrations at which annealing activity is impaired. Thus, it is unclear which oligomeric form is responsible for annealing. We combined single-molecule mass photometry with biochemical assays to determine the in vitro oligomeric states of human RAD52. We found that RAD52 was mostly monomeric at lower nanomolar concentrations. With increasing concentration, RAD52 oligomerized and formed rings with a variable stoichiometry from heptamers to tridecamers consistent with an oligomerization model of noncooperative assembly coupled with preferential cyclization. Under conditions where hardly any rings were present, RAD52 already promoted single-strand annealing in vitro. Our findings indicate that in vitro single-strand annealing can be mediated by monomers and short oligomers of RAD52. The oligomerization model suggests that ring formation is similar to a phase transition whereby rings are a reservoir to replenish the monomer and short oligomer pool. This pool has a nearly constant concentration which may be optimal for annealing and would be independent, for example, of the amount of DNA damage, protein upregulation, or the cell cycle.
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Affiliation(s)
- Maria A. Kharlamova
- Cellular Nanoscience, Center for Plant Molecular Biology, University of Tübingen, Tübingen72076, Germany
| | - Manish S. Kushwah
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Tobias J. Jachowski
- Cellular Nanoscience, Center for Plant Molecular Biology, University of Tübingen, Tübingen72076, Germany
| | - Sivaraman Subramaniam
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden01307, Germany
| | - Viktor Schiff
- Cellular Nanoscience, Center for Plant Molecular Biology, University of Tübingen, Tübingen72076, Germany
| | - A. Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden01307, Germany
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney2052, NSW, Australia
- State Key Laboratory of Microbial Research, Shandong University, Qingdao266237, China
| | - Philipp Kukura
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Erik Schäffer
- Cellular Nanoscience, Center for Plant Molecular Biology, University of Tübingen, Tübingen72076, Germany
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Mentani A, Maresca M, Shiriaeva A. Prime Editing: Mechanistic Insights and DNA Repair Modulation. Cells 2025; 14:277. [PMID: 39996750 PMCID: PMC11853414 DOI: 10.3390/cells14040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/15/2025] [Accepted: 01/24/2025] [Indexed: 02/26/2025] Open
Abstract
Prime editing is a genome editing technique that allows precise modifications of cellular DNA without relying on donor DNA templates. Recently, several different prime editor proteins have been published in the literature, relying on single- or double-strand breaks. When prime editing occurs, the DNA undergoes one of several DNA repair pathways, and these processes can be modulated with the use of inhibitors. Firstly, this review provides an overview of several DNA repair mechanisms and their modulation by known inhibitors. In addition, we summarize different published prime editors and provide a comprehensive overview of associated DNA repair mechanisms. Finally, we discuss the delivery and safety aspects of prime editing.
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Affiliation(s)
- Astrid Mentani
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Anna Shiriaeva
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
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Alshareedah I, Pangeni S, Dewan PA, Honda M, Liao TW, Spies M, Ha T. The human RAD52 complex undergoes phase separation and facilitates bundling and end-to-end tethering of RAD51 presynaptic filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.09.627445. [PMID: 39713334 PMCID: PMC11661238 DOI: 10.1101/2024.12.09.627445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Human RAD52 is a prime target for synthetical lethality approaches to treat cancers with deficiency in homologous recombination. Among multiple cellular roles of RAD52, its functions in homologous recombination repair and protection of stalled replication forks appear to substitute those of the tumor suppressor protein BRCA2. However, the mechanistic details of how RAD52 can substitute BRCA2 functions are only beginning to emerge. RAD52 forms an undecameric ring that is enveloped by eleven ~200 residue-long disordered regions, making it a highly multivalent and branched protein complex that potentiates supramolecular assembly. Here, we show that RAD52 exhibits homotypic phase separation capacity, and its condensates recruit key players in homologous recombination such as single-stranded (ss)DNA, RPA, and the RAD51 recombinase. Moreover, we show that RAD52 phase separation is regulated by its interaction partners such as ssDNA and RPA. Using fluorescence microscopy, we show that RAD52 can induce the formation of RAD51-ssDNA fibrillar structures. To probe the fine structure of these fibrils, we utilized single-molecule super-resolution imaging via DNA-PAINT and atomic force microscopy and showed that RAD51 fibrils are bundles of individual RAD51 nucleoprotein filaments. We further show that RAD52 induces end-to-end tethering of RAD51 nucleoprotein filaments. Overall, we demonstrate unique macromolecular organizational features of RAD52 that may underlie its various functions in the cell.
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Affiliation(s)
- Ibraheem Alshareedah
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sushil Pangeni
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Paul A. Dewan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Biophysics, Harvard University, Cambridge, MA, USA
| | - Masayoshi Honda
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Ting-Wei Liao
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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Rinaldi F, Girotto S. Structure-based approaches in synthetic lethality strategies. Curr Opin Struct Biol 2024; 88:102895. [PMID: 39137490 DOI: 10.1016/j.sbi.2024.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Evolution has fostered robust DNA damage response (DDR) mechanisms to combat DNA lesions. However, disruptions in this intricate machinery can render cells overly reliant on the remaining functional but often less accurate DNA repair pathways. This increased dependence on error-prone pathways may result in improper repair and the accumulation of mutations, fostering genomic instability and facilitating the uncontrolled cell proliferation characteristic of cancer initiation and progression. Strategies based on the concept of synthetic lethality (SL) leverage the inherent genomic instability of cancer cells by targeting alternative pathways, thereby inducing selective death of cancer cells. This review emphasizes recent advancements in structural investigations of pivotal SL targets. The significant contribution of structure-based methodologies to SL research underscores their potential impact in characterizing the growing number of SL targets, largely due to advances in next-generation sequencing. Harnessing these approaches is essential for advancing the development of precise and personalized SL therapeutic strategies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics Facility, Istituto Italiano di Tecnologia, 16163 Genoa, Italy.
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