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 2024:10.1038/s41594-024-01339-x. [PMID: 38898102 DOI: 10.1038/s41594-024-01339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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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: 20] [Impact Index Per Article: 5.0] [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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3
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Gonzalez-Rodriguez Y, Bunting SF. XLF extends its range from DNA repair to replication. J Cell Biol 2019; 218:2075-2076. [PMID: 31189608 PMCID: PMC6605802 DOI: 10.1083/jcb.201905221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The close interplay between DNA replication and repair is underscored by a report from Chen et al. (2019. J. Cell Biol. https://doi.org/10.1083/jcb.201808134) in this issue. The authors demonstrate that the non-homologous end-joining factor XLF promotes the stability of replication forks.
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Affiliation(s)
- Yanira Gonzalez-Rodriguez
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Samuel F Bunting
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ
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4
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Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB. XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat Struct Mol Biol 2018; 25:971-980. [PMID: 30291363 PMCID: PMC6234012 DOI: 10.1038/s41594-018-0133-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.
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Affiliation(s)
- Clement Nemoz
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Amandine Gontier
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pascal Drevet
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jinchao Yu
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurelien Pitois
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Audrey Comte
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christine Delteil
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Nadia Barboule
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Pierre Legrand
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Sonia Baconnais
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126, CNRS, Université Paris-Sud, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Yandong Yin
- New York University School of Medicine, Perlmutter Cancer Center, New York, USA
| | - Satish Tadi
- Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | | | - Imre Berger
- BrisSynBio Centre, School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Eric Le Cam
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126, CNRS, Université Paris-Sud, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Eli Rothenberg
- New York University School of Medicine, Perlmutter Cancer Center, New York, USA
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France.
| | - Jean Baptiste Charbonnier
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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5
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Menon V, Povirk LF. XLF/Cernunnos: An important but puzzling participant in the nonhomologous end joining DNA repair pathway. DNA Repair (Amst) 2017; 58:29-37. [PMID: 28846869 DOI: 10.1016/j.dnarep.2017.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/24/2017] [Accepted: 08/07/2017] [Indexed: 01/15/2023]
Abstract
DNA double strand breaks (DSBs) are one of the most deleterious DNA lesions that promote cell death, genomic instability and carcinogenesis. The two major cellular mechanisms that repair DSBs are Nonhomologous End-Joining (NHEJ) and Homologous Recombination Repair (HRR). NHEJ is the predominant pathway, in which XLF (also called Cernunnos) is a key player. Patients with XLF mutation exhibit microcephaly, lymphopenia, and growth retardation, and are immunodeficient and radiosensitive. During NHEJ, XLF interacts with XRCC4-Ligase IV, stimulates its ligase activity, and forms DNA-binding filaments of alternating XLF and XRCC4 dimers that may serve to align broken DNA and promote ligation of noncomplementary ends. Despite its central role in NHEJ, the effects of XLF deficiency are surprisingly variable in different biological contexts, and different individual cell lines. This review summarizes the role of XLF in NHEJ, and the unexpected complexity of its interplay with other repair factors in supporting radiosurvival and V(D)J recombination.
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Affiliation(s)
- Vijay Menon
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, VA, USA
| | - Lawrence F Povirk
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, VA, USA; Department of Pharmacology and Toxicology, Virginia Commonwealth University, VA, USA.
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6
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Rulten SL, Grundy GJ. Non-homologous end joining: Common interaction sites and exchange of multiple factors in the DNA repair process. Bioessays 2017; 39. [PMID: 28133776 DOI: 10.1002/bies.201600209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-homologous end-joining (NHEJ) is the dominant means of repairing chromosomal DNA double strand breaks (DSBs), and is essential in human cells. Fifteen or more proteins can be involved in the detection, signalling, synapsis, end-processing and ligation events required to repair a DSB, and must be assembled in the confined space around the DNA ends. We review here a number of interaction points between the core NHEJ components (Ku70, Ku80, DNA-PKcs, XRCC4 and Ligase IV) and accessory factors such as kinases, phosphatases, polymerases and structural proteins. Conserved protein-protein interaction sites such as Ku-binding motifs (KBMs), XLF-like motifs (XLMs), FHA and BRCT domains illustrate that different proteins compete for the same binding sites on the core machinery, and must be spatially and temporally regulated. We discuss how post-translational modifications such as phosphorylation, ADP-ribosylation and ubiquitinylation may regulate sequential steps in the NHEJ pathway or control repair at different types of DNA breaks.
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Affiliation(s)
- Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gabrielle J Grundy
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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7
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XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation. Mol Cell Biol 2015; 35:3017-28. [PMID: 26100018 DOI: 10.1128/mcb.01503-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/15/2015] [Indexed: 01/21/2023] Open
Abstract
The classic nonhomologous end-joining (c-NHEJ) pathway is largely responsible for repairing double-strand breaks (DSBs) in mammalian cells. XLF stimulates the XRCC4/DNA ligase IV complex by an unknown mechanism. XLF interacts with XRCC4 to form filaments of alternating XRCC4 and XLF dimers that bridge DNA ends in vitro, providing a mechanism by which XLF might stimulate ligation. Here, we characterize two XLF mutants that do not interact with XRCC4 and cannot form filaments or bridge DNA in vitro. One mutant is fully sufficient in stimulating ligation by XRCC4/Lig4 in vitro; the other is not. This separation-of-function mutant (which must function as an XLF homodimer) fully complements the c-NHEJ deficits of some XLF-deficient cell strains but not others, suggesting a variable requirement for XRCC4/XLF interaction in living cells. To determine whether the lack of XRCC4/XLF interaction (and potential bridging) can be compensated for by other factors, candidate repair factors were disrupted in XLF- or XRCC4-deficient cells. The loss of either ATM or the newly described XRCC4/XLF-like factor, PAXX, accentuates the requirement for XLF. However, in the case of ATM/XLF loss (but not PAXX/XLF loss), this reflects a greater requirement for XRCC4/XLF interaction.
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8
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Koike M, Yutoku Y, Koike A. Dynamic changes in subcellular localization of cattle XLF during cell cycle, and focus formation of cattle XLF at DNA damage sites immediately after irradiation. J Vet Med Sci 2015; 77:1109-14. [PMID: 25947322 PMCID: PMC4591152 DOI: 10.1292/jvms.14-0516] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Clinically, many chemotherapeutics and ionizing radiation (IR) have been applied for the treatment of various types of human and animal malignancies. These treatments kill tumor cells by causing DNA double-strand breaks (DSBs). Core factors of classical nonhomologous DNA-end joining (C-NHEJ) play a vital role in DSB repair. Thus, it is indispensable to clarify the mechanisms of C-NHEJ in order to develop next-generation chemotherapeutics for cancer. The XRCC4-like factor (XLF; also called Cernunnos or NHEJ1) is the lastly identified core NHEJ factor. The localization of core NHEJ factors might play a critical role in regulating NHEJ activity. The localization and function of XLF have not been elucidated in animal species other than mice and humans. Domestic cattle (Bos taurus) are the most common and vital domestic animals in many countries. Here, we show that the localization of cattle XLF changes dynamically during the cell cycle. Furthermore, EYFP-cattle XLF accumulates quickly at microirradiated sites and colocalizes with the DSB marker γH2AX. Moreover, nuclear localization and accumulation of cattle XLF at DSB sites are dependent on 12 amino acids (288-299) of the C-terminal region of XLF (XLF CTR). Furthermore, basic amino acids on the XLF CTR are highly conserved among domestic animals including cattle, goat and horses, suggesting that the CTR is essential for the function of XLF in domestic animals. These findings might be useful to develop the molecular-targeting therapeutic drug taking XLF as a target molecule for human and domestic animals.
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Affiliation(s)
- Manabu Koike
- Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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9
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Francis DB, Kozlov M, Chavez J, Chu J, Malu S, Hanna M, Cortes P. DNA Ligase IV regulates XRCC4 nuclear localization. DNA Repair (Amst) 2014; 21:36-42. [PMID: 24984242 DOI: 10.1016/j.dnarep.2014.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022]
Abstract
DNA Ligase IV, along with its interacting partner XRCC4, are essential for repairing DNA double strand breaks by non-homologous end joining (NHEJ). Together, they complete the final ligation step resolving the DNA break. Ligase IV is regulated by XRCC4 and XLF. However, the mechanism(s) by which Ligase IV control the NHEJ reaction and other NHEJ factor(s) remains poorly characterized. Here, we show that a C-terminal region of Ligase IV (aa 620-800), which encompasses a NLS, the BRCT I, and the XRCC4 interacting region (XIR), is essential for nuclear localization of its co-factor XRCC4. In Ligase IV deficient cells, XRCC4 showed deregulated localization remaining in the cytosol even after induction of DNA double strand breaks. DNA Ligase IV was also required for efficient localization of XLF into the nucleus. Additionally, human fibroblasts that harbor hypomorphic mutations within the Ligase IV gene displayed decreased levels of XRCC4 protein, implicating that DNA Ligase IV is also regulating XRCC4 stability. Our results provide evidence for a role of DNA Ligase IV in controlling the cellular localization and protein levels of XRCC4.
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Affiliation(s)
- Dailia B Francis
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mikhail Kozlov
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jose Chavez
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jennifer Chu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Shruti Malu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mary Hanna
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Patricia Cortes
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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10
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Mahaney BL, Lees-Miller SP, Cobb JA. The C-terminus of Nej1 is critical for nuclear localization and non-homologous end-joining. DNA Repair (Amst) 2013; 14:9-16. [PMID: 24369855 DOI: 10.1016/j.dnarep.2013.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 11/14/2013] [Accepted: 12/03/2013] [Indexed: 11/25/2022]
Abstract
Nej1 is an essential factor in the non-homologous end-joining (NHEJ) pathway and interacts with the DNA ligase complex, Lif1-Dnl4, through interactions with Lif1. We have mapped K331-V338 in the C-terminal region of Nej1 to be critical for its functionality during repair. Truncation and alanine scanning mutagenesis have been used to identify a motif in Nej1, KKRK (331-334), which is important for both nuclear targeting and NHEJ repair after localization. We have identified F335-V338 to be important for proper interaction with Lif1, however this region is not required for Nej1 recruitment to HO endonuclease-induced DNA double-strand breaks in vivo. Phenylalanine at position 335 is particularly important for the role of Nej1 in repair and the loss of association between Nej1 and Lif1 correlates with a decrease in cell survival upon either transient or continuous HO expression in nej1 mutants.
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Affiliation(s)
- Brandi L Mahaney
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Jennifer A Cobb
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1.
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11
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Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol 2013; 91:31-41. [PMID: 23442139 DOI: 10.1139/bcb-2012-0058] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) pathway. One of the most critical steps in NHEJ is ligation of DNA ends by DNA ligase IV (LIG4), which interacts with, and is stabilized by, the scaffolding protein X-ray cross-complementing gene 4 (XRCC4). XRCC4 also interacts with XRCC4-like factor (XLF, also called Cernunnos); yet, XLF has been one of the least mechanistically understood proteins and precisely how XLF functions in NHEJ has been enigmatic. Here, we examine current combined structural and mutational findings that uncover integrated functions of XRCC4 and XLF and reveal their interactions to form long, helical protein filaments suitable to protect and align DSB ends. XLF-XRCC4 provides a global structural scaffold for ligating DSBs without requiring long DNA ends, thus ensuring accurate and efficient ligation and repair. The assembly of these XRCC4-XLF filaments, providing both DNA end protection and alignment, may commit cells to NHEJ with general biological implications for NHEJ and DSB repair processes and their links to cancer predispositions and interventions.
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Affiliation(s)
- Brandi L Mahaney
- Department of Biochemistry, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions. Biochem Soc Trans 2012; 39:1387-92, suppl 2 p following 1392. [PMID: 21936820 DOI: 10.1042/bst0391387] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
XRCC4 (X-ray cross-complementation group 4) and XLF (XRCC4-like factor) are two essential interacting proteins in the human NHEJ (non-homologous end-joining) pathway that repairs DNA DSBs (double-strand breaks). The individual crystal structures show that the dimeric proteins are homologues with protomers containing head domains and helical coiled-coil tails related by approximate two-fold symmetry. Biochemical, mutagenesis, biophysical and structural studies have identified the regions of interaction between the two proteins and suggested models for the XLF-XRCC4 complex. An 8.5 Å (1 Å = 0.1 nm) resolution crystal structure of XLF-XRCC4 solved by molecular replacement, together with gel filtration and nano-ESI (nano-electrospray ionization)-MS results, demonstrates that XLF and XRCC4 dimers interact through their head domains and form an alternating left-handed helical structure with polypeptide coiled coils and pseudo-dyads of individual XLF and XRCC4 dimers at right angles to the helical axis.
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13
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Hammel M, Rey M, Yu Y, Mani RS, Classen S, Liu M, Pique ME, Fang S, Mahaney BL, Weinfeld M, Schriemer DC, Lees-Miller SP, Tainer JA. XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J Biol Chem 2011; 286:32638-50. [PMID: 21775435 PMCID: PMC3173232 DOI: 10.1074/jbc.m111.272641] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/07/2011] [Indexed: 11/06/2022] Open
Abstract
The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, we report the XLF-XRCC4 complex crystal structure in combination with biophysical and mutational analyses to define the XLF-XRCC4 interactions. Crystal and solution structures plus mutations characterize alternating XRCC4 and XLF head domain interfaces forming parallel super-helical filaments. XLF Leu-115 ("Leu-lock") inserts into a hydrophobic pocket formed by XRCC4 Met-59, Met-61, Lys-65, Lys-99, Phe-106, and Leu-108 in synergy with pseudo-symmetric β-zipper hydrogen bonds to drive specificity. XLF C terminus and DNA enhance parallel filament formation. Super-helical XLF-XRCC4 filaments form a positively charged channel to bind DNA and align ends for efficient ligation. Collective results reveal how human XLF and XRCC4 interact to bind DNA, suggest consequences of patient mutations, and support a unified molecular mechanism for XLF-XRCC4 stimulation of DNA ligation.
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Affiliation(s)
- Michal Hammel
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Martial Rey
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Yaping Yu
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Rajam S. Mani
- the Department of Oncology, University of Alberta and the Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Scott Classen
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mona Liu
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael E. Pique
- the Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, and
| | - Shujuan Fang
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Brandi L. Mahaney
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Michael Weinfeld
- the Department of Oncology, University of Alberta and the Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - David C. Schriemer
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Susan P. Lees-Miller
- the Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - John A. Tainer
- the Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, and
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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14
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Yano KI, Morotomi-Yano K, Lee KJ, Chen DJ. Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF. FEBS Lett 2011; 585:841-6. [PMID: 21349273 DOI: 10.1016/j.febslet.2011.02.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/28/2011] [Accepted: 02/14/2011] [Indexed: 11/25/2022]
Abstract
Ku heterodimer is essential for the repair of DNA double-strand breaks (DSBs) by non-homologous end-joining (NHEJ). Ku recruits XLF, also known as Cernunnos, to DSBs. Here we report domain analyses of Ku-XLF interaction. The heterodimeric domain of Ku was found to be sufficient for the recruitment of XLF to DSBs and for the interaction of Ku with XLF. A small C-terminal deletion of XLF completely abolished recruitment of XLF to DSBs and Ku-XLF interaction. This deletion also led to marked reduction of XLF-XRCC4 interaction although the XRCC4-binding site on the XLF N-terminal domain remained intact. These results demonstrate the significance of Ku-XLF interaction in the molecular assembly of NHEJ factors.
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Affiliation(s)
- Ken-ichi Yano
- Bioelectrics Research Center, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.
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Malivert L, Ropars V, Nunez M, Drevet P, Miron S, Faure G, Guerois R, Mornon JP, Revy P, Charbonnier JB, Callebaut I, de Villartay JP. Delineation of the Xrcc4-interacting region in the globular head domain of cernunnos/XLF. J Biol Chem 2010; 285:26475-83. [PMID: 20558749 DOI: 10.1074/jbc.m110.138156] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In mammals, the majority of DNA double-strand breaks are processed by the nonhomologous end-joining (NHEJ) pathway, composed of seven factors: Ku70, Ku80, DNA-PKcs, Artemis, Xrcc4 (X4), DNA-ligase IV (L4), and Cernunnos/XLF. Cernunnos is part of the ligation complex, constituted by X4 and L4. To improve our knowledge on the structure and function of Cernunnos, we performed a systematic mutagenesis study on positions selected from an analysis of the recent three-dimensional structures of this factor. Ten of 27 screened mutants were nonfunctional in several DNA repair assays. Outside amino acids critical for the expression and stability of Cernunnos, we identified three amino acids (Arg(64), Leu(65), and Leu(115)) essential for the interaction with X4 and the proper function of Cernunnos. Docking the crystal structures of the two factors further validated this probable interaction surface of Cernunnos with X4.
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Affiliation(s)
- Laurent Malivert
- INSERM, Hôpital Necker-Enfants Malades U768, Unité de Développement Normal et Pathologique du Système Immunitaire, Paris, France
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