1
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Bacurio JHT, Yawson P, Thomforde J, Zhang Q, Kumar HV, Den Hartog H, Tretyakova NY, Basu AK. 5-Formylcytosine mediated DNA-peptide cross-link induces predominantly semi-targeted mutations in both Escherichia coli and human cells. J Biol Chem 2024; 300:105786. [PMID: 38401843 PMCID: PMC10966706 DOI: 10.1016/j.jbc.2024.105786] [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: 12/29/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Histone proteins can become trapped on DNA in the presence of 5-formylcytosine (5fC) to form toxic DNA-protein conjugates. Their repair may involve proteolytic digestion resulting in DNA-peptide cross-links (DpCs). Here, we have investigated replication of a model DpC comprised of an 11-mer peptide (NH2-GGGKGLGK∗GGA) containing an oxy-lysine residue (K∗) conjugated to 5fC in DNA. Both CXG and CXT (where X = 5fC-DpC) sequence contexts were examined. Replication of both constructs gave low viability (<10%) in Escherichia coli, whereas TLS efficiency was high (72%) in HEK 293T cells. In E. coli, the DpC was bypassed largely error-free, inducing only 2 to 3% mutations, which increased to 4 to 5% with SOS. For both sequences, semi-targeted mutations were dominant, and for CXG, the predominant mutations were G→T and G→C at the 3'-base to the 5fC-DpC. In HEK 293T cells, 7 to 9% mutations occurred, and the dominant mutations were the semi-targeted G → T for CXG and T → G for CXT. These mutations were reduced drastically in cells deficient in hPol η, hPol ι or hPol ζ, suggesting a role of these TLS polymerases in mutagenic TLS. Steady-state kinetics studies using hPol η confirmed that this polymerase induces G → T and T → G transversions at the base immediately 3' to the DpC. This study reveals a unique replication pattern of 5fC-conjugated DpCs, which are bypassed largely error-free in both E. coli and human cells and induce mostly semi-targeted mutations at the 3' position to the lesion.
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Affiliation(s)
| | - Priscilla Yawson
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Jenna Thomforde
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Honnaiah Vijay Kumar
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Holly Den Hartog
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA.
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2
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Li J, Dai L, Feng Y, Cao Z, Ding Y, Xu H, Xu A, Du H. Multigenerational effects and mutagenicity of three flame retardants on germ cells in Caenorhabditis elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115815. [PMID: 38091675 DOI: 10.1016/j.ecoenv.2023.115815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024]
Abstract
Flame retardants (FRs) have raised public concerns because of their environmental persistence and negative impacts on human health. Recent evidence has revealed that many FRs exhibit reproductive toxicities and transgenerational impacts, whereas the toxic effects of FRs on germ cells remain barely explored. Here we investigated the multigenerational effects of three flame retardants (TBBPA, TCEP and TCPP) on germ cell development in Caenorhabditis elegans, and examined the germ cell mutagenicity of these FRs by using whole genome sequencing. Parental exposure to three FRs markedly increased germ cell apoptosis, and impeded oogenesis in F1-F6 offspring. In addition, the double-increased mutation frequencies observed in progeny genomes uncover the mutagenic actions of FRs on germ cells. Analysis of mutation spectra revealed that these FRs predominantly induced point mutations at A:T base pairs, whereas both small and large indels were almost unaffected. These results revealed the long-term effects of FRs on development and genomic stability of germ cells, which may pose risks to environmental organisms and human reproductive health. Taken together, our findings suggest that germ cell mutagenicity should be carefully examined for the environmental risk assessment of FRs and other emerging pollutants.
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Affiliation(s)
- Jiali Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China
| | - Linglong Dai
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Yu Feng
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Science Island Branch, Graduate School of USTC, Hefei 230026, Anhui, China
| | - Zhenxiao Cao
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Yuting Ding
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Hao Xu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China
| | - An Xu
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
| | - Hua Du
- Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, China.
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3
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Li J, Hu Z, Liu D, Wang P. Mass spectrometry-based assays for assessing replicative bypass and repair of DNA alkylation in cells. RSC Adv 2023; 13:15490-15497. [PMID: 37223415 PMCID: PMC10201546 DOI: 10.1039/d2ra08340j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
Endogenous metabolism and environmental exposure can give rise to DNA alkylation, which can elicit deleterious biological consequences. In the search for reliable and quantitative analytical methods to elucidate the impact of DNA alkylation on the flow of genetic information, mass spectrometry (MS) has attracted increasing attention, owing to its unambiguous determination of molecular mass. The MS-based assays obviate conventional colony-picking methods and Sanger sequencing procedures, and retained the high sensitivity of postlabeling methods. With the help of the CRISPR/Cas9 gene editing method, MS-based assays showed high potential in studying individual functions of repair proteins and translesion synthesis (TLS) polymerases in DNA replication. In this mini-review, we have summarized the development of MS-based competitive and replicative adduct bypass (CRAB) assays and their recent applications in assessing the impact of alkylation on DNA replication. With further development of MS instruments for high resolving power and high throughput, these assays should be generally applicable and efficient in quantitative measurement of the biological consequences and repair of other DNA lesions.
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Affiliation(s)
- Jiaxian Li
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Zhihai Hu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Dandan Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
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4
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Stanio S, Bacurio JHT, Yang H, Greenberg MM, Basu AK. 8-Oxo-2'-deoxyguanosine Replication in Mutational Hot Spot Sequences of the p53 Gene in Human Cells Is Less Mutagenic than That of the Corresponding Formamidopyrimidine. Chem Res Toxicol 2023; 36:782-789. [PMID: 37093780 PMCID: PMC10192040 DOI: 10.1021/acs.chemrestox.3c00069] [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] [Indexed: 04/25/2023]
Abstract
7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo) is a ubiquitous DNA damage formed by oxidation of 2'-deoxyguanosine. In this study, plasmid DNA containing 8-OxodGuo located in three mutational hot spots of human cancers, codons 248, 249, and 273 of the Tp53 tumor suppressor gene, was replicated in HEK 293T cells. 8-OxodGuo was only a weak block of replication, and the bypass was largely error-free. The mutations (1-5%) were primarily G → T transversions, and the mutation frequency was generally lower than that of the chemically related Fapy·dG. A unique 8-OxodGuo mutation spectrum was observed at each site, as reflected by replication in translesion synthesis (TLS) polymerase- or hPol λ-deficient cells. In codon 248 (CG*G) and 249 (AG*G), where G* denotes 8-OxodGuo, hPol η and hPol ζ carried out largely error-free bypass of the lesion, whereas hPol κ and hPol ι were involved mostly in error-prone TLS, resulting in G → T mutations. 8-OxodGuo bypass in codon 273 (CG*T) was unlike the other two sites, as hPol κ participated in the mostly error-free bypass of the lesion. Yet, in all three sites, including codon 273, simultaneous deficiency of hpol κ and hPol ι resulted in reduction of G → T transversions. This indicates a convincing role of these two TLS polymerases in error-prone bypass of 8-OxodGuo. Although the dominant mutation was G → T in each site, in codon 249, and to a lesser extent in codon 248, significant semi-targeted single-base deletions also occurred, which suggests that 8-OxodGuo can initiate slippage of a base near the lesion site. This study underscores the importance of sequence context in 8-OxodGuo mutagenesis in human cells. It also provides a more comprehensive comparison between 8-OxodGuo and the sister lesion, Fapy·dG. The greater mutagenicity of the latter in the same sequence contexts indicates that Fapy·dG is a biologically significant lesion and biomarker on par with 8-OxodGuo.
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Affiliation(s)
- Stephen Stanio
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | | | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ashis K. Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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5
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Fahrer J, Christmann M. DNA Alkylation Damage by Nitrosamines and Relevant DNA Repair Pathways. Int J Mol Sci 2023; 24:ijms24054684. [PMID: 36902118 PMCID: PMC10003415 DOI: 10.3390/ijms24054684] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023] Open
Abstract
Nitrosamines occur widespread in food, drinking water, cosmetics, as well as tobacco smoke and can arise endogenously. More recently, nitrosamines have been detected as impurities in various drugs. This is of particular concern as nitrosamines are alkylating agents that are genotoxic and carcinogenic. We first summarize the current knowledge on the different sources and chemical nature of alkylating agents with a focus on relevant nitrosamines. Subsequently, we present the major DNA alkylation adducts induced by nitrosamines upon their metabolic activation by CYP450 monooxygenases. We then describe the DNA repair pathways engaged by the various DNA alkylation adducts, which include base excision repair, direct damage reversal by MGMT and ALKBH, as well as nucleotide excision repair. Their roles in the protection against the genotoxic and carcinogenic effects of nitrosamines are highlighted. Finally, we address DNA translesion synthesis as a DNA damage tolerance mechanism relevant to DNA alkylation adducts.
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Affiliation(s)
- Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schrödinger Strasse 52, D-67663 Kaiserslautern, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| | - Markus Christmann
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
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6
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Kan Y, Jin Z, Ke Y, Lin D, Yan L, Wu L, He Y. Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell. Sci Rep 2022; 12:21183. [PMID: 36476762 PMCID: PMC9729220 DOI: 10.1038/s41598-022-24802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.
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Affiliation(s)
- Yuhe Kan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, 010021 Inner Mongolia People’s Republic of China ,Qilu Pharmaceutical (Inner Mongolia) CO., LTD., Hohhot, 010080 Inner Mongolia People’s Republic of China
| | - Zhaoyang Jin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yongqi Ke
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Dao Lin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Liang Yan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Li Wu
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China
| | - Yujian He
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China ,grid.410726.60000 0004 1797 8419School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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7
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Cao Z, Wang M, Zhou T, Xu A, Du H. Whole-Genome Sequencing Reveals Germ Cell Mutagenicity of α-Endosulfan in Caenorhabditis elegans. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16024-16032. [PMID: 36239620 DOI: 10.1021/acs.est.2c06817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Endosulfan is an extensively used organochlorine pesticide around the world, which was classified as a persistent organic pollutant (POP) in 2009. Although previous studies have documented the reproductive toxicity of endosulfan in a variety of organisms, little is known about the influence of endosulfan on the genome stability of germ cells and nonexposed progeny. Here we applied whole-genome sequencing to explore the germ cell mutagenicity of α-endosulfan in Caenorhabditis elegans (C. elegans). We found that, although low doses of α-endosulfan exhibited a minor effect on the reproductive capacity of C. elegans, chronic exposure to 1 μM α-endosulfan significantly increased the mutation frequencies of nonexposed progeny. Further analysis of genome-wide mutation spectra demonstrated that α-endosulfan preferentially elicited A:T → G:C substitutions and clustered mutations. By using worms deficient in DNA damage response genes, our results suggest the involvement of translesion synthesis polymerase η in modulating α-endosulfan-induced mutations in germ cells. Together, these observations reveal the germ cell mutagenicity of α-endosulfan in C. elegans and the possible underlying mechanism. In addition, our findings implicate that germ cell mutagenicity might be a necessary consideration for the health risk assessment of environmental chemicals such as POPs.
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Affiliation(s)
- Zhenxiao Cao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - Meimei Wang
- Department of Pathophysiology, School of Basic Medical Science, Anhui Medical University, No. 81 Mei-Shan Rd, Hefei 230032, Anhui, P. R. China
| | - Tong Zhou
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
| | - Hua Du
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS; Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei 230031, Anhui, P. R. China
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8
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Bolleddula J, Gopalakrishnan S, Hu P, Dong J, Venkatakrishnan K. Alternatives to rifampicin: A review and perspectives on the choice of strong CYP3A inducers for clinical drug-drug interaction studies. Clin Transl Sci 2022; 15:2075-2095. [PMID: 35722783 PMCID: PMC9468573 DOI: 10.1111/cts.13357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023] Open
Abstract
N-Nitrosamine (NA) impurities are considered genotoxic and have gained attention due to the recall of several marketed drug products associated with higher-than-permitted limits of these impurities. Rifampicin is an index inducer of multiple cytochrome P450s (CYPs) including CYP2B6, 2C8, 2C9, 2C19, and 3A4/5 and an inhibitor of OATP1B transporters (single dose). Hence, rifampicin is used extensively in clinical studies to assess drug-drug interactions (DDIs). Despite NA impurities being reported in rifampicin and rifapentine above the acceptable limits, these critical anti-infective drugs are available for therapeutic use considering their benefit-risk profile. Reports of NA impurities in rifampicin products have created uncertainty around using rifampicin in clinical DDI studies, especially in healthy volunteers. Hence, a systematic investigation through a literature search was performed to determine possible alternative index inducer(s) to rifampicin. The available strong CYP3A inducers were selected from the University of Washington DDI Database and their in vivo DDI potential assessed using the data from clinical DDI studies with sensitive CYP3A substrates. To propose potential alternative CYP3A inducers, factors including lack of genotoxic potential, adequate safety, feasibility of multiple dose administration to healthy volunteers, and robust in vivo evidence of induction of CYP3A were considered. Based on the qualifying criteria, carbamazepine, phenytoin, and lumacaftor were identified to be the most promising alternatives to rifampicin for conducting CYP3A induction DDI studies. Strengths and limitations of the proposed alternative CYP3A inducers, the magnitude of in vivo CYP3A induction, appropriate study designs for each alternative inducer, and future perspectives are presented in this paper.
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Affiliation(s)
- Jayaprakasam Bolleddula
- Quantitative PharmacologyEMD Serono Research & Development Institute, Inc.BillericaMassachusettsUSA
| | | | - Ping Hu
- Quantitative PharmacologyEMD Serono Research & Development Institute, Inc.BillericaMassachusettsUSA
| | - Jennifer Dong
- Quantitative PharmacologyEMD Serono Research & Development Institute, Inc.BillericaMassachusettsUSA
| | - Karthik Venkatakrishnan
- Quantitative PharmacologyEMD Serono Research & Development Institute, Inc.BillericaMassachusettsUSA
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9
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Wilson KA, Jeong YER, Wetmore SD. Multiscale computational investigations of the translesion synthesis bypass of tobacco-derived DNA adducts: critical insights that complement experimental biochemical studies. Phys Chem Chem Phys 2022; 24:10667-10683. [PMID: 35502640 DOI: 10.1039/d2cp00481j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Among the numerous agents that damage DNA, tobacco products remain one of the most lethal and result in the most diverse set of DNA lesions. This perspective aims to provide an overview of computational work conducted to complement experimental biochemical studies on the mutagenicity of adducts derived from the most potent tobacco carcinogen, namely 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (nicotine-derived nitrosaminoketone or NNK). Lesions ranging from the smallest methylated thymine derivatives to the larger, flexible pyridyloxobutyl (POB) guanine adducts are considered. Insights are obtained from density functional theory (DFT) calculations and molecular dynamics (MD) simulations into the damaged nucleobase and nucleoside structures, the accommodation of the lesions in the active site of key human polymerases, the intrinsic base pairing potentials of the adducts, and dNTP incorporation opposite the lesions. Overall, the computational data provide atomic level information that can rationalize the differential mutagenic properties of tobacco-derived lesions and uncover important insights into the impact of adduct size, nucleobase, position, and chemical composition of the bulky moiety.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI) and Southern Alberta Genome Sciences Center (SAGSC), University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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10
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Li Y, Hecht SS. Metabolism and DNA Adduct Formation of Tobacco-Specific N-Nitrosamines. Int J Mol Sci 2022; 23:5109. [PMID: 35563500 PMCID: PMC9104174 DOI: 10.3390/ijms23095109] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 01/06/2023] Open
Abstract
The tobacco-specific N-nitrosamines 4-(N-nitrosomethylamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) always occur together and exclusively in tobacco products or in environments contaminated by tobacco smoke. They have been classified as "carcinogenic to humans" by the International Agency for Research on Cancer. In 1998, we published a review of the biochemistry, biology and carcinogenicity of tobacco-specific nitrosamines. Over the past 20 years, considerable progress has been made in our understanding of the mechanisms of metabolism and DNA adduct formation by these two important carcinogens, along with progress on their carcinogenicity and mutagenicity. In this review, we aim to provide an update on the carcinogenicity and mechanisms of the metabolism and DNA interactions of NNK and NNN.
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Affiliation(s)
- Yupeng Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
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11
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Hecht SS, Hatsukami DK. Smokeless tobacco and cigarette smoking: chemical mechanisms and cancer prevention. Nat Rev Cancer 2022; 22:143-155. [PMID: 34980891 PMCID: PMC9308447 DOI: 10.1038/s41568-021-00423-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 12/19/2022]
Abstract
Tobacco products present a deadly combination of nicotine addiction and carcinogen exposure resulting in millions of cancer deaths per year worldwide. A plethora of smokeless tobacco products lead to unacceptable exposure to multiple carcinogens, including the tobacco-specific nitrosamine N'-nitrosonornicotine, a likely cause of the commonly occurring oral cavity cancers observed particularly in South-East Asian countries. Cigarettes continue to deliver a large number of carcinogens, including tobacco-specific nitrosamines, polycyclic aromatic hydrocarbons and volatile organic compounds. The multiple carcinogens in cigarette smoke are responsible for the complex mutations observed in critical cancer genes. The exposure of smokeless tobacco users and smokers to carcinogens and toxicants can now be monitored by urinary and DNA adduct biomarkers that may be able to identify those individuals at highest risk of cancer so that effective cancer prevention interventions can be initiated. Regulation of the levels of carcinogens, toxicants and nicotine in tobacco products and evidence-based tobacco control efforts are now recognized as established pathways to preventing tobacco related cancer.
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Affiliation(s)
- Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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12
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Bacurio JHT, Yang H, Naldiga S, Powell BV, Ryan BJ, Freudenthal BD, Greenberg MM, Basu AK. Sequence context effects of replication of Fapy•dG in three mutational hot spot sequences of the p53 gene in human cells. DNA Repair (Amst) 2021; 108:103213. [PMID: 34464900 DOI: 10.1016/j.dnarep.2021.103213] [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: 07/16/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 01/01/2023]
Abstract
Fapy•dG and 8-OxodGuo are formed in DNA from a common N7-dG radical intermediate by reaction with hydroxyl radical. Although cellular levels of Fapy•dG are often greater, its effects on replication are less well understood than those of 8-OxodGuo. In this study plasmid DNA containing Fapy•dG in three mutational hotspots of human cancers, codons 248, 249, and 273 of the p53 tumor suppressor gene, was replicated in HEK 293T cells. TLS efficiencies for the Fapy•dG containing plasmids varied from 72 to 89%, and were further reduced in polymerase-deficient cells. The mutation frequency (MF) of Fapy•dG ranged from 7.3 to 11.6%, with G→T and G→A as major mutations in codons 248 and 249 compared to primarily G→T in codon 273. Increased MF in hPol ι-, hPol κ-, and hPol ζ-deficient cells suggested that these polymerases more frequently insert the correct nucleotide dC opposite Fapy•dG, whereas decreased G→A in codons 248 and 249 and reduction of all mutations in codon 273 in hPol λ-deficient cells indicated hPol λ's involvement in Fapy•dG mutagenesis. In vitro kinetic analysis using isolated translesion synthesis polymerases and hPol λ incompletely corroborated the mutagenesis experiments, indicating codependence on other proteins in the cellular milieu. In conclusion, Fapy•dG mutagenesis is dependent on the DNA sequence context, but its bypass by the TLS polymerases is largely error-free.
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Affiliation(s)
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Spandana Naldiga
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Brent V Powell
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA.
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13
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Bhutani P, Murray MT, Sommer CW, Wilson KA, Wetmore SD. Structural Rationalization for the Nonmutagenic and Mutagenic Bypass of the Tobacco-Derived O4-4-(3-Pyridyl)-4-oxobut-1-yl-thymine Lesion by Human Polymerase η: A Multiscale Computational Study. Chem Res Toxicol 2021; 34:1619-1629. [PMID: 33856186 DOI: 10.1021/acs.chemrestox.1c00063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tobacco-derived pyridyloxobutyl (POB) DNA adducts are unique due to the large size and flexibility of the alkyl chain connecting the pyridyl ring to the nucleobase. Recent experimental work suggests that the O4-4-(3-pyridyl)-4-oxobut-1-yl-T (O4-POB-T) lesion can undergo both nonmutagenic (dATP) and mutagenic (dGTP) insertion by the translesion synthesis (TLS) polymerase (pol) η in human cells. Interestingly, the mutagenic rate for O4-POB-T replication is reduced compared to that for the smaller O4-methylthymine (O4-Me-T) lesion, and O4-POB-T yields a different mutagenic profile than the O2-POB-T variant (dTTP insertion). The present work uses a combination of density functional theory calculations and molecular dynamics simulations to probe the impact of the size and flexibility of O4-POB-T on pol η replication outcomes. Due to changes in the Watson-Crick binding face upon damage of canonical T, O4-POB-T does not form favorable hydrogen-bonding interactions with A. Nevertheless, dATP is positioned for insertion in the pol η active site by a water chain to the template strand, which suggests a pol η replication pathway similar to that for abasic sites. Although a favorable O4-POB-T:G mispair forms in the pol η active site and DNA duplexes, the inherent dynamical nature of O4-POB-T periodically disrupts interstrand hydrogen bonding that would otherwise facilitate dGTP insertion and stabilize damaged DNA duplexes. In addition to explaining the origin of the experimentally reported pol η outcomes associated with O4-POB-T replication, comparison to structural data for the O4-Me-T and O2-POB-T adducts highlights an emerging common pathway for the nonmutagenic replication of thymine alkylated lesions by pol η, yet underscores the broader impacts of bulky moiety size, flexibility, and position on the associated mutagenic outcomes.
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Affiliation(s)
- Priya Bhutani
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Makay T Murray
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Craig W Sommer
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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14
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Nookaew I, Jenjaroenpun P, Du H, Wang P, Wu J, Wongsurawat T, Moon SH, Huang E, Wang Y, Boysen G. Detection and Discrimination of DNA Adducts Differing in Size, Regiochemistry, and Functional Group by Nanopore Sequencing. Chem Res Toxicol 2020; 33:2944-2952. [PMID: 32799528 DOI: 10.1021/acs.chemrestox.0c00202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chemically induced DNA adducts can lead to mutations and cancer. Unfortunately, because common analytical methods (e.g., liquid chromatography-mass spectrometry) require adducts to be digested or liberated from DNA before quantification, information about their positions within the DNA sequence is lost. Advances in nanopore sequencing technologies allow individual DNA molecules to be analyzed at single-nucleobase resolution, enabling us to study the dynamic of epigenetic modifications and exposure-induced DNA adducts in their native forms on the DNA strand. We applied and evaluated the commercially available Oxford Nanopore Technology (ONT) sequencing platform for site-specific detection of DNA adducts and for distinguishing individual alkylated DNA adducts. Using ONT and the publicly available ELIGOS software, we analyzed a library of 15 plasmids containing site-specifically inserted O6- or N2-alkyl-2'-deoxyguanosine lesions differing in sizes and regiochemistries. Positions of DNA adducts were correctly located, and individual DNA adducts were clearly distinguished from each other.
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Affiliation(s)
- Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Hua Du
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Jun Wu
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Sun Hee Moon
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - En Huang
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Gunnar Boysen
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
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15
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Kan Y, Chen L, Lin D, Bu X, Mo M, Yan L, Yang Z, Yuan L, Wu L, He Y. Replication of DNA Containing Mirror-Image Thymidine in E. coli Cells. Chem Res Toxicol 2020; 33:2276-2285. [PMID: 32812424 DOI: 10.1021/acs.chemrestox.9b00502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA damage can occur naturally or through environmental factors, leading to mutations in DNA replication and genomic instability in cells. Normally, natural d-nucleotides were selected by DNA polymerases. The template l-thymidine (l-T) has been shown to be bypassed by several types of DNA polymerases. However, DNA replication fidelity of nucleotide incorporation opposite l-thymidine in vivo remains unknown. Here, we constructed plasmids containing a restriction enzyme (PstI) recognition site in which the l-T lesion was site-specifically located within the PstI recognition sequence (CTGCAG). Further, we assessed the efficiencies of nucleotide incorporation opposite the l-T site and l-T lesion bypass replication in vitro and in vivo. We found that recombinants containing the l-T lesion site inhibited DNA replication. In addition, A was incorporated opposite the l-T lesion by routine PCR assay, whereas preference for nucleotide incorporation opposite the l-T site was A (13%), T (22%), C (46%), and G (19%), and no nucleotide insertion and deletions were detected in E. coli cells. In particular, a novel restriction enzyme-mediated method for detection of the mutagenic properties of DNA lesion was established, which allows us to readily detect restriction-digestion of the l-T-bearing plasmids. The study provided significant insight into how mirror-image nucleosides perturb the fidelity of DNA replication in vivo and whether they elicit mutagenic effects, which may help to understand both how DNA damage interferes with the flow of genetic information during DNA replication and development of diseases caused by gene mutation.
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Affiliation(s)
- Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lu Chen
- School of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 110000, P. R. China
| | - Dao Lin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinya Bu
- School of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 110000, P. R. China
| | - Mengwu Mo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Longfei Yuan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
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16
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Powell BV, Bacurio JHT, Basu AK. Translesion synthesis of 6-nitrochrysene-derived 2'-deoxyadenosine adduct in human cells. DNA Repair (Amst) 2020; 95:102935. [PMID: 32721818 DOI: 10.1016/j.dnarep.2020.102935] [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: 06/09/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 10/23/2022]
Abstract
6-Nitrochrysene (6-NC) is a potent mutagen in bacteria and carcinogenic in animals. It is the most potent carcinogen ever tested in newborn mouse assay. DNA lesions resulting from 6-NC modification are likely to induce mutations if they are not removed by cellular defense pathways prior to DNA replication. Earlier studies showed that 6-NC-derived C8-2'-deoxyadenosine adduct, N-(dA-8-yl)-6-AC, is very slowly repaired in human cells. In this study, we have investigated replication of N-(dA-8-yl)-6-AC in human embryonic kidney (HEK 293T) cells and the roles of translesion synthesis (TLS) DNA polymerases in bypassing it. Replication of a plasmid containing a single site-specific N-(dA-8-yl)-6-AC adduct in HEK 293 T cells showed that human DNA polymerase (hPol) η and hPol κ played important roles in bypassing the adduct, since TLS efficiency was reduced to 26 % in the absence of these two polymerases compared to 83 % in polymerase-competent HEK 293T cells. The progeny from HEK 293T cells provided 12.7 % mutants predominantly containing A→T transversions. Mutation frequency (MF) was increased to 17.8 % in hPol η-deficient cells, whereas it was decreased to 3.3 % and 3.9 % when the adduct containing plasmid was replicated in hPol κ- and hPol ζ-deficient cells, respectively. The greatest reduction in MF by more than 90 % (to MF 1.2 %) was observed in hPol ζ-knockout cells in which hPol κ was knocked down. Taken together, these results suggest that hPol κ and hPol ζ are involved in the error-prone TLS of N-(dA-8-yl)-6-AC, while hPol η performs error-free bypass.
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Affiliation(s)
- Brent V Powell
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, United States
| | - Jan Henric T Bacurio
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, United States
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, United States.
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17
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Du H, Wang P, Wu J, He X, Wang Y. The roles of polymerases ν and θ in replicative bypass of O6- and N2-alkyl-2'-deoxyguanosine lesions in human cells. J Biol Chem 2020; 295:4556-4562. [PMID: 32098870 PMCID: PMC7135994 DOI: 10.1074/jbc.ra120.012830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/20/2020] [Indexed: 12/28/2022] Open
Abstract
Exogenous and endogenous chemicals can react with DNA to produce DNA lesions that may block DNA replication. Not much is known about the roles of polymerase (Pol) ν and Pol θ in translesion synthesis (TLS) in cells. Here we examined the functions of these two polymerases in bypassing major-groove O6-alkyl-2'-deoxyguanosine (O6-alkyl-dG) and minor-groove N2-alkyl-dG lesions in human cells, where the alkyl groups are ethyl, n-butyl (nBu), and, for O6-alkyl-dG, pyridyloxobutyl. We found that Pol ν and Pol θ promote TLS across major-groove O6-alkyl-dG lesions. O6-alkyl-dG lesions mainly induced G→A mutations that were modulated by the two TLS polymerases and the structures of the alkyl groups. Simultaneous ablation of Pol ν and Pol θ resulted in diminished mutation frequencies for all three O6-alkyl-dG lesions. Depletion of Pol ν alone reduced mutations only for O6-nBu-dG, and sole loss of Pol θ attenuated the mutation rates for O6-nBu-dG and O6-pyridyloxobutyl-dG. Replication across the two N2-alkyl-dG lesions was error-free, and Pol ν and Pol θ were dispensable for their replicative bypass. Together, our results provide critical knowledge about the involvement of Pol ν and Pol θ in bypassing alkylated guanine lesions in human cells.
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Affiliation(s)
- Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Jun Wu
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Xiaomei He
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403
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18
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Abstract
Genome integrity is constantly challenged by endogenous or exogenous genotoxic agents, which can give rise to various DNA adducts. After metabolic activation, tobacco-specific nitrosamines N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) can lead to pyridyloxobutylphosphotriesters (POB-PTEs) in DNA. Here, we synthesized oligodeoxyribonucleotides containing a site-specifically inserted SP- or RP-POB-PTE flanked by two thymidines, and we examined the impact that these lesions have on DNA replication in Escherichia coli cells. We found that these two lesions are not strong impediments to DNA replication, and their replicative bypass is not modulated by genetic depletion of the three SOS-induced DNA polymerases or Ada protein. In addition, neither SP- nor RP-POB-PTEs was mutagenic in E. coli cells. Together, our study unveiled, for the first time, the influence of tobacco-specific nitrosamine-induced POB-PTE lesions on DNA replication in vivo.
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19
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Naldiga S, Huang H, Greenberg MM, Basu AK. Mutagenic Effects of a 2-Deoxyribonolactone-Thymine Glycol Tandem DNA Lesion in Human Cells. Biochemistry 2019; 59:417-424. [PMID: 31860280 DOI: 10.1021/acs.biochem.9b01058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tandem DNA lesions containing two contiguously damaged nucleotides are commonly formed by ionizing radiation. Their effects on replication in mammalian cells are largely unknown. Replication of isolated 2-deoxyribonolactone (L), thymine glycol (Tg), and tandem lesion 5'-LTg was examined in human cells. Although nearly 100% of Tg was bypassed in HEK 293T cells, L was a significant replication block. 5'-LTg was an even stronger replication block with 5% TLS efficiency. The mutation frequency (MF) of Tg was 3.4%, which increased to 3.9% and 4.8% in pol ι- and pol κ-deficient cells, respectively. An even greater increase in the MF of Tg (to ∼5.5%) was observed in cells deficient in both pol κ and pol ζ, suggesting that they work together to bypass Tg in an error-free manner. Isolated L bypass generated 12-18% one-base deletions, which increased as much as 60% in TLS polymerase-deficient cells. The fraction of deletion products also increased in TLS polymerase-deficient cells upon 5'-LTg bypass. In full-length products and in all cell types, dA was preferentially incorporated opposite an isolated L as well as when it was part of a tandem lesion. However, misincorporation opposite Tg increased significantly when it was part of a tandem lesion. In wild type cells, targeted mutations increased about 3-fold to 9.7% and to 17.4, 15.9, and 28.8% in pol κ-, pol ζ-, and pol ι-deficient cells, respectively. Overall, Tg is significantly more miscoding as part of a tandem lesion, and error-free Tg replication in HEK 293T cells requires participation of the TLS polymerases.
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Affiliation(s)
- Spandana Naldiga
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Haidong Huang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Ashis K Basu
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
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20
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Bhutani P, Nikkel DJ, Wilson KA, Wetmore SD. Computational Insight into the Differential Mutagenic Patterns of O-Methylthymine Lesions. Chem Res Toxicol 2019; 32:2107-2117. [DOI: 10.1021/acs.chemrestox.9b00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Priya Bhutani
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J. Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta T1K 3M4, Canada
| | - Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta T1K 3M4, Canada
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21
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Wilson KA, Garden JL, Wetmore NT, Felske LR, Wetmore SD. DFT and MD Studies of Formaldehyde-Derived DNA Adducts: Molecular-Level Insights into the Differential Mispairing Potentials of the Adenine, Cytosine, and Guanine Lesions. J Phys Chem A 2019; 123:6229-6240. [PMID: 31241337 DOI: 10.1021/acs.jpca.9b03899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Josh L. Garden
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Natasha T. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Lindey R. Felske
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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22
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Du H, Wang P, Li L, Wang Y. Repair and translesion synthesis of O 6-alkylguanine DNA lesions in human cells. J Biol Chem 2019; 294:11144-11153. [PMID: 31167778 DOI: 10.1074/jbc.ra119.009054] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
O 6-alkyl-2'-deoxyguanosine (O 6-alkyl-dG) lesions are among the most mutagenic and prevalent alkylated DNA lesions that are associated with cancer initiation and progression. In this study, using a shuttle vector-based strand-specific PCR-competitive replication and adduct bypass assay in conjunction with tandem MS for product identification, we systematically assessed the repair and replicative bypass of a series of O 6-alkyl-dG lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu, or sBu, in several human cell lines. We found that the extent of replication-blocking effects of these lesions is influenced by the size of the alkyl groups situated on the O 6 position of the guanine base. We also noted involvement of distinct DNA repair pathways and translesion synthesis polymerases (Pols) in ameliorating the replication blockage effects elicited by the straight- and branched-chain O 6-alkyl-dG lesions. We observed that O 6-methylguanine DNA methyltransferase is effective in removing the smaller alkyl groups from the O 6 position of guanine, whereas repair of the branched-chain lesions relied on nucleotide excision repair. Moreover, these lesions were highly mutagenic during cellular replication and exclusively directed G→A mutations; Pol η and Pol ζ participated in error-prone bypass of the straight-chain lesions, whereas Pol κ preferentially incorporated the correct dCMP opposite the branched-chain lesions. Together, these results uncover key cellular proteins involved in repair and translesion synthesis of O 6-alkyl-dG lesions and provide a better understanding of the roles of these types of lesions in the etiology of human cancer.
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Affiliation(s)
- Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403
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23
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Du H, Wang P, Li L, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C1' and C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Human Cells. ACS Chem Biol 2019; 14:478-485. [PMID: 30768892 DOI: 10.1021/acschembio.8b01126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomic integrity is constantly challenged by exposure to environmental and endogenous genotoxic agents. Reactive oxygen species (ROS) represent one of the most common types of DNA damaging agents. While ROS mainly induce single-nucleobase lesions, epimeric 2-deoxyribose lesions can also be induced upon hydrogen atom abstraction from the C1', C3', or C4' carbon and the subsequent incorrect chemical repair of the resulting carbon-centered radicals. Herein, we investigated the replicative bypass of the C1'- and C3'-epimeric lesions of the four 2'-deoxynucleosides in HEK293T human embryonic kidney epithelial cells. Our results revealed distinct bypass efficiencies and mutagenic properties of these two types of epimeric lesions. Replicative bypasses of all C1'-epimeric lesions except α-dA are mutagenic in HEK293T cells, and their mutagenic properties are further modulated by translesion synthesis (TLS) DNA polymerases. By contrast, none of the four C3'-epimeric lesions are mutagenic, and the replicative bypass of these lesions is not compromised upon depletion of polymerase η, ι, κ, or ζ. Together, our results provide important new knowledge about the cytotoxic and mutagenic properties of C1' and C3' epimeric lesions, and reveal the roles of TLS DNA polymerases in bypassing these lesions in human cells.
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Affiliation(s)
- Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- 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
| | - Nicholas J. Amato
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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24
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Su Y, Ghodke PP, Egli M, Li L, Wang Y, Guengerich FP. Human DNA polymerase η has reverse transcriptase activity in cellular environments. J Biol Chem 2019; 294:6073-6081. [PMID: 30842261 DOI: 10.1074/jbc.ra119.007925] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Indexed: 12/24/2022] Open
Abstract
Classical DNA and RNA polymerase (pol) enzymes have defined roles with their respective substrates, but several pols have been found to have multiple functions. We reported previously that purified human DNA pol η (hpol η) can incorporate both deoxyribonucleoside triphosphates (dNTPs) and ribonucleoside triphosphates (rNTPs) and can use both DNA and RNA as substrates. X-ray crystal structures revealed that two pol η residues, Phe-18 and Tyr-92, behave as steric gates to influence sugar selectivity. However, the physiological relevance of these phenomena has not been established. Here, we show that purified hpol η adds rNTPs to DNA primers at physiological rNTP concentrations and in the presence of competing dNTPs. When two rATPs were inserted opposite a cyclobutane pyrimidine dimer, the substrate was less efficiently cleaved by human RNase H2. Human XP-V fibroblast extracts, devoid of hpol η, could not add rNTPs to a DNA primer, but the expression of transfected hpol η in the cells restored this ability. XP-V cell extracts did not add dNTPs to DNA primers hybridized to RNA, but could when hpol η was expressed in the cells. HEK293T cell extracts could add dNTPs to DNA primers hybridized to RNA, but lost this ability if hpol η was deleted. Interestingly, a similar phenomenon was not observed when other translesion synthesis (TLS) DNA polymerases-hpol ι, κ, or ζ-were individually deleted. These results suggest that hpol η is one of the major reverse transcriptases involved in physiological processes in human cells.
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Affiliation(s)
- Yan Su
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Pratibha P Ghodke
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Lin Li
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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25
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Wilson KA, Holland CD, Wetmore SD. Uncovering a unique approach for damaged DNA replication: A computational investigation of a mutagenic tobacco-derived thymine lesion. Nucleic Acids Res 2019; 47:1871-1879. [PMID: 30605521 PMCID: PMC6393286 DOI: 10.1093/nar/gky1265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 01/01/2023] Open
Abstract
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone is a potent nicotine carcinogen that leads to many DNA lesions, the most persistent being the O2-[4-oxo-4-(3-pyridyl)butyl]thymine adduct (POB-T). Although the experimental mutagenic profile for the minor groove POB-T lesion has been previously reported, the findings are puzzling in terms of the human polymerases involved. Specifically, while pol κ typically replicates minor groove adducts, in vivo studies indicate pol η replicates POB-T despite being known for processing major groove adducts. Our multiscale modeling approach reveals that the canonical (anti) glycosidic orientation of POB-T can fit in the pol κ active site, but only a unique (syn) POB-T conformation is accommodated by pol η. These distinct binding orientations rationalize the differential in vitro mutagenic spectra based on the preferential stabilization of dGTP and dTTP opposite the lesion for pol κ and η, respectively. Overall, by uncovering the first evidence for the replication of a damaged pyrimidine in the syn glycosidic orientation, the current work provides the insight necessary to clarify a discrepancy in the DNA replication literature, expand the biological role of the critical human pol η, and understand the mutational signature in human cancers associated with tobacco exposure.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Carl D Holland
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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26
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Guo S, Leng J, Tan Y, Price NE, Wang Y. Quantification of DNA Lesions Induced by 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol in Mammalian Cells. Chem Res Toxicol 2019; 32:708-717. [PMID: 30714728 DOI: 10.1021/acs.chemrestox.8b00374] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quantitative measurement of DNA adducts in carcinogen-exposed cells provides the information about the frequency of formation and the rate of removal of DNA lesions in vivo, which yields insights into the initial events of mutagenesis. Metabolic activation of tobacco-specific nitrosamines, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and its reduction product 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), leads to pyridyloxobutylation and pyridylhydroxybutylation of DNA. In this study, we employed a highly robust nanoflow liquid chromatography-nanoelectrospray ionization-tandem mass spectrometry (nLC-nESI-MS/MS) coupled with the isotope-dilution method for simultaneous quantification of O6-[4-(3-pyridyl)-4-hydroxylbut-1-yl]-2'-deoxyguanosine ( O6-PHBdG) and O2- and O4-[4-(3-pyridyl)-4-hydroxylbut-1-yl]-thymidine ( O2-PHBdT and O4-PHBdT). Cultured mammalian cells were exposed to a model pyridylhydroxybutylating agent, 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanol (NNALOAc), followed by DNA extraction, enzymatic digestion, and sample enrichment prior to nLC-nESI-MS/MS quantification. Our results demonstrate, for the first time, that O4-PHBdT is quantifiable in cellular DNA and naked DNA upon NNALOAc exposure. We also show that nucleotide excision repair (NER) machinery may counteract the formation of O2-PHBdT and O4-PHBdT, and O6-alkylguanine DNA alkyltransferase (AGT) may be responsible for the repair of O6-PHBdG and O4-PHBdT in mammalian cells. Together, our study provides new knowledge about the occurrence and repair of NNAL-induced DNA lesions in mammalian cells.
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27
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Wang P, Leng J, Wang Y. DNA replication studies of N-nitroso compound-induced O 6-alkyl-2'-deoxyguanosine lesions in Escherichia coli. J Biol Chem 2019; 294:3899-3908. [PMID: 30655287 DOI: 10.1074/jbc.ra118.007358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
N-Nitroso compounds (NOCs) are common DNA-alkylating agents, are abundantly present in food and tobacco, and can also be generated endogenously. Metabolic activation of some NOCs can give rise to carboxymethylation and pyridyloxobutylation/pyridylhydroxybutylation of DNA, which are known to be carcinogenic and can lead to gastrointestinal and lung cancer, respectively. Herein, using the competitive replication and adduct bypass (CRAB) assay, along with MS- and NMR-based approaches, we assessed the cytotoxic and mutagenic properties of three O 6-alkyl-2'-deoxyguanosine (O 6-alkyl-dG) adducts, i.e. O 6-pyridyloxobutyl-dG (O 6-POB-dG) and O 6-pyridylhydroxybutyl-dG (O 6-PHB-dG), derived from tobacco-specific nitrosamines, and O 6-carboxymethyl-dG (O 6-CM-dG), induced by endogenous N-nitroso compounds. We also investigated two neutral analogs of O 6-CM-dG, i.e. O 6-aminocarbonylmethyl-dG (O 6-ACM-dG) and O 6-hydroxyethyl-dG (O 6-HOEt-dG). We found that, in Escherichia coli cells, these lesions mildly (O 6-POB-dG), moderately (O 6-PHB-dG), or strongly (O 6-CM-dG, O 6-ACM-dG, and O 6-HOEt-dG) impede DNA replication. The strong blockage effects of the last three lesions were attributable to the presence of hydrogen-bonding donor(s) located on the alkyl functionality of these lesions. Except for O 6-POB-dG, which also induced a low frequency of G → T transversions, all other lesions exclusively stimulated G → A transitions. SOS-induced DNA polymerases played redundant roles in bypassing all the O 6-alkyl-dG lesions investigated. DNA polymerase IV (Pol IV) and Pol V, however, were uniquely required for inducing the G → A transition for O 6-CM-dG exposure. Together, our study expands our knowledge about the recognition of important NOC-derived O 6-alkyl-dG lesions by the E. coli DNA replication machinery.
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Affiliation(s)
- Pengcheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and.,the Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, China
| | - Jiapeng Leng
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and
| | - Yinsheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and
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