1
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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; 19:2891-2914. [PMID: 38890499 DOI: 10.1038/s41596-024-01004-z] [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: 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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2
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Wojtaszek JL, Williams RS. From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks. DNA Repair (Amst) 2024; 142:103751. [PMID: 39180935 PMCID: PMC11404304 DOI: 10.1016/j.dnarep.2024.103751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Since the report of "DNA untwisting" activity in 1972, ∼50 years of research has revealed seven topoisomerases in humans (TOP1, TOP1mt, TOP2α, TOP2β, TOP3α, TOP3β and Spo11). These conserved regulators of DNA topology catalyze controlled breakage to the DNA backbone to relieve the torsional stress that accumulates during essential DNA transactions including DNA replication, transcription, and DNA repair. Each topoisomerase-catalyzed reaction involves the formation of a topoisomerase cleavage complex (TOPcc), a covalent protein-DNA reaction intermediate formed between the DNA phosphodiester backbone and a topoisomerase catalytic tyrosine residue. A variety of perturbations to topoisomerase reaction cycles can trigger failure of the enzyme to re-ligate the broken DNA strand(s), thereby generating topoisomerase DNA-protein crosslinks (TOP-DPC). TOP-DPCs pose unique threats to genomic integrity. These complex lesions are comprised of structurally diverse protein components covalently linked to genomic DNA, which are bulky DNA adducts that can directly impact progression of the transcription and DNA replication apparatus. A variety of genome maintenance pathways have evolved to recognize and resolve TOP-DPCs. Eukaryotic cells harbor tyrosyl DNA phosphodiesterases (TDPs) that directly reverse 3'-phosphotyrosyl (TDP1) and 5'-phoshotyrosyl (TDP2) protein-DNA linkages. The broad specificity Mre11-Rad50-Nbs1 and APE2 nucleases are also critical for mitigating topoisomerase-generated DNA damage. These DNA-protein crosslink metabolizing enzymes are further enabled by proteolytic degradation, with the proteasome, Spartan, GCNA, Ddi2, and FAM111A proteases implicated thus far. Strategies to target, unfold, and degrade the protein component of TOP-DPCs have evolved as well. Here we survey mechanisms for addressing Topoisomerase 1 (TOP1) and Topoisomerase 2 (TOP2) DPCs, highlighting systems for which molecular structure information has illuminated function of these critical DNA damage response pathways.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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3
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Li L. Transcription reprogramming and endogenous DNA damage. DNA Repair (Amst) 2024; 142:103754. [PMID: 39232366 DOI: 10.1016/j.dnarep.2024.103754] [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: 04/01/2024] [Revised: 07/18/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024]
Abstract
Transcription reprogramming is essential to carry out a variety of cell dynamics such as differentiation and stress response. During reprogramming of transcription, a number of adverse effects occur and potentially compromise genomic stability. Formaldehyde as an obligatory byproduct is generated in the nucleus via oxidative protein demethylation at regulatory regions, leading to the formation of DNA crosslinking damage. Elevated levels of transcription activities can result in the accumulation of unscheduled R-loop. DNA strand breaks can form if processed 5-methylcytosines are exercised by DNA glycosylase during imprint reversal. When cellular differentiation involves a large number of genes undergoing transcription reprogramming, these endogenous DNA lesions and damage-prone structures may pose a significant threat to genome stability. In this review, we discuss how DNA damage is formed during cellular differentiation, cellular mechanisms for their removal, and diseases associated with transcription reprogramming.
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Affiliation(s)
- Lei Li
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China.
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4
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Blouin T, Saini N. Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis. Front Oncol 2024; 14:1478373. [PMID: 39328207 PMCID: PMC11424613 DOI: 10.3389/fonc.2024.1478373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.
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Affiliation(s)
- Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
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5
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Noireterre A, Soudet J, Bagdiul I, Stutz F. The cullin Rtt101 promotes ubiquitin-dependent DNA-protein crosslink repair across the cell cycle. Nucleic Acids Res 2024; 52:9654-9670. [PMID: 39077933 PMCID: PMC11381328 DOI: 10.1093/nar/gkae658] [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: 12/06/2023] [Revised: 06/28/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
DNA-protein crosslinks (DPCs) challenge faithful DNA replication and smooth passage of genomic information. Our study unveils the cullin E3 ubiquitin ligase Rtt101 as a DPC repair factor. Genetic analyses demonstrate that Rtt101 is essential for resistance to a wide range of DPC types including topoisomerase 1 crosslinks, in the same pathway as the ubiquitin-dependent aspartic protease Ddi1. Using an in vivo inducible Top1-mimicking DPC system, we reveal the significant impact of Rtt101 ubiquitination on DPC removal across different cell cycle phases. High-throughput methods coupled with next-generation sequencing specifically highlight the association of Rtt101 with replisomes as well as colocalization with DPCs. Our findings establish Rtt101 as a main contributor to DPC repair throughout the yeast cell cycle.
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Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Julien Soudet
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
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6
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Anticevic I, Otten C, Popovic M. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) repairs DNA-protein crosslinks and protects against double strand breaks in vivo. Front Cell Dev Biol 2024; 12:1394531. [PMID: 39228401 PMCID: PMC11369425 DOI: 10.3389/fcell.2024.1394531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 09/05/2024] Open
Abstract
DNA-protein crosslinks pose a significant challenge to genome stability and cell viability. Efficient repair of DPCs is crucial for preserving genomic integrity and preventing the accumulation of DNA damage. Despite recent advances in our understanding of DPC repair, many aspects of this process, especially at the organismal level, remain elusive. In this study, we used zebrafish as a model organism to investigate the role of TDP2 (Tyrosyl-DNA phosphodiesterase 2) in DPC repair. We characterized the two tdp2 orthologs in zebrafish using phylogenetic, syntenic and expression analysis and investigated the phenotypic consequences of tdp2 silencing in zebrafish embryos. We then quantified the effects of tdp2a and tdp2b silencing on cellular DPC levels and DSB accumulation in zebrafish embryos. Our findings revealed that tdp2b is the main ortholog during embryonic development, while both orthologs are ubiquitously present in adult tissues. Notably, the tdp2b ortholog is phylogenetically closer to human TDP2. Silencing of tdp2b, but not tdp2a, resulted in the loss of Tdp2 activity in zebrafish embryos, accompanied by the accumulation of DPCs and DSBs. Our findings contribute to a more comprehensive understanding of DPC repair at the organismal level and underscore the significance of TDP2 in maintaining genome stability.
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Affiliation(s)
| | | | - Marta Popovic
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruder Boskovic, Zagreb, Croatia
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7
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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [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: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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8
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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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9
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Hurben AK, Zhang Q, Galligan JJ, Tretyakova N, Erber L. Endogenous Cellular Metabolite Methylglyoxal Induces DNA-Protein Cross-Links in Living Cells. ACS Chem Biol 2024; 19:1291-1302. [PMID: 38752800 PMCID: PMC11353540 DOI: 10.1021/acschembio.4c00100] [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: 06/22/2024]
Abstract
Methylglyoxal (MGO) is an electrophilic α-oxoaldehyde generated endogenously through metabolism of carbohydrates and exogenously due to autoxidation of sugars, degradation of lipids, and fermentation during food and drink processing. MGO can react with nucleophilic sites within proteins and DNA to form covalent adducts. MGO-induced advanced glycation end-products such as protein and DNA adducts are thought to be involved in oxidative stress, inflammation, diabetes, cancer, renal failure, and neurodegenerative diseases. Additionally, MGO has been hypothesized to form toxic DNA-protein cross-links (DPC), but the identities of proteins participating in such cross-linking in cells have not been determined. In the present work, we quantified DPC formation in human cells exposed to MGO and identified proteins trapped on DNA upon MGO exposure using mass spectrometry-based proteomics. A total of 265 proteins were found to participate in MGO-derived DPC formation including gene products engaged in telomere organization, nucleosome assembly, and gene expression. In vitro experiments confirmed DPC formation between DNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as well as histone proteins H3.1 and H4. Collectively, our study provides the first evidence for MGO-mediated DNA-protein cross-linking in living cells, prompting future studies regarding the relevance of these toxic lesions in cancer, diabetes, and other diseases linked to elevated MGO levels.
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Affiliation(s)
- Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Present Address: Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke Erber
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Li BZ, Kolodner RD, Putnam CD. Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers. G3 (BETHESDA, MD.) 2024; 14:jkae064. [PMID: 38526099 PMCID: PMC11152081 DOI: 10.1093/g3journal/jkae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
Cellular pathways that detect DNA damage are useful for identifying genes that suppress DNA damage, which can cause genome instability and cancer predisposition syndromes when mutated. We identified 199 high-confidence and 530 low-confidence DNA damage-suppressing (DDS) genes in Saccharomyces cerevisiae through a whole-genome screen for mutations inducing Hug1 expression, a focused screen for mutations inducing Ddc2 foci, and data from previous screens for mutations causing Rad52 foci accumulation and Rnr3 induction. We also identified 286 high-confidence and 394 low-confidence diverse genome instability-suppressing (DGIS) genes through a whole-genome screen for mutations resulting in increased gross chromosomal rearrangements and data from previous screens for mutations causing increased genome instability as assessed in a diversity of genome instability assays. Genes that suppress both pathways (DDS+ DGIS+) prevent or repair DNA replication damage and likely include genes preventing collisions between the replication and transcription machineries. DDS+ DGIS- genes, including many transcription-related genes, likely suppress damage that is normally repaired properly or prevent inappropriate signaling, whereas DDS- DGIS+ genes, like PIF1, do not suppress damage but likely promote its proper, nonmutagenic repair. Thus, induction of DNA damage markers is not a reliable indicator of increased genome instability, and the DDS and DGIS categories define mechanistically distinct groups of genes.
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Affiliation(s)
- Bin-Zhong Li
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
- Moores-UCSD Cancer Center, University of California San Diego, La Jolla, CA 92093-0669, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0669, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093-0669, USA
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11
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Radisky ES. Extracellular proteolysis in cancer: Proteases, substrates, and mechanisms in tumor progression and metastasis. J Biol Chem 2024; 300:107347. [PMID: 38718867 PMCID: PMC11170211 DOI: 10.1016/j.jbc.2024.107347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
A vast ensemble of extracellular proteins influences the development and progression of cancer, shaped and reshaped by a complex network of extracellular proteases. These proteases, belonging to the distinct classes of metalloproteases, serine proteases, cysteine proteases, and aspartic proteases, play a critical role in cancer. They often become dysregulated in cancer, with increases in pathological protease activity frequently driven by the loss of normal latency controls, diminished regulation by endogenous protease inhibitors, and changes in localization. Dysregulated proteases accelerate tumor progression and metastasis by degrading protein barriers within the extracellular matrix (ECM), stimulating tumor growth, reactivating dormant tumor cells, facilitating tumor cell escape from immune surveillance, and shifting stromal cells toward cancer-promoting behaviors through the precise proteolysis of specific substrates to alter their functions. These crucial substrates include ECM proteins and proteoglycans, soluble proteins secreted by tumor and stromal cells, and extracellular domains of cell surface proteins, including membrane receptors and adhesion proteins. The complexity of the extracellular protease web presents a significant challenge to untangle. Nevertheless, technological strides in proteomics, chemical biology, and the development of new probes and reagents are enabling progress and advancing our understanding of the pivotal importance of extracellular proteolysis in cancer.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA.
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12
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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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13
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Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024; 41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [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: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Genevieve T Oliver
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabella Z Farkas
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Buszczak
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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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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15
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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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16
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Palani S, Machida Y, Alvey JR, Mishra V, Welter AL, Cui G, Bragantini B, Botuyan MV, Cong ATQ, Mer G, Schellenberg MJ, Machida YJ. Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes. Nat Commun 2024; 15:2064. [PMID: 38453899 PMCID: PMC10920703 DOI: 10.1038/s41467-024-46207-w] [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: 03/30/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A's function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
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Affiliation(s)
- Sowmiya Palani
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Yuka Machida
- Department of Oncology, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Julia R Alvey
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Vandana Mishra
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Allison L Welter
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Anh T Q Cong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Yuichi J Machida
- Department of Oncology, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA.
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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17
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Batel A, Polović M, Glumac M, Šuman O, Jadrijević S, Lozić B, Petrović M, Samardžija B, Bradshaw NJ, Skube K, Palada V, Acman M, Marinović Terzić I. SPRTN is involved in hepatocellular carcinoma development through the ER stress response. Cancer Gene Ther 2024; 31:376-386. [PMID: 38086993 DOI: 10.1038/s41417-023-00708-w] [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: 07/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 03/16/2024]
Abstract
Endoplasmic reticulum (ER) stress, prompted by the accumulation of misfolded or unfolded proteins, triggers the activation of the unfolded protein response (UPR) pathway to restore ER homeostasis. This stress response is implicated in the development of hepatocellular carcinoma (HCC). A biallelic mutation in SPRTN is currently the only known single-gene mutation implicated in the early onset of HCC. However, the exact mechanism linking SPRTN mutations to HCC remains unclear. In our study, we analyzed SPRTN and UPR in 21 human HCC tissue samples using RT-qPCR, immunoblot, and immunohistochemistry. We found alterations in the expression levels of SPRTN and UPR-related genes and proteins in HCC samples. The impact of SPRTN on the ER stress response was assessed in SPRTN-depleted HepG2 cells through RNA sequencing, pull-down assay, comet assay, and mitotic index calculation. We demonstrated that SPRTN interacts with the UPR sensor GRP78. Furthermore, we observed a decrease in SPRTN levels during ER stress, and increased sensitivity to ER stress in SPRTN-depleted cells. These findings suggest an essential role for SPRTN in the ER stress response and provide new insights into HCC pathogenesis. This newly discovered function of SPRTN could significantly enhance our understanding and treatment of HCC.
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Affiliation(s)
- Anja Batel
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mirjana Polović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mateo Glumac
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Oliver Šuman
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Stipislav Jadrijević
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Bernarda Lozić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Marija Petrović
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Bobana Samardžija
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Nicholas J Bradshaw
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Karlo Skube
- Selvita, Prilaz baruna Filipovića 29, 10000, Zagreb, Croatia
| | - Vinko Palada
- Department of Physiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Mislav Acman
- Omics solutions, trg 101. Brigade HV 1, 10000, Zagreb, Croatia
| | - Ivana Marinović Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia.
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18
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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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19
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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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20
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Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [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: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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21
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Essawy M, Chesner L, Alshareef D, Ji S, Tretyakova N, Campbell C. Ubiquitin signaling and the proteasome drive human DNA-protein crosslink repair. Nucleic Acids Res 2023; 51:12174-12184. [PMID: 37843153 PMCID: PMC10711432 DOI: 10.1093/nar/gkad860] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are large cytotoxic DNA lesions that form following exposure to chemotherapeutic drugs and environmental chemicals. Nucleotide excision repair (NER) and homologous recombination (HR) promote survival following exposure to DPC-inducing agents. However, it is not known how cells recognize DPC lesions, or what mechanisms selectively target DPC lesions to these respective repair pathways. To address these questions, we examined DPC recognition and repair by transfecting a synthetic DPC lesion comprised of the human oxoguanine glycosylase (OGG1) protein crosslinked to double-stranded M13MP18 into human cells. In wild-type cells, this lesion is efficiently repaired, whereas cells deficient in NER can only repair this lesion if an un-damaged homologous donor is co-transfected. Transfected DPC is subject to rapid K63 polyubiquitination. In NER proficient cells, the DPC is subject to K48 polyubiquitination, and is removed via a proteasome-dependent mechanism. In NER-deficient cells, the DNA-conjugated protein is not subject to K48 polyubiquitination. Instead, the K63 tag remains attached, and is only lost when a homologous donor molecule is present. Taken together, these results support a model in which selective addition of polyubiquitin chains to DNA-crosslinked protein leads to selective recruitment of the proteasome and the cellular NER and recombinational DNA repair machinery.
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Affiliation(s)
- Maram Essawy
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Lisa Chesner
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Duha Alshareef
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Shaofei Ji
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
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22
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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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23
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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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24
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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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25
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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26
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Shimizu N, Hamada Y, Morozumi R, Yamamoto J, Iwai S, Sugiyama KI, Ide H, Tsuda M. Repair of topoisomerase 1-induced DNA damage by tyrosyl-DNA phosphodiesterase 2 (TDP2) is dependent on its magnesium binding. J Biol Chem 2023; 299:104988. [PMID: 37392847 PMCID: PMC10407441 DOI: 10.1016/j.jbc.2023.104988] [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: 01/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023] Open
Abstract
Topoisomerases are enzymes that relax DNA supercoiling during replication and transcription. Camptothecin, a topoisomerase 1 (TOP1) inhibitor, and its analogs trap TOP1 at the 3'-end of DNA as a DNA-bound intermediate, resulting in DNA damage that can kill cells. Drugs with this mechanism of action are widely used to treat cancers. It has previously been shown that tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs TOP1-induced DNA damage generated by camptothecin. In addition, tyrosyl-DNA phosphodiesterase 2 (TDP2) plays critical roles in repairing topoisomerase 2 (TOP2)-induced DNA damage at the 5'-end of DNA and in promoting the repair of TOP1-induced DNA damage in the absence of TDP1. However, the catalytic mechanism by which TDP2 processes TOP1-induced DNA damage has not been elucidated. In this study, we found that a similar catalytic mechanism underlies the repair of TOP1- and TOP2-induced DNA damage by TDP2, with Mg2+-TDP2 binding playing a role in both repair mechanisms. We show chain-terminating nucleoside analogs are incorporated into DNA at the 3'-end and abort DNA replication to kill cells. Furthermore, we found that Mg2+-TDP2 binding also contributes to the repair of incorporated chain-terminating nucleoside analogs. Overall, these findings reveal the role played by Mg2+-TDP2 binding in the repair of both 3'- and 5'-blocking DNA damage.
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Affiliation(s)
- Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yusaku Hamada
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kei-Ichi Sugiyama
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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27
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Vijayraghavan S, Saini N. Aldehyde-Associated Mutagenesis─Current State of Knowledge. Chem Res Toxicol 2023. [PMID: 37363863 DOI: 10.1021/acs.chemrestox.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Aldehydes are widespread in the environment, with multiple sources such as food and beverages, industrial effluents, cigarette smoke, and additives. The toxic effects of exposure to several aldehydes have been observed in numerous studies. At the molecular level, aldehydes damage DNA, cross-link DNA and proteins, lead to lipid peroxidation, and are associated with increased disease risk including cancer. People genetically predisposed to aldehyde sensitivity exhibit severe health outcomes. In various diseases such as Fanconi's anemia and Cockayne syndrome, loss of aldehyde-metabolizing pathways in conjunction with defects in DNA repair leads to widespread DNA damage. Importantly, aldehyde-associated mutagenicity is being explored in a growing number of studies, which could offer key insights into how they potentially contribute to tumorigenesis. Here, we review the genotoxic effects of various aldehydes, focusing particularly on the DNA adducts underlying the mutagenicity of environmentally derived aldehydes. We summarize the chemical structures of the aldehydes and their predominant DNA adducts, discuss various methodologies, in vitro and in vivo, commonly used in measuring aldehyde-associated mutagenesis, and highlight some recent studies looking at aldehyde-associated mutation signatures and spectra. We conclude the Review with a discussion on the challenges and future perspectives of investigating aldehyde-associated mutagenesis.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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28
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Sun Y, Baechler SA, Zhang X, Kumar S, Factor VM, Arakawa Y, Chau CH, Okamoto K, Parikh A, Walker B, Su YP, Chen J, Ting T, Huang SYN, Beck E, Itkin Z, McKnight C, Xie C, Roper N, Nijhawan D, Figg WD, Meltzer PS, Yang JC, Thomas CJ, Pommier Y. Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex. Nat Commun 2023; 14:3762. [PMID: 37353483 PMCID: PMC10290057 DOI: 10.1038/s41467-023-39374-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
Colorectal cancers (CRCs) are prevalent worldwide, yet current treatments remain inadequate. Using chemical genetic screens, we identify that co-inhibition of topoisomerase I (TOP1) and NEDD8 is synergistically cytotoxic in human CRC cells. Combination of the TOP1 inhibitor irinotecan or its bioactive metabolite SN38 with the NEDD8-activating enzyme inhibitor pevonedistat exhibits synergy in CRC patient-derived organoids and xenografts. Mechanistically, we show that pevonedistat blocks the ubiquitin/proteasome-dependent repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors and that the CUL4-RBX1 complex (CRL4) is a prominent ubiquitin ligase acting on TOP1-DPCs for proteasomal degradation upon auto-NEDD8 modification during replication. We identify DCAF13, a DDB1 and Cullin Associated Factor, as the receptor of TOP1-DPCs for CRL4. Our study not only uncovers a replication-coupled ubiquitin-proteasome pathway for the repair of TOP1-DPCs but also provides molecular and translational rationale for combining TOP1 inhibitors and pevonedistat for CRC and other types of cancers.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Simone A Baechler
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Valentina M Factor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yasuhiro Arakawa
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cindy H Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kanako Okamoto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anup Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bob Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun P Su
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tabitha Ting
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Erin Beck
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Zina Itkin
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Crystal McKnight
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Deepak Nijhawan
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William Douglas Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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29
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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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30
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Kumari P, Sahu SR, Utkalaja BG, Dutta A, Acharya N. RAD51-WSS1-dependent genetic pathways are essential for DNA-Protein crosslink repair and pathogenesis in Candida albicans. J Biol Chem 2023; 299:104728. [PMID: 37080389 DOI: 10.1016/j.jbc.2023.104728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/22/2023] Open
Abstract
Genetic analyses in Saccharomyces cerevisiae suggest that nucleotide excision repair (NER), homologous recombination (HR), and proteases-dependent repair (PDR) pathways coordinately function to remove DNA-protein crosslinks (DPCs) from the genome. DPCs are genomic cytotoxic lesions generated due to the covalent linkage of proteins with DNA. Although NER and HR processes have been studied in pathogenic Candida albicans, their roles in DPCs repair (DPCR) are yet to be explored. Proteases like Wss1 and Tdp1 are known to be involved in DPCR, however, Tdp1 that selectively removes topoisomerase-DNA complexes is intrinsically absent in C. albicans. Therefore, the mechanism of DPCR might have evolved differently in C. albicans. Herein, we investigated the interplay of three genetic pathways and found that RAD51-WSS1 dependent HR and PDR pathways are essential for DPCs removal, and their absence caused an increased rate of loss of heterozygosity in C. albicans. RAD1 but not RAD2 of NER is critical for DPCR. Additionally, we observed truncation of chromosome#6 in the cells defective in both RAD51 and WSS1 genes. While the protease and DNA binding activities are essential, a direct interaction of Wss1 with the eukaryotic DNA clamp PCNA is not a requisite for Wss1's function. DPCR-defective C. albicans cells exhibited filamentous morphology, reduced immune cell evasion, and attenuation in virulence. Thus, we concluded that RAD51-WSS1-dependent DPCR pathways are essential for genome stability and candidiasis development. Since no vaccine against candidiasis is available for human use yet, we propose to explore DPCR defective attenuated strains (rad51ΔΔwss1ΔΔ and rad2ΔΔrad51ΔΔwss1ΔΔ) for whole-cell vaccine development.
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Affiliation(s)
- Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India; Regional center of Biotechnology, Faridabad, India
| | - Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India; Regional center of Biotechnology, Faridabad, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India; Regional center of Biotechnology, Faridabad, India
| | - Abinash Dutta
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India.
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31
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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32
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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: 14] [Impact Index Per Article: 14.0] [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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33
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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: 22] [Impact Index Per Article: 22.0] [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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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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35
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Welter AL, Machida YJ. Functions and evolution of FAM111 serine proteases. Front Mol Biosci 2022; 9:1081166. [PMID: 36589246 PMCID: PMC9798293 DOI: 10.3389/fmolb.2022.1081166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Proteolysis plays fundamental and regulatory roles in diverse cellular processes. The serine protease FAM111A (FAM111 trypsin-like peptidase A) emerged recently as a protease involved in two seemingly distinct processes: DNA replication and antiviral defense. FAM111A localizes to nascent DNA and plays a role at the DNA replication fork. At the fork, FAM111A is hypothesized to promote DNA replication at DNA-protein crosslinks (DPCs) and protein obstacles. On the other hand, FAM111A has also been identified as a host restriction factor for mutants of SV40 and orthopoxviruses. FAM111A also has a paralog, FAM111B, a serine protease with unknown cellular functions. Furthermore, heterozygous missense mutations in FAM111A and FAM111B cause distinct genetic disorders. In this review, we discuss possible models that could explain how FAM111A can function as a protease in both DNA replication and antiviral defense. We also review the consequences of FAM111A and FAM111B mutations and explore possible mechanisms underlying the diseases. Additionally, we propose a possible explanation for what drove the evolution of FAM111 proteins and discuss why some species have two FAM111 proteases. Altogether, studies of FAM111 proteases in DNA repair, antiviral defense, and genetic diseases will help us elucidate their functions and the regulatory mechanisms.
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Affiliation(s)
- Allison L. Welter
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Yuichi J. Machida
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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36
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Meroni A, Grosser J, Agashe S, Ramakrishnan N, Jackson J, Verma P, Baranello L, Vindigni A. NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors. SCIENCE ADVANCES 2022; 8:eabq0648. [PMID: 36490343 PMCID: PMC9733930 DOI: 10.1126/sciadv.abq0648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/26/2022] [Indexed: 05/30/2023]
Abstract
DNA topoisomerase 1 (TOP11) inhibitors are mainstays of anticancer therapy. These drugs trap TOP1 on DNA, stabilizing the TOP1-cleavage complex (TOP1-cc). The accumulation of TOP1-ccs perturbs DNA replication fork progression, leading to DNA breaks and cell death. By analyzing the genomic occupancy and activity of TOP1, we show that cells adapt to treatment with multiple doses of TOP1 inhibitor by promoting the degradation of TOP1-ccs, allowing cells to better tolerate subsequent doses of TOP1 inhibitor. The E3-RING Cullin 3 ligase in complex with the BTBD1 and BTBD2 adaptor proteins promotes TOP1-cc ubiquitination and subsequent proteasomal degradation. NEDDylation of Cullin 3 activates this pathway, and inhibition of protein NEDDylation or depletion of Cullin 3 sensitizes cancer cells to TOP1 inhibitors. Collectively, our data uncover a previously unidentified NEDD8-Cullin 3 pathway involved in the adaptive response to TOP1 inhibitors, which can be targeted to improve the efficacy of TOP1 drugs in cancer therapy.
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Affiliation(s)
- Alice Meroni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jan Grosser
- Karolinska Institutet, CMB, 171 65 Solna, Sweden
| | - Sumedha Agashe
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Natasha Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Priyanka Verma
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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37
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Bolgi O, Silva-Garcia M, Ross B, Pilla E, Kari V, Killisch M, Spitzner M, Stark N, Lenz C, Weiss K, Donzelli L, Gorrell MD, Grade M, Riemer J, Urlaub H, Dobbelstein M, Huber R, Geiss-Friedlander R. Dipeptidyl peptidase 9 triggers BRCA2 degradation and promotes DNA damage repair. EMBO Rep 2022; 23:e54136. [PMID: 35912982 PMCID: PMC9535758 DOI: 10.15252/embr.202154136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/30/2022] Open
Abstract
N-terminal sequences are important sites for post-translational modifications that alter protein localization, activity, and stability. Dipeptidyl peptidase 9 (DPP9) is a serine aminopeptidase with the rare ability to cleave off N-terminal dipeptides with imino acid proline in the second position. Here, we identify the tumor-suppressor BRCA2 as a DPP9 substrate and show this interaction to be induced by DNA damage. We present crystallographic structures documenting intracrystalline enzymatic activity of DPP9, with the N-terminal Met1-Pro2 of a BRCA21-40 peptide captured in its active site. Intriguingly, DPP9-depleted cells are hypersensitive to genotoxic agents and are impaired in the repair of DNA double-strand breaks by homologous recombination. Mechanistically, DPP9 targets BRCA2 for degradation and promotes the formation of RAD51 foci, the downstream function of BRCA2. N-terminal truncation mutants of BRCA2 that mimic a DPP9 product phenocopy reduced BRCA2 stability and rescue RAD51 foci formation in DPP9-deficient cells. Taken together, we present DPP9 as a regulator of BRCA2 stability and propose that by fine-tuning the cellular concentrations of BRCA2, DPP9 alters the BRCA2 interactome, providing a possible explanation for DPP9's role in cancer.
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Affiliation(s)
- Oguz Bolgi
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Maria Silva-Garcia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Breyan Ross
- Max Planck Institut für Biochemie, Martinsried, Germany.,Proteros Biostructures GmbH, Martinsried, Germany
| | - Esther Pilla
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Killisch
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Melanie Spitzner
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Nadine Stark
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Konstantin Weiss
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Mark D Gorrell
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Robert Huber
- Max Planck Institut für Biochemie, Martinsried, Germany.,Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Essen, Germany.,Fakultät für Chemie, Technische Universität München, Garching, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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38
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Brand CL, Levine MT. Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity. Curr Biol 2022; 32:2962-2971.e4. [PMID: 35643081 PMCID: PMC9283324 DOI: 10.1016/j.cub.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
Satellite DNA spans megabases of eukaryotic sequence and evolves rapidly.1-6 Paradoxically, satellite-rich genomic regions mediate strictly conserved, essential processes such as chromosome segregation and nuclear structure.7-10 A leading resolution to this paradox posits that satellite DNA and satellite-associated chromosomal proteins coevolve to preserve these essential functions.11 We experimentally test this model of intragenomic coevolution by conducting the first evolution-guided manipulation of both chromosomal protein and DNA satellite. The 359bp satellite spans an 11 Mb array in Drosophila melanogaster that is absent from its sister species, Drosophila simulans.12-14 This species-specific DNA satellite colocalizes with the adaptively evolving, ovary-enriched protein, maternal haploid (MH), the Drosophila homolog of Spartan.15 To determine if MH and 359bp coevolve, we swapped the D. simulans version of MH ("MH[sim]") into D. melanogaster. MH[sim] triggers ovarian cell death, reduced ovary size, and loss of mature eggs. Surprisingly, the D. melanogaster mh-null mutant has no such ovary phenotypes,15 suggesting that MH[sim] is toxic in a D. melanogaster background. Using both cell biology and genetics, we discovered that MH[sim] poisons oogenesis through a DNA-damage pathway. Remarkably, deleting the D. melanogaster-specific 359bp satellite array completely restores mh[sim] germline genome integrity and fertility, consistent with a history of coevolution between these two fast-evolving loci. Germline genome integrity and fertility are also restored by overexpressing topoisomerase II (Top2), suggesting that MH[sim] interferes with Top2-mediated processing of 359bp. The observed 359bp-MH[sim] cross-species incompatibility supports a model under which seemingly inert repetitive DNA and essential chromosomal proteins must coevolve to preserve germline genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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39
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Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
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40
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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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41
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Kröning A, van den Boom J, Kracht M, Kueck AF, Meyer H. Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN. J Biol Chem 2022; 298:101976. [PMID: 35469923 PMCID: PMC9127365 DOI: 10.1016/j.jbc.2022.101976] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/02/2022] Open
Abstract
The protease SPRTN degrades DNA-protein crosslinks (DPCs) that threaten genome stability. SPRTN has been connected to the ubiquitin-directed protein unfoldase p97 (also called VCP or Cdc48), but a functional cooperation has not been demonstrated directly. Here, we biochemically reconstituted p97-assisted proteolysis with purified proteins and showed that p97 targets ubiquitin-modified DPCs and unfolds them to prepare them for proteolysis by SPRTN. We demonstrate that purified SPRTN alone was unable to degrade a tightly-folded Eos fluorescent reporter protein even when Eos was crosslinked to DNA (Eos-DPC). However, when present, p97 unfolded poly-ubiquitinated Eos-DPC in a manner requiring its ubiquitin adapter, Ufd1-Npl4. Notably, we show that, in cooperation with p97 and Ufd1-Npl4, SPRTN proteolyzed unfolded Eos-DPC, which relied on recognition of the DNA-crosslink by SPRTN. In a simplified unfolding assay, we further demonstrate that p97, while unfolding a protein substrate, can surmount the obstacle of a DNA crosslink site in the substrate. Thus, our data demonstrate that p97, in conjunction with Ufd1-Npl4, assists SPRTN-mediated proteolysis of tightly-folded proteins crosslinked to DNA, even threading bulky protein-DNA adducts. These findings will be relevant for understanding how cells handle DPCs to ensure genome stability and for designing strategies that target p97 in combination cancer therapy.
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Affiliation(s)
- Alexander Kröning
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Matthias Kracht
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anja F Kueck
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hemmo Meyer
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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42
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Wang M, Dingler FA, Patel KJ. Genotoxic aldehydes in the hematopoietic system. Blood 2022; 139:2119-2129. [PMID: 35148375 DOI: 10.1182/blood.2019004316] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Reactive aldehydes are potent genotoxins that threaten the integrity of hematopoietic stem cells and blood production. To protect against aldehydes, mammals have evolved a family of enzymes to detoxify aldehydes, and the Fanconi anemia DNA repair pathway to process aldehyde-induced DNA damage. Loss of either protection mechanisms in humans results in defective hematopoiesis and predisposition to leukemia. This review will focus on the impact of genotoxic aldehydes on hematopoiesis, the sources of endogenous aldehydes, and potential novel protective pathways.
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Affiliation(s)
- Meng Wang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Department of Haematology and
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom; and
| | - Felix A Dingler
- Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - K J Patel
- Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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43
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USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nat Commun 2022; 13:1740. [PMID: 35365626 PMCID: PMC8975806 DOI: 10.1038/s41467-022-29369-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
The deubiquitinase USP1 is a critical regulator of genome integrity through the deubiquitylation of Fanconi Anemia proteins and the DNA replication processivity factor, proliferating cell nuclear antigen (PCNA). Uniquely, following UV irradiation, USP1 self-inactivates through autocleavage, which enables its own degradation and in turn, upregulates PCNA monoubiquitylation. However, the functional role for this autocleavage event during physiological conditions remains elusive. Herein, we discover that cells harboring an autocleavage-defective USP1 mutant, while still able to robustly deubiquitylate PCNA, experience more replication fork-stalling and premature fork termination events. Using super-resolution microscopy and live-cell single-molecule tracking, we show that these defects are related to the inability of this USP1 mutant to be properly recycled from sites of active DNA synthesis, resulting in replication-associated lesions. Furthermore, we find that the removal of USP1 molecules from DNA is facilitated by the DNA-dependent metalloprotease Spartan to counteract the cytotoxicity caused by “USP1-trapping”. We propose a utility of USP1 inhibitors in cancer therapy based on their ability to induce USP1-trapping lesions and consequent replication stress and genomic instability in cancer cells, similar to how non-covalent DNA-protein crosslinks cause cytotoxicity by imposing steric hindrances upon proteins involved in DNA transactions. Here the authors provide mechanistic insights into how auto-cleavage of the USP1 deubiquitinase regulates DNA replication and genome stability. Implications for the targeting of USP1 activity via protein-DNA trapping in cancer therapy are discussed.
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Abstract
Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
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Hacker L, Dorn A, Enderle J, Puchta H. The repair of topoisomerase 2 cleavage complexes in Arabidopsis. THE PLANT CELL 2022; 34:287-301. [PMID: 34524446 PMCID: PMC8773952 DOI: 10.1093/plcell/koab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/08/2021] [Indexed: 05/04/2023]
Abstract
DNA-protein crosslinks (DPCs) and DNA double-stranded breaks (DSBs), including those produced by stalled topoisomerase 2 cleavage complexes (TOP2ccs), must be repaired to ensure genome stability. The basic mechanisms of TOP2cc repair have been characterized in other eukaryotes, but we lack information for plants. Using CRISPR/Cas-induced mutants, we show that Arabidopsis thaliana has two main TOP2cc repair pathways: one is defined by TYROSYL-DNA-PHOSPHODIESTERASE 2 (TDP2), which hydrolyzes TOP2-DNA linkages, the other by the DNA-dependent protease WSS1A (a homolog of human SPARTAN/yeast weak suppressor of smt3 [Wss1]), which also functions in DPC repair. TDP1 and TDP2 function nonredundantly in TOP1cc repair, indicating that they act specifically on their respective stalled cleavage complexes. The nuclease METHYL METHANESULFONATE AND UV-SENSITIVE PROTEIN 81 (MUS81) plays a major role in global DPC repair and a minor role in TOP2cc repair. DSBs arise as intermediates of TOP2cc repair and are repaired by classical and alternative nonhomologous end joining (NHEJ) pathways. Double-mutant analysis indicates that "clean" DNA ends caused by TDP2 hydrolysis are mainly religated by classical NHEJ, which helps avoid mutation. In contrast, the mutagenic alternative NHEJ pathway mainly processes nonligateable DNA ends. Thus, TDP2 promotes maintenance of plant genome integrity by error-free repair of TOP2cc.
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Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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Go AC, Civetta A. Divergence of X-linked trans regulatory proteins and the misexpression of gene targets in sterile Drosophila pseudoobscura hybrids. BMC Genomics 2022; 23:30. [PMID: 34991488 PMCID: PMC8740060 DOI: 10.1186/s12864-021-08267-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The genetic basis of hybrid incompatibilities is characterized by pervasive cases of gene interactions. Sex chromosomes play a major role in speciation and X-linked hybrid male sterility (HMS) genes have been identified. Interestingly, some of these genes code for proteins with DNA binding domains, suggesting a capability to act as trans-regulatory elements and disturb the expression of a large number of gene targets. To understand how interactions between trans- and cis-regulatory elements contribute to speciation, we aimed to map putative X-linked trans-regulatory elements and to identify gene targets with disrupted gene expression in sterile hybrids between the subspecies Drosophila pseudoobscura pseudoobscura and D. p. bogotana. RESULTS We find six putative trans-regulatory proteins within previously mapped X chromosome HMS loci with sequence changes that differentiate the two subspecies. Among them, the previously characterized HMS gene Overdrive (Ovd) had the largest number of amino acid changes between subspecies, with some substitutions localized within the protein's DNA binding domain. Using an introgression approach, we detected transcriptional responses associated with a sterility/fertility Ovd allele swap. We found a network of 52 targets of Ovd and identified cis-regulatory effects among target genes with disrupted expression in sterile hybrids. However, a combined analysis of polymorphism and divergence in non-coding sequences immediately upstream of target genes found no evidence of changes in candidate regulatory proximal cis-elements. Finally, peptidases were over-represented among target genes. CONCLUSIONS We provide evidence of divergence between subspecies within the DNA binding domain of the HMS protein Ovd and identify trans effects on the expression of 52 gene targets. Our results identify a network of trans-cis interactions with possible effects on HMS. This network provides molecular evidence of gene × gene incompatibilities as contributors to hybrid dysfunction.
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Affiliation(s)
- Alwyn C Go
- Department of Biology, University of Winnipeg, 515 Portage Ave, Winnipeg, MB, R3B 2E9, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, 515 Portage Ave, Winnipeg, MB, R3B 2E9, Canada.
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Campos JTADM, Oliveira MSD, Soares LP, Medeiros KAD, Campos LRDS, Lima JG. DNA repair-related genes and adipogenesis: Lessons from congenital lipodystrophies. Genet Mol Biol 2022; 45:e20220086. [DOI: 10.1590/1678-4685-gmb-2022-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
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Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Mol Syst Biol 2022; 18:e10584. [PMID: 35044719 PMCID: PMC8769072 DOI: 10.15252/msb.202110584] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
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Affiliation(s)
- Caroline Benz
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Muhammad Ali
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | | | | | - Ahmed Sayadi
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Filip Mihalic
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Johanna Kliche
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Eva Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Per Jemth
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
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49
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Bhattacharjee S, Rehman I, Nandy S, Das BB. Post-translational regulation of Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) for the repair of the trapped topoisomerase-DNA covalent complex. DNA Repair (Amst) 2022; 111:103277. [DOI: 10.1016/j.dnarep.2022.103277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/24/2021] [Accepted: 01/20/2022] [Indexed: 12/23/2022]
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50
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Ruggiano A, Vaz B, Kilgas S, Popović M, Rodriguez-Berriguete G, Singh AN, Higgins GS, Kiltie AE, Ramadan K. The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability. Cell Rep 2021; 37:110080. [PMID: 34879279 PMCID: PMC8674535 DOI: 10.1016/j.celrep.2021.110080] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 09/22/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are a specific type of DNA lesion in which proteins are covalently attached to DNA. Unrepaired DPCs lead to genomic instability, cancer, neurodegeneration, and accelerated aging. DPC proteolysis was recently identified as a specialized pathway for DPC repair. The DNA-dependent protease SPRTN and the 26S proteasome emerged as two independent proteolytic systems. DPCs are also repaired by homologous recombination (HR), a canonical DNA repair pathway. While studying the cellular response to DPC formation, we identify ubiquitylation and SUMOylation as two major signaling events in DNA replication-coupled DPC repair. DPC ubiquitylation recruits SPRTN to repair sites, promoting DPC removal. DPC SUMOylation prevents DNA double-strand break formation, HR activation, and potentially deleterious genomic rearrangements. In this way, SUMOylation channels DPC repair toward SPRTN proteolysis, which is a safer pathway choice for DPC repair and prevention of genomic instability.
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Affiliation(s)
- Annamaria Ruggiano
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Bruno Vaz
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Susan Kilgas
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Marta Popović
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK; Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Gonzalo Rodriguez-Berriguete
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Abhay N Singh
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Geoff S Higgins
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Anne E Kiltie
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.
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