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Boldinova EO, Ghodke PP, Sudhakar S, Mishra VK, Manukyan AA, Miropolskaya N, Pradeepkumar PI, Makarova AV. Translesion Synthesis across the N2-Ethyl-deoxyguanosine Adduct by Human PrimPol. ACS Chem Biol 2022; 17:3238-3250. [PMID: 36318733 DOI: 10.1021/acschembio.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Primase-DNA polymerase (PrimPol) is involved in reinitiating DNA synthesis at stalled replication forks. PrimPol also possesses DNA translesion (TLS) activity and bypasses several endogenous nonbulky DNA lesions in vitro. Little is known about the TLS activity of PrimPol across bulky carcinogenic adducts. We analyzed the DNA polymerase activity of human PrimPol on DNA templates with seven N2-dG lesions of different steric bulkiness. In the presence of Mg2+ ions, bulky N2-isobutyl-dG, N2-benzyl-dG, N2-methyl(1-naphthyl)-dG, N2-methyl(9-anthracenyl)-dG, N2-methyl(1-pyrenyl)-dG, and N2-methyl(1,3-dimethoxyanthraquinone)-dG adducts fully blocked PrimPol activity. At the same time, PrimPol incorporated complementary deoxycytidine monophosphate (dCMP) opposite N2-ethyl-dG with moderate efficiency but did not extend DNA beyond the lesion. We also demonstrated that mutation of the Arg288 residue abrogated dCMP incorporation opposite the lesion in the presence of Mn2+ ions. When Mn2+ replaced Mg2+, PrimPol carried out DNA synthesis on all DNA templates with N2-dG adducts in standing start reactions with low efficiency and accuracy, possibly utilizing a lesion "skipping" mechanism. The TLS activity of PrimPol opposite N2-ethyl-dG but not bulkier adducts was stimulated by accessory proteins, polymerase delta-interacting protein 2 (PolDIP2), and replication protein A (RPA). Molecular dynamics studies demonstrated the absence of stable interactions with deoxycytidine triphosphate (dCTP), large reactions, and C1'-C1' distances for the N2-isobutyl-dG and N2-benzyl-dG PrimPol complexes, suggesting that the size of the adduct is a limiting factor for efficient TLS across minor groove adducts by PrimPol.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Pratibha P Ghodke
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | | | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
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Sar D, Kim B, Ostadhossein F, Misra SK, Pan D. Revisiting Polyarenes and Related Molecules: An Update of Synthetic Approaches and Structure-Activity-Mechanistic Correlation for Carcinogenesis. CHEM REC 2018; 18:619-658. [DOI: 10.1002/tcr.201700110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Dinabandhu Sar
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | | | - Fatemeh Ostadhossein
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | - Santosh K. Misra
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | - Dipanjan Pan
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
- Department of Materials Science and Engineering; University of Illinois at Urbana-Champaign, Urbana, Illinois; 61801 USA
- Beckman Institute; University of Illinois at Urbana-Champaign; Urbana, Illinois 61801 USA
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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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Moore AFT, Goicoechea HC, Barbosa F, Campiglia AD. Parallel Factor Analysis of 4.2 K Excitation–Emission Matrices for the Direct Determination of Dibenzopyrene Isomers in Coal-Tar Samples with a Cryogenic Fiber-Optic Probe Coupled to a Commercial Spectrofluorimeter. Anal Chem 2015; 87:5232-9. [DOI: 10.1021/acs.analchem.5b00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Anthony F. T. Moore
- University of Central Florida, Department of Chemistry, 4111 Libra Drive, Physical Sciences Building Room 255, Orlando, Florida 32816-2366, United States
| | - Hector C. Goicoechea
- Laboratorio
de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra
de Química Analítica I, Facultad de Bioquímica
y Ciencias Biológicas, Universidad Nacional de Litoral, Santa Fe S3000ZAA, Argentina
| | - Fernando Barbosa
- Laboratório
de Toxicologia e Essencialidade de Metais, Faculdade de Ciências
Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, Monte Alegre, 1404903, Ribeirão Preto-SP, Brazil
| | - Andres D. Campiglia
- University of Central Florida, Department of Chemistry, 4111 Libra Drive, Physical Sciences Building Room 255, Orlando, Florida 32816-2366, United States
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Martins M, Santos JM, Diniz MS, Ferreira AM, Costa MH, Costa PM. Effects of carcinogenic versus non-carcinogenic AHR-active PAHs and their mixtures: lessons from ecological relevance. ENVIRONMENTAL RESEARCH 2015; 138:101-111. [PMID: 25704830 DOI: 10.1016/j.envres.2015.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/02/2015] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are priority environmental mutagens and carcinogens that occur in the aquatic environment as mixtures rather than the individual compounds for which guidelines are issued. The present work aimed at understanding the interaction effects between carcinogenic and non-carcinogenic PAHs in a model marine fish (Dicentrarchus labrax) in realistic scenarios. Laboratory assays under ecologically-relevant parameters were conducted for 28 days with sediments spiked with low-moderate concentrations (250-800ngg(-1)) of two model PAHs, phenanthrene (non-carcinogenic) and benzo[b]fluoranthene (carcinogenic to experimental animals). Both PAHs induced hepatic histopathological changes that indicate metabolic failure and inflammation, especially in animals exposed to mixtures. Phenanthrene elicited biochemical changes better related to oxidative stress (lipid peroxidation, glutathione and glutathione S-transferase activity) and CYP function, whereas B[b]F disrupted metabolic responses and defences to toxicological challenge. Conversely, mixed PAHs yielded lesions and responses that, altogether, are compatible with the AHR dependent pathway (the basis of PAH mutagenicity), potentially generating supra-additive effects. Nonetheless, the low, ecologically-relevant, concentrations of PAHs diluted dose and time-response relations. Overall, although seemingly predicting the risk of individual PAHs, environmental guidelines may not apply to mixtures by underestimating adverse effects, which calls for a redefinition of standards when determining the true risk of toxicants under realistic circumstances.
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Affiliation(s)
- Marta Martins
- MARE - Marine and Environmental Sciences Centre, Departamento de Ciências e Engenharia do Ambiente, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; IPMA-Instituto Português do Mar e da Atmosfera, Avenida do Brasil, 1449-006 Lisboa, Portugal.
| | - José M Santos
- MARE - Marine and Environmental Sciences Centre, Departamento de Ciências e Engenharia do Ambiente, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Mário S Diniz
- UCIBIO-Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Ana M Ferreira
- IPMA-Instituto Português do Mar e da Atmosfera, Avenida do Brasil, 1449-006 Lisboa, Portugal
| | - Maria H Costa
- MARE - Marine and Environmental Sciences Centre, Departamento de Ciências e Engenharia do Ambiente, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro M Costa
- MARE - Marine and Environmental Sciences Centre, Departamento de Ciências e Engenharia do Ambiente, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Lee YC, Cai Y, Mu H, Broyde S, Amin S, Chen X, Min JH, Geacintov NE. The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation? DNA Repair (Amst) 2014; 19:55-63. [PMID: 24784728 DOI: 10.1016/j.dnarep.2014.03.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The first eukaryotic NER factor that recognizes NER substrates is the heterodimeric XPC-RAD23B protein. The currently accepted hypothesis is that this protein recognizes the distortions/destabilization caused by DNA lesions rather than the lesions themselves. The resulting XPC-RAD23B-DNA complexes serve as scaffolds for the recruitment of subsequent NER factors that lead to the excision of the oligonucleotide sequences containing the lesions. Based on several well-known examples of DNA lesions like the UV radiation-induced CPD and 6-4 photodimers, as well as cisplatin-derived intrastrand cross-linked lesions, it is generally believed that the differences in excision activities in human cell extracts is correlated with the binding affinities of XPC-RAD23B to these DNA lesions. However, using electrophoretic mobility shift assays, we have found that XPC-RAD23B binding affinities of certain bulky lesions derived from metabolically activated polycyclic aromatic hydrocarbon compounds such as benzo[a]pyrene and dibenzo[a,l]pyrene, are not directly, or necessarily correlated with NER excision activities observed in cell-free extracts. These findings point to features of XPC-RAD23B-bulky DNA adduct complexes that may involve the formation of NER-productive or unproductive forms of binding that depend on the structural and stereochemical properties of the DNA adducts studied. The pronounced differences in NER cleavage efficiencies observed in cell-free extracts may be due to differences in the successful recruitment of subsequent NER factors by the XPC-RAD23B-DNA adduct complexes, and/or in the verification step. These phenomena appear to depend on the structural and conformational properties of the class of bulky DNA adducts studied.
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Affiliation(s)
- Yuan-Cho Lee
- Chemistry Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Yuqin Cai
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Hong Mu
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Suse Broyde
- Biology Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Xuejing Chen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nicholas E Geacintov
- Chemistry Department, New York University, Silver Complex, 100 Washington Square East, New York, NY 10012, USA.
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