1
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Noireterre A, Stutz F. Cdc48/p97 segregase: Spotlight on DNA-protein crosslinks. DNA Repair (Amst) 2024; 139:103691. [PMID: 38744091 DOI: 10.1016/j.dnarep.2024.103691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
The ATP-dependent molecular chaperone Cdc48 (in yeast) and its human counterpart p97 (also known as VCP), are essential for a variety of cellular processes, including the removal of DNA-protein crosslinks (DPCs) from the DNA. Growing evidence demonstrates in the last years that Cdc48/p97 is pivotal in targeting ubiquitinated and SUMOylated substrates on chromatin, thereby supporting the DNA damage response. Along with its cofactors, notably Ufd1-Npl4, Cdc48/p97 has emerged as a central player in the unfolding and processing of DPCs. This review introduces the detailed structure, mechanism and cellular functions of Cdc48/p97 with an emphasis on the current knowledge of DNA-protein crosslink repair pathways across several organisms. The review concludes by discussing the potential therapeutic relevance of targeting p97 in DPC repair.
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Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 4 1211, Switzerland.
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2
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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3
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Oka Y, Nakazawa Y, Shimada M, Ogi T. Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair. Nat Cell Biol 2024; 26:784-796. [PMID: 38600234 PMCID: PMC11098742 DOI: 10.1038/s41556-024-01401-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair and aldehyde clearance processes cause progeria, including Ruijs-Aalfs syndrome (RJALS) and AMeD syndrome (AMeDS) in humans. Although the elimination of DPC during replication has been well established, how cells overcome DPC lesions in transcription remains elusive. Here we show that endogenous aldehyde-induced DPC roadblocks are efficiently resolved by transcription-coupled repair (TCR). We develop a high-throughput sequencing technique to measure the genome-wide distribution of DPCs (DPC-seq). Using proteomics and DPC-seq, we demonstrate that the conventional TCR complex as well as VCP/p97 and the proteasome are required for the removal of formaldehyde-induced DPCs. TFIIS-dependent cleavage of RNAPII transcripts protects against transcription obstacles. Finally, a mouse model lacking both aldehyde clearance and TCR confirms endogenous DPC accumulation in actively transcribed regions. Collectively, our data provide evidence that transcription-coupled DPC repair (TC-DPCR) as well as aldehyde clearance are crucial for protecting against metabolic genotoxin, thus explaining the molecular pathogenesis of AMeDS and other disorders associated with defects in TCR, such as Cockayne syndrome.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan.
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
- Division of Molecular Physiology and Dynamics, Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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4
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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: 2] [Impact Index Per Article: 2.0] [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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5
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. The Response of the Replication Apparatus to Leading Template Strand Blocks. Cells 2023; 12:2607. [PMID: 37998342 PMCID: PMC10670059 DOI: 10.3390/cells12222607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Duplication of the genome requires the replication apparatus to overcome a variety of impediments, including covalent DNA adducts, the most challenging of which is on the leading template strand. Replisomes consist of two functional units, a helicase to unwind DNA and polymerases to synthesize it. The helicase is a multi-protein complex that encircles the leading template strand and makes the first contact with a leading strand adduct. The size of the channel in the helicase would appear to preclude transit by large adducts such as DNA: protein complexes (DPC). Here we discuss some of the extensively studied pathways that support replication restart after replisome encounters with leading template strand adducts. We also call attention to recent work that highlights the tolerance of the helicase for adducts ostensibly too large to pass through the central channel.
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Affiliation(s)
| | | | | | | | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (M.A.B.)
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6
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Yudkina A, Bulgakov N, Kim D, Baranova S, Ishchenko A, Saparbaev M, Koval V, Zharkov D. Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases. Nucleic Acids Res 2023; 51:6321-6336. [PMID: 37216593 PMCID: PMC10325907 DOI: 10.1093/nar/gkad423] [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: 12/20/2022] [Revised: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites are abundant DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and as base excision repair (BER) intermediates. AP sites and their derivatives readily trap DNA-bound proteins, resulting in DNA-protein cross-links. Those are subject to proteolysis but the fate of the resulting AP-peptide cross-links (APPXLs) is unclear. Here, we report two in vitro models of APPXLs synthesized by cross-linking of DNA glycosylases Fpg and OGG1 to DNA followed by trypsinolysis. The reaction with Fpg produces a 10-mer peptide cross-linked through its N-terminus, while OGG1 yields a 23-mer peptide attached through an internal lysine. Both adducts strongly blocked Klenow fragment, phage RB69 polymerase, Saccharolobus solfataricus Dpo4, and African swine fever virus PolX. In the residual lesion bypass, mostly dAMP and dGMP were incorporated by Klenow and RB69 polymerases, while Dpo4 and PolX used primer/template misalignment. Of AP endonucleases involved in BER, Escherichia coli endonuclease IV and its yeast homolog Apn1p efficiently hydrolyzed both adducts. In contrast, E. coli exonuclease III and human APE1 showed little activity on APPXL substrates. Our data suggest that APPXLs produced by proteolysis of AP site-trapped proteins may be removed by the BER pathway, at least in bacterial and yeast cells.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikita A Bulgakov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Daria V Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana V Baranova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Groupe “Mechanisms of DNA Repair and Carcinogenesis”, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France
| | - Murat K Saparbaev
- Groupe “Mechanisms of DNA Repair and Carcinogenesis”, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France
| | - Vladimir V Koval
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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7
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Noireterre A, Serbyn N, Bagdiul I, Stutz F. Ubx5-Cdc48 assists the protease Wss1 at DNA-protein crosslink sites in yeast. EMBO J 2023:e113609. [PMID: 37144685 DOI: 10.15252/embj.2023113609] [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: 01/25/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
DNA-protein crosslinks (DPCs) pose a serious threat to genome stability. The yeast proteases Wss1, 26S proteasome, and Ddi1 are safeguards of genome integrity by acting on a plethora of DNA-bound proteins in different cellular contexts. The AAA ATPase Cdc48/p97 is known to assist Wss1/SPRTN in clearing DNA-bound complexes; however, its contribution to DPC proteolysis remains unclear. Here, we show that the Cdc48 adaptor Ubx5 is detrimental in yeast mutants defective in DPC processing. Using an inducible site-specific crosslink, we show that Ubx5 accumulates at persistent DPC lesions in the absence of Wss1, which prevents their efficient removal from the DNA. Abolishing Cdc48 binding or complete loss of Ubx5 suppresses sensitivity of wss1∆ cells to DPC-inducing agents by favoring alternate repair pathways. We provide evidence for cooperation of Ubx5-Cdc48 and Wss1 in the genotoxin-induced degradation of RNA polymerase II (RNAPII), a described candidate substrate of Wss1. We propose that Ubx5-Cdc48 assists Wss1 for proteolysis of a subset of DNA-bound proteins. Together, our findings reveal a central role for Ubx5 in DPC clearance and repair.
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Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Nataliia Serbyn
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Ivona Bagdiul
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
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8
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Bryan C, Le J, Wei X, Yang K. Saccharomyces cerevisiae apurinic/apyrimidinic endonuclease 1 repairs abasic site-mediated DNA-peptide/protein cross-links. DNA Repair (Amst) 2023; 126:103501. [PMID: 37075541 DOI: 10.1016/j.dnarep.2023.103501] [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: 10/26/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
Saccharomyces cerevisiae apurinic/apyrimidinic (AP) endonuclease 1 (yApn1) is a key player of the base excision repair pathway. This multifunctional enzyme is an AP endonuclease, 3'-5' exonuclease, 3'-phosphodiesterase, and participates in nucleotide incision repair. To the best of our knowledge, the known substrates of yApn1 are small DNA lesions such as AP sites and 3'-phospho-α,β-unsaturated aldehyde (3'-PUA). Here, we wish to report in vitro findings that yApn1 repairs bulky DNA-peptide cross-links (DpCs) and DNA-protein cross-links (DPCs) arising from AP sites and 3'-PUA. We chemically synthesized stable and linkage-defined DpCs and DPCs by oxime ligation and reductive amination, respectively. Our steady-state kinetic data showed that yApn1 repairs a 10-mer peptide-conjugated AP site and 3'-PUA with comparable efficiencies to that of processing the unconjugated lesions. We demonstrated that yApn1 is the predominant enzyme that incises AP-DpC in yeast cell extracts. We also demonstrated that yApn1 incises AP-DPCs in a DPC size-dependent manner, and prior DPC proteolysis by trypsin facilitates the repair. We further found that yApn1 removes 3'-PUA-histone DPCs with moderate efficiencies. Together, our results uncovered a novel role of yApn1 in DPC repair, and support the emerging model that proteolysis is required for efficient DPC repair.
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Affiliation(s)
- Cameron Bryan
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Jennifer Le
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Xiaoying Wei
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States.
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9
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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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10
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In vitro eradication of abasic site-mediated DNA-peptide/protein cross-links by Escherichia coli long-patch base excision repair. J Biol Chem 2022; 298:102055. [PMID: 35605665 PMCID: PMC9234237 DOI: 10.1016/j.jbc.2022.102055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Apurinic/apyrimidinic (AP or abasic) sites are among the most abundant DNA lesions. Numerous proteins within different organisms ranging from bacteria to human have been demonstrated to react with AP sites to form covalent Schiff base DNA–protein cross-links (DPCs). These DPCs are unstable due to their spontaneous hydrolysis, but the half-lives of these cross-links can be as long as several hours. Such long-lived DPCs are extremely toxic due to their large sizes, which physically block DNA replication. Therefore, these adducts must be promptly eradicated to maintain genome integrity. Herein, we used in vitro reconstitution experiments with chemically synthesized, stable, and site-specific Schiff base AP-peptide/protein cross-link analogs to demonstrate for the first time that this type of DPC can be repaired by Escherichia coli (E. coli) long-patch base excision repair. We demonstrated that the repair process requires a minimum of three enzymes and five consecutive steps, including: (1) 5′-DNA strand incision of the DPC by endonuclease IV; (2 to 4) strand-displacement DNA synthesis, removal of the 5′-deoxyribose phosphate-peptide/protein adduct-containing flap, and gap-filling DNA synthesis by DNA polymerase I; and (5) strand ligation by a ligase. We further demonstrated that endonuclease IV plays a major role in incising an AP-peptide cross-link within E. coli cell extracts. We also report that eradicating model AP-protein (11.2–36.1 kDa) DPCs is less efficient than that of an AP-peptide10mer cross-link, supporting the emerging model that proteolysis is likely required for efficient DPC repair.
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11
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Pujari SS, Wu M, Thomforde J, Wang ZA, Chao C, Olson NM, Erber L, Pomerantz WCK, Cole P, Tretyakova NY. Site‐Specific 5‐Formyl Cytosine Mediated DNA‐Histone Cross‐Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Suresh S. Pujari
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Mingxuan Wu
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
- Current address: School of Science Westlake University Institute of Natural Sciences, Westlake Institute for Advanced Study 18 Shilongshan Road, 310024 Hangzhou Zhejiang Province China
| | - Jenna Thomforde
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Zhipeng A. Wang
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
| | - Christopher Chao
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | - Noelle M. Olson
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | - Luke Erber
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
| | | | - Philip Cole
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115 USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry College of Pharmacy, and Masonic Cancer Center University of Minnesota Minneapolis MN 55455 USA
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12
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Pujari SS, Wu M, Thomforde J, Wang ZA, Chao C, Olson N, Erber L, Pomerantz WCK, Cole P, Tretyakova NY. Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angew Chem Int Ed Engl 2021; 60:26489-26494. [PMID: 34634172 PMCID: PMC8775767 DOI: 10.1002/anie.202109418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/06/2021] [Indexed: 01/16/2023]
Abstract
DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.
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Affiliation(s)
- Suresh S. Pujari
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mingxuan Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Jenna Thomforde
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhipeng A. Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Christopher Chao
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Noelle Olson
- Department of Chemistry, University of Minnesota, Minnesota 55455, USA
| | - Luke Erber
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - Philip Cole
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA. 02115, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, College of Pharmacy, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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13
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Wei X, Peng Y, Bryan C, Yang K. Mechanisms of DNA-protein cross-link formation and repair. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140669. [PMID: 33957291 DOI: 10.1016/j.bbapap.2021.140669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Covalent binding of DNA to proteins produces DNA-protein cross-links (DPCs). DPCs are formed as intermediates of enzymatic processes, generated from the reactions of protein nucleophiles with DNA electrophiles, and produced by endogenous and exogenous cross-linking agents. DPCs are heterogeneous due to the variations of DNA conjugation sites, flanking DNA structures, protein sizes, and cross-link bonds. Unrepaired DPCs are toxic because their bulky sizes physically block DNA replication and transcription, resulting in impaired genomic integrity. Compared to other types of DNA lesions, DPC repair is less understood. Emerging evidence suggests a general repair model that DPCs are proteolyzed by the proteasome and/or DPC proteases, followed by the peptide removal through canonical repair pathways. Herein, we first describe the recently discovered DPCs. We then review the mechanisms of DPC proteolysis with the focus on recently identified DPC proteases. Finally, distinct pathways that bypass or remove the cross-linked peptides following proteolysis are discussed.
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Affiliation(s)
- Xiaoying Wei
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States; Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ying Peng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Cameron Bryan
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States.
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14
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Hu Q, Klages-Mundt N, Wang R, Lynn E, Kuma Saha L, Zhang H, Srivastava M, Shen X, Tian Y, Kim H, Ye Y, Paull T, Takeda S, Chen J, Li L. The ARK Assay Is a Sensitive and Versatile Method for the Global Detection of DNA-Protein Crosslinks. Cell Rep 2020; 30:1235-1245.e4. [PMID: 31995761 PMCID: PMC7069250 DOI: 10.1016/j.celrep.2019.12.067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/03/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are a frequent form of DNA lesion and are strongly inhibitive in diverse DNA transactions. Despite recent developments, the biochemical detection of DPCs remains a limiting factor for the in-depth mechanistic understanding of DPC repair. Here, we develop a sensitive and versatile assay, designated ARK, for the quantitative analysis of DPCs in cells. ARK uses sequential chaotropic and detergent-based isolation of DPCs and substantially enhances sample purity, resulting in a 5-fold increase in detection sensitivity and a 10-fold reduction in background reading. We validate the ARK assay with genetic mutants with established deficiencies in DPC repair and demonstrate its robustness by using common DPC-inducing reagents, including formaldehyde, camptothecin, and etoposide. In addition, we show that the Fanconi anemia pathway contributes to the repair of DPCs. Thus, ARK is expected to facilitate various studies aimed at understanding both fundamental biology and translational applications of DNA-protein crosslink repair. Hu et al. develop a protocol to analyze DNA-protein crosslinking (DPC) damage. Designated the ARK assay, this method outperforms widely used assays by allowing the detection of global DPCs with improved sensitivity and expanded readout. Defective DPC repair is detected in Fanconi anemia mutant cells by this protocol.
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Affiliation(s)
- Qianghua Hu
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Naeh Klages-Mundt
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Wang
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica Lynn
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Liton Kuma Saha
- Department of Radiation Genetics, Kyoto University, Kyoto, Japan
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanyan Tian
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyeung Kim
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yin Ye
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanya Paull
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Kyoto, Japan
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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15
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Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nat Commun 2020; 11:5250. [PMID: 33067435 PMCID: PMC7567871 DOI: 10.1038/s41467-020-19047-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future. Cross-linking mass spectrometry (XLMS) allows mapping of protein-protein and protein-RNA interactions, but the analysis of protein-DNA complexes remains challenging. Here, the authors develop a UV light-based XLMS workflow to determine protein-DNA interfaces in reconstituted chromatin and isolated nuclei.
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Affiliation(s)
- Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Monika Raabe
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Christin Kappert
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Andy M Lau
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Stefan-Sebastian David
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Argyris Politis
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.
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16
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Kühbacher U, Duxin JP. How to fix DNA-protein crosslinks. DNA Repair (Amst) 2020; 94:102924. [PMID: 32683310 PMCID: PMC7511601 DOI: 10.1016/j.dnarep.2020.102924] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemotherapeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the catalytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage.
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Affiliation(s)
- Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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17
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Kojima Y, Machida YJ. DNA-protein crosslinks from environmental exposure: Mechanisms of formation and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:716-729. [PMID: 32329115 PMCID: PMC7575214 DOI: 10.1002/em.22381] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 05/19/2023]
Abstract
Many environmental carcinogens cause DNA damage, which can result in mutations and other alterations in genomic DNA if not repaired promptly. Because of the bulkiness of the lesions, DNA-protein crosslinks (DPCs) are one of the types of toxic DNA damage with potentially deleterious consequences. Despite the importance of DPCs, how cells remove these complex DNA adducts has been incompletely understood. However, major progress in the DPC repair field over the past 5 years now supports the view that cells are equipped with multiple mechanisms to cope with DPCs. Here, we first provide an overview of environmental substances that induce DPCs, describing the sources of exposure and mechanisms of DPC formation. We then review current models of DPC repair and discuss their significance for environmental carcinogens.
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Affiliation(s)
- Yusuke Kojima
- Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Yuichi J. Machida
- Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
- Correspondence to Yuichi J. Machida.
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18
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Ji S, Park D, Kropachev K, Kolbanovskiy M, Fu I, Broyde S, Essawy M, Geacintov NE, Tretyakova NY. 5-Formylcytosine-induced DNA-peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells. J Biol Chem 2019; 294:18387-18397. [PMID: 31597704 DOI: 10.1074/jbc.ra119.009834] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/26/2019] [Indexed: 11/06/2022] Open
Abstract
5-Formylcytosine (5fC) is an endogenous epigenetic DNA mark introduced via enzymatic oxidation of 5-methyl-dC in DNA. We and others recently reported that 5fC can form reversible DNA-protein conjugates with histone proteins, likely contributing to regulation of nucleosomal organization and gene expression. The protein component of DNA-protein cross-links can be proteolytically degraded, resulting in smaller DNA-peptide cross-links. Unlike full-size DNA-protein cross-links that completely block replication and transcription, DNA-peptide cross-links can be bypassed by DNA and RNA polymerases and can potentially be repaired via the nucleotide excision repair (NER) pathway. In the present work, we constructed plasmid molecules containing reductively stabilized, site-specific 5fC-polypeptide lesions and employed a quantitative MS-based assay to assess their effects on transcription in cells. Our results revealed that the presence of DNA-peptide cross-link significantly inhibits transcription in human HEK293T cells but does not induce transcription errors. Furthermore, transcription efficiency was similar in WT and NER-deficient human cell lines, suggesting that the 5fC-polypeptide lesion is a weak substrate for NER. This finding was confirmed by in vitro NER assays in cell-free extracts from human HeLa cells, suggesting that another mechanism is required for 5fC-polypeptide lesion removal. In summary, our findings indicate that 5fC-mediated DNA-peptide cross-links dramatically reduce transcription efficiency, are poor NER substrates, and do not cause transcription errors.
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Affiliation(s)
- Shaofei Ji
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daeyoon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | | | | | - Iwen Fu
- Department of Biology, New York University, New York, New York 10003
| | - Suse Broyde
- Department of Biology, New York University, New York, New York 10003
| | - Maram Essawy
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455.
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19
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Slyskova J, Sabatella M, Ribeiro-Silva C, Stok C, Theil AF, Vermeulen W, Lans H. Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage. Nucleic Acids Res 2019; 46:9537-9549. [PMID: 30137419 PMCID: PMC6182164 DOI: 10.1093/nar/gky764] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Sensitivity and resistance of cells to platinum drug chemotherapy are to a large extent determined by activity of the DNA damage response (DDR). Combining chemotherapy with inhibition of specific DDR pathways could therefore improve treatment efficacy. Multiple DDR pathways have been implicated in removal of platinum-DNA lesions, but it is unclear which exact pathways are most important to cellular platinum drug resistance. Here, we used CRISPR/Cas9 screening to identify DDR proteins that protect colorectal cancer cells against the clinically applied platinum drug oxaliplatin. We find that besides the expected homologous recombination, Fanconi anemia and translesion synthesis pathways, in particular also transcription-coupled nucleotide excision repair (TC-NER) and base excision repair (BER) protect against platinum-induced cytotoxicity. Both repair pathways are required to overcome oxaliplatin- and cisplatin-induced transcription arrest. In addition to the generation of DNA crosslinks, exposure to platinum drugs leads to reactive oxygen species production that induces oxidative DNA lesions, explaining the requirement for BER. Our findings highlight the importance of transcriptional integrity in cells exposed to platinum drugs and suggest that both TC-NER and BER should be considered as targets for novel combinatorial treatment strategies.
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Affiliation(s)
- Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Colin Stok
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- To whom correspondence should be addressed. Tel: +31 10 7038169; Fax: +31 10 7044743;
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20
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Ghodke PP, Albertolle ME, Johnson KM, Guengerich FP. Synthesis and Characterization of Site-Specific O 6 -Alkylguanine DNA-Alkyl Transferase-Oligonucleotide Crosslinks. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2019; 76:e74. [PMID: 30657645 PMCID: PMC6504252 DOI: 10.1002/cpnc.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O6 -Alkylguanine DNA-alkyltransferase (AGT), a DNA repair protein, can form crosslinks with DNA. The AGT-DNA crosslinks are known to be mutagenic when AGT is heterologously expressed in Escherichia coli, as well as in mammalian cells. To understand the biological consequences, reliable access to AGT-oligonucleotide crosslinks is needed. This article describes the synthesis and characterization of site-specific AGT-oligonucleotide crosslinks at the N2-position of deoxyguanosine and N6-position of deoxyadenosine. We developed a post-oligomerization strategy for the synthesis of propargyl-modified oligonucleotides. Copper-catalyzed azide-alkyne cycloaddition was used as a key step to obtain the iodoacetamide-linked oligonucleotides, which serve as good electrophiles for the crosslinking reaction with cysteine-145 of the active site of AGT. Trypsinization of AGT and hydrolysis of oligonucleotides, combined with analysis by liquid chromatography-tandem mass spectrometry, was utilized to confirm the nucleobase-adducted peptides. This method provides a useful strategy for the synthesis and characterization of site-specific DNA-protein crosslinks, which can be further used to understand proteolytic degradation-coupled DNA repair mechanisms. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Matthew E Albertolle
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kevin M Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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21
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Chesner LN, Campbell C. A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells. J Vis Exp 2018. [PMID: 29553515 PMCID: PMC5898435 DOI: 10.3791/57413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The purpose of this method is to provide a flexible, rapid, and quantitative technique to examine the kinetics of DNA-protein crosslink (DPC) repair in mammalian cell lines. Rather than globally assaying removal of xenobiotic-induced or spontaneous chromosomal DPC removal, this assay examines the repair of a homogeneous, chemically defined lesion specifically introduced at one site within a plasmid DNA substrate. Importantly, this approach avoids the use of radioactive materials and is not dependent on expensive or highly-specialized technology. Instead, it relies on standard recombinant DNA procedures and widely available real-time, quantitative polymerase chain reaction (qPCR) instrumentation. Given the inherent flexibility of the strategy utilized, the size of the crosslinked protein, as well as the nature of the chemical linkage and the precise DNA sequence context of the attachment site can be varied to address the respective contributions of these parameters to the overall efficiency of DPC repair. Using this method, plasmids containing a site-specific DPC were transfected into cells and low molecular weight DNA recovered at various times post-transfection. Recovered DNA is then subjected to strand-specific primer extension (SSPE) using a primer complementary to the damaged strand of the plasmid. Since the DPC lesion blocks Taq DNA polymerase, the ratio of repaired to un-repaired DNA can be quantitatively assessed using qPCR. Cycle threshold (CT) values are used to calculate percent repair at various time points in the respective cell lines. This SSPE-qPCR method can also be used to quantitatively assess the repair kinetics of any DNA adduct that blocks Taq polymerase.
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22
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Chesner LN, Campbell C. A quantitative PCR-based assay reveals that nucleotide excision repair plays a predominant role in the removal of DNA-protein crosslinks from plasmids transfected into mammalian cells. DNA Repair (Amst) 2018; 62:18-27. [PMID: 29413806 DOI: 10.1016/j.dnarep.2018.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
DNA-protein crosslinks (DPCs) are complex DNA lesions that induce mutagenesis and cell death. DPCs are created by common antitumor drugs, reactive oxygen species, and endogenous aldehydes. Since these agents create other types of DNA damage in addition to DPCs, identification of the mechanisms of DPC repair is challenging. In this study, we created plasmid substrates containing site-specific DPC lesions, as well as plasmids harboring lesions that are selectively repaired by the base excision or nucleotide excision repair (NER) pathways. These substrates were transfected into mammalian cells and a quantitative real-time PCR assay employed to study their repair. This assay revealed that DPC lesions were rapidly repaired in wild-type human and Chinese hamster derived cells, as were plasmids harboring an oxoguanine residue (base excision repair substrate) or cholesterol lesion (NER substrate). Interestingly, the DPC substrate was repaired in human cells nearly three times as efficiently as in Chinese hamster cells (>75% vs ∼25% repair at 8 h post-transfection), while there was no significant species-specific difference in the efficiency with which the cholesterol lesion was repaired (∼60% repair). Experiments revealed that both human and hamster cells deficient in NER due to mutations in the xeroderma pigmentosum A or D genes were five to ten-fold less able to repair the cholesterol and DPC lesions than were wild-type control clones, and that both the global genome and transcription-coupled sub-pathways of NER were capable of repairing DPCs. In addition, analyses using this PCR-based assay revealed that a 4 kDa peptide DNA crosslink was repaired nearly twice as efficiently as was a ∼38 kDa DPC, suggesting that proteolytic degradation of crosslinked proteins occurs during DPC repair. These results highlight the utility of this PCR-based assay to study DNA repair and indicate that the NER machinery rapidly and efficiently repairs plasmid DPC lesions in mammalian cells.
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Affiliation(s)
- Lisa N Chesner
- Department of Pharmacology, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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23
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ASH1L histone methyltransferase regulates the handoff between damage recognition factors in global-genome nucleotide excision repair. Nat Commun 2017; 8:1333. [PMID: 29109511 PMCID: PMC5673894 DOI: 10.1038/s41467-017-01080-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
Global-genome nucleotide excision repair (GG-NER) prevents ultraviolet (UV) light-induced skin cancer by removing mutagenic cyclobutane pyrimidine dimers (CPDs). These lesions are formed abundantly on DNA wrapped around histone octamers in nucleosomes, but a specialized damage sensor known as DDB2 ensures that they are accessed by the XPC initiator of GG-NER activity. We report that DDB2 promotes CPD excision by recruiting the histone methyltransferase ASH1L, which methylates lysine 4 of histone H3. In turn, methylated H3 facilitates the docking of the XPC complex to nucleosomal histone octamers. Consequently, DDB2, ASH1L and XPC proteins co-localize transiently on histone H3-methylated nucleosomes of UV-exposed cells. In the absence of ASH1L, the chromatin binding of XPC is impaired and its ability to recruit downstream GG-NER effectors diminished. Also, ASH1L depletion suppresses CPD excision and confers UV hypersensitivity. These findings show that ASH1L configures chromatin for the effective handoff between damage recognition factors during GG-NER activity.
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24
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Klages-Mundt NL, Li L. Formation and repair of DNA-protein crosslink damage. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1065-1076. [PMID: 29098631 DOI: 10.1007/s11427-017-9183-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/26/2017] [Indexed: 12/15/2022]
Abstract
DNA is constantly exposed to a wide array of genotoxic agents, generating a variety of forms of DNA damage. DNA-protein crosslinks (DPCs)-the covalent linkage of proteins with a DNA strand-are one of the most deleterious and understudied forms of DNA damage, posing as steric blockades to transcription and replication. If not properly repaired, these lesions can lead to mutations, genomic instability, and cell death. DPCs can be induced endogenously or through environmental carcinogens and chemotherapeutic agents. Endogenously, DPCs are commonly derived through reactions with aldehydes, as well as through trapping of various enzymatic intermediates onto the DNA. Proteolytic cleavage of the protein moiety of a DPC is a general strategy for removing the lesion. This can be accomplished through a DPC-specific protease and and/or proteasome-mediated degradation. Nucleotide excision repair and homologous recombination are each involved in repairing DPCs, with their respective roles likely dependent on the nature and size of the adduct. The Fanconi anemia pathway may also have a role in processing DPC repair intermediates. In this review, we discuss how these lesions are formed, strategies and mechanisms for their removal, and diseases associated with defective DPC repair.
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Affiliation(s)
- Naeh L Klages-Mundt
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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25
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Vaz B, Popovic M, Ramadan K. DNA-Protein Crosslink Proteolysis Repair. Trends Biochem Sci 2017; 42:483-495. [PMID: 28416269 DOI: 10.1016/j.tibs.2017.03.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 01/18/2023]
Abstract
Proteins that are covalently bound to DNA constitute a specific type of DNA lesion known as DNA-protein crosslinks (DPCs). DPCs represent physical obstacles to the progression of DNA replication. If not repaired, DPCs cause stalling of DNA replication forks that consequently leads to DNA double-strand breaks, the most cytotoxic DNA lesion. Although DPCs are common DNA lesions, the mechanism of DPC repair was unclear until now. Recent work unveiled that DPC repair is orchestrated by proteolysis performed by two distinct metalloproteases, SPARTAN in metazoans and Wss1 in yeast. This review summarizes recent discoveries on two proteases in DNA replication-coupled DPC repair and establishes DPC proteolysis repair as a separate DNA repair pathway for genome stability and protection from accelerated aging and cancer.
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Affiliation(s)
- Bruno Vaz
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Marta Popovic
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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26
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Ming X, Groehler A, Michaelson-Richie ED, Villalta PW, Campbell C, Tretyakova NY. Mass Spectrometry Based Proteomics Study of Cisplatin-Induced DNA-Protein Cross-Linking in Human Fibrosarcoma (HT1080) Cells. Chem Res Toxicol 2017; 30:980-995. [PMID: 28282121 DOI: 10.1021/acs.chemrestox.6b00389] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Platinum-based antitumor drugs such as 1,1,2,2-cis-diamminedichloroplatinum(II) (cisplatin), carboplatin, and oxaliplatin are currently used to treat nearly 50% of all cancer cases, and novel platinum based agents are under development. The antitumor effects of cisplatin and other platinum compounds are attributed to their ability to induce interstrand DNA-DNA cross-links, which are thought to inhibit tumor cell growth by blocking DNA replication and/or preventing transcription. However, platinum agents also induce significant numbers of unusually bulky and helix-distorting DNA-protein cross-links (DPCs), which are poorly characterized because of their unusual complexity. We and others have previously shown that DPCs block DNA replication and transcription and causes toxicity in human cells, potentially contributing to the biological effects of platinum agents. In the present work, we have undertaken a system-wide investigation of cisplatin-mediated DNA-protein cross-linking in human fibrosarcoma (HT1080) cells using mass spectrometry-based proteomics. DPCs were isolated from cisplatin-treated cells using a modified phenol/chloroform DNA extraction in the presence of protease inhibitors. Proteins were released from DNA strands and identified by mass spectrometry-based proteomics and immunological detection. Over 250 nuclear proteins captured on chromosomal DNA following treatment with cisplatin were identified, including high mobility group (HMG) proteins, histone proteins, and elongation factors. To reveal the exact molecular structures of cisplatin-mediated DPCs, isotope dilution HPLC-ESI+-MS/MS was employed to detect 1,1-cis-diammine-2-(5-amino-5-carboxypentyl)amino-2-(2'-deoxyguanosine-7-yl)-platinum(II) (dG-Pt-Lys) conjugates between the N7 guanine of DNA and the ε-amino group of lysine. Our results demonstrate that therapeutic levels of cisplatin induce a wide range of DPC lesions, which likely contribute to both target and off target effects of this clinically important drug.
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Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Arnold Groehler
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Erin D Michaelson-Richie
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Mass Spectrometry Core at the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
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27
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Poletini MO, de Assis LVM, Moraes MN, Castrucci AMDL. Estradiol differently affects melanin synthesis of malignant and normal melanocytes: a relationship with clock and clock-controlled genes. Mol Cell Biochem 2016; 421:29-39. [DOI: 10.1007/s11010-016-2781-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/05/2016] [Indexed: 12/20/2022]
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28
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Sancar A. Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel Lecture). Angew Chem Int Ed Engl 2016; 55:8502-27. [PMID: 27337655 DOI: 10.1002/anie.201601524] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/27/2023]
Abstract
Ultraviolet light damages DNA by converting two adjacent thymines into a thymine dimer which is potentially mutagenic, carcinogenic, or lethal to the organism. This damage is repaired by photolyase and the nucleotide excision repair system in E. coli by nucleotide excision repair in humans. The work leading to these results is presented by Aziz Sancar in his Nobel Lecture.
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Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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29
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Sancar A. Mechanismen der DNA-Reparatur durch Photolyasen und Exzisionsnukleasen (Nobel-Aufsatz). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics; University of North Carolina School of Medicine; Chapel Hill North Carolina USA
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30
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Lai Y, Yu R, Hartwell HJ, Moeller BC, Bodnar WM, Swenberg JA. Measurement of Endogenous versus Exogenous Formaldehyde-Induced DNA-Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry. Cancer Res 2016; 76:2652-61. [PMID: 26984759 DOI: 10.1158/0008-5472.can-15-2527] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/14/2016] [Indexed: 12/24/2022]
Abstract
DNA-protein crosslinks (DPC) arise from a wide range of endogenous and exogenous chemicals, such as chemotherapeutic drugs and formaldehyde. Importantly, recent identification of aldehydes as endogenous genotoxins in Fanconi anemia has provided new insight into disease causation. Because of their bulky nature, DPCs pose severe threats to genome stability, but previous methods to measure formaldehyde-induced DPCs were incapable of discriminating between endogenous and exogenous sources of chemical. In this study, we developed methods that provide accurate and distinct measurements of both exogenous and endogenous DPCs in a structurally specific manner. We exposed experimental animals to stable isotope-labeled formaldehyde ([(13)CD2]-formaldehyde) by inhalation and performed ultrasensitive mass spectrometry to measure endogenous (unlabeled) and exogenous ((13)CD2-labeled) DPCs. We found that exogenous DPCs readily accumulated in nasal respiratory tissues but were absent in tissues distant to the site of contact. This observation, together with the finding that endogenous formaldehyde-induced DPCs were present in all tissues examined, suggests that endogenous DPCs may be responsible for increased risks of bone marrow toxicity and leukemia. Furthermore, the slow rate of DPC repair provided evidence for the persistence of DPCs. In conclusion, our method for measuring endogenous and exogenous DPCs presents a new perspective for the potential health risks inflicted by endogenous formaldehyde and may inform improved disease prevention and treatment strategies. Cancer Res; 76(9); 2652-61. ©2016 AACR.
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Affiliation(s)
- Yongquan Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Rui Yu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hadley J Hartwell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Wanda M Bodnar
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - James A Swenberg
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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31
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Duxin JP, Walter JC. What is the DNA repair defect underlying Fanconi anemia? Curr Opin Cell Biol 2015; 37:49-60. [PMID: 26512453 PMCID: PMC4688103 DOI: 10.1016/j.ceb.2015.09.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 12/14/2022]
Abstract
Fanconi anemia (FA) is a rare human genetic disease characterized by bone marrow failure, cancer predisposition, and genomic instability. It has been known for many years that FA patient-derived cells are exquisitely sensitive to DNA interstrand cross-linking agents such as cisplatin and mitomycin C. On this basis, it was widely assumed that failure to repair endogenous interstrand cross-links (ICLs) causes FA, although the endogenous mutagen that generates these lesions remained elusive. Recent genetic evidence now suggests that endogenous aldehydes are the driving force behind FA. Importantly, aldehydes cause a variety of DNA lesions, including ICLs and DNA protein cross-links (DPCs), re-kindling the debate about which DNA lesions cause FA. In this review, we discuss new developments in our understanding of DPC and ICL repair, and how these findings bear on the question of which DNA lesion underlies FA.
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Affiliation(s)
- Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - 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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32
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Ortega-Atienza S, Green SE, Zhitkovich A. Proteasome activity is important for replication recovery, CHK1 phosphorylation and prevention of G2 arrest after low-dose formaldehyde. Toxicol Appl Pharmacol 2015; 286:135-41. [PMID: 25817892 PMCID: PMC4458209 DOI: 10.1016/j.taap.2015.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 11/24/2022]
Abstract
Formaldehyde (FA) is a human carcinogen with numerous sources of environmental and occupational exposures. This reactive aldehyde is also produced endogenously during metabolism of drugs and other processes. DNA-protein crosslinks (DPCs) are considered to be the main genotoxic lesions for FA. Accumulating evidence suggests that DPC repair in high eukaryotes involves proteolysis of crosslinked proteins. Here, we examined a role of the main cellular proteolytic machinery proteasomes in toxic responses of human lung cells to low FA doses. We found that transient inhibition of proteasome activity increased cytotoxicity and diminished clonogenic viability of FA-treated cells. Proteasome inactivation exacerbated suppressive effects of FA on DNA replication and increased the levels of the genotoxic stress marker γ-H2AX in normal human cells. A transient loss of proteasome activity in FA-exposed cells also caused delayed perturbations of cell cycle, which included G2 arrest and a depletion of S-phase populations at FA doses that had no effects in control cells. Proteasome activity diminished p53-Ser15 phosphorylation but was important for FA-induced CHK1 phosphorylation, which is a biochemical marker of DPC proteolysis in replicating cells. Unlike FA, proteasome inhibition had no effect on cell survival and CHK1 phosphorylation by the non-DPC replication stressor hydroxyurea. Overall, we obtained evidence for the importance of proteasomes in protection of human cells against biologically relevant doses of FA. Biochemically, our findings indicate the involvement of proteasomes in proteolytic repair of DPC, which removes replication blockage by these highly bulky lesions.
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Affiliation(s)
- Sara Ortega-Atienza
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Samantha E Green
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA.
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33
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Chowdhury G, Guengerich FP. Characterization of thioether-linked protein adducts of DNA using a Raney-Ni-mediated desulfurization method and liquid chromatography-electrospray-tandem mass spectrometry. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2015; 60:10.15.1-10.15.14. [PMID: 25754888 DOI: 10.1002/0471142700.nc1015s60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This unit contains a complete procedure for the detection and structural characterization of DNA protein crosslinks (DPCs). The procedure also describes an approach for the quantitation of the various structurally distinct DPCs. Although various methods have been described in the literature for labile DPCs, characterization of nonlabile adducts remain a challenge. Here we present a novel approach for characterization of both labile and non-labile adducts by the use of a combination of chemical, enzymatic, and mass spectrometric approaches. A Raney Ni-catalyzed reductive desulfurization method was used for removal of the bulky peptide adducts, enzymatic digestion was used to digest the protein to smaller peptides and DNA to nucleosides, and finally LC-ESI-tandem mass spectrometry (MS) was utilized for detection and characterization of nucleoside adducts.
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Affiliation(s)
- Goutam Chowdhury
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, G. B. Nagar, UP 201314, India
| | - F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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34
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Krasich R, Wu SY, Kuo HK, Kreuzer KN. Functions that protect Escherichia coli from DNA-protein crosslinks. DNA Repair (Amst) 2015; 28:48-59. [PMID: 25731940 DOI: 10.1016/j.dnarep.2015.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) treatment in cells overexpressing cytosine methyltransferase; hypersensitivity was verified to depend on methyltransferase expression. We isolated hypersensitive mutants that were uncovered in previous studies (recA, recBC, recG, and uvrD), hypersensitive mutants that apparently activate phage Mu Gam expression, and novel hypersensitive mutants in genes involved in DNA metabolism, cell division, and tRNA modification (dinG, ftsK, xerD, dnaJ, hflC, miaA, mnmE, mnmG, and ssrA). Inactivation of SbcCD, which can cleave DNA at protein-DNA complexes, did not cause hypersensitivity. We previously showed that tmRNA pathway defects cause aza-C hypersensitivity, implying that DPCs block coupled transcription/translation complexes. Here, we show that mutants in tRNA modification functions miaA, mnmE and mnmG cause defects in aza-C-induced tmRNA tagging, explaining their hypersensitivity. In order for tmRNA to access a stalled ribosome, the mRNA must be cleaved or released from RNA polymerase. Mutational inactivation of functions involved in mRNA processing and RNA polymerase elongation/release (RNase II, RNaseD, RNase PH, RNase LS, Rep, HepA, GreA, GreB) did not cause aza-C hypersensitivity; the mechanism of tmRNA access remains unclear.
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Affiliation(s)
- Rachel Krasich
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Sunny Yang Wu
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - H Kenny Kuo
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States.
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35
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Nakano T, Mitsusada Y, Salem AMH, Shoulkamy MI, Sugimoto T, Hirayama R, Uzawa A, Furusawa Y, Ide H. Induction of DNA-protein cross-links by ionizing radiation and their elimination from the genome. Mutat Res 2015; 771:45-50. [PMID: 25771979 DOI: 10.1016/j.mrfmmm.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Ionizing radiation produces various types of DNA lesions, such as base damage, single-strand breaks, double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, DSBs are the most critical lesions underlying the lethal effects of ionizing radiation. With DPCs, proteins covalently trapped in DNA constitute strong roadblocks to replication and transcription machineries, and hence can be lethal to cells. The formation of DPCs by ionizing radiation is promoted in the absence of oxygen, whereas that of DSBs is retarded. Accordingly, the contribution of DPCs to the lethal events in irradiated cells may not be negligible for hypoxic cells, such as those present in tumors. However, the role of DPCs in the lethal effects of ionizing radiation remains largely equivocal. In the present study, normoxic and hypoxic mouse tumors were irradiated with X-rays [low linear energy transfer (LET) radiation] and carbon (C)-ion beams (high LET radiation), and the resulting induction of DPCs and DSBs and their removal from the genome were analyzed. X-rays and C-ion beams produced more DPCs in hypoxic tumors than in normoxic tumors. Interestingly, the yield of DPCs was slightly but statistically significantly greater (1.3- to 1.5-fold) for C-ion beams than for X-rays. Both X-rays and C-ion beams generated two types of DPC that differed according to their rate of removal from the genome. This was also the case for DSBs. The half-lives of the rapidly removed components of DPCs and DSBs were similar (<1 h), but those of the slowly removed components of DPCs and DSBs were markedly different (3.9-5 h for DSBs versus 63-70 h for DPCs). The long half-life and abundance of the slowly removed DPCs render them persistent in DNA, which may impede DNA transactions and confer deleterious effects on cells in conjunction with DSBs.
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Affiliation(s)
- Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Yusuke Mitsusada
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Amir M H Salem
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Pathology, Medical Research Division, National Research Centre, El-Bohouth St., Dokki, Giza 12311, Egypt
| | - Mahmoud I Shoulkamy
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Zoology, Biological Science Building, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Tatsuya Sugimoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ryoichi Hirayama
- Research Center for Charged Particle Therapy, National Institute of Radiological Sciences (NIRS), Chiba 263-8555, Japan
| | - Akiko Uzawa
- Research Center for Charged Particle Therapy, National Institute of Radiological Sciences (NIRS), Chiba 263-8555, Japan
| | - Yoshiya Furusawa
- Development and Support Center, National Institute of Radiological Sciences (NIRS), Chiba 263-8555, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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36
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Wickramaratne S, Boldry EJ, Buehler C, Wang YC, Distefano MD, Tretyakova NY. Error-prone translesion synthesis past DNA-peptide cross-links conjugated to the major groove of DNA via C5 of thymidine. J Biol Chem 2014; 290:775-87. [PMID: 25391658 DOI: 10.1074/jbc.m114.613638] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are exceptionally bulky, structurally diverse DNA adducts formed in cells upon exposure to endogenous and exogenous bis-electrophiles, reactive oxygen species, and ionizing radiation. If not repaired, DPCs can induce toxicity and mutations. It has been proposed that the protein component of a DPC is proteolytically degraded, giving rise to smaller DNA-peptide conjugates, which can be subject to nucleotide excision repair and replication bypass. In this study, polymerase bypass of model DNA-peptide conjugates structurally analogous to the lesions induced by reactive oxygen species and DNA methyltransferase inhibitors was examined. DNA oligomers containing site-specific DNA-peptide conjugates were generated by copper-catalyzed [3 + 2] Huisgen cyclo-addition between an alkyne-functionalized C5-thymidine in DNA and an azide-containing 10-mer peptide. The resulting DNA-peptide conjugates were subjected to steady-state kinetic experiments in the presence of recombinant human lesion bypass polymerases κ and η, followed by PAGE-based assays to determine the catalytic efficiency and the misinsertion frequency opposite the lesion. We found that human polymerase κ and η can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, whereas human polymerase η preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI(-)-MS/MS sequencing of the extension products has revealed that post-lesion synthesis was highly error-prone, resulting in mutations opposite the adducted site or at the +1 position from the adduct and multiple deletions. Collectively, our results indicate that replication bypass of peptides conjugated to the C5 position of thymine by human translesion synthesis polymerases leads to large numbers of base substitution and frameshift mutations.
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Affiliation(s)
- Susith Wickramaratne
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily J Boldry
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and
| | - Charles Buehler
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Yen-Chih Wang
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark D Distefano
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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37
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Duxin JP, Dewar JM, Yardimci H, Walter JC. Repair of a DNA-protein crosslink by replication-coupled proteolysis. Cell 2014; 159:346-57. [PMID: 25303529 PMCID: PMC4229047 DOI: 10.1016/j.cell.2014.09.024] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 12/24/2022]
Abstract
DNA-protein crosslinks (DPCs) are caused by environmental, endogenous, and chemotherapeutic agents and pose a severe threat to genome stability. We use Xenopus egg extracts to recapitulate DPC repair in vitro and show that this process is coupled to DNA replication. A DPC on the leading strand template arrests the replisome by stalling the CMG helicase. The DPC is then degraded on DNA, yielding a peptide-DNA adduct that is bypassed by CMG. The leading strand subsequently resumes synthesis, stalls again at the adduct, and then progresses past the adduct using DNA polymerase ζ. A DPC on the lagging strand template only transiently stalls the replisome, but it too is degraded, allowing Okazaki fragment bypass. Our experiments describe a versatile, proteolysis-based mechanism of S phase DPC repair that avoids replication fork collapse.
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Affiliation(s)
- Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hasan Yardimci
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, UK
| | - 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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Yeo JE, Wickramaratne S, Khatwani S, Wang YC, Vervacke J, Distefano MD, Tretyakova NY. Synthesis of site-specific DNA-protein conjugates and their effects on DNA replication. ACS Chem Biol 2014; 9:1860-8. [PMID: 24918113 PMCID: PMC4136702 DOI: 10.1021/cb5001795] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
DNA–protein
cross-links (DPCs) are bulky, helix-distorting
DNA lesions that form in the genome upon exposure to common antitumor
drugs, environmental/occupational toxins, ionizing radiation, and
endogenous free-radical-generating systems. As a result of their considerable
size and their pronounced effects on DNA–protein interactions,
DPCs can interfere with DNA replication, transcription, and repair,
potentially leading to mutagenesis, genotoxicity, and cytotoxicity.
However, the biological consequences of these ubiquitous lesions are
not fully understood due to the difficulty of generating DNA substrates
containing structurally defined, site-specific DPCs. In the present
study, site-specific cross-links between the two biomolecules were
generated by copper-catalyzed [3 + 2] Huisgen cycloaddition (click
reaction) between an alkyne group from 5-(octa-1,7-diynyl)-uracil
in DNA and an azide group within engineered proteins/polypeptides.
The resulting DPC substrates were subjected to in vitro primer extension in the presence of human lesion bypass DNA polymerases
η, κ, ν, and ι. We found that DPC lesions
to the green fluorescent protein and a 23-mer peptide completely blocked
DNA replication, while the cross-link to a 10-mer peptide was bypassed.
These results indicate that the polymerases cannot read through the
larger DPC lesions and further suggest that proteolytic degradation
may be required to remove the replication block imposed by bulky DPC
adducts.
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Affiliation(s)
- Jung Eun Yeo
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Susith Wickramaratne
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Santoshkumar Khatwani
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yen-Chih Wang
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jeffrey Vervacke
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D. Distefano
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Natalia Y. Tretyakova
- Masonic Cancer Center and Departments of †Medicinal Chemistry and ‡Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Chowdhury G, Cho SH, Pegg AE, Guengerich FP. Detection and Characterization of 1,2-Dibromoethane-Derived DNA Crosslinks Formed with O6-Alkylguanine-DNA Alkyltransferase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Chowdhury G, Cho SH, Pegg AE, Guengerich FP. Detection and characterization of 1,2-dibromoethane-derived DNA crosslinks formed with O(6) -alkylguanine-DNA alkyltransferase. Angew Chem Int Ed Engl 2013; 52:12879-82. [PMID: 24130045 DOI: 10.1002/anie.201307580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Indexed: 01/05/2023]
Abstract
A combination of chemical modifications and LC-tandem MS was used for the structure elucidation of various ethylene crosslinks of DNA with O(6) -alkylguanine-DNA alkyltransferase (AGT, see picture). The elucidation of the chemical structures of such DNA-protein crosslinks is necessary to understand mechanisms of mutagenesis.
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Affiliation(s)
- Goutam Chowdhury
- Department of Biochemistry, Vanderbilt University School of Medicine, 638 RRB, 2220 Pierce Ave., Nashville, TN 37232 (USA)
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Fang Q. DNA-protein crosslinks processed by nucleotide excision repair and homologous recombination with base and strand preference in E. coli model system. Mutat Res 2013; 741-742:1-10. [PMID: 23500083 DOI: 10.1016/j.mrfmmm.2013.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 01/24/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
Abstract
Bis-electrophiles including dibromoethane and epibromohydrin can react with O(6)-alkylguanine-DNA alkyltransferase (AGT) and form AGT-DNA crosslinks in vitro and in vivo. The presence of human AGT (hAGT) paradoxically increases the mutagenicity and cytotoxicity of bis-electrophiles in cells. Here we establish a bacterial system to study the repair mechanism and cellular responses to DNA-protein crosslinks (DPCs) in vivo. Results show that both nucleotide excision repair (NER) and homologous recombination (HR) pathways can process hAGT-DNA crosslinks with HR playing a dominant role. Mutation spectra show that HR has no strand preference but NER favors processing of the DPCs in the transcribed strand; UvrA, UvrB and Mfd can interfere with small size DPCs but only UvrA can interfere with large size DPCs in the transcribed strand processed by HR. Further, we found that DPCs at TA deoxynucleotide sites are very inefficiently processed by NER and the presence of NER can interfere with these DNA lesions processed by HR. These data indicate that NER and HR can process DPCs cooperatively and competitively and NER processes DPCs with base and strand preference. Therefore, the formation of hAGT-DNA crosslinks can be a plausible and specific system to study the repair mechanism and effects of DPCs precisely in vivo.
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Affiliation(s)
- Qingming Fang
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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42
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Wong VCL, Cash HL, Morse JL, Lu S, Zhitkovich A. S-phase sensing of DNA-protein crosslinks triggers TopBP1-independent ATR activation and p53-mediated cell death by formaldehyde. Cell Cycle 2012; 11:2526-37. [PMID: 22722496 DOI: 10.4161/cc.20905] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined genotoxic signaling and cell fate decisions in response to a potent DNA-protein crosslinker formaldehyde (FA). DNA-protein crosslinks (DPC) are poorly understood lesions produced by bifunctional carcinogens and several cancer drugs. FA-treated human cells showed a rapid activation of ATR kinase that preferentially targeted the p53 transcription factor at low doses and CHK1 kinase at more severe damage, producing bell-shaped and sublinear responses, respectively. CHK1 phosphorylation was transient, and its loss was accompanied by increased p53 accumulation and Ser15 phosphorylation. Activation of p53 was insensitive to inhibition of mismatch repair and nucleotide and base excision repair, excluding the role of small DNA adducts in this response. The p53-targeted signaling was transcription-independent, absent in quiescent cells and specific to S-phase in cycling populations. Unlike other S-phase stressors, FA-activated p53 was functional transcriptionally, promoted apoptosis in lung epithelial cells and caused senescence in normal lung fibroblasts. FA did not induce ATR, RAD1 or RPA foci, and p53 phosphorylation was TopBP1-independent, indicating a noncanonical mode of ATR activation. Replication arrest by FA caused a dissociation of ATR from a chromatin-loaded MCM helicase but no PCNA monoubiquitination associated with stalled polymerases. These results suggest that unlike typical DNA adducts that stall DNA polymerases, replication inhibition by bulkier DPC largely results from blocking upstream MCM helicase, which prevents accumulation of ssDNA. Overall, our findings indicate that S-phase-specific, TopBP1-independent activation of the ATR-p53 axis is a critical stress response to FA-DPC, which has implications for understanding of FA carcinogenesis.
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Affiliation(s)
- Victor Chun-Lam Wong
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
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43
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Shoulkamy MI, Nakano T, Ohshima M, Hirayama R, Uzawa A, Furusawa Y, Ide H. Detection of DNA-protein crosslinks (DPCs) by novel direct fluorescence labeling methods: distinct stabilities of aldehyde and radiation-induced DPCs. Nucleic Acids Res 2012; 40:e143. [PMID: 22730301 PMCID: PMC3467041 DOI: 10.1093/nar/gks601] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteins are covalently trapped on DNA to form DNA-protein crosslinks (DPCs) when cells are exposed to DNA-damaging agents. DPCs interfere with many aspects of DNA transactions. The current DPC detection methods indirectly measure crosslinked proteins (CLPs) through DNA tethered to proteins. However, a major drawback of such methods is the non-linear relationship between the amounts of DNA and CLPs, which makes quantitative data interpretation difficult. Here we developed novel methods of DPC detection based on direct CLP measurement, whereby CLPs in DNA isolated from cells are labeled with fluorescein isothiocyanate (FITC) and quantified by fluorometry or western blotting using anti-FITC antibodies. Both formats successfully monitored the induction and elimination of DPCs in cultured cells exposed to aldehydes and mouse tumors exposed to ionizing radiation (carbon-ion beams). The fluorometric and western blotting formats require 30 and 0.3 μg of DNA, respectively. Analyses of the isolated genomic DPCs revealed that both aldehydes and ionizing radiation produce two types of DPC with distinct stabilities. The stable components of aldehyde-induced DPCs have half-lives of up to days. Interestingly, that of radiation-induced DPCs has an infinite half-life, suggesting that the stable DPC component exerts a profound effect on DNA transactions over many cell cycles.
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Affiliation(s)
- Mahmoud I Shoulkamy
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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44
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Reelfs O, Karran P, Young AR. 4-Thiothymidine sensitization of DNA to UVA offers potential for a novel photochemotherapy. Photochem Photobiol Sci 2012; 11:148-54. [PMID: 22044942 DOI: 10.1039/c1pp05188a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 09/23/2011] [Indexed: 02/11/2024]
Abstract
Photochemotherapy, in which ultraviolet radiation (UVR: 280-400 nm) or visible light is combined with a photosensitizing drug to produce a therapeutic effect that neither drug or radiation can achieve alone, is a proven therapeutic strategy for a number of non-malignant hyperproliferative skin conditions and various cancers. Examples are psoralen plus UVA (320-400 nm) radiation (PUVA) and photodynamic therapy (PDT). All existing photochemotherapies have drawbacks - for example the association of PUVA with the development of skin cancer, and pain that is often associated with PDT treatment of skin lesions. There is a clear need to develop alternative approaches that involve lower radiation doses and/or improved selectivity for target cells. In this review, we explore the possibility to address this need by exploiting thionucleoside-mediated DNA photosensitisation to low, non toxic doses of UVA radiation.
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Affiliation(s)
- Olivier Reelfs
- King's College London, King's College London School of Medicine, Division of Genetics and Molecular Medicine, St John's Institute of Dermatology, London, UK SE19RT.
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45
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Grogan D, Jinks-Robertson S. Formaldehyde-induced mutagenesis in Saccharomyces cerevisiae: molecular properties and the roles of repair and bypass systems. Mutat Res 2011; 731:92-8. [PMID: 22197481 DOI: 10.1016/j.mrfmmm.2011.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 10/14/2022]
Abstract
Although DNA-protein cross-links (DPCs) pose a significant threat to genome stability, they remain a poorly understood class of DNA lesions. To define genetic impacts of DPCs on eukaryotic cells in molecular terms, we used a sensitive Saccharomyces cerevisiae frameshift-detection assay to analyze mutagenesis by formaldehyde (HCHO), and its response to nucleotide excision repair (NER) and translesion DNA synthesis (TLS). Brief exposure to HCHO was mutagenic for NER-defective rad14 strains but not for a corresponding RAD14 strain, nor for a rad14 strain lacking both Polζ and Polη TLS polymerases. This confirmed that HCHO-generated DNA lesions can trigger error-prone TLS and are substrates for the NER pathway. Sequencing revealed that HCHO-induced single-base-pair insertions occurred primarily at one hotspot; most of these insertions were also complex, changing an additional base-pair nearby. Most of the HCHO-induced mutations required both Polζ and Polη, providing a striking example of cooperativity between these two TLS polymerases during bypass of a DNA lesion formed in vivo. The similar molecular properties of HCHO-induced and spontaneous complex +1 insertions detected by this system suggest that DPCs which form in vivo during normal metabolism may contribute characteristic events to the spectra of spontaneous mutations in NER-deficient cells.
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Affiliation(s)
- Dennis Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati OH 45221-0006, USA.
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46
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Gueranger Q, Kia A, Frith D, Karran P. Crosslinking of DNA repair and replication proteins to DNA in cells treated with 6-thioguanine and UVA. Nucleic Acids Res 2011; 39:5057-66. [PMID: 21398635 PMCID: PMC3130278 DOI: 10.1093/nar/gkr112] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 12/15/2022] Open
Abstract
The DNA of patients taking immunosuppressive and anti-inflammatory thiopurines contains 6-thioguanine (6-TG) and their skin is hypersensitive to ultraviolet A (UVA) radiation. DNA 6-TG absorbs UVA and generates reactive oxygen species that damage DNA and proteins. Here, we show that the DNA damage includes covalent DNA-protein crosslinks. An oligonucleotide containing a single 6-TG is photochemically crosslinked to cysteine-containing oligopeptides by low doses of UVA. Crosslinking is significantly more efficient if guanine sulphonate (G(SO3))--an oxidized 6-TG and a previously identified UVA photoproduct--replaces 6-TG, suggesting that G(SO3) is an important reaction intermediate. Crosslinking occurs via oligopeptide sulphydryl and free amino groups. The oligonucleotide-oligopeptide adducts are heat stable but are partially reversed by reducing treatments. UVA irradiation of human cells containing DNA 6-TG induces extensive heat- and reducing agent-resistant covalent DNA-protein crosslinks and diminishes the recovery of some DNA repair and replication proteins from nuclear extracts. DNA-protein crosslinked material has an altered buoyant density and can be purified by banding in cesium chloride (CsCl) gradients. PCNA, the MSH2 mismatch repair protein and the XPA nucleotide excision repair (NER) factor are among the proteins detectable in the DNA-crosslinked material. These findings suggest that the 6-TG/UVA combination might compromise DNA repair by sequestering essential proteins.
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Affiliation(s)
| | | | | | - Peter Karran
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, UK
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47
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Ide H, Shoulkamy MI, Nakano T, Miyamoto-Matsubara M, Salem AMH. Repair and biochemical effects of DNA-protein crosslinks. Mutat Res 2011; 711:113-122. [PMID: 21185846 DOI: 10.1016/j.mrfmmm.2010.12.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 12/11/2010] [Accepted: 12/17/2010] [Indexed: 05/30/2023]
Abstract
Genomic DNA is associated with various structural, regulatory, and transaction proteins. The dynamic and reversible association between proteins and DNA ensures the accurate expression and propagation of genetic information. However, various endogenous, environmental, and chemotherapeutic agents induce DNA-protein crosslinks (DPCs), and hence covalently trap proteins on DNA. Since DPCs are extremely large compared to conventional DNA lesions, they probably impair many aspects of DNA transactions such as replication, transcription, and repair due to steric hindrance. Recent genetic and biochemical studies have shed light on the elaborate molecular mechanism by which cells repair or tolerate DPCs. This review summarizes the current knowledge regarding the repair and biochemical effects of the most ubiquitous form of DPCs, which are associated with no flanked DNA strand breaks. In bacteria small DPCs are eliminated by nucleotide excision repair (NER), whereas oversized DPCs are processed by RecBCD-dependent homologous recombination (HR). NER does not participate in the repair of DPCs in mammalian cells, since the upper size limit of DPCs amenable to mammalian NER is smaller than that of bacterial NER. Thus, DPCs are processed exclusively by HR. The reactivation of the stalled replication fork at DPCs by HR seems to involve fork breakage in mammalian cells but not in bacterial cells. In addition, recent proteomic studies have identified the numbers of proteins in DPCs induced by environmental and chemotherapeutic agents. However, it remains largely elusive how DPCs affect replication and transcription at the molecular level. Considering the extremely large nature of DPCs, it is possible that they impede the progression of replication and transcription machineries by mechanisms different from those for conventional DNA lesions. This might also be true for the DNA damage response and signaling mechanism.
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Affiliation(s)
- Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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48
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Rapid DNA-protein cross-linking and strand scission by an abasic site in a nucleosome core particle. Proc Natl Acad Sci U S A 2010; 107:22475-80. [PMID: 21149689 DOI: 10.1073/pnas.1012860108] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites are ubiquitous DNA lesions that are highly mutagenic and cytotoxic if not repaired. In addition, clusters of two or more abasic lesions within one to two turns of DNA, a hallmark of ionizing radiation, are repaired much less efficiently and thus present greater mutagenic potential. Abasic sites are chemically labile, but naked DNA containing them undergoes strand scission slowly with a half-life on the order of weeks. We find that independently generated AP sites within nucleosome core particles are highly destabilized, with strand scission occurring ∼60-fold more rapidly than in naked DNA. The majority of core particles containing single AP lesions accumulate DNA-protein cross-links, which persist following strand scission. The N-terminal region of histone protein H4 contributes significantly to DNA-protein cross-links and strand scission when AP sites are produced approximately 1.5 helical turns from the nucleosome dyad, which is a known hot spot for nucleosomal DNA damage. Reaction rates for AP sites at two positions within this region differ by ∼4-fold. However, the strand scission of the slowest reacting AP site is accelerated when it is part of a repair resistant bistranded lesion composed of two AP sites, resulting in rapid formation of double strand breaks in high yields. Multiple lysine residues within a single H4 protein catalyze double strand cleavage through a mechanism believed to involve a templating effect. These results show that AP sites within the nucleosome produce significant amounts of DNA-protein cross-links and generate double strand breaks, the most deleterious form of DNA damage.
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49
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Molecular response prediction in multimodality treatment for adenocarcinoma of the esophagus and esophagogastric junction. Recent Results Cancer Res 2010; 182:179-91. [PMID: 20676881 DOI: 10.1007/978-3-540-70579-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cancers arising from the esophagus are becoming more common in the United States and Europe. In 2009, an estimate of 14,530 new cases will be diagnosed and more than 90% will die of their disease. Esophageal cancer is currently the most rapidly increasing cancer in the western world and is coinciding with a shift in histological type and primary tumor location. Despite recent improvements in the detection, surgical resection, and (radio-) chemotherapy, the overall survival (OS) of esophageal cancer remains relatively poor. It is becoming increasingly apparent that neoadjuvant chemoradiation followed by surgery may be beneficial in terms of increasing resectability and OS compared to surgery alone. Results from clinical trials are encouraging; however, they also demonstrated that only patients with major histopathological response (pCR) will benefit from neoadjuvant therapy. In addition, these therapies are expensive and the prognoses of patients who do not respond to trimodality treatment strategies appear to be inferior to that of patients who had surgery alone. Accordingly, the development of validated predictive molecular markers may not only be helpful in identifying EA patients who are more likely to respond, but they will also be critical in selecting more efficient treatment strategies with the means of a tailored, targeted, and effective therapy to the molecular profile of both the patient and their disease while minimizing and avoiding life-threatening toxicities.
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50
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Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage. Biochemistry 2010; 49:6155-64. [PMID: 20604523 PMCID: PMC2907095 DOI: 10.1021/bi100364f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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DNA−protein conjugates are potentially repaired via proteolytic digestion to DNA−peptide conjugates. The latter have been modeled with the amino-terminal lysine of the peptide KWKK conjugated via a trimethylene linkage to the N2-dG amine positioned in 5′-d(GCTAGCXAGTCC)-3′·5′-d(GGACTCGCTAGC)-3′ (X = N2-dG−trimethylene link−KWKK). This linkage is a surrogate for the reversible linkage formed by the γ-OH-1,N2-propanodeoxyguanosine (γ-OH-PdG) adduct. This conjugated KWKK stabilizes the DNA. Amino acids K26, W27, K28, and K29 are in the minor groove. The W27 indolyl group does not intercalate into the DNA. The G7N2 amine and the K26 N-terminal amine nitrogens are in the trans configuration with respect to the Cα or Cγ of the trimethylene tether, respectively. The structure of this DNA−KWKK conjugate is discussed in the context of its biological processing.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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