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Vijayraghavan S, Porcher L, Mieczkowski PA, Saini N. Acetaldehyde makes a distinct mutation signature in single-stranded DNA. Nucleic Acids Res 2022; 50:7451-7464. [PMID: 35776120 PMCID: PMC9303387 DOI: 10.1093/nar/gkac570] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/09/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
Acetaldehyde (AA), a by-product of ethanol metabolism, is acutely toxic due to its ability to react with various biological molecules including DNA and proteins, which can greatly impede key processes such as replication and transcription and lead to DNA damage. As such AA is classified as a group 1 carcinogen by the International Agency for Research on Cancer (IARC). Previous in vitro studies have shown that AA generates bulky adducts on DNA, with signature guanine-centered (GG→TT) mutations. However, due to its weak mutagenicity, short chemical half-life, and the absence of powerful genetic assays, there is considerable variability in reporting the mutagenic effects of AA in vivo. Here, we used an established yeast genetic reporter system and demonstrate that AA treatment is highly mutagenic to cells and leads to strand-biased mutations on guanines (G→T) at a high frequency on single stranded DNA (ssDNA). We further demonstrate that AA-derived mutations occur through lesion bypass on ssDNA by the translesion polymerase Polζ. Finally, we describe a unique mutation signature for AA, which we then identify in several whole-genome and -exome sequenced cancers, particularly those associated with alcohol consumption. Our study proposes a key mechanism underlying carcinogenesis by acetaldehyde—mutagenesis of single-stranded DNA.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Latarsha Porcher
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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2
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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3
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Tan Y, Guo S, Wu J, Du H, Li L, You C, Wang Y. DNA Polymerase η Promotes the Transcriptional Bypass of N2-Alkyl-2'-deoxyguanosine Adducts in Human Cells. J Am Chem Soc 2021; 143:16197-16205. [PMID: 34555898 DOI: 10.1021/jacs.1c07374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To cope with unrepaired DNA lesions, cells are equipped with DNA damage tolerance mechanisms, including translesion synthesis (TLS). While TLS polymerases are well documented in facilitating replication across damaged DNA templates, it remains unknown whether TLS polymerases participate in transcriptional bypass of DNA lesions in cells. Herein, we employed the competitive transcription and adduct bypass assay to examine the efficiencies and fidelities of transcription across N2-alkyl-2'-deoxyguanosine (N2-alkyl-dG, alkyl = methyl, ethyl, n-propyl, or n-butyl) lesions in HEK293T cells. We found that N2-alkyl-dG lesions strongly blocked transcription and elicited CC → AA tandem mutations in nascent transcripts, where adenosines were misincorporated opposite the lesions and their adjacent 5' nucleoside. Additionally, genetic ablation of Pol η, but not Pol κ, Pol ι, or Pol ζ, conferred marked diminutions in the transcriptional bypass efficiencies of the N2-alkyl-dG lesions, which is exacerbated by codepletion of Rev1 in Pol η-deficient background. We also observed that the repair of N2-nBu-dG was not pronouncedly affected by genetic depletion of Pol η or Rev1. Hence, our results provided insights into transcriptional perturbations induced by N2-alkyl-dG lesions and expanded the biological functions of TLS DNA polymerases.
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Affiliation(s)
- Ying Tan
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Su Guo
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Jun Wu
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Changjun You
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States.,Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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4
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Mišík M, Ferk F, Schaar H, Yamada M, Jaeger W, Knasmueller S, Kreuzinger N. Genotoxic activities of wastewater after ozonation and activated carbon filtration: Different effects in liver-derived cells and bacterial indicators. WATER RESEARCH 2020; 186:116328. [PMID: 32866931 DOI: 10.1016/j.watres.2020.116328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Aim of this study was to investigate the impact of advanced wastewater treatment techniques (combining ozonation with activated carbon filtration) on acute and genotoxic activities of tertiary treated wastewater. Concentrated samples were tested in Salmonella/microsome assays. Furthermore, induction of DNA damage was measured in liver-derived cells (human hepatoma and primary rat hepatocytes) in single cell gel electrophoresis experiments, which are based on the measurement of DNA migration in an electric field. These cell types possess phase I and phase II enzymes, which catalyze the activation/detoxification of mutagens. Acute toxicity was determined with the trypan blue exclusion technique. We found no evidence for mutagenic effects of non-ozonated samples in several bacterial tester strains (TA98, TA100, YG7108, YG7104, YG7112 and YG7113) but clear induction of His+ mutants after O3 treatment in two strains with defective genes encoding for DNA repair, which are highly sensitive towards alkylating agents (YG7108 and YG7104). These effects were reduced after activated carbon filtration. Furthermore, we detected a slight increase of mutagenic activity in strain YG1024 with increased acetyltransferase activity, which is sensitive towards aromatic amines and nitro compounds in untreated water, which was not reduced by O3 treatment. A completely different pattern of mutagenic activity was seen in liver-derived cells; non ozonated samples caused in both cell types pronounced DNA damage, which was reduced (by ca. 25%) after ozonation. Activated carbon treatment did not cause a substantial further reduction of DNA damage. Additional experiments with liver homogenate indicate that the compounds which cause the effects in the human cells are promutagens which require enzymatic activation. None of the waters caused acute toxicity in the liver-derived cells and in the bacterial indicators. Assuming that hepatic mammalian cells reflect the genotoxic properties of the waters in vertebrates (including humans) more adequately as genetically modified bacterial indicators, we conclude that ozonation has beneficial effects in regard to the reduction of genotoxic properties of treated wastewaters.
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Affiliation(s)
- Miroslav Mišík
- Institute of Cancer Research, Department of Internal Medicine I, Borschkegasse 8a, Vienna 1090, Austria
| | - Franziska Ferk
- Institute of Cancer Research, Department of Internal Medicine I, Borschkegasse 8a, Vienna 1090, Austria
| | - Heidemarie Schaar
- Technische Universität Wien, Institute for Water Quality and Resource Management, Karlsplatz 13/226-1, Austria
| | | | - Walter Jaeger
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Siegfried Knasmueller
- Institute of Cancer Research, Department of Internal Medicine I, Borschkegasse 8a, Vienna 1090, Austria.
| | - Norbert Kreuzinger
- Technische Universität Wien, Institute for Water Quality and Resource Management, Karlsplatz 13/226-1, Austria
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5
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Agapov A, Ignatov A, Turtola M, Belogurov G, Esyunina D, Kulbachinskiy A. Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase. J Biol Chem 2020; 295:9583-9595. [PMID: 32439804 DOI: 10.1074/jbc.ra119.011844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 05/20/2020] [Indexed: 11/06/2022] Open
Abstract
DNA lesions can severely compromise transcription and block RNA synthesis by RNA polymerase (RNAP), leading to subsequent recruitment of DNA repair factors to the stalled transcription complex. Recent structural studies have uncovered molecular interactions of several DNA lesions within the transcription elongation complex. However, little is known about the role of key elements of the RNAP active site in translesion transcription. Here, using recombinantly expressed proteins, in vitro transcription, kinetic analyses, and in vivo cell viability assays, we report that point amino acid substitutions in the trigger loop, a flexible element of the active site involved in nucleotide addition, can stimulate translesion RNA synthesis by Escherichia coli RNAP without altering the fidelity of nucleotide incorporation. We show that these substitutions also decrease transcriptional pausing and strongly affect the nucleotide addition cycle of RNAP by increasing the rate of nucleotide addition but also decreasing the rate of translocation. The secondary channel factors DksA and GreA modulated translesion transcription by RNAP, depending on changes in the trigger loop structure. We observed that although the mutant RNAPs stimulate translesion synthesis, their expression is toxic in vivo, especially under stress conditions. We conclude that the efficiency of translesion transcription can be significantly modulated by mutations affecting the conformational dynamics of the active site of RNAP, with potential effects on cellular stress responses and survival.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Jillella GK, Khan K, Roy K. Application of QSARs in identification of mutagenicity mechanisms of nitro and amino aromatic compounds against Salmonella typhimurium species. Toxicol In Vitro 2020; 65:104768. [PMID: 31926304 DOI: 10.1016/j.tiv.2020.104768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
In an attempt to describe the underlying causes of mutagenicity mainly due to organic chemicals, quantitative structure-activity relationship (QSAR) models have been developed using two different Salmonella typhimurium mutagenicity endpoints with or without presence of liver metabolic microsomal enzymes (S9) namely TA98-S9 and TA98 + S9. The models were developed using simple 2D variables having definite physicochemical meaning calculated from Dragon, SiRMS, and PaDEL-descriptor software tools. Stepwise regression followed by partial least squares (PLS) regression was used in model development following the strict OECD guidelines for QSAR model development and validation. The models were validated using coefficient of determination R2, cross-validation coefficient Q2LOO (leave one out) while the test set predictions were analyzed using Q2F1 (coefficient of determination for the test set). Several other internationally accepted validation metrics like MAE95%train, average rm(LOO)2 and Δrm(LOO)2 (for the training set) were used to check model robustness while predictive efficiency was evaluated using MAE95%test, average rm2 and Δrm2 (for the test set). The scope of predictions was defined by applicability domain analysis using the DModX approach, a recommended tool for PLS models. The major contributing features related to mutagenicity include lipophilicity, electronegativity, branching and unsaturation, etc. The present manuscript is the first attempt to undertake modeling of two different endpoints (TA98-S9 and TA98 + S9) in order to explore major contributing molecular features linked directly or indirectly to mutagenicity.
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Affiliation(s)
- Gopala Krishna Jillella
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Educational and Research (NIPER), Chunilal Bhawan, 168, Manikata Main Road, 700054 Kolkata, India
| | - Kabiruddin Khan
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, 188 Raja S C Mullick Road, 700032 Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, 188 Raja S C Mullick Road, 700032 Kolkata, India.
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7
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Tsuruta H, Sonohara Y, Tohashi K, Aoki Shioi N, Iwai S, Kuraoka I. Effects of acetaldehyde-induced DNA lesions on DNA metabolism. Genes Environ 2020; 42:2. [PMID: 31921374 PMCID: PMC6945695 DOI: 10.1186/s41021-019-0142-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/26/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Acetaldehyde, produced upon exposure to alcohol, cigarette smoke, polluted air and sugar, is a highly reactive compound that is carcinogenic to humans and causes a variety of DNA lesions in living human cells. Previously, we reported that acetaldehyde reacts with adjacent deoxyguanosine residues on oligonucleotides, but not with single deoxyguanosine residues or other deoxyadenosine, deoxycytosine, or thymidine residues, and revealed that it forms reversible intrastrand crosslinks with the dGpdG sequence (GG dimer). RESULTS Here, we show that restriction enzymes that recognize a GG sequence digested acetaldehyde-treated plasmid DNA with low but significant efficiencies, whereas restriction enzymes that recognize other sequences were able to digest such DNA. This suggested that acetaldehyde produced GG dimers in plasmid DNA. Additionally, acetaldehyde-treated oligonucleotides were efficient in preventing digestion by the exonuclease function of T4 DNA polymerase compared to non-treated oligonucleotides, suggesting structural distortions of DNA caused by acetaldehyde-treatment. Neither in vitro DNA synthesis reactions of phi29 DNA polymerase nor in vitro RNA synthesis reactions of T7 RNA polymerase were observed when acetaldehyde-treated plasmid DNA was used, compared to when non-treated plasmid DNA was used, suggesting that acetaldehyde-induced DNA lesions inhibited replication and transcription in DNA metabolism. CONCLUSIONS Acetaldehyde-induced DNA lesions could affect the relative resistance to endo- and exo-nucleolytic activity and also inhibit in vitro replication and in vitro transcription. Thus, investigating the effects of acetaldehyde-induced DNA lesions may enable a better understanding of the toxicity and carcinogenicity of acetaldehyde.
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Affiliation(s)
- Haruka Tsuruta
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Yuina Sonohara
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Kosuke Tohashi
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Narumi Aoki Shioi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 Japan
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
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8
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Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E7082-E7091. [PMID: 28784758 DOI: 10.1073/pnas.1708748114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O2-, N3-, and O4-ethylthymidine (O2-, N3-, and O4-EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O2-EtdT and N3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O2-EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O4-EtdT lesion. For the N3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove-sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.
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9
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Liu B, Xue Q, Tang Y, Cao J, Guengerich FP, Zhang H. Mechanisms of mutagenesis: DNA replication in the presence of DNA damage. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2016; 768:53-67. [PMID: 27234563 PMCID: PMC5237373 DOI: 10.1016/j.mrrev.2016.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 02/07/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
Environmental mutagens cause DNA damage that disturbs replication and produces mutations, leading to cancer and other diseases. We discuss mechanisms of mutagenesis resulting from DNA damage, from the level of DNA replication by a single polymerase to the complex DNA replisome of some typical model organisms (including bacteriophage T7, T4, Sulfolobus solfataricus, Escherichia coli, yeast and human). For a single DNA polymerase, DNA damage can affect replication in three major ways: reducing replication fidelity, causing frameshift mutations, and blocking replication. For the DNA replisome, protein interactions and the functions of accessory proteins can yield rather different results even with a single DNA polymerase. The mechanism of mutation during replication performed by the DNA replisome is a long-standing question. Using new methods and techniques, the replisomes of certain organisms and human cell extracts can now be investigated with regard to the bypass of DNA damage. In this review, we consider the molecular mechanism of mutagenesis resulting from DNA damage in replication at the levels of single DNA polymerases and complex DNA replisomes, including translesion DNA synthesis.
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Affiliation(s)
- Binyan Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Qizhen Xue
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Yong Tang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Huidong Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China.
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10
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Soni SK, Kabir KMM, Babarao R, Coyle VE, Sarkar S, Sabri YM, Bhargava SK. A QCM-based ‘on–off’ mechanistic study of gas adsorption by plasmid DNA and DNA–[Bmim][PF6] construct. RSC Adv 2016. [DOI: 10.1039/c6ra14759c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study of the adsorption behavior of disease markers such as ammonia (NH3) and acetaldehyde (CH3CHO) with biomaterials has been presented to enable the development of self-diagnosis technologies, among others.
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Affiliation(s)
- Sarvesh Kumar Soni
- Centre for Advanced Materials and Industrial Chemistry
- School of Science
- RMIT University
- Melbourne
- Australia
| | - K. M. Mohibul Kabir
- Centre for Advanced Materials and Industrial Chemistry
- School of Science
- RMIT University
- Melbourne
- Australia
| | - Ravichandar Babarao
- CSIRO Manufacturing Flagship
- Australia
- School of Science
- RMIT University
- Melbourne
| | - Victoria E. Coyle
- Centre for Advanced Materials and Industrial Chemistry
- School of Science
- RMIT University
- Melbourne
- Australia
| | - Sampa Sarkar
- School of Science
- RMIT University
- Melbourne
- Australia
| | - Ylias M. Sabri
- Centre for Advanced Materials and Industrial Chemistry
- School of Science
- RMIT University
- Melbourne
- Australia
| | - Suresh K. Bhargava
- Centre for Advanced Materials and Industrial Chemistry
- School of Science
- RMIT University
- Melbourne
- Australia
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11
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Shrivastav N, Fedeles BI, Li D, Delaney JC, Frick LE, Foti JJ, Walker GC, Essigmann JM. A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo. PLoS One 2014; 9:e94716. [PMID: 24733044 PMCID: PMC3986394 DOI: 10.1371/journal.pone.0094716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 03/18/2014] [Indexed: 01/06/2023] Open
Abstract
DinB, the E. coli translesion synthesis polymerase, has been shown to bypass several N2-alkylguanine adducts in vitro, including N2-furfurylguanine, the structural analog of the DNA adduct formed by the antibacterial agent nitrofurazone. Recently, it was demonstrated that the Fe(II)- and α-ketoglutarate-dependent dioxygenase AlkB, a DNA repair enzyme, can dealkylate in vitro a series of N2-alkyguanines, including N2-furfurylguanine. The present study explored, head to head, the in vivo relative contributions of these two DNA maintenance pathways (replicative bypass vs. repair) as they processed a series of structurally varied, biologically relevant N2-alkylguanine lesions: N2-furfurylguanine (FF), 2-tetrahydrofuran-2-yl-methylguanine (HF), 2-methylguanine, and 2-ethylguanine. Each lesion was chemically synthesized and incorporated site-specifically into an M13 bacteriophage genome, which was then replicated in E. coli cells deficient or proficient for DinB and AlkB (4 strains in total). Biochemical tools were employed to analyze the relative replication efficiencies of the phage (a measure of the bypass efficiency of each lesion) and the base composition at the lesion site after replication (a measure of the mutagenesis profile of each lesion). The main findings were: 1) Among the lesions studied, the bulky FF and HF lesions proved to be strong replication blocks when introduced site-specifically on a single-stranded vector in DinB deficient cells. This toxic effect disappeared in the strains expressing physiological levels of DinB. 2) AlkB is known to repair N2-alkylguanine lesions in vitro; however, the presence of AlkB showed no relief from the replication blocks induced by FF and HF in vivo. 3) The mutagenic properties of the entire series of N2-alkyguanines adducts were investigated in vivo for the first time. None of the adducts were mutagenic under the conditions evaluated, regardless of the DinB or AlkB cellular status. Taken together, the data indicated that the cellular pathway to combat bulky N2-alkylguanine DNA adducts was DinB-dependent lesion bypass.
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Affiliation(s)
- Nidhi Shrivastav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bogdan I. Fedeles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James C. Delaney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lauren E. Frick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - James J. Foti
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John M. Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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12
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Brooks PJ, Zakhari S. Acetaldehyde and the genome: beyond nuclear DNA adducts and carcinogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:77-91. [PMID: 24282063 DOI: 10.1002/em.21824] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
The designation of acetaldehyde associated with the consumption of alcoholic beverages as "carcinogenic to humans" (Group 1) by the International Agency for Research on Cancer (IARC) has brought renewed attention to the biological effects of acetaldehyde, as the primary oxidative metabolite of alcohol. Therefore, the overall focus of this review is on acetaldehyde and its direct and indirect effects on the nuclear and mitochondrial genome. We first consider different acetaldehyde-DNA adducts, including a critical assessment of the evidence supporting a role for acetaldehyde-DNA adducts in alcohol related carcinogenesis, and consideration of additional data needed to make a conclusion. We also review recent data on the role of the Fanconi anemia DNA repair pathway in protecting against acetaldehyde genotoxicity and carcinogenicity, as well as teratogenicity. We also review evidence from the older literature that acetaldehyde may impact the genome indirectly, via the formation of adducts with proteins that are themselves critically involved in the maintenance of genetic and epigenetic stability. Finally, we note the lack of information regarding acetaldehyde effects on the mitochondrial genome, which is notable since aldehyde dehydrogenase 2 (ALDH2), the primary acetaldehyde metabolic enzyme, is located in the mitochondrion, and roughly 30% of East Asian individuals are deficient in ALDH2 activity due to a genetic variant in the ALDH2 gene. In summary, a comprehensive understanding of all of the mechanisms by which acetaldehyde impacts the function of the genome has implications not only for alcohol and cancer, but types of alcohol related pathologies as well.
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Affiliation(s)
- Philip J Brooks
- Division of Metabolism and Health Effects, National Institute on Alcohol Abuse and Alcoholism, Bethesda, Maryland
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A quantitative assay for assessing the effects of DNA lesions on transcription. Nat Chem Biol 2013; 8:817-22. [PMID: 22902614 PMCID: PMC3509257 DOI: 10.1038/nchembio.1046] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/22/2012] [Indexed: 12/12/2022]
Abstract
Most mammalian cells in nature are quiescent but actively transcribing mRNA for normal physiological processes; thus, it is important to investigate how endogenous and exogenous DNA damage compromises transcription in cells. Here we describe a new competitive transcription and adduct bypass (CTAB) assay to determine the effects of DNA lesions on the fidelity and efficiency of transcription. Using this strategy, we demonstrate that the oxidatively induced lesions 8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine (cdG) and the methylglyoxal-induced lesion N(2)-(1-carboxyethyl)-2'-deoxyguanosine (N(2)-CEdG) strongly inhibited transcription in vitro and in mammalian cells. In addition, cdA and cdG, but not N(2)-CEdG, induced transcriptional mutagenesis in vitro and in vivo. Furthermore, when located on the template DNA strand, all examined lesions were primarily repaired by transcription-coupled nucleotide excision repair in mammalian cells. This newly developed CTAB assay should be generally applicable for quantitatively assessing how other DNA lesions affect DNA transcription in vitro and in cells.
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Nakanishi N, Fukuoh A, Kang D, Iwai S, Kuraoka I. Effects of DNA lesions on the transcription reaction of mitochondrial RNA polymerase: implications for bypass RNA synthesis on oxidative DNA lesions. Mutagenesis 2012; 28:117-23. [PMID: 23053822 DOI: 10.1093/mutage/ges060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Oxidative DNA lesions inhibit the transcription of RNA polymerase II, but in the presence of transcription elongation factors, the transcription can bypass the lesions. Single-subunit mitochondrial RNA polymerase (mtRNAP) catalyses the synthesis of essential transcripts in mitochondria where reactive oxidative species (ROS) are generated as by-products. The occurrence of RNA synthesis by mtRNAP at oxidative DNA lesions remains unknown. Purified mtRNAP and a complex of RNA primer/DNA template containing a single DNA lesion, such as ROS-induced 8-oxoguanine (8-oxoG), two isomeric thymine glycols (5R-Tg or 5S-Tg), the UV-induced cis-syn cyclobutane pyrimidine dimer (CPD) and the pyrimidine(6-4)pyrimidone photoproduct (6-4pp), or a spontaneous common DNA lesion, a base-loss-induced apurinic/apyrimidinic (AP) site, were used for in vitro RNA synthesis assays. In this report, we show that mtRNAP bypassed the oxidative DNA lesions of non-bulky 8-oxoG and 5R-Tg and 5S-Tg with pausing sites but did not bypass the UV-induced DNA lesions and the AP site. The bacteriophage T7 phage RNA polymerase, which is homologous to mtRNAP, bypassed 8-oxoG but stalled at 5R-Tg and 5S-Tg. As expected, although translesion RNA synthesis in 8-oxoG on the DNA templates generated incorrect transcripts with a G:C to T:A transversion, the synthesis in Tg could lead to the correct transcripts with no transcriptional mutagenesis. Collectively, these data suggest that mtRNAP may tolerate the mitochondrial genome containing oxidative DNA lesions induced by ROS from the side effects of an ATP generation reaction.
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Affiliation(s)
- Nozomi Nakanishi
- Graduate School of Engineering Science, Osaka University Graduate School of Engineering Science, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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Berquist BR, Wilson DM. Pathways for repairing and tolerating the spectrum of oxidative DNA lesions. Cancer Lett 2012; 327:61-72. [PMID: 22353689 DOI: 10.1016/j.canlet.2012.02.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/26/2012] [Accepted: 02/01/2012] [Indexed: 01/03/2023]
Abstract
Reactive oxygen species (ROS) arise from both endogenous and exogenous sources. These reactive molecules possess the ability to damage both the DNA nucleobases and the sugar phosphate backbone, leading to a wide spectrum of lesions, including non-bulky (8-oxoguanine and formamidopyrimidine) and bulky (cyclopurine and etheno adducts) base modifications, abasic sites, non-conventional single-strand breaks, protein-DNA adducts, and intra/interstrand DNA crosslinks. Unrepaired oxidative DNA damage can result in bypass mutagenesis during genome copying or gene expression, or blockage of the essential cellular processes of DNA replication or transcription. Such outcomes underlie numerous pathologies, including, but not limited to, carcinogenesis and neurodegeneration, as well as the aging process. Cells have adapted and evolved defense systems against the deleterious effects of ROS, and specifically devote a number of cellular DNA repair and tolerance pathways to combat oxidative DNA damage. Defects in these protective pathways trigger hereditary human diseases that exhibit increased cancer incidence, developmental defects, neurological abnormalities, and/or premature aging. We review herein classic and atypical oxidative DNA lesions, outcomes of encountering these damages during DNA replication and transcription, and the consequences of losing the ability to repair the different forms of oxidative DNA damage. We particularly focus on the hereditary human diseases Xeroderma Pigmentosum, Cockayne Syndrome and Fanconi Anemia, which may involve defects in the efficient repair of oxidative modifications to chromosomal DNA.
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Affiliation(s)
- Brian R Berquist
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, 77843, United States
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Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP. Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-alkylguanine adducts. J Biol Chem 2008; 284:3563-76. [PMID: 19059910 DOI: 10.1074/jbc.m807778200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In contrast to replicative DNA polymerases, Sulfolobus solfataricus Dpo4 showed a limited decrease in catalytic efficiency (k(cat)/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity was maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increased slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. Pre-steady-state kinetic bursts were observed for dCTP incorporation throughout the series (N2-MeG to N2-AnthG), with a decrease in the burst amplitude and k(pol), the rate of single-turnover incorporation. The pre-steady-state kinetic courses with G and all of the six N2-alkyl G adducts could be fit to a general DNA polymerase scheme to which was added an inactive complex in equilibrium with the active ternary Dpo4.DNA.dNTP complex, and only the rates of equilibrium with the inactive complex and phosphodiester bond formation were altered. Two crystal structures of Dpo4 with a template N2-NaphG (in a post-insertion register opposite a 3'-terminal C in the primer) were solved. One showed N2-NaphG in a syn conformation, with the naphthyl group located between the template and the Dpo4 "little finger" domain. The Hoogsteen face was within hydrogen bonding distance of the N4 atoms of the cytosine opposite N2-NaphG and the cytosine at the -2 position. The second structure showed N2-Naph G in an anti conformation with the primer terminus largely disordered. Collectively these results explain the versatility of Dpo4 in bypassing bulky G lesions.
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Affiliation(s)
- Huidong Zhang
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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