1
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Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, Ferrage F. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro. Nat Struct Mol Biol 2024; 31:1732-1744. [PMID: 38898102 DOI: 10.1038/s41594-024-01339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70-Ku80 heterodimer (Ku), X-ray repair cross complementing 4 (XRCC4) in complex with DNA ligase 4 (X4L4) and XRCC4-like factor (XLF) form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were recently obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at residue resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs lead to the formation of XLF and X4L4 condensates in vitro, which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome-editing strategies.
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Affiliation(s)
- Duc-Duy Vu
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Manon Brenière
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Philippe Pelupessy
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ziqing Wang
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ludovic Carlier
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Guillaume Bouvignies
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, New York, NY, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), Grenoble Alpes University, CNRS, CEA, Grenoble, France
| | - Zoher Gueroui
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France.
| | - Fabien Ferrage
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France.
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2
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Sergeeva SV, Loshchenova PS, Oshchepkov DY, Orishchenko KE. Crosstalk between BER and NHEJ in XRCC4-Deficient Cells Depending on hTERT Overexpression. Int J Mol Sci 2024; 25:10405. [PMID: 39408734 PMCID: PMC11476898 DOI: 10.3390/ijms251910405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/21/2024] [Accepted: 09/25/2024] [Indexed: 10/20/2024] Open
Abstract
Targeting DNA repair pathways is an important strategy in anticancer therapy. However, the unrevealed interactions between different DNA repair systems may interfere with the desired therapeutic effect. Among DNA repair systems, BER and NHEJ protect genome integrity through the entire cell cycle. BER is involved in the repair of DNA base lesions and DNA single-strand breaks (SSBs), while NHEJ is responsible for the repair of DNA double-strand breaks (DSBs). Previously, we showed that BER deficiency leads to downregulation of NHEJ gene expression. Here, we studied BER's response to NHEJ deficiency induced by knockdown of NHEJ scaffold protein XRCC4 and compared the knockdown effects in normal (TIG-1) and hTERT-modified cells (NBE1). We investigated the expression of the XRCC1, LIG3, and APE1 genes of BER and LIG4; the Ku70/Ku80 genes of NHEJ at the mRNA and protein levels; as well as p53, Sp1 and PARP1. We found that, in both cell lines, XRCC4 knockdown leads to a decrease in the mRNA levels of both BER and NHEJ genes, though the effect on protein level is not uniform. XRCC4 knockdown caused an increase in p53 and Sp1 proteins, but caused G1/S delay only in normal cells. Despite the increased p53 protein, p21 did not significantly increase in NBE1 cells with overexpressed hTERT, and this correlated with the absence of G1/S delay in these cells. The data highlight the regulatory function of the XRCC4 scaffold protein and imply its connection to a transcriptional regulatory network or mRNA metabolism.
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Affiliation(s)
- Svetlana V. Sergeeva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentieva 10, Novosibirsk 630090, Russia; (P.S.L.); (K.E.O.)
- Department of Genetic Technologies, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Polina S. Loshchenova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentieva 10, Novosibirsk 630090, Russia; (P.S.L.); (K.E.O.)
- Department of Genetic Technologies, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Dmitry Yu. Oshchepkov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentieva 10, Novosibirsk 630090, Russia; (P.S.L.); (K.E.O.)
| | - Konstantin E. Orishchenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentieva 10, Novosibirsk 630090, Russia; (P.S.L.); (K.E.O.)
- Department of Genetic Technologies, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
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3
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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4
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Amin H, Zahid S, Hall C, Chaplin AK. Cold snapshots of DNA repair: Cryo-EM structures of DNA-PKcs and NHEJ machinery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:1-13. [PMID: 38036101 DOI: 10.1016/j.pbiomolbio.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/03/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The proteins and protein assemblies involved in DNA repair have been the focus of a multitude of structural studies for the past few decades. Historically, the structures of these protein complexes have been resolved by X-ray crystallography. However, more recently with the advancements in cryo-electron microscopy (cryo-EM) ranging from optimising the methodology for sample preparation to the development of improved electron detectors, the focus has shifted from X-ray crystallography to cryo-EM. This methodological transition has allowed for the structural determination of larger, more complex protein assemblies involved in DNA repair pathways and has subsequently led to a deeper understanding of the mechanisms utilised by these fascinating molecular machines. Here, we review some of the key structural advancements that have been gained in the study of non-homologous end joining (NHEJ) by the use of cryo-EM, with a focus on assemblies composed of DNA-PKcs and Ku70/80 (Ku) and the various methodologies utilised to obtain these structures.
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Affiliation(s)
- Himani Amin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Sayma Zahid
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Chloe Hall
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Amanda K Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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5
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De Bragança S, Dillingham MS, Moreno-Herrero F. Recent insights into eukaryotic double-strand DNA break repair unveiled by single-molecule methods. Trends Genet 2023; 39:924-940. [PMID: 37806853 DOI: 10.1016/j.tig.2023.09.004] [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: 06/14/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Genome integrity and maintenance are essential for the viability of all organisms. A wide variety of DNA damage types have been described, but double-strand breaks (DSBs) stand out as one of the most toxic DNA lesions. Two major pathways account for the repair of DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Both pathways involve complex DNA transactions catalyzed by proteins that sequentially or cooperatively work to repair the damage. Single-molecule methods allow visualization of these complex transactions and characterization of the protein:DNA intermediates of DNA repair, ultimately allowing a comprehensive breakdown of the mechanisms underlying each pathway. We review current understanding of the HR and NHEJ responses to DSBs in eukaryotic cells, with a particular emphasis on recent advances through the use of single-molecule techniques.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Mark S Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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6
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Vogt A, He Y, Lees-Miller SP. How to fix DNA breaks: new insights into the mechanism of non-homologous end joining. Biochem Soc Trans 2023; 51:1789-1800. [PMID: 37787023 PMCID: PMC10657183 DOI: 10.1042/bst20220741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation-induced DNA double-strand breaks (DSBs) in human cells and is essential for the generation of mature T and B cells in the adaptive immune system via the process of V(D)J recombination. Here, we review how recently determined structures shed light on how NHEJ complexes function at DNA DSBs, emphasizing how multiple structures containing the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) may function in NHEJ. Together, these studies provide an explanation for how NHEJ proteins assemble to detect and protect DSB ends, then proceed, through DNA-PKcs-dependent autophosphorylation, to a ligation-competent complex.
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Affiliation(s)
- Alex Vogt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, U.S.A
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, U.S.A
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, U.S.A
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, U.S.A
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, U.S.A
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, U.S.A
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre and Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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7
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Prabhu D, Ray U, Rajeev A, Joy R, George AT, George J, Raghavan SC, John F. Design and Synthesis of Ketenimine Sulfonamide Conjugates through Multicomponent Reactions; A Combined Cytotoxic Analysis and Computational Exploration. ACS OMEGA 2023; 8:38619-38631. [PMID: 37867708 PMCID: PMC10586297 DOI: 10.1021/acsomega.3c05816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023]
Abstract
Multicomponent reactions involving zwitterion generated from dimethyl acetylenedicarboxylate, aryl sulfonamide, and isocyanide to generate sulfonamide-conjugated ketenimines is reported. The synthetic strategy adopted is highly atom economical and stereoselective. Ketenimine sulfonamide analogues are key intermediates for further synthetic conversions to generate a combinatorial library of compounds. Furthermore, sulfonamide compounds are known to possess a broad spectrum of biological applications. All the novel molecules synthesized exhibit the potential to target the nonhomologous DNA end-joining (NHEJ) pathway with cytotoxic ability. Computational studies compliment the in vitro biological assays of the 8 small-molecule inhibitors. DNA double-strand breaks (DSBs) are considered as the most lethal among different DNA damages. NHEJ repairs about 70% of the DSBs generated in cells within mammals. The DNA-dependent protein kinase catalytic subunit is one of the PI3 kinases associated with NHEJ. Compounds DK01-DK08 were investigated for their ability to induce cancer cell death by treating with two leukemic cell lines where NHEJ is high. Results showed that bromoaryl (DK04)- and nitroaryl (DK05)-conjugated molecules showed excellent biological activity, having IC50 values of ∼2 μM in Nalm6 cell lines.
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Affiliation(s)
- Deepak
J. Prabhu
- Post
Graduate Research Department of Chemistry, Maharajas College, Ernakulam, Ernakulam, Kerala 682011, India
| | - Ujjayinee Ray
- Department
of Microbiology, Techno India University,
Kolkata, West Bengal 700091, India
| | - Anjaly Rajeev
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Reshma Joy
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Abi Thoppilan George
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Jinu George
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
| | - Sathees C. Raghavan
- Department
of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Franklin John
- Post
Graduate and Research Department of Chemistry, Sacred Heart college (M.G University), Thevara, Kerala 682013, India
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8
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Vogt A, He Y. Structure and mechanism in non-homologous end joining. DNA Repair (Amst) 2023; 130:103547. [PMID: 37556875 PMCID: PMC10528545 DOI: 10.1016/j.dnarep.2023.103547] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
DNA double-stranded breaks (DSBs) are a particularly challenging form of DNA damage to repair because the damaged DNA must not only undergo the chemical reactions responsible for returning it to its original state, but, additionally, the two free ends can become physically separated in the nucleus and must be bridged prior to repair. In nonhomologous end joining (NHEJ), one of the major pathways of DSB repair, repair is carried out by a number of repair factors capable of binding to and directly joining DNA ends. It has been unclear how these processes are carried out at a molecular level, owing in part to the lack of structural evidence describing the coordination of the NHEJ factors with each other and a DNA substrate. Advances in cryo-Electron Microscopy (cryo-EM), allowing for the structural characterization of large protein complexes that would be intractable using other techniques, have led to the visualization several key steps of the NHEJ process, which support a model of sequential assembly of repair factors at the DSB, followed by end-bridging mediated by protein-protein complexes and transition to full synapsis. Here we examine the structural evidence for these models, devoting particular attention to recent work identifying a new NHEJ intermediate state and incorporating new NHEJ factors into the general mechanism. We also discuss the evolving understanding of end-bridging mechanisms in NHEJ and DNA-PKcs's role in mediating DSB repair.
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Affiliation(s)
- Alex Vogt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, USA.
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9
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Loparo JJ. Holding it together: DNA end synapsis during non-homologous end joining. DNA Repair (Amst) 2023; 130:103553. [PMID: 37572577 PMCID: PMC10530278 DOI: 10.1016/j.dnarep.2023.103553] [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: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023]
Abstract
DNA double strand breaks (DSBs) are common lesions whose misrepair are drivers of oncogenic transformations. The non-homologous end joining (NHEJ) pathway repairs the majority of these breaks in vertebrates by directly ligating DNA ends back together. Upon formation of a DSB, a multiprotein complex is assembled on DNA ends which tethers them together within a synaptic complex. Synapsis is a critical step of the NHEJ pathway as loss of synapsis can result in mispairing of DNA ends and chromosome translocations. As DNA ends are commonly incompatible for ligation, the NHEJ machinery must also process ends to enable rejoining. This review describes how recent progress in single-molecule approaches and cryo-EM have advanced our molecular understanding of DNA end synapsis during NHEJ and how synapsis is coordinated with end processing to determine the fidelity of repair.
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Affiliation(s)
- Joseph J Loparo
- Dept. of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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10
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Hardwick SW, Stavridi AK, Chirgadze DY, De Oliveira TM, Charbonnier JB, Ropars V, Meek K, Blundell TL, Chaplin AK. Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ. Structure 2023; 31:895-902.e3. [PMID: 37311458 DOI: 10.1016/j.str.2023.05.013] [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: 02/07/2023] [Revised: 04/11/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ultimately lead to diseases including cancer. Non-homologous end joining (NHEJ) is one of two core mechanisms utilized to repair DSBs. DNA-PK is a key component in this process and has recently been shown to form alternate long-range synaptic dimers. This has led to the proposal that these complexes can be formed before transitioning to a short-range synaptic complex. Here we present cryo-EM data representing an NHEJ supercomplex consisting of a trimer of DNA-PK in complex with XLF, XRCC4, and DNA Ligase IV. This trimer represents a complex of both long-range synaptic dimers. We discuss the potential role of the trimeric structure, and possible higher order oligomers, as structural intermediates in the NHEJ mechanism, or as functional DNA repair centers.
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Affiliation(s)
- Steven W Hardwick
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Dimitri Y Chirgadze
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | | | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Amanda K Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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11
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Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, Ferrage F. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548668. [PMID: 37503201 PMCID: PMC10369993 DOI: 10.1101/2023.07.12.548668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70/80 heterodimer (Ku), XRCC4 in complex with DNA Ligase 4 (X4L4), and XLF form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) have recently been obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here, we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at atomic resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs led to the formation of XLF and X4L4 condensates in vitro which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome editing strategies.
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Affiliation(s)
- Duc-Duy Vu
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Manon Brenière
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Philippe Pelupessy
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ziqing Wang
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ludovic Carlier
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Guillaume Bouvignies
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, 160 Convent Avenue, New York, NY 10029, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Martin Blackledge
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Zoher Gueroui
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Fabien Ferrage
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
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12
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Watanabe G, Lieber MR. The flexible and iterative steps within the NHEJ pathway. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:105-119. [PMID: 37150451 PMCID: PMC10205690 DOI: 10.1016/j.pbiomolbio.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Cellular and biochemical studies of nonhomologous DNA end joining (NHEJ) have long established that nuclease and polymerase action are necessary for the repair of a very large fraction of naturally-arising double-strand breaks (DSBs). This conclusion is derived from NHEJ studies ranging from yeast to humans and all genetically-tractable model organisms. Biochemical models derived from recent real-time and structural studies have yet to incorporate physical space or timing for DNA end processing. In real-time single molecule FRET (smFRET) studies, we analyzed NHEJ synapsis of DNA ends in a defined biochemical system. We described a Flexible Synapsis (FS) state in which the DNA ends were in proximity via only Ku and XRCC4:DNA ligase 4 (X4L4), and in an orientation that would not yet permit ligation until base pairing between one or more nucleotides of microhomology (MH) occurred, thereby allowing an in-line Close Synapsis (CS) state. If no MH was achievable, then XLF was critical for ligation. Neither FS or CS required DNA-PKcs, unless Artemis activation was necessary to permit local resection and subsequent base pairing between the two DNA ends being joined. Here we conjecture on possible 3D configurations for this FS state, which would spatially accommodate the nuclease and polymerase processing steps in an iterative manner. The FS model permits repeated attempts at ligation of at least one strand at the DSB after each round of nuclease or polymerase action. In addition to activation of Artemis, other possible roles for DNA-PKcs are discussed.
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Affiliation(s)
- Go Watanabe
- Departments of Pathology, Biochemistry, Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), University of Southern California, Los Angeles, CA, 90089-9176, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry, Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), University of Southern California, Los Angeles, CA, 90089-9176, USA.
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13
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Nishikubo K, Hasegawa M, Izumi Y, Fujii K, Matsuo K, Matsumoto Y, Yokoya A. Structural study of wild-type and phospho-mimic XRCC4 dimer and multimer proteins using circular dichroism spectroscopy. Int J Radiat Biol 2023; 99:1684-1691. [PMID: 37171809 DOI: 10.1080/09553002.2023.2214210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE To investigate the structural features of wild-type and phospho-mimicking mutated XRCC4 protein, a protein involved in DNA double-strand break repair. MATERIALS AND METHODS XRCC4 with a HisTag were expressed by E. coli harboring plasmid DNA and purified. Phospho-mimicking mutants in which one phosphorylation site was replaced with aspartic acid were also prepared in order to reproduce the negative charge resulting from phosphorylation. The proteins were separated into dimers and multimers by gel filtration chromatography. Circular dichroism (CD) spectroscopy was performed in the region from ultraviolet to vacuum-ultraviolet. The CD spectra were analyzed with two analysis programs to evaluate the secondary structures of the wild-type and phospho-mimicked dimers and multimers. RESULT AND DISCUSSION The proportion of β-strand in the wild-type dimers was very low, particularly in their C-terminal region, including the five phosphorylation sites. The secondary structure of the phospho-mimic hardly changed in the dimeric form. In contrast, the β-strand content increased and the α-helix content decreased upon multimerization of the wild-type protein. The structural change of multimers slightly depended on the phospho-mimic site. These results suggest that the β-strand structure stabilizes the multimerization of XRCC4 and it is regulated by phosphorylation at the C-terminal site in living cells. CONCLUSION An increase in the β-strand content in XRCC4 is essential for stabilization of the multimeric form through C-terminal phosphorylation, allowing the formation of the large double-strand break repair machinery.
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Affiliation(s)
- Kai Nishikubo
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Maho Hasegawa
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Yudai Izumi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Kentaro Fujii
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Akinari Yokoya
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
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14
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De Bragança S, Aicart-Ramos C, Arribas-Bosacoma R, Rivera-Calzada A, Unfried JP, Prats-Mari L, Marin-Baquero M, Fortes P, Llorca O, Moreno-Herrero F. APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining. Cell Rep 2023; 42:111917. [PMID: 36640344 DOI: 10.1016/j.celrep.2022.111917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023] Open
Abstract
The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). This is performed by a multicomponent protein complex assembled around Ku70-Ku80 heterodimers and regulated by accessory factors, including long non-coding RNAs, through poorly understood mechanisms. Here, we use magnetic tweezers to investigate the contributions of core NHEJ proteins and APLF and lncRNA NIHCOLE to DNA synapsis. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis for several minutes under piconewton forces. We find the C-terminal acidic region of APLF to be critical for bridging. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF. This effect is further enhanced by a small and structured RNA domain within NIHCOLE. We propose a model where Ku70-Ku80 can simultaneously bind DNA, APLF, and structured RNAs to promote the stable joining of DNA ends.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Juan Pablo Unfried
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain.
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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15
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Cisneros-Aguirre M, Lopezcolorado FW, Tsai LJ, Bhargava R, Stark JM. The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened. Nat Commun 2022; 13:3662. [PMID: 35760797 PMCID: PMC9237100 DOI: 10.1038/s41467-022-31365-6] [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: 01/20/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
Canonical non-homologous end joining (C-NHEJ) factors can assemble into a long-range (LR) complex with DNA ends relatively far apart that contains DNAPKcs, XLF, XRCC4, LIG4, and the KU heterodimer and a short-range (SR) complex lacking DNAPKcs that has the ends positioned for ligation. Since the SR complex can form de novo, the role of the LR complex (i.e., DNAPKcs) for chromosomal EJ is unclear. We have examined EJ of chromosomal blunt DNA double-strand breaks (DSBs), and found that DNAPKcs is significantly less important than XLF for such EJ. However, weakening XLF via disrupting interaction interfaces causes a marked requirement for DNAPKcs, its kinase activity, and its ABCDE-cluster autophosphorylation sites for blunt DSB EJ. In contrast, other aspects of genome maintenance are sensitive to DNAPKcs kinase inhibition in a manner that is not further enhanced by XLF loss (i.e., suppression of homology-directed repair and structural variants, and IR-resistance). We suggest that DNAPKcs is required to position a weakened XLF in an LR complex that can transition into a functional SR complex for blunt DSB EJ, but also has distinct functions for other aspects of genome maintenance. DNAPKcs and its kinase activity are required for blunt DNA break end joining when the bridging factor XLF is weakened, but for homologous recombination and radiation resistance, the influence of DNAPKcs is not further enhanced with loss of XLF.
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Affiliation(s)
- Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Felicia Wednesday Lopezcolorado
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Linda Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA. .,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.
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16
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Cabello-Lobato MJ, Jenner M, Cisneros-Aguirre M, Brüninghoff K, Sandy Z, da Costa I, Jowitt T, Loch C, Jackson S, Wu Q, Mootz H, Stark J, Cliff M, Schmidt C. Microarray screening reveals two non-conventional SUMO-binding modules linked to DNA repair by non-homologous end-joining. Nucleic Acids Res 2022; 50:4732-4754. [PMID: 35420136 PMCID: PMC9071424 DOI: 10.1093/nar/gkac237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
SUMOylation is critical for numerous cellular signalling pathways, including the maintenance of genome integrity via the repair of DNA double-strand breaks (DSBs). If misrepaired, DSBs can lead to cancer, neurodegeneration, immunodeficiency and premature ageing. Using systematic human proteome microarray screening combined with widely applicable carbene footprinting, genetic code expansion and high-resolution structural profiling, we define two non-conventional and topology-selective SUMO2-binding regions on XRCC4, a DNA repair protein important for DSB repair by non-homologous end-joining (NHEJ). Mechanistically, the interaction of SUMO2 and XRCC4 is incompatible with XRCC4 binding to three other proteins important for NHEJ-mediated DSB repair. These findings are consistent with SUMO2 forming a redundant NHEJ layer with the potential to regulate different NHEJ complexes at distinct levels including, but not limited to, XRCC4 interactions with XLF, LIG4 and IFFO1. Regulation of NHEJ is not only relevant for carcinogenesis, but also for the design of precision anti-cancer medicines and the optimisation of CRISPR/Cas9-based gene editing. In addition to providing molecular insights into NHEJ, this work uncovers a conserved SUMO-binding module and provides a rich resource on direct SUMO binders exploitable towards uncovering SUMOylation pathways in a wide array of cellular processes.
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Affiliation(s)
- Maria Jose Cabello-Lobato
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Kira Brüninghoff
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149 Muenster, Germany
| | - Zac Sandy
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Isabelle C da Costa
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Qian Wu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149 Muenster, Germany
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Matthew J Cliff
- Manchester Institute of Biotechnology (MIB) and School of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Christine K Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
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17
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Libri A, Marton T, Deriano L. The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination. Front Genet 2022; 12:823943. [PMID: 35082840 PMCID: PMC8785701 DOI: 10.3389/fgene.2021.823943] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
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Affiliation(s)
- Alice Libri
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Timea Marton
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
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18
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WASH interacts with Ku to regulate DNA double-stranded break repair. iScience 2022; 25:103676. [PMID: 35036867 PMCID: PMC8749218 DOI: 10.1016/j.isci.2021.103676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/12/2021] [Accepted: 12/20/2021] [Indexed: 12/28/2022] Open
Abstract
The Wiskott-Aldrich syndrome protein and SCAR homolog (WASH), an actin nucleation-promoting factor, is present in the nucleus where it regulates gene transcription and maintains nuclear organization. Here, we show that WASH interacts with core non-homologous end-joining (NHEJ) factors including Ku70/Ku80 and DNA-PKcs, and Ku70/Ku80 is involved in the recruitment of WASH to the sites of DNA double-stranded break (DSB). WASH depletion leads to increased cell sensitivity and impaired DNA repair capacity in response to etoposide-induced DSBs and reduces NHEJ efficiency. Mechanistically, we show that loss of WASH inhibits the phosphorylation of DNA-PKcs, H2AX, and KAP1 after DSB induction and reduces chromatin relaxation and the recruitment of several downstream NHEJ factors to DSBs. Moreover, WASH role in DSB repair depends on its conserved C-terminal VCA domain and Arp2/3 activation. Our findings reveal a function and mechanistic insight for WASH in DNA DSB repair by the NHEJ pathway.
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19
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Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods Mol Biol 2022; 2444:43-68. [PMID: 35290631 PMCID: PMC9020468 DOI: 10.1007/978-1-0716-2063-2_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kathryn H Burnett
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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20
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Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Front Immunol 2021; 12:797880. [PMID: 34970273 PMCID: PMC8712645 DOI: 10.3389/fimmu.2021.797880] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
The DNA damage response (DDR) is an organized network of multiple interwoven components evolved to repair damaged DNA and maintain genome fidelity. Conceptually the DDR includes damage sensors, transducer kinases, and effectors to maintain genomic stability and accurate transmission of genetic information. We have recently gained a substantially improved molecular and mechanistic understanding of how DDR components are interconnected to inflammatory and immune responses to stress. DDR shapes both innate and adaptive immune pathways: (i) in the context of innate immunity, DDR components mainly enhance cytosolic DNA sensing and its downstream STimulator of INterferon Genes (STING)-dependent signaling; (ii) in the context of adaptive immunity, the DDR is needed for the assembly and diversification of antigen receptor genes that is requisite for T and B lymphocyte development. Imbalances between DNA damage and repair impair tissue homeostasis and lead to replication and transcription stress, mutation accumulation, and even cell death. These impacts from DDR defects can then drive tumorigenesis, secretion of inflammatory cytokines, and aberrant immune responses. Yet, DDR deficiency or inhibition can also directly enhance innate immune responses. Furthermore, DDR defects plus the higher mutation load in tumor cells synergistically produce primarily tumor-specific neoantigens, which are powerfully targeted in cancer immunotherapy by employing immune checkpoint inhibitors to amplify immune responses. Thus, elucidating DDR-immune response interplay may provide critical connections for harnessing immunomodulatory effects plus targeted inhibition to improve efficacy of radiation and chemotherapies, of immune checkpoint blockade, and of combined therapeutic strategies.
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Affiliation(s)
- Zu Ye
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yin Shi
- Department of Immunology, Zhejiang University School of Medicine, Hangzhou, China
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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21
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DNA Repair in Haploid Context. Int J Mol Sci 2021; 22:ijms222212418. [PMID: 34830299 PMCID: PMC8620282 DOI: 10.3390/ijms222212418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 12/15/2022] Open
Abstract
DNA repair is a well-covered topic as alteration of genetic integrity underlies many pathological conditions and important transgenerational consequences. Surprisingly, the ploidy status is rarely considered although the presence of homologous chromosomes dramatically impacts the repair capacities of cells. This is especially important for the haploid gametes as they must transfer genetic information to the offspring. An understanding of the different mechanisms monitoring genetic integrity in this context is, therefore, essential as differences in repair pathways exist that differentiate the gamete’s role in transgenerational inheritance. Hence, the oocyte must have the most reliable repair capacity while sperm, produced in large numbers and from many differentiation steps, are expected to carry de novo variations. This review describes the main DNA repair pathways with a special emphasis on ploidy. Differences between Saccharomyces cerevisiae and Schizosaccharomyces pombe are especially useful to this aim as they can maintain a diploid and haploid life cycle respectively.
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22
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Kong M, Greene EC. Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks. Front Cell Dev Biol 2021; 9:745311. [PMID: 34869333 PMCID: PMC8636147 DOI: 10.3389/fcell.2021.745311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
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23
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Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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24
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Joshi JS, Vora HH, Ghosh NR, Tankshali RN, Jetly DH, Trivedi TI. Nonhomologous end joining repair pathway molecules as predictive biomarkers for patients with oral squamous cell carcinoma. J Cancer Res Ther 2021; 17:1031-1038. [PMID: 34528560 DOI: 10.4103/jcrt.jcrt_582_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose Nonhomologous end-joining (NHEJ) is critical for the repair of either pathologic double-strand breaks (DSBs) and/or for the repair of physiologic DSBs created during radiotherapy to kill the tumor cell. Therefore, patients with higher expression of NHEJ repair proteins might develop resistance to ionizing radiation, allowing the disease to recur. As cancer of the oral cavity is a serious health problem globally, the present study aimed to examine the expression of Ku70/80, X-ray repair cross-complementing protein 4 (XRCC4) and DNA ligase IV-core molecules of the NHEJ pathway in patients with oral cancer. Materials and Methods Protein expression of Ku70/80, XRCC4, and DNA ligase IV were studied by Immunohistochemistry and mRNA expression of Ku70 and Ku80 were studied using reverse transcription polymerase chain reaction. Data were analyzed statistically using SPSS. Results A univariate survival analysis revealed an association of Ku70 mRNA with shorter overall survival (OS). While protein expression of XRCC4 showed an association with reduced relapse-free survival and shorter OS. Multivariate survival analysis demonstrated that XRCC4 and DNA ligase IV are independent prognosticators for predicting adverse disease outcomes. Conclusion Strong expression of repair proteins - XRCC4 and DNA ligase IV is associated with unfavorable disease outcome in patients with oral squamous cell carcinoma.
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Affiliation(s)
- Jigna S Joshi
- Stem Cell Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Immunohematology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Nandita R Ghosh
- Tumor Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Rajen N Tankshali
- Department of Surgical Oncology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Dhaval H Jetly
- Department of Onco-Pathology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Trupti I Trivedi
- Clinical Carcinogenesis Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
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25
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Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL. Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Mol Cell 2021; 81:3400-3409.e3. [PMID: 34352203 PMCID: PMC9006396 DOI: 10.1016/j.molcel.2021.07.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair.
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Affiliation(s)
- Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Steven W Hardwick
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Christopher J Buehl
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Noah J Goff
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Shikang Liang
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Dimitri Y Chirgadze
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK.
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26
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McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
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27
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Liang S, Chaplin AK, Stavridi AK, Appleby R, Hnizda A, Blundell TL. Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:60-73. [PMID: 33285184 PMCID: PMC8224183 DOI: 10.1016/j.pbiomolbio.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/26/2020] [Indexed: 01/10/2023]
Abstract
Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspects of the repair pathway: stages, scaffolds and strings. We discuss the orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades, not only using X-ray diffraction, but also increasingly exploiting cryo-EM to investigate the macromolecular assemblies.
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Affiliation(s)
- Shikang Liang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK.
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28
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Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
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Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
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29
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Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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30
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Jensen RB, Rothenberg E. Preserving genome integrity in human cells via DNA double-strand break repair. Mol Biol Cell 2021; 31:859-865. [PMID: 32286930 PMCID: PMC7185975 DOI: 10.1091/mbc.e18-10-0668] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The efficient maintenance of genome integrity in the face of cellular stress is vital to protect against human diseases such as cancer. DNA replication, chromatin dynamics, cellular signaling, nuclear architecture, cell cycle checkpoints, and other cellular activities contribute to the delicate spatiotemporal control that cells utilize to regulate and maintain genome stability. This perspective will highlight DNA double-strand break (DSB) repair pathways in human cells, how DNA repair failures can lead to human disease, and how PARP inhibitors have emerged as a novel clinical therapy to treat homologous recombination-deficient tumors. We briefly discuss how failures in DNA repair produce a permissive genetic environment in which preneoplastic cells evolve to reach their full tumorigenic potential. Finally, we conclude that an in-depth understanding of DNA DSB repair pathways in human cells will lead to novel therapeutic strategies to treat cancer and potentially other human diseases.
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Affiliation(s)
- Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
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31
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Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y. Structural basis of long-range to short-range synaptic transition in NHEJ. Nature 2021; 593:294-298. [PMID: 33854234 PMCID: PMC8122075 DOI: 10.1038/s41586-021-03458-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis1,2. The conserved error-prone non-homologous end joining (NHEJ) pathway has a key role in determining the effects of DSB-inducing agents that are used to treat cancer as well as the generation of the diversity in antibodies and T cell receptors2,3. Here we applied single-particle cryo-electron microscopy to visualize two key DNA-protein complexes that are formed by human NHEJ factors. The Ku70/80 heterodimer (Ku), the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), DNA ligase IV (LigIV), XRCC4 and XLF form a long-range synaptic complex, in which the DNA ends are held approximately 115 Å apart. Two DNA end-bound subcomplexes comprising Ku and DNA-PKcs are linked by interactions between the DNA-PKcs subunits and a scaffold comprising LigIV, XRCC4, XLF, XRCC4 and LigIV. The relative orientation of the DNA-PKcs molecules suggests a mechanism for autophosphorylation in trans, which leads to the dissociation of DNA-PKcs and the transition into the short-range synaptic complex. Within this complex, the Ku-bound DNA ends are aligned for processing and ligation by the XLF-anchored scaffold, and a single catalytic domain of LigIV is stably associated with a nick between the two Ku molecules, which suggests that the joining of both strands of a DSB involves both LigIV molecules.
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Affiliation(s)
- Siyu Chen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Tasmin Naila
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
- Department of Molecular Genetics & Microbiology, University of New Mexico, Albuquerque, NM, USA
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Susan Fishbain
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Annie Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alan E Tomkinson
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
- Department of Molecular Genetics & Microbiology, University of New Mexico, Albuquerque, NM, USA
- University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
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32
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Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
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33
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Stinson BM, Loparo JJ. Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. Annu Rev Biochem 2021; 90:137-164. [PMID: 33556282 DOI: 10.1146/annurev-biochem-080320-110356] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.
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Affiliation(s)
- Benjamin M Stinson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
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34
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Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure 2021; 29:467-478.e6. [PMID: 33412091 DOI: 10.1016/j.str.2020.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/14/2020] [Accepted: 12/09/2020] [Indexed: 01/06/2023]
Abstract
In the non-homologous end-joining (NHEJ) of a DNA double-strand break, DNA ends are bound and protected by DNA-PK, which synapses across the break to tether the broken ends and initiate repair. There is little clarity surrounding the nature of the synaptic complex and the mechanism governing the transition to repair. We report an integrative structure of the synaptic complex at a precision of 13.5 Å, revealing a symmetric head-to-head arrangement with a large offset in the DNA ends and an extensive end-protection mechanism involving a previously uncharacterized plug domain. Hydrogen/deuterium exchange mass spectrometry identifies an allosteric pathway connecting DNA end-binding with the kinase domain that places DNA-PK under tension in the kinase-active state. We present a model for the transition from end-protection to repair, where the synaptic complex supports hierarchical processing of the ends and scaffold assembly, requiring displacement of the catalytic subunit and tension release through kinase activity.
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Affiliation(s)
- Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Shujuan Fang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Claire Atkinson
- Department of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada; Department of Chemistry, University of Calgary, Calgary, AB, Canada.
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Lee W, Park JW, Go YJ, Kim WJ, Rhee YM. Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers. RSC Adv 2021; 11:9315-9326. [PMID: 35423456 PMCID: PMC8695334 DOI: 10.1039/d0ra10106k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 11/21/2022] Open
Abstract
Considering both small and large scale motions of VEGF is crucial to predict its relative binding affinities to DNA aptamer variants with docking.
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Affiliation(s)
- Wook Lee
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Korea
- Department of Chemistry
| | - Jae Whee Park
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
| | - Yeon Ju Go
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
| | - Won Jong Kim
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Korea
| | - Young Min Rhee
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
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Carney SM, Moreno AT, Piatt SC, Cisneros-Aguirre M, Lopezcolorado FW, Stark JM, Loparo JJ. XLF acts as a flexible connector during non-homologous end joining. eLife 2020; 9:e61920. [PMID: 33289484 PMCID: PMC7744095 DOI: 10.7554/elife.61920] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/07/2020] [Indexed: 01/01/2023] Open
Abstract
Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-strand breaks in vertebrates. During NHEJ DNA ends are held together by a multi-protein synaptic complex until they are ligated. Here, we use Xenopus laevis egg extract to investigate the role of the intrinsically disordered C-terminal tail of the XRCC4-like factor (XLF), a critical factor in end synapsis. We demonstrate that the XLF tail along with the Ku-binding motif (KBM) at the extreme C-terminus are required for end joining. Although the underlying sequence of the tail can be varied, a minimal tail length is required for NHEJ. Single-molecule FRET experiments that observe end synapsis in real-time show that this defect is due to a failure to closely align DNA ends. Our data supports a model in which a single C-terminal tail tethers XLF to Ku, while allowing XLF to form interactions with XRCC4 that enable synaptic complex formation.
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Affiliation(s)
- Sean M Carney
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Andrew T Moreno
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Sadie C Piatt
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
- Harvard Graduate Program in Biophysics, Harvard Medical SchoolBostonUnited States
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of HopeDuarteUnited States
| | | | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of HopeDuarteUnited States
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
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Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat Struct Mol Biol 2020; 28:13-19. [DOI: 10.1038/s41594-020-00517-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/08/2020] [Indexed: 11/08/2022]
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Hammel M, Rosenberg DJ, Bierma J, Hura GL, Thapar R, Lees-Miller SP, Tainer JA. Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:74-86. [PMID: 32966823 DOI: 10.1016/j.pbiomolbio.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022]
Abstract
Assembly of KU and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) at DNA double strand breaks (DSBs) forms DNA-PK holoenzyme as a critical initiating step for non-homologous end joining (NHEJ) repair of DSBs produced by radiation and chemotherapies. Advanced cryo-electron microscopy (cryo-EM) imaging together with breakthrough macromolecular X-ray crystal (MX) structures of KU and DNA-PKcs recently enabled visualization of the ∼600 kDa DNA-PK assembly at near atomic resolution. These important static structures provide the foundation for definition and interpretation of functional movements crucial to mechanistic understanding that can be tested through solution state structure analysis. We herein therefore leverage Cryo-EM and MX structures for the interpretation of synchrotron small-angle X-ray scattering (SAXS) data on DNA-PK conformations in solution to inform the structural mechanism for NHEJ initiation. SAXS, which measures thermodynamic solution-state conformational states and assemblies outside of cryo- and solid-state conditions, unveils the inherent flexibility of KU, DNA-PKcs and DNA-PK. The combined structural measurements reveal mobility of KU80 C-terminal region (KU80CTR), motion/plasticity of HEAT (DNA-PKcs Huntingtin, Elongation Factor 3, PP2 A, and TOR1) regions, allosteric switching upon DNA-PKcs autophosphorylation, and dimeric arrangements of DNA-PK assembly. Importantly, the results uncover displacement of the N-terminal HEAT domain during autophosphorylation as suitable for a regulated release mechanism of DNA-PKcs from DNA-PK to control unproductive access to toxic and mutagenic DNA repair intermediates. These integrated analyses show that the marriage of SAXS with cryo-EM leverages the strengths of both techniques to enable assessment of functional conformations and flexibility defining atomic-resolution molecular mechanisms for DSB repair.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Graduate Group in Biophysics, University of California, Berkeley, CA, 94720, USA
| | - Jan Bierma
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Gregory L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Roopa Thapar
- Department of Cancer Biology, Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, T2N 4N1, Canada
| | - John A Tainer
- Department of Cancer Biology, Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Vujin A, Jones SJ, Zetka M. NHJ-1 Is Required for Canonical Nonhomologous End Joining in Caenorhabditis elegans. Genetics 2020; 215:635-651. [PMID: 32457132 PMCID: PMC7337088 DOI: 10.1534/genetics.120.303328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a particularly lethal form of DNA damage that must be repaired to restore genomic integrity. Canonical nonhomologous end joining (NHEJ), is a widely conserved pathway that detects and directly ligates the broken ends to repair the DSB. These events globally require the two proteins that form the Ku ring complex, Ku70 and Ku80, and the terminal ligase LIG4. While the NHEJ pathway in vertebrates is elaborated by more than a dozen factors of varying conservation and is similarly complex in other eukaryotes, the entire known NHEJ toolkit in Caenorhabditis elegans consists only of the core components CKU-70, CKU-80, and LIG-4 Here, we report the discovery of the first accessory NHEJ factor in C. elegans Our analysis of the DNA damage response in young larvae revealed that the canonical wild-type N2 strain consisted of two lines that exhibited a differential phenotypic response to ionizing radiation (IR). Following the mapping of the causative locus to a candidate on chromosome V and clustered regularly interspaced short palindromic repeats-Cas9 mutagenesis, we show that disruption of the nhj-1 sequence induces IR sensitivity in the N2 line that previously exhibited IR resistance. Using genetic and cytological analyses, we demonstrate that nhj-1 functions in the NHEJ pathway to repair DSBs. Double mutants of nhj-1 and lig-4 or cku-80 do not exhibit additive IR sensitivity, and the post-IR somatic and fertility phenotypes of nhj-1 mimic those of the other NHEJ factors. Furthermore, in com-1 mutants that permit repair of meiotic DSBs by NHEJ instead of restricting their repair to the homologous recombination pathway, loss of nhj-1 mimics the consequences of loss of lig-4 Diakinesis-stage nuclei in nhj-1; com-1 and nhj-1; lig-4 mutant germlines exhibit increased numbers of DAPI-staining bodies, consistent with increased chromosome fragmentation in the absence of NHEJ-mediated meiotic DSB repair. Finally, we show that NHJ-1 and LIG-4 localize to somatic nuclei in larvae, but are excluded from the germline progenitor cells, consistent with NHEJ being the dominant DNA repair pathway in the soma. nhj-1 shares no sequence homology with other known eukaryotic NHEJ factors and is taxonomically restricted to the Rhabditid family, underscoring the evolutionary plasticity of even highly conserved pathways.
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Affiliation(s)
- Aleksandar Vujin
- Department of Biology, McGill University, Montreal, Quebec H3K 1M4, Canada
| | - Steven J Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Monique Zetka
- Department of Biology, McGill University, Montreal, Quebec H3K 1M4, Canada
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Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining. Curr Opin Struct Biol 2020; 61:9-16. [DOI: 10.1016/j.sbi.2019.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 01/19/2023]
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Structural mechanism of DNA-end synapsis in the non-homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends. Biochem Soc Trans 2020; 47:1609-1619. [PMID: 31829407 DOI: 10.1042/bst20180518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022]
Abstract
Non-homologous end joining (NHEJ) is a major repair pathway for DNA double-strand breaks (DSBs), which is the most toxic DNA damage in cells. Unrepaired DSBs can cause genome instability, tumorigenesis or cell death. DNA end synapsis is the first and probably the most important step of the NHEJ pathway, aiming to bring two broken DNA ends close together and provide structural stability for end processing and ligation. This process is mediated through a group of NHEJ proteins forming higher-order complexes, to recognise and bridge two DNA ends. Spatial and temporal understanding of the structural mechanism of DNA-end synapsis has been largely advanced through recent structural and single-molecule studies of NHEJ proteins. This review focuses on core NHEJ proteins that mediate DNA end synapsis through their unique structures and interaction properties, as well as how they play roles as anchor and linker proteins during the process of 'bridge over troubled ends'.
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Ruis B, Molan A, Takasugi T, Hendrickson EA. Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination. DNA Repair (Amst) 2019; 85:102738. [PMID: 31731258 DOI: 10.1016/j.dnarep.2019.102738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
The repair of DNA double-stranded breaks (DSBs) is an essential function performed by the Classical Non-Homologous End-Joining (C-NHEJ) pathway in higher eukaryotes. C-NHEJ, in fact, does double duty as it is also required for the repair of the intermediates formed during lymphoid B- and T-cell recombination. Consequently, the failure to properly repair DSBs leads to both genomic instability and immunodeficiency. A critical DSB protein required for C-NHEJ is the DNA Ligase IV (LIGIV) accessory factor, X-Ray Cross Complementing 4 (XRCC4). XRCC4 is believed to stabilize LIGIV, participate in LIGIV activation, and to help tether the broken DSB ends together. XRCC4's role in these processes has been muddied by the identification of two additional XRCC4 paralogs, XRCC4-Like Factor (XLF), and Paralog of XRCC4 and XLF (PAXX). The roles that these paralogs play in C-NHEJ is partially understood, but, in turn, has itself been obscured by species-specific differences observed in the absence of one or the other paralogs. In order to investigate the role(s) that XRCC4 may play, with or without XLF and/or PAXX, in lymphoid variable(diversity)joining [V(D)J] recombination as well as in DNA DSB repair in human somatic cells, we utilized gene targeting to inactivate the XRCC4 gene in both parental and XLF- HCT116 cells and then inactivated PAXX in those same cell lines. The loss of XRCC4 expression by itself led, as anticipated, to increased sensitivity to DNA damaging agents as well as an increased dependence on microhomology-mediated DNA repair whether in the context of DSB repair or during V(D)J recombination. The additional loss of XLF in these cell lines sensitized the cells even more whereas the presence or absence of PAXX was scarcely negligible. These studies demonstrate that, of the three LIG4 accessory factor paralogs, the absence of XRCC4 influences DNA repair and recombination the most in human cells.
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Affiliation(s)
- Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Amy Molan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States.
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Liu Z, Yu M, Fei B, Sun J, Wang D. Identification Of Natural Compound Derivative For Inhibition Of XLF And Overcoming Chemoresistance In Colorectal Cancer Cells. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:3823-3834. [PMID: 31806933 PMCID: PMC6847993 DOI: 10.2147/dddt.s215967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022]
Abstract
Purpose A previous study has identified that XRCC4-like factor (XLF) is a potential target to overcome resistance to 5-fluorouracil (5-Fu) and oxaliplatin (OXA) in colorectal cancer (CRC). The purpose of this study is to develop potent XLF inhibitors to chemoresistance in CRC. Methods Virtual screening was adopted to identify novel XLF-binding compounds by initially testing 6800 molecules in Chemical Entities of Biological Interest library. Hit compounds were further validated by Western blot assay. Cell sensitivity to 5-Fu and OXA was measured using sulforhodamine B assay. The effect of XLF inhibitor on DNA repair efficiency was evaluated by comet assay, fluorescent-based nonhomologous end joining (NHEJ) and homologous recombination (HR) reporter assays. DNA-binding activity of NHEJ key factors was examined by chromatin fractionation assay. Results We identified G3, a novel and potent XLF inhibitor (IC50 0.47±0.02 µM). G3 induced XLF protein degradation in CRC cells. Significantly, G3 improved cell sensitivity to 5-Fu and OXA in chemoresistant CRC cell lines. Mechanistically, G3 depleted XLF expression, severely compromised NHEJ efficiency by up to 65% and inhibited NHEJ key factor assembly on DNA. G3 also inhibited HR efficiency in a time-dependent manner. Conclusion These results suggest that G3 overcomes 5-Fu and OXA resistance in CRC cells by inhibiting XLF expression. Thus, XLF is a promising target and its inhibitor G3 is a potential candidate for treatment of chemoresistant CRC patients.
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Affiliation(s)
- Zhuo Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Miao Yu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Bingyuan Fei
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Jing Sun
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Dongxin Wang
- Department of Anesthesiology, Jilin Cancer Hospital, Jilin, People's Republic of China
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Li W, Bai X, Li J, Zhao Y, Liu J, Zhao H, Liu L, Ding M, Wang Q, Shi FY, Hou M, Ji J, Gao G, Guo R, Sun Y, Liu Y, Xu D. The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis. Nat Cell Biol 2019; 21:1273-1285. [DOI: 10.1038/s41556-019-0388-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 01/19/2023]
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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: 14] [Impact Index Per Article: 2.3] [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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46
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Chen BR, Quinet A, Byrum AK, Jackson J, Berti M, Thangavel S, Bredemeyer AL, Hindi I, Mosammaparast N, Tyler JK, Vindigni A, Sleckman BP. XLF and H2AX function in series to promote replication fork stability. J Cell Biol 2019; 218:2113-2123. [PMID: 31123184 PMCID: PMC6605786 DOI: 10.1083/jcb.201808134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/03/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Chen et al. show that XLF functions to limit fork reversal during DNA replication. H2AX prevents MRE11-dependent replication stress in XLF-deficient cells, suggesting that H2AX prevents the resection of regressed arms at reversed forks. XRCC4-like factor (XLF) is a non-homologous end joining (NHEJ) DNA double strand break repair protein. However, XLF deficiency leads to phenotypes in mice and humans that are not necessarily consistent with an isolated defect in NHEJ. Here we show that XLF functions during DNA replication. XLF undergoes cell division cycle 7–dependent phosphorylation; associates with the replication factor C complex, a critical component of the replisome; and is found at replication forks. XLF deficiency leads to defects in replication fork progression and an increase in fork reversal. The additional loss of H2AX, which protects DNA ends from resection, leads to a requirement for ATR to prevent an MRE11-dependent loss of newly synthesized DNA and activation of DNA damage response. Moreover, H2ax−/−:Xlf−/− cells exhibit a marked dependence on the ATR kinase for survival. We propose that XLF and H2AX function in series to prevent replication stress induced by the MRE11-dependent resection of regressed arms at reversed replication forks.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea K Byrum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Matteo Berti
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Saravanabhavan Thangavel
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea L Bredemeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Issa Hindi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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Xue R, Peng Y, Han B, Li X, Chen Y, Pei H. Metastasis suppressor NME1 promotes non-homologous end joining of DNA double-strand breaks. DNA Repair (Amst) 2019; 77:27-35. [DOI: 10.1016/j.dnarep.2019.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/03/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
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Multicomponent assemblies in DNA-double-strand break repair by NHEJ. Curr Opin Struct Biol 2019; 55:154-160. [DOI: 10.1016/j.sbi.2019.03.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 03/06/2019] [Accepted: 03/27/2019] [Indexed: 11/17/2022]
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49
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Plugged into the Ku-DNA hub: The NHEJ network. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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50
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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