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Miron S, Legrand P, Dupaigne P, van Rossum-Fikkert SE, Ristic D, Majeed A, Kanaar R, Zinn-Justin S, Zelensky AN. DMC1 and RAD51 bind FxxA and FxPP motifs of BRCA2 via two separate interfaces. Nucleic Acids Res 2024:gkae452. [PMID: 38828772 DOI: 10.1093/nar/gkae452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/29/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
In vertebrates, the BRCA2 protein is essential for meiotic and somatic homologous recombination due to its interaction with the RAD51 and DMC1 recombinases through FxxA and FxPP motifs (here named A- and P-motifs, respectively). The A-motifs present in the eight BRC repeats of BRCA2 compete with the A-motif of RAD51, which is responsible for its self-oligomerization. BRCs thus disrupt RAD51 nucleoprotein filaments in vitro. The role of the P-motifs is less studied. We recently found that deletion of Brca2 exons 12-14 encoding one of them (the prototypical 'PhePP' motif), disrupts DMC1 but not RAD51 function in mouse meiosis. Here we provide a mechanistic explanation for this phenotype by solving the crystal structure of the complex between a BRCA2 fragment containing the PhePP motif and DMC1. Our structure reveals that, despite sharing a conserved phenylalanine, the A- and P-motifs bind to distinct sites on the ATPase domain of the recombinases. The P-motif interacts with a site that is accessible in DMC1 octamers and nucleoprotein filaments. Moreover, we show that this interaction also involves the adjacent protomer and thus increases the stability of the DMC1 nucleoprotein filaments. We extend our analysis to other P-motifs from RAD51AP1 and FIGNL1.
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Affiliation(s)
- Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, Gif sur-Yvette, France
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Sari E van Rossum-Fikkert
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
| | - Dejan Ristic
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
| | - Atifa Majeed
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Alex N Zelensky
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands
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2
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Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
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Kopa P, Macieja A, Galita G, Witczak ZJ, Poplawski T. DNA Double Strand Breaks Repair Inhibitors: Relevance as Potential New Anticancer Therapeutics. Curr Med Chem 2019; 26:1483-1493. [PMID: 29446719 DOI: 10.2174/0929867325666180214113154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/19/2022]
Abstract
DNA double-strand breaks are considered one of the most lethal forms of DNA damage. Many effective anticancer therapeutic approaches used chemical and physical methods to generate DNA double-strand breaks in the cancer cells. They include: IR and drugs which mimetic its action, topoisomerase poisons, some alkylating agents or drugs which affected DNA replication process. On the other hand, cancer cells are mostly characterized by highly effective systems of DNA damage repair. There are two main DNA repair pathways used to fix double-strand breaks: NHEJ and HRR. Their activity leads to a decreased effect of chemotherapy. Targeting directly or indirectly the DNA double-strand breaks response by inhibitors seems to be an exciting option for anticancer therapy and is a part of novel trends that arise after the clinical success of PARP inhibitors. These trends will provide great opportunities for the development of DNA repair inhibitors as new potential anticancer drugs. The main objective of this article is to address these new promising advances.
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Affiliation(s)
- Paulina Kopa
- Department of Immunopathology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz 90-752, Poland
| | - Anna Macieja
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
| | - Grzegorz Galita
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
| | - Zbigniew J Witczak
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, Wilkes-Barre, PA 18766, United States
| | - Tomasz Poplawski
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
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Sidhu A, Ristic D, Sánchez H, Wyman C. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF). Methods Enzymol 2018; 600:347-374. [DOI: 10.1016/bs.mie.2017.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Marrese M, Guarino V, Ambrosio L. Atomic Force Microscopy: A Powerful Tool to Address Scaffold Design in Tissue Engineering. J Funct Biomater 2017; 8:E7. [PMID: 28208801 PMCID: PMC5371880 DOI: 10.3390/jfb8010007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022] Open
Abstract
Functional polymers currently represent a basic component of a large range of biological and biomedical applications including molecular release, tissue engineering, bio-sensing and medical imaging. Advancements in these fields are driven by the use of a wide set of biodegradable polymers with controlled physical and bio-interactive properties. In this context, microscopy techniques such as Atomic Force Microscopy (AFM) are emerging as fundamental tools to deeply investigate morphology and structural properties at micro and sub-micrometric scale, in order to evaluate the in time relationship between physicochemical properties of biomaterials and biological response. In particular, AFM is not only a mere tool for screening surface topography, but may offer a significant contribution to understand surface and interface properties, thus concurring to the optimization of biomaterials performance, processes, physical and chemical properties at the micro and nanoscale. This is possible by capitalizing the recent discoveries in nanotechnologies applied to soft matter such as atomic force spectroscopy to measure surface forces through force curves. By tip-sample local interactions, several information can be collected such as elasticity, viscoelasticity, surface charge densities and wettability. This paper overviews recent developments in AFM technology and imaging techniques by remarking differences in operational modes, the implementation of advanced tools and their current application in biomaterials science, in terms of characterization of polymeric devices in different forms (i.e., fibres, films or particles).
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Affiliation(s)
- Marica Marrese
- Faculty of Sciences, Biophotonics and Medical Imaging group and Laser Lab, VU University Amsterdam, De Boelelaan 1081 HV Amsterdam, The Netherlands.
| | - Vincenzo Guarino
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le Kennedy 54, Pad 20, Mostra d'Oltremare, Naples 80125, Italy.
| | - Luigi Ambrosio
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le Kennedy 54, Pad 20, Mostra d'Oltremare, Naples 80125, Italy.
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Abe T, Branzei D. High levels of BRC4 induced by a Tet-On 3G system suppress DNA repair and impair cell proliferation in vertebrate cells. DNA Repair (Amst) 2014; 22:153-64. [PMID: 25218467 PMCID: PMC4194320 DOI: 10.1016/j.dnarep.2014.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/27/2022]
Abstract
The Tet-On 3G system is useful for conditional gene overexpression studies in DT40. The Tet-On-I-SceI effectively induces DSB formation in vertebrate cells. BRC4 overexpression induces chromosomal breaks and G2-arrest. BRC4 cytotoxicity is mediated by endogenous BRCA2, but independent of NHEJ. BRC4 inhibits cancer cell proliferation and exacerbates the effects of chemotherapy.
Transient induction or suppression of target genes is useful to study the function of toxic or essential genes in cells. Here we apply a Tet-On 3G system to DT40 lymphoma B cell lines, validating it for three different genes. Using this tool, we then show that overexpression of the chicken BRC4 repeat of the tumor suppressor BRCA2 impairs cell proliferation and induces chromosomal breaks. Mechanistically, high levels of BRC4 suppress double strand break-induced homologous recombination, inhibit the formation of RAD51 recombination repair foci, reduce cellular resistance to DNA damaging agents and induce a G2 damage checkpoint-mediated cell-cycle arrest. The above phenotypes are mediated by BRC4 capability to bind and inhibit RAD51. The toxicity associated with BRC4 overexpression is exacerbated by chemotherapeutic agents and reversed by RAD51 overexpression, but it is neither aggravated nor suppressed by a deficit in the non-homologous end-joining pathway of double strand break repair. We further find that the endogenous BRCA2 mediates the cytotoxicity associated with BRC4 induction, thus underscoring the possibility that BRC4 or other domains of BRCA2 cooperate with ectopic BRC4 in regulating repair activities or mitotic cell division. In all, the results demonstrate the utility of the Tet-On 3G system in DT40 research and underpin a model in which BRC4 role on cell proliferation and chromosome repair arises primarily from its suppressive role on RAD51 functions.
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Affiliation(s)
- Takuya Abe
- IFOM, The FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
| | - Dana Branzei
- IFOM, The FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
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Goodarzi AA, Jeggo PA. The repair and signaling responses to DNA double-strand breaks. ADVANCES IN GENETICS 2013; 82:1-45. [PMID: 23721719 DOI: 10.1016/b978-0-12-407676-1.00001-9] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A DNA double-strand break (DSB) has long been recognized as a severe cellular lesion, potentially representing an initiating event for carcinogenesis or cell death. The evolution of DSB repair pathways as well as additional processes, such as cell cycle checkpoint arrest, to minimize the cellular impact of DSB formation was, therefore, not surprising. However, the depth and complexity of the DNA damage responses being revealed by current studies were unexpected. Perhaps the most surprising finding to emerge is the dramatic changes to chromatin architecture that arise in the DSB vicinity. In this review, we overview the cellular response to DSBs focusing on DNA repair pathways and the interface between them. We consider additional events which impact upon these DSB repair pathways, including regulated arrest of cell cycle progression and chromatin architecture alterations. Finally, we discuss the impact of defects in these processes to human disease.
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Affiliation(s)
- Aaron A Goodarzi
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
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Tessmer I, Kaur P, Lin J, Wang H. Investigating bioconjugation by atomic force microscopy. J Nanobiotechnology 2013; 11:25. [PMID: 23855448 PMCID: PMC3723498 DOI: 10.1186/1477-3155-11-25] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 07/05/2013] [Indexed: 12/15/2022] Open
Abstract
Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str, 2, 97080, Würzburg, Germany.
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Zarkov A, Vasilev A, Deligeorgiev T, Stoynov S, Nedelcheva-Veleva M. Novel Fluorescent Dyes for Single DNA Molecule Techniques. Mol Imaging 2013. [DOI: 10.2310/7290.2012.00018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander Zarkov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Aleksey Vasilev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Todor Deligeorgiev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Stoyno Stoynov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Marina Nedelcheva-Veleva
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
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De Vlaminck I, Henighan T, van Loenhout MTJ, Burnham DR, Dekker C. Magnetic forces and DNA mechanics in multiplexed magnetic tweezers. PLoS One 2012; 7:e41432. [PMID: 22870220 PMCID: PMC3411724 DOI: 10.1371/journal.pone.0041432] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/26/2012] [Indexed: 12/02/2022] Open
Abstract
Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization where large numbers of molecules (say 103) are addressed in the same amount of time required by a single-molecule measurement. We apply offline analysis of recorded images and show that this approach provides a scalable solution for parallel tracking of the xyz-positions of many beads simultaneously. We employ a large field-of-view imaging system to address many DNA-bead tethers in parallel. We model the 3D magnetic field generated by the magnets and derive the magnetic force experienced by DNA-bead tethers across the large field of view from first principles. We furthermore experimentally demonstrate that a DNA-bead tether subject to a rotating magnetic field describes a bicircular, Limaçon rotation pattern and that an analysis of this pattern simultaneously yields information about the force angle and the position of attachment of the DNA on the bead. Finally, we apply MMT in the high-throughput investigation of the distribution of the induced magnetic moment, the position of attachment of DNA on the beads, and DNA flexibility. The methods described herein pave the way to kilo-molecule level magnetic tweezers experiments.
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Affiliation(s)
- Iwijn De Vlaminck
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Thomas Henighan
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Daniel R. Burnham
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- * E-mail:
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Affiliation(s)
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2628 CJ, The Netherlands;
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