1
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Noireterre A, Stutz F. Cdc48/p97 segregase: Spotlight on DNA-protein crosslinks. DNA Repair (Amst) 2024; 139:103691. [PMID: 38744091 DOI: 10.1016/j.dnarep.2024.103691] [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: 12/22/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
The ATP-dependent molecular chaperone Cdc48 (in yeast) and its human counterpart p97 (also known as VCP), are essential for a variety of cellular processes, including the removal of DNA-protein crosslinks (DPCs) from the DNA. Growing evidence demonstrates in the last years that Cdc48/p97 is pivotal in targeting ubiquitinated and SUMOylated substrates on chromatin, thereby supporting the DNA damage response. Along with its cofactors, notably Ufd1-Npl4, Cdc48/p97 has emerged as a central player in the unfolding and processing of DPCs. This review introduces the detailed structure, mechanism and cellular functions of Cdc48/p97 with an emphasis on the current knowledge of DNA-protein crosslink repair pathways across several organisms. The review concludes by discussing the potential therapeutic relevance of targeting p97 in DPC repair.
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Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland.
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2
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Weickert P, Dürauer S, Götz MJ, Li HY, Stingele J. Electro-elution-based purification of covalent DNA-protein cross-links. Nat Protoc 2024:10.1038/s41596-024-01004-z. [PMID: 38890499 DOI: 10.1038/s41596-024-01004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/19/2024] [Indexed: 06/20/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are pervasive DNA lesions that challenge genome stability and can be induced by metabolic or chemotherapeutic cross-linking agents including reactive aldehydes, topoisomerase poisons and DNMT1 inhibitors. The purification of x-linked proteins (PxP), where DNA-cross-linked proteins are separated from soluble proteins via electro-elution, can be used to identify DPCs. Here we describe a versatile and sensitive strategy for PxP. Mammalian cells are collected following exposure to a DPC-inducing agent, embedded in low-melt agarose plugs and lysed under denaturing conditions. Following lysis, the soluble proteins are extracted from the agarose plug by electro-elution, while genomic DNA and cross-linked proteins are retained in the plug. The cross-linked proteins can then be analyzed by standard analytical techniques such as sodium dodecyl-sulfate-polyacrylamide gel electrophoresis followed by western blotting or fluorescent staining. Alternatively, quantitative mass spectrometry-based proteomics can be used for the unbiased identification of DPCs. The isolation and analysis of DPCs by PxP overcomes the limitations of alternative methods to analyze DPCs that rely on precipitation as the separating principle and can be performed by users trained in molecular or cell biology within 2-3 d. The protocol has been optimized to study DPC induction and repair in mammalian cells but may also be adapted to other sample types including bacteria, yeast and tissue samples.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sophie Dürauer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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3
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Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP. Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J 2024; 43:2397-2423. [PMID: 38760575 PMCID: PMC11183266 DOI: 10.1038/s44318-024-00108-2] [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: 09/19/2023] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Amy Wanders
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hao-Yi Li
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sean L Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nadia Gueorguieva
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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4
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [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: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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5
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Wen T, Zhao S, Stingele J, Ravanat JL, Greenberg MM. Quantification of Intracellular DNA-Protein Cross-Links with N7-Methyl-2'-Deoxyguanosine and Their Contribution to Cytotoxicity. Chem Res Toxicol 2024; 37:814-823. [PMID: 38652696 PMCID: PMC11105979 DOI: 10.1021/acs.chemrestox.4c00076] [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] [Indexed: 04/25/2024]
Abstract
The major product of DNA-methylating agents, N7-methyl-2'-deoxyguanosine (MdG), is a persistent lesion in vivo, but it is not believed to have a large direct physiological impact. However, MdG reacts with histone proteins to form reversible DNA-protein cross-links (DPCMdG), a family of DNA lesions that can significantly threaten cell survival. In this paper, we developed a tandem mass spectrometry method for quantifying the amounts of MdG and DPCMdG in nuclear DNA by taking advantage of their chemical lability and the concurrent release of N7-methylguanine. Using this method, we determined that DPCMdG is formed in less than 1% yield based upon the levels of MdG in methyl methanesulfonate (MMS)-treated HeLa cells. Despite its low chemical yield, DPCMdG contributes to MMS cytotoxicity. Consequently, cells that lack efficient DPC repair by the DPC protease SPRTN are hypersensitive to MMS. This investigation shows that the downstream chemical and biochemical effects of initially formed DNA damage can have significant biological consequences. With respect to MdG formation, the initial DNA lesion is only the beginning.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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6
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Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J. Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB. Nat Cell Biol 2024; 26:797-810. [PMID: 38600235 PMCID: PMC11098753 DOI: 10.1038/s41556-024-01391-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA-protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Aleida C Acampora
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aldo S Bader
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elnatan Bitensky
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fatih Aygenli
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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7
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van Sluis M, Yu Q, van der Woude M, Gonzalo-Hansen C, Dealy SC, Janssens RC, Somsen HB, Ramadhin AR, Dekkers DHW, Wienecke HL, Demmers JJPG, Raams A, Davó-Martínez C, Llerena Schiffmacher DA, van Toorn M, Häckes D, Thijssen KL, Zhou D, Lammers JG, Pines A, Vermeulen W, Pothof J, Demmers JAA, van den Berg DLC, Lans H, Marteijn JA. Transcription-coupled DNA-protein crosslink repair by CSB and CRL4 CSA-mediated degradation. Nat Cell Biol 2024; 26:770-783. [PMID: 38600236 PMCID: PMC11098752 DOI: 10.1038/s41556-024-01394-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 03/01/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) arise from enzymatic intermediates, metabolism or chemicals like chemotherapeutics. DPCs are highly cytotoxic as they impede DNA-based processes such as replication, which is counteracted through proteolysis-mediated DPC removal by spartan (SPRTN) or the proteasome. However, whether DPCs affect transcription and how transcription-blocking DPCs are repaired remains largely unknown. Here we show that DPCs severely impede RNA polymerase II-mediated transcription and are preferentially repaired in active genes by transcription-coupled DPC (TC-DPC) repair. TC-DPC repair is initiated by recruiting the transcription-coupled nucleotide excision repair (TC-NER) factors CSB and CSA to DPC-stalled RNA polymerase II. CSA and CSB are indispensable for TC-DPC repair; however, the downstream TC-NER factors UVSSA and XPA are not, a result indicative of a non-canonical TC-NER mechanism. TC-DPC repair functions independently of SPRTN but is mediated by the ubiquitin ligase CRL4CSA and the proteasome. Thus, DPCs in genes are preferentially repaired in a transcription-coupled manner to facilitate unperturbed transcription.
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Affiliation(s)
- Marjolein van Sluis
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Qing Yu
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shannon C Dealy
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hedda B Somsen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anisha R Ramadhin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannah Lena Wienecke
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Diana A Llerena Schiffmacher
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith G Lammers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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8
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Liu JCY, Ackermann L, Hoffmann S, Gál Z, Hendriks IA, Jain C, Morlot L, Tatham MH, McLelland GL, Hay RT, Nielsen ML, Brummelkamp T, Haahr P, Mailand N. Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01294-7. [PMID: 38649616 DOI: 10.1038/s41594-024-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Protein SUMOylation provides a principal driving force for cellular stress responses, including DNA-protein crosslink (DPC) repair and arsenic-induced PML body degradation. In this study, using genome-scale screens, we identified the human E3 ligase TOPORS as a key effector of SUMO-dependent DPC resolution. We demonstrate that TOPORS promotes DPC repair by functioning as a SUMO-targeted ubiquitin ligase (STUbL), combining ubiquitin ligase activity through its RING domain with poly-SUMO binding via SUMO-interacting motifs, analogous to the STUbL RNF4. Mechanistically, TOPORS is a SUMO1-selective STUbL that complements RNF4 in generating complex ubiquitin landscapes on SUMOylated targets, including DPCs and PML, stimulating efficient p97/VCP unfoldase recruitment and proteasomal degradation. Combined loss of TOPORS and RNF4 is synthetic lethal even in unstressed cells, involving defective clearance of SUMOylated proteins from chromatin accompanied by cell cycle arrest and apoptosis. Our findings establish TOPORS as a STUbL whose parallel action with RNF4 defines a general mechanistic principle in crucial cellular processes governed by direct SUMO-ubiquitin crosstalk.
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Affiliation(s)
- Julio C Y Liu
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leena Ackermann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Saskia Hoffmann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zita Gál
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Charu Jain
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Louise Morlot
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gian-Luca McLelland
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Lund Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thijn Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Peter Haahr
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Cellular and Molecular Medicine, Center for Gene Expression, University of Copenhagen, Copenhagen, Denmark.
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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9
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Price NE, Gates KS. Novel Processes Associated with the Repair of Interstrand Cross-Links Derived from Abasic Sites in Duplex DNA: Roles for the Base Excision Repair Glycosylase NEIL3 and the SRAP Protein HMCES. Chem Res Toxicol 2024; 37:199-207. [PMID: 38198604 DOI: 10.1021/acs.chemrestox.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Recent studies have defined a novel pathway for the repair of interstrand cross-links derived from the reaction of an adenine residue with an apurinic/apyrimidinic (AP) site on the opposing strand of DNA (dA-AP ICL). Stalling of a replication fork at the dA-AP ICL triggers TRAIP-dependent ubiquitylation of the CMG helicase that recruits the base excision repair glycosylase NEIL3 to the lesion. NEIL3 unhooks the dA-AP ICL to regenerate the native adenine residue on one strand and an AP site on the other strand. Covalent capture of the abasic site by the SRAP protein HMCES protects against genomic instability that would result from cleavage of the abasic site in the context of single-stranded DNA at the replication fork. After repair synthesis moves the HMCES-AP adduct into the context of double-stranded DNA, the DNA-protein cross-link is resolved by a nonproteolytic mechanism involving dissociation of thiazolidine attachment. The AP site in duplex DNA is then repaired by the base excision repair pathway.
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Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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10
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Torrecilla I, Ruggiano A, Kiianitsa K, Aljarbou F, Lascaux P, Hoslett G, Song W, Maizels N, Ramadan K. Isolation and detection of DNA-protein crosslinks in mammalian cells. Nucleic Acids Res 2024; 52:525-547. [PMID: 38084926 PMCID: PMC10810220 DOI: 10.1093/nar/gkad1178] [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: 07/10/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.
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Affiliation(s)
- Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
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11
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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12
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Ruiz PD, Smogorzewska A. Temporary HMCES-DNA cross-link prevents permanent DNA damage. Cell Rep 2024; 43:113594. [PMID: 38141170 PMCID: PMC10986309 DOI: 10.1016/j.celrep.2023.113594] [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: 11/25/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/25/2023] Open
Abstract
HMCES, a recently discovered but ancient protein, covalently attaches to damaged single-stranded DNA and shields it from nucleases. Rua-Fernandez and colleagues now show that HMCES catalyzes its own recycling, permitting normal growth and non-mutagenic DNA repair.1.
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Affiliation(s)
- Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA.
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13
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Essawy MM, Campbell C. Enzymatic Processing of DNA-Protein Crosslinks. Genes (Basel) 2024; 15:85. [PMID: 38254974 PMCID: PMC10815813 DOI: 10.3390/genes15010085] [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: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
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Affiliation(s)
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA;
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14
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Zhao S, Cordes J, Caban KM, Götz MJ, Mackens-Kiani T, Veltri AJ, Sinha NK, Weickert P, Kaya S, Hewitt G, Nedialkova DD, Fröhlich T, Beckmann R, Buskirk AR, Green R, Stingele J. RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks. Mol Cell 2023; 83:4290-4303.e9. [PMID: 37951216 PMCID: PMC10783637 DOI: 10.1016/j.molcel.2023.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are abundant endogenous metabolites that challenge homeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA damage requires repair to prevent cancer and premature aging, but it is unknown whether cells also possess mechanisms that resolve aldehyde-induced RNA lesions. Here, we establish photoactivatable ribonucleoside-enhanced crosslinking (PAR-CL) as a model system to study RNA crosslinking damage in the absence of confounding DNA damage in human cells. We find that such RNA damage causes translation stress by stalling elongating ribosomes, which leads to collisions with trailing ribosomes and activation of multiple stress response pathways. Moreover, we discovered a translation-coupled quality control mechanism that resolves covalent RNA-protein crosslinks. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their modification with atypical K6- and K48-linked ubiquitin chains. Ubiquitylation requires the E3 ligase RNF14 and leads to proteasomal degradation of the protein adduct. Our findings identify RNA lesion-induced translational stress as a central component of crosslinking damage.
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Affiliation(s)
- Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karolina M Caban
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timur Mackens-Kiani
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anthony J Veltri
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Selay Kaya
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Graeme Hewitt
- King's College London School of Cancer & Pharmaceutical Sciences, London, UK
| | - Danny D Nedialkova
- Max Planck Institute of Biochemistry, Martinsried, Germany; Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Thomas Fröhlich
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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15
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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16
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Han J, Mu Y, Huang J. Preserving genome integrity: The vital role of SUMO-targeted ubiquitin ligases. CELL INSIGHT 2023; 2:100128. [PMID: 38047137 PMCID: PMC10692494 DOI: 10.1016/j.cellin.2023.100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/05/2023]
Abstract
Various post-translational modifications (PTMs) collaboratively fine-tune protein activities. SUMO-targeted ubiquitin E3 ligases (STUbLs) emerge as specialized enzymes that recognize SUMO-modified substrates through SUMO-interaction motifs and subsequently ubiquitinate them via the RING domain, thereby bridging the SUMO and ubiquitin signaling pathways. STUbLs participate in a wide array of molecular processes, including cell cycle regulation, DNA repair, replication, and mitosis, operating under both normal conditions and in response to challenges such as genotoxic stress. Their ability to catalyze various types of ubiquitin chains results in diverse proteolytic and non-proteolytic outcomes for target substrates. Importantly, STUbLs are strategically positioned in close proximity to SUMO proteases and deubiquitinases (DUBs), ensuring precise and dynamic control over their target proteins. In this review, we provide insights into the unique properties and indispensable roles of STUbLs, with a particular emphasis on their significance in preserving genome integrity in humans.
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Affiliation(s)
- Jinhua Han
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yanhua Mu
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Jun Huang
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
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17
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. The Response of the Replication Apparatus to Leading Template Strand Blocks. Cells 2023; 12:2607. [PMID: 37998342 PMCID: PMC10670059 DOI: 10.3390/cells12222607] [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: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Duplication of the genome requires the replication apparatus to overcome a variety of impediments, including covalent DNA adducts, the most challenging of which is on the leading template strand. Replisomes consist of two functional units, a helicase to unwind DNA and polymerases to synthesize it. The helicase is a multi-protein complex that encircles the leading template strand and makes the first contact with a leading strand adduct. The size of the channel in the helicase would appear to preclude transit by large adducts such as DNA: protein complexes (DPC). Here we discuss some of the extensively studied pathways that support replication restart after replisome encounters with leading template strand adducts. We also call attention to recent work that highlights the tolerance of the helicase for adducts ostensibly too large to pass through the central channel.
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Affiliation(s)
| | | | | | | | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (M.A.B.)
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18
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Wang R, Sun Y, Li C, Xue Y, Ba X. Targeting the DNA Damage Response for Cancer Therapy. Int J Mol Sci 2023; 24:15907. [PMID: 37958890 PMCID: PMC10648182 DOI: 10.3390/ijms242115907] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Over the course of long-term evolution, cells have developed intricate defense mechanisms in response to DNA damage; these mechanisms play a pivotal role in maintaining genomic stability. Defects in the DNA damage response pathways can give rise to various diseases, including cancer. The DNA damage response (DDR) system is instrumental in safeguarding genomic stability. The accumulation of DNA damage and the weakening of DDR function both promote the initiation and progression of tumors. Simultaneously, they offer opportunities and targets for cancer therapeutics. This article primarily elucidates the DNA damage repair pathways and the progress made in targeting key proteins within these pathways for cancer treatment. Among them, poly (ADP-ribose) polymerase 1 (PARP1) plays a crucial role in DDR, and inhibitors targeting PARP1 have garnered extensive attention in anticancer research. By delving into the realms of DNA damage and repair, we aspire to explore more precise and effective strategies for cancer therapy and to seek novel avenues for intervention.
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Affiliation(s)
- Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Yating Sun
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Chunshuang Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Yaoyao Xue
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
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19
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Gasser SM, Stutz F. SUMO in the regulation of DNA repair and transcription at nuclear pores. FEBS Lett 2023; 597:2833-2850. [PMID: 37805446 DOI: 10.1002/1873-3468.14751] [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: 07/16/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
Two related post-translational modifications, the covalent linkage of Ubiquitin and the Small Ubiquitin-related MOdifier (SUMO) to lysine residues, play key roles in the regulation of both DNA repair pathway choice and transcription. Whereas ubiquitination is generally associated with proteasome-mediated protein degradation, the impact of sumoylation has been more mysterious. In the cell nucleus, sumoylation effects are largely mediated by the relocalization of the modified targets, particularly in response to DNA damage. This is governed in part by the concentration of SUMO protease at nuclear pores [Melchior, F et al. (2003) Trends Biochem Sci 28, 612-618; Ptak, C and Wozniak, RW (2017) Adv Exp Med Biol 963, 111-126]. We review here the roles of sumoylation in determining genomic locus positioning relative to the nuclear envelope and to nuclear pores, to facilitate repair and regulate transcription.
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Affiliation(s)
- Susan M Gasser
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- ISREC Foundation, Agora Cancer Research Center, Lausanne, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Switzerland
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20
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Wen T, Kermarrec M, Dumont E, Gillet N, Greenberg MM. DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles. J Am Chem Soc 2023; 145:23702-23714. [PMID: 37856159 PMCID: PMC10652223 DOI: 10.1021/jacs.3c08135] [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] [Indexed: 10/20/2023]
Abstract
Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA-protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone N-terminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Maxime Kermarrec
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice UMR 7272, Université Côte d'Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
| | - Natacha Gillet
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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21
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Donsbach M, Dürauer S, Grünert F, Nguyen KT, Nigam R, Yaneva D, Weickert P, Bezalel‐Buch R, Semlow DR, Stingele J. A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks. EMBO J 2023; 42:e113360. [PMID: 37519246 PMCID: PMC10505908 DOI: 10.15252/embj.2022113360] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
The conserved protein HMCES crosslinks to abasic (AP) sites in ssDNA to prevent strand scission and the formation of toxic dsDNA breaks during replication. Here, we report a non-proteolytic release mechanism for HMCES-DNA-protein crosslinks (DPCs), which is regulated by DNA context. In ssDNA and at ssDNA-dsDNA junctions, HMCES-DPCs are stable, which efficiently protects AP sites against spontaneous incisions or cleavage by APE1 endonuclease. In contrast, HMCES-DPCs are released in dsDNA, allowing APE1 to initiate downstream repair. Mechanistically, we show that release is governed by two components. First, a conserved glutamate residue, within HMCES' active site, catalyses reversal of the crosslink. Second, affinity to the underlying DNA structure determines whether HMCES re-crosslinks or dissociates. Our study reveals that the protective role of HMCES-DPCs involves their controlled release upon bypass by replication forks, which restricts DPC formation to a necessary minimum.
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Affiliation(s)
- Maximilian Donsbach
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Sophie Dürauer
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Florian Grünert
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Kha T Nguyen
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Richa Nigam
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Denitsa Yaneva
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Pedro Weickert
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
| | - Rachel Bezalel‐Buch
- Department of Biological Chemistry and Molecular BiophysicsWashington University School of MedicalSaint LouisMOUSA
| | - Daniel R Semlow
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Julian Stingele
- Department of BiochemistryLudwig‐Maximilians‐University MunichMunichGermany
- Gene Center, Ludwig‐Maximilians‐University MunichMunichGermany
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22
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Lewicky JD, Martel AL, Gupta MR, Roy R, Rodriguez GM, Vanderhyden BC, Le HT. Conventional DNA-Damaging Cancer Therapies and Emerging cGAS-STING Activation: A Review and Perspectives Regarding Immunotherapeutic Potential. Cancers (Basel) 2023; 15:4127. [PMID: 37627155 PMCID: PMC10453198 DOI: 10.3390/cancers15164127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Many traditional cancer treatments such as radiation and chemotherapy are known to induce cellular DNA damage as part of their cytotoxic activity. The cGAS-STING signaling axis, a key member of the DNA damage response that acts as a sensor of foreign or aberrant cytosolic DNA, is helping to rationalize the DNA-damaging activity of these treatments and their emerging immunostimulatory capacity. Moreover, cGAS-STING, which is attracting considerable attention for its ability to promote antitumor immune responses, may fundamentally be able to address many of the barriers limiting the success of cancer immunotherapy strategies, including the immunosuppressive tumor microenvironment. Herein, we review the traditional cancer therapies that have been linked with cGAS-STING activation, highlighting their targets with respect to their role and function in the DNA damage response. As part of the review, an emerging "chemoimmunotherapy" concept whereby DNA-damaging agents are used for the indirect activation of STING is discussed as an alternative to the direct molecular agonism strategies that are in development, but have yet to achieve clinical approval. The potential of this approach to address some of the inherent and emerging limitations of cGAS-STING signaling in cancer immunotherapy is also discussed. Ultimately, it is becoming clear that in order to successfully employ the immunotherapeutic potential of the cGAS-STING axis, a balance between its contrasting antitumor and protumor/inflammatory activities will need to be achieved.
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Affiliation(s)
- Jordan D. Lewicky
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
| | - Alexandrine L. Martel
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
| | - Mukul Raj Gupta
- Glycosciences and Nanomaterial Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (M.R.G.); (R.R.)
| | - René Roy
- Glycosciences and Nanomaterial Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (M.R.G.); (R.R.)
| | - Galaxia M. Rodriguez
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Rd., Ottawa, ON K1H 8L6, Canada; (G.M.R.); (B.C.V.)
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Rd., Ottawa, ON K1H 8M5, Canada
| | - Barbara C. Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Rd., Ottawa, ON K1H 8L6, Canada; (G.M.R.); (B.C.V.)
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Rd., Ottawa, ON K1H 8M5, Canada
| | - Hoang-Thanh Le
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
- Medicinal Sciences Division, NOSM University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
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23
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Berger S, Chistol G. Visualizing the dynamics of DNA replication and repair at the single-molecule level. Methods Cell Biol 2023; 182:109-165. [PMID: 38359974 DOI: 10.1016/bs.mcb.2023.07.001] [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] [Indexed: 02/17/2024]
Abstract
During cell division, the genome of each eukaryotic cell is copied by thousands of replisomes-large protein complexes consisting of several dozen proteins. Recent studies suggest that the eukaryotic replisome is much more dynamic than previously thought. To directly visualize replisome dynamics in a physiological context, we recently developed a single-molecule approach for imaging replication proteins in Xenopus egg extracts. These extracts contain all the soluble nuclear proteins and faithfully recapitulate DNA replication and repair in vitro, serving as a powerful platform for studying the mechanisms of genome maintenance. Here we present detailed protocols for conducting single-molecule experiments in nuclear egg extracts and preparing key reagents. This workflow can be easily adapted to visualize the dynamics and function of other proteins implicated in DNA replication and repair.
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Affiliation(s)
- Scott Berger
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States
| | - Gheorghe Chistol
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States; Chemical and Systems Biology Department, Cancer Biology Program, Stanford School of Medicine, Stanford, CA, United States.
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24
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Marini V, Nikulenkov F, Samadder P, Juul S, Knudsen BR, Krejci L. MUS81 cleaves TOP1-derived lesions and other DNA-protein cross-links. BMC Biol 2023; 21:110. [PMID: 37194054 DOI: 10.1186/s12915-023-01614-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND DNA-protein cross-links (DPCs) are one of the most deleterious DNA lesions, originating from various sources, including enzymatic activity. For instance, topoisomerases, which play a fundamental role in DNA metabolic processes such as replication and transcription, can be trapped and remain covalently bound to DNA in the presence of poisons or nearby DNA damage. Given the complexity of individual DPCs, numerous repair pathways have been described. The protein tyrosyl-DNA phosphodiesterase 1 (Tdp1) has been demonstrated to be responsible for removing topoisomerase 1 (Top1). Nevertheless, studies in budding yeast have indicated that alternative pathways involving Mus81, a structure-specific DNA endonuclease, could also remove Top1 and other DPCs. RESULTS This study shows that MUS81 can efficiently cleave various DNA substrates modified by fluorescein, streptavidin or proteolytically processed topoisomerase. Furthermore, the inability of MUS81 to cleave substrates bearing native TOP1 suggests that TOP1 must be either dislodged or partially degraded prior to MUS81 cleavage. We demonstrated that MUS81 could cleave a model DPC in nuclear extracts and that depletion of TDP1 in MUS81-KO cells induces sensitivity to the TOP1 poison camptothecin (CPT) and affects cell proliferation. This sensitivity is only partially suppressed by TOP1 depletion, indicating that other DPCs might require the MUS81 activity for cell proliferation. CONCLUSIONS Our data indicate that MUS81 and TDP1 play independent roles in the repair of CPT-induced lesions, thus representing new therapeutic targets for cancer cell sensitisation in combination with TOP1 inhibitors.
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Affiliation(s)
- Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekařská 53, Brno, 60200, Czech Republic
| | - Fedor Nikulenkov
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
| | - Pounami Samadder
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic
| | - Sissel Juul
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, 8000, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus, 8000, Denmark
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/B07, Brno, 62500, Czech Republic.
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekařská 53, Brno, 60200, Czech Republic.
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/C04, Brno, 625 00, Czech Republic.
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25
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Dvořák Tomaštíková E, Prochazkova K, Yang F, Jemelkova J, Finke A, Dorn A, Said M, Puchta H, Pecinka A. SMC5/6 complex-mediated SUMOylation stimulates DNA-protein cross-link repair in Arabidopsis. THE PLANT CELL 2023; 35:1532-1547. [PMID: 36705512 PMCID: PMC10118267 DOI: 10.1093/plcell/koad020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 05/10/2023]
Abstract
DNA-protein cross-links (DPCs) are highly toxic DNA lesions consisting of proteins covalently attached to chromosomal DNA. Unrepaired DPCs physically block DNA replication and transcription. Three DPC repair pathways have been identified in Arabidopsis (Arabidopsis thaliana) to date: the endonucleolytic cleavage of DNA by the structure-specific endonuclease MUS81; proteolytic degradation of the crosslinked protein by the metalloprotease WSS1A; and cleavage of the cross-link phosphodiester bonds by the tyrosyl phosphodiesterases TDP1 and TDP2. Here we describe the evolutionary conserved STRUCTURAL MAINTENANCE OF CHROMOSOMEs SMC5/6 complex as a crucial component involved in DPC repair. We identified multiple alleles of the SMC5/6 complex core subunit gene SMC6B via a forward-directed genetic screen designed to identify the factors involved in the repair of DPCs induced by the cytidine analog zebularine. We monitored plant growth and cell death in response to DPC-inducing chemicals, which revealed that the SMC5/6 complex is essential for the repair of several types of DPCs. Genetic interaction and sensitivity assays showed that the SMC5/6 complex works in parallel to the endonucleolytic and proteolytic pathways. The repair of zebularine-induced DPCs was associated with SMC5/6-dependent SUMOylation of the damage sites. Thus, we present the SMC5/6 complex as an important factor in plant DPC repair.
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Affiliation(s)
| | - Klara Prochazkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Fen Yang
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 77900 Olomouc, Czech Republic
| | - Jitka Jemelkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Functional Genomics and Proteomics, National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, 12619, Cairo, Egypt
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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26
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Weickert P, Li HY, Götz MJ, Dürauer S, Yaneva D, Zhao S, Cordes J, Acampora AC, Forne I, Imhof A, Stingele J. SPRTN patient variants cause global-genome DNA-protein crosslink repair defects. Nat Commun 2023; 14:352. [PMID: 36681662 PMCID: PMC9867749 DOI: 10.1038/s41467-023-35988-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are pervasive DNA lesions that are induced by reactive metabolites and various chemotherapeutic agents. Here, we develop a technique for the Purification of x-linked Proteins (PxP), which allows identification and tracking of diverse DPCs in mammalian cells. Using PxP, we investigate DPC repair in cells genetically-engineered to express variants of the SPRTN protease that cause premature ageing and early-onset liver cancer in Ruijs-Aalfs syndrome patients. We find an unexpected role for SPRTN in global-genome DPC repair, that does not rely on replication-coupled detection of the lesion. Mechanistically, we demonstrate that replication-independent DPC cleavage by SPRTN requires SUMO-targeted ubiquitylation of the protein adduct and occurs in addition to proteasomal DPC degradation. Defective ubiquitin binding of SPRTN patient variants compromises global-genome DPC repair and causes synthetic lethality in combination with a reduction in proteasomal DPC repair capacity.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Sophie Dürauer
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Denitsa Yaneva
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Jacqueline Cordes
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Aleida C Acampora
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Ignasi Forne
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig-Maximilians-University, 82152, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig-Maximilians-University, 82152, Martinsried, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-University, 81377, Munich, Germany.
- Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany.
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27
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Cooke MS, Chang YJ, Chen YR, Hu CW, Chao MR. Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159192. [PMID: 36195140 DOI: 10.1016/j.scitotenv.2022.159192] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/07/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
This Discussion article aims to explore the potential for a new generation of assay to emerge from cellular and urinary DNA adductomics which brings together DNA-RNA- and, to some extent, protein adductomics, to better understand the role of the exposome in environmental health. Components of the exposome have been linked to an increased risk of various, major diseases, and to identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and a goal of cellular DNA adductomics is to evaluate the totality of DNA modifications in the genome, on the basis that this will be most informative. Consequently, an approach which encompasses modifications of all nucleic acids (NA) would be potentially yet more informative. This article focuses on NA adductomics, which brings together the assessment of both DNA and RNA modifications, including modified (2'-deoxy)ribonucleosides (2'-dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). We discuss the need for NA adductomics, plus the pros and cons of cellular vs. urinary NA adductomics, and present some evidence for the feasibility of this approach. We propose that NA adductomics provides a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.
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Affiliation(s)
- Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan.
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan.
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28
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Yaneva D, Sparks JL, Donsbach M, Zhao S, Weickert P, Bezalel-Buch R, Stingele J, Walter JC. The FANCJ helicase unfolds DNA-protein crosslinks to promote their repair. Mol Cell 2023; 83:43-56.e10. [PMID: 36608669 PMCID: PMC9881729 DOI: 10.1016/j.molcel.2022.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
Endogenous and exogenous agents generate DNA-protein crosslinks (DPCs), whose replication-dependent degradation by the SPRTN protease suppresses aging and liver cancer. SPRTN is activated after the replicative CMG helicase bypasses a DPC and polymerase extends the nascent strand to the adduct. Here, we identify a role for the 5'-to-3' helicase FANCJ in DPC repair. In addition to supporting CMG bypass, FANCJ is essential for SPRTN activation. FANCJ binds ssDNA downstream of the DPC and uses its ATPase activity to unfold the protein adduct, which exposes the underlying DNA and enables cleavage of the adduct. FANCJ-dependent DPC unfolding is also essential for translesion DNA synthesis past DPCs that cannot be degraded. In summary, our results show that helicase-mediated protein unfolding enables multiple events in DPC repair.
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Affiliation(s)
- Denitsa Yaneva
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Maximilian Donsbach
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Rachel Bezalel-Buch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany.
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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29
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Sun Y, Nitiss JL, Pommier Y. Editorial: The repair of DNA-protein crosslinks. Front Mol Biosci 2023; 10:1203479. [PMID: 37187895 PMCID: PMC10175854 DOI: 10.3389/fmolb.2023.1203479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Affiliation(s)
- Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
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30
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Xu W, Tang J, Zhao L. DNA-protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM). Nucleic Acids Res 2022; 51:41-53. [PMID: 36583367 PMCID: PMC9841407 DOI: 10.1093/nar/gkac1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential organelles for energy production, metabolism, and signaling. Mitochondrial DNA (mtDNA) encodes 13 protein subunits for oxidative phosphorylation and a set of tRNAs and rRNAs. mtDNA damage, sourced from endogenous chemicals and environmental factors, contributes to mitochondrial genomic instability, which has been associated with various mitochondrial diseases. DNA-protein cross-links (DPCs) are deleterious DNA lesions that threaten genomic integrity. Although much has been learned about the formation and repair of DPCs in the nucleus, little is known about DPCs in mitochondria. Here, we present in vitro and in cellulo data to demonstrate the formation of DPCs between a prevalent abasic (AP) DNA lesion and a DNA-packaging protein, mitochondrial transcription factor A (TFAM). TFAM cleaves AP-DNA and forms DPCs and single-strand breaks (SSB). Lys residues of TFAM are critical for the formation of TFAM-DPC and a reactive 3'-phospho-α,β-unsaturated aldehyde (3'pUA) residue on SSB. The 3'pUA residue reacts with two Cys of TFAM and contributes to the stable TFAM-DPC formation. Glutathione reacts with 3'pUA and competes with TFAM-DPC formation, corroborating our cellular experiments showing the accumulation of TFAM-DPCs under limiting glutathione. Our data point to the involvement of TFAM in AP-DNA turnover and fill a knowledge gap regarding the protein factors in processing damaged mtDNA.
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Affiliation(s)
- Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- To whom correspondence should be addressed. Tel: +1 951 827 9081;
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31
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Xu W, Zhao L. An Enzyme-Linked Immunosorbent Assay for the Detection of Mitochondrial DNA-Protein Cross-Links from Mammalian Cells. DNA 2022; 2:264-278. [PMID: 37601565 PMCID: PMC10438828 DOI: 10.3390/dna2040019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
DNA-Protein cross-links (DPCs) are cytotoxic DNA lesions with a protein covalently bound to the DNA. Although much has been learned about the formation, repair, and biological consequences of DPCs in the nucleus, little is known regarding mitochondrial DPCs. This is due in part to the lack of robust and specific methods to measure mitochondrial DPCs. Herein, we reported an enzyme-linked immunosorbent assay (ELISA)-based method for detecting mitochondrial DPCs formed between DNA and mitochondrial transcription factor A (TFAM) in cultured human cells. To optimize the purification and detection workflow, we prepared model TFAM-DPCs via Schiff base chemistry using recombinant human TFAM and a DNA substrate containing an abasic (AP) lesion. We optimized the isolation of TFAM-DPCs using commercial silica gel-based columns to achieve a high recovery yield for DPCs. We evaluated the microplate, DNA-coating solution, and HRP substrate for specific and sensitive detection of TFAM-DPCs. Additionally, we optimized the mtDNA isolation procedure to eliminate almost all nuclear DNA contaminants. For proof of concept, we detected the different levels of TFAM-DPCs in mtDNA from HEK293 cells under different biological conditions. The method is based on commercially available materials and can be amended to detect other types of DPCs in mitochondria.
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Affiliation(s)
- Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, 92521, United States
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32
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Sun Y, Soans E, Mishina M, Petricci E, Pommier Y, Nitiss KC, Nitiss JL. Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells. Front Mol Biosci 2022; 9:1007064. [PMID: 36213114 PMCID: PMC9537633 DOI: 10.3389/fmolb.2022.1007064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.
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Affiliation(s)
- Yilun Sun
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
| | - Eroica Soans
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | - Margarita Mishina
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | | | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
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Kabbaha S, Al-Azzam S, Karasneh RA, Khassawneh BY, Al-Mistarehi AH, Lattyak WJ, Aldiab M, Hasan SS, Conway BR, Aldeyab MA. Predictors of invasive mechanical ventilation in hospitalized COVID-19 patients: a retrospective study from Jordan. Expert Rev Respir Med 2022; 16:945-952. [PMID: 35929952 DOI: 10.1080/17476348.2022.2108796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To identify early indicators for invasive mechanical ventilation utilization among COVID-19 patients. METHODS This retrospective study evaluated COVID-19 patients who were admitted to hospital from September 20, 2020, to August 8, 2021. Patients' clinical characteristics, demographics, comorbidities, and laboratory results were evaluated. Multivariable logistic regression and machine learning (ML) methods were employed to assess variable significance. RESULTS Among 1,613 confirmed COVID-19 patients, 365 patients (22.6%) received invasive mechanical ventilation (IMV). Factors associated with IMV included older age >65 years (OR,1.46; 95%CI, 1.13 - 1.89), current smoking status (OR, 1.71; 95%CI, 1.22-2.41), critical disease at admission (OR, 1.97; 95%CI, 1.28-3.03), and chronic kidney disease (OR, 2.07; 95%CI, 1.37-3.13). Laboratory abnormalities that were associated with increased risk for IMV included high leukocyte count (OR, 2.19; 95%CI, 1.68 - 2.87), low albumin (OR, 1.76; 95%CI, 1.33 - 2.34) and high AST (OR, 1.71; 95%CI, 1.31 - 2.22). CONCLUSION Our study suggests that there are several factors associated with the increased need for IMV among COVID-19 patients including older age, current smoking status, critical disease status on admission, and chronic kidney disease. In addition, laboratory markers such as high leukocyte count, low albumin and high AST were determined. These findings will help in early identification of patients at high risk for IMV and reallocation of hospital resources towards patients who need them the most to improve their outcomes.
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Affiliation(s)
- Suad Kabbaha
- Department of Health Research Methods, Evidence & Impact (HEI), McMaster University, Hamilton, Canada
| | - Sayer Al-Azzam
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Reema A Karasneh
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Basheer Y Khassawneh
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Abdel-Hameed Al-Mistarehi
- Department of Public Health and Family Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | | | - Motasem Aldiab
- Department of Computing, British Columbia Institute of Technology, Vancouver, Canada
| | - Syed Shahzad Hasan
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Barbara R Conway
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom.,Institute of Skin Integrity and Infection Prevention, University of Huddersfield, Huddersfield, United Kingdom
| | - Mamoon A Aldeyab
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity. Curr Biol 2022; 32:2962-2971.e4. [DOI: 10.1016/j.cub.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
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