1
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Zinflou C, Rochette PJ. Indenopyrene and Blue-Light Co-Exposure Impairs the Tightly Controlled Activation of Xenobiotic Metabolism in Retinal Pigment Epithelial Cells: A Mechanism for Synergistic Toxicity. Int J Mol Sci 2023; 24:17385. [PMID: 38139215 PMCID: PMC10744144 DOI: 10.3390/ijms242417385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
High energy visible (HEV) blue light is an increasing source of concern for visual health. Polycyclic aromatic hydrocarbons (PAH), a group of compounds found in high concentrations in smokers and polluted environments, accumulate in the retinal pigment epithelium (RPE). HEV absorption by indeno [1,2,3-cd]pyrene (IcdP), a common PAH, synergizes their toxicities and promotes degenerative changes in RPE cells comparable to the ones observed in age-related macular degeneration. In this study, we decipher the processes underlying IcdP and HEV synergic toxicity in human RPE cells. We found that IcdP-HEV toxicity is caused by the loss of the tight coupling between the two metabolic phases ensuring IcdP efficient detoxification. Indeed, IcdP/HEV co-exposure induces an overactivation of key actors in phase I metabolism. IcdP/HEV interaction is also associated with a downregulation of proteins involved in phase II. Our data thus indicate that phase II is hindered in response to co-exposure and that it is insufficient to sustain the enhanced phase I induction. This is reflected by an accelerated production of endogenous reactive oxygen species (ROS) and an increased accumulation of IcdP-related bulky DNA damage. Our work raises the prospect that lifestyle and environmental pollution may be significant modulators of HEV toxicity in the retina.
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Affiliation(s)
- Corinne Zinflou
- Axe Médecine Régénératrice, Centre de Recherche du CHU de Québec, Hôpital du Saint-Sacrement, Université Laval, Quebec, QC G1S 4L8, Canada;
- Centre de Recherche en Organogénèse Expérimentale de l’Université Laval/LOEX, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Patrick J. Rochette
- Axe Médecine Régénératrice, Centre de Recherche du CHU de Québec, Hôpital du Saint-Sacrement, Université Laval, Quebec, QC G1S 4L8, Canada;
- Centre de Recherche en Organogénèse Expérimentale de l’Université Laval/LOEX, Université Laval, Quebec, QC G1V 0A6, Canada
- Département d’Ophtalmologie et ORL—Chirurgie Cervico-Faciale, Université Laval, Quebec, QC G1V 0A6, Canada
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2
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Oscorbin I, Filipenko M. Bst polymerase - a humble relative of Taq polymerase. Comput Struct Biotechnol J 2023; 21:4519-4535. [PMID: 37767105 PMCID: PMC10520511 DOI: 10.1016/j.csbj.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
DNA polymerases are a superfamily of enzymes synthesizing DNA using DNA as a template. They are essential for nucleic acid metabolism and for DNA replication and repair. Modern biotechnology and molecular diagnostics rely heavily on DNA polymerases in analyzing nucleic acids. Among a variety of discovered DNA polymerases, Bst polymerase, a large fragment of DNA polymerase I from Geobacillus stearothermophilus, is one of the most commonly used but is not as well studied as Taq polymerase. The ability of Bst polymerase to displace an upstream DNA strand during synthesis, coupled with its moderate thermal stability, has provided the basis for several isothermal DNA amplification methods, including LAMP, WGA, RCA, and many others. Bst polymerase is one of the key components defining the robustness and analytical characteristics of diagnostic test systems based on isothermal amplification. Here, we present an overview of the biochemical and structural features of Bst polymerase and provide information on its mutated analogs.
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Affiliation(s)
- Igor Oscorbin
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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3
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Ge Y, Yan H, Shi X, Wu Z, Wang Y, Zhang Z, Luo Q, Liu W, Liang L, Peng L, Hu J. Study on dietary intake, risk assessment, and molecular toxicity mechanism of benzo[α]pyrene in college students in China Bashu area. Food Sci Nutr 2022; 10:4155-4167. [PMID: 36514765 PMCID: PMC9731532 DOI: 10.1002/fsn3.3007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022] Open
Abstract
As an extremely strong polycyclic aromatic hydrocarbon carcinogen, benzo[α]pyrene (BaP) is often produced during food processing at high temperatures. Recently, food safety, as well as toxicity mechanism and risk assessment of BaP, has received extensive attention. We first constructed the database of BaP pollution concentration in Chinese daily food with over 104 data items; collected dietary intake data using online survey; then assessed dietary exposure risk; and finally revealed the possible toxicity mechanism through four comparative molecular dynamics (MD) simulations. The statistical results showed that the concentration of BaP in olive oil was the highest, followed by that in fried meat products. The margins of exposure and incremental lifetime cancer risk both indicated that the dietary exposure to BaP of the participants was generally safe, but there were still some people with certain carcinogenic risks. Specifically, the health risk of the core district population was higher than that of the noncore district in Bashu area, and the female postgraduate group was higher than the male group with bachelor degree or below. From MD trajectories, BaP binding does not affect the global motion of individual nucleic acid sequences, but local weak noncovalent interactions changed greatly; it also weakens molecular interactions of nucleic acid with Bacillus stearothermophilus DNA polymerase I large fragment (BF), and significantly changes the cavity structure of recognition interface. This work not only reveals the possible toxicity mechanism of BaP, but also provides theoretical guidance for the subsequent optimization of food safety standards and reference of rational diet.
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Affiliation(s)
- Yutong Ge
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Hailian Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Zhixiang Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Yueteng Wang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Zelan Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Qing Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Wei Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Li Liang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Jianping Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
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4
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Changmei L, Gengrui W, Haizhen W, Yuxiao W, Shuang Z, Chaohai W. Kinetics and molecular mechanism of enhanced fluoranthene biodegradation by co-substrate phenol in co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9. ENVIRONMENTAL RESEARCH 2022; 205:112413. [PMID: 34861230 DOI: 10.1016/j.envres.2021.112413] [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: 09/27/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and phenol are persistent pollutants that coexist in coking wastewater (CWW). Fluoranthene (Flu) is the predominant PAH species in the CWW treatment system. Our work emphasized on distinguishing the effects of phenol on Flu biodegradation by co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9 and illustrated the molecular mechanisms. Results showed Flu biodegradation by co-culture was enhanced by phenol. According to the first-order degradation kinetic analysis of Flu, phenol significantly increased the biodegradation rate constant and shortened the half-life of Flu. Transcriptome analysis pointed out the up-regulation of DNA repair activity and 3717 significantly differentially expressed genes (DEGs), were triggered by 800 mg/L phenol. GO enrichment analysis suggested these DEGs are mainly concentrated in biochemical processes such as metal ion binding and alpha-amino acid biosynthesis, which are closely associated with Flu biodegradation, indicating that phenol promotes DNA repair activity and reduces Flu genotoxicity. qRT-PCR was performed to detect the gene expression of aromatic ring-opening dioxygenase. Combined with transcriptome analysis, the qRT-PCR results suggested phenol did not induce the expression of related PAHs-degrading enzymes. RNA extraction and microbial growth curves of COC and COC + Ph provided further evidence that phenol serves as co-substrate which increases biomass and the concentration of degrading enzymes, therefore promoting the Flu degradation.
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Affiliation(s)
- Li Changmei
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wei Gengrui
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Wu Haizhen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Wang Yuxiao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zhu Shuang
- Cener for Bioresources & Drug Discovery and School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Wei Chaohai
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
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5
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Nemcakova I, Jirka I, Doubkova M, Bacakova L. Heat treatment dependent cytotoxicity of silicalite-1 films deposited on Ti-6Al-4V alloy evaluated by bone-derived cells. Sci Rep 2020; 10:9456. [PMID: 32528137 PMCID: PMC7289882 DOI: 10.1038/s41598-020-66228-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/18/2020] [Indexed: 11/24/2022] Open
Abstract
A silicalite-1 film (SF) deposited on Ti-6Al-4V alloy was investigated in this study as a promising coating for metallic implants. Two forms of SFs were prepared: as-synthesized SFs (SF-RT), and SFs heated up to 500 °C (SF-500) to remove the excess of template species from the SF surface. The SFs were characterized in detail by X-ray photoelectron spectroscopy (XPS), by Fourier transform infrared spectroscopy (FTIR), by scanning electron microscopy (SEM) and water contact angle measurements (WCA). Two types of bone-derived cells (hFOB 1.19 non-tumor fetal osteoblast cell line and U-2 OS osteosarcoma cell line) were used for a biocompatibility assessment. The initial adhesion of hFOB 1.19 cells, evaluated by cell numbers and cell spreading area, was better supported by SF-500 than by SF-RT. While no increase in cell membrane damage, in ROS generation and in TNF-alpha secretion of bone-derived cells grown on both SFs was found, gamma H2AX staining revealed an elevated DNA damage response of U-2 OS cells grown on heat-treated samples (SF-500). This study also discusses differences between osteosarcoma cell lines and non-tumor osteoblastic cells, stressing the importance of choosing the right cell type model.
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Affiliation(s)
- Ivana Nemcakova
- Institute of Physiology of the Czech Academy of Sciences, v.v.i., Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Ivan Jirka
- J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i., Dolejskova 3, 182 23, Prague 8, Czech Republic
| | - Martina Doubkova
- Institute of Physiology of the Czech Academy of Sciences, v.v.i., Videnska 1083, 142 20, Prague 4, Czech Republic.,Second Faculty of Medicine, Charles University, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Lucie Bacakova
- Institute of Physiology of the Czech Academy of Sciences, v.v.i., Videnska 1083, 142 20, Prague 4, Czech Republic
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6
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Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
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7
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BP[dG]-induced distortions to DNA polymerase and DNA duplex: A detailed mechanism of BP adducts blocking replication. Food Chem Toxicol 2020; 140:111325. [DOI: 10.1016/j.fct.2020.111325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/15/2020] [Accepted: 04/04/2020] [Indexed: 01/21/2023]
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8
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Jirka I, Kopová I, Kubát P, Tabor E, Bačáková L, Bouša M, Sajdl P. The Photodynamic Properties and the Genotoxicity of Heat-Treated Silicalite-1 Films. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E567. [PMID: 30769806 PMCID: PMC6416588 DOI: 10.3390/ma12040567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/31/2019] [Accepted: 02/10/2019] [Indexed: 11/17/2022]
Abstract
We investigated the use of a supported silicalite-1 film (SF) as a promising coating for metallic materials used in the fabrication of prostheses. The role of carbonaceous residua present on high-temperature calcined-SF in generating singlet oxygen for future use as a sterilization method has also been addressed, and the potential genotoxicity of these residua in osteoblast-like cells has been investigated. Calcination of as-synthesized SF induced the appearance of a rather complicated mixture of aliphatic and aromatic species on its outer surface. A series of variously volatile polycyclic aromatic hydrocarbons (PAH), including naphthalene, fluorene, phenanthrene, anthracene, fluoranthene, and pyrene, were identified in micromole concentrations. Irradiation of these PAHs on calcined-SF immersed in air-saturated chloroform led to the formation of very low concentrations of singlet oxygen. However, an increased level of DNA damage was observed on calcined-SF by immunofluorescence staining of phosphorylated histone H2AX analyzed by flow cytometry.
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Affiliation(s)
- Ivan Jirka
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i, Dolejškova 3, 182 23 Prague 8, Czech Republic.
| | - Ivana Kopová
- Institute of Physiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Pavel Kubát
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i, Dolejškova 3, 182 23 Prague 8, Czech Republic.
| | - Edyta Tabor
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i, Dolejškova 3, 182 23 Prague 8, Czech Republic.
| | - Lucie Bačáková
- Institute of Physiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Milan Bouša
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i, Dolejškova 3, 182 23 Prague 8, Czech Republic.
| | - Petr Sajdl
- Power Engineering Department, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Czech Republic.
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9
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Thangavel N, Ganesan VV, Nair BU. Conformation Specific Binding of [Ru(phen)2
(dppz)]2+
with Mono- and Cluster Arylamine-DNA Adducts. ChemistrySelect 2018. [DOI: 10.1002/slct.201802172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nandhini Thangavel
- Inorganic and Physical Chemistry Laboratory; CSIR-Central Leather Research Institute, Adyar; Chennai 600 020 India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Central Leather Research Institute, Adyar; Chennai 600 020 India
| | - Vaidyanathan V. Ganesan
- Advanced Materials Laboratory; CSIR-Central Leather Research Institute, Adyar; Chennai 600 020 India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Central Leather Research Institute, Adyar; Chennai 600 020 India
| | - Balachandran U. Nair
- Inorganic and Physical Chemistry Laboratory; CSIR-Central Leather Research Institute, Adyar; Chennai 600 020 India
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10
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Prakasha Gowda AS, Spratt TE. Active Site Interactions Impact Phosphoryl Transfer during Replication of Damaged and Undamaged DNA by Escherichia coli DNA Polymerase I. Chem Res Toxicol 2017; 30:2033-2043. [PMID: 29053918 DOI: 10.1021/acs.chemrestox.7b00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replicative DNA polymerases are able to discriminate between very similar substrates with high accuracy. One mechanism by which E. coli DNA polymerase I checks for Watson-Crick geometry is through a hydrogen bonding fork between Arg668 and the incoming dNTP and the minor groove of the primer terminus. The importance of the Arg-fork was examined by disrupting it with either a guanine to 3-deazaguanine substitution at the primer terminus or the use of a carbocyclic deoxyribose analog of dUTP. Using thio-substituted dNTPs and differential quench techniques, we determined that when the Arg-fork was disrupted, the rate-limiting step changed from a conformational change to phosphodiester bond formation. This result indicates that Arg668 is involved in the phosphoryl transfer step. We examined the role of the Arg-fork in the replication of four DNA damaged templates, O6-methylguanine (O6-mG), 8-oxo-7,8-dihydroguanine (oxoG), O2-[4-(3-pyridyl)-4-oxobutyl]thymine (O2-POB-T), and N2-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-8,9,10-trihydroxybenzo[a]pyren-7-yl]-guanine (N2-BP-G). In general, the guanine to 3-deazaguanine substitution caused a decrease in kpol that was proportional to kpol over five orders of magnitude. The linear relationship indicates that the Arg668-fork helps catalyze phosphoryl transfer by the same mechanism with all the substrates. Exceptions to the linear relationship were the incorporations of dTTP opposite G, oxoG, and O6mG, which showed large decreases in kpol, similar to that exhibited by the Watson-Crick base pairs. It was proposed that the incorporation of dTTP opposite G, oxoG, and O6mG occurred via Watson-Crick-like structures.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
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11
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Gahlon HL, Romano LJ, Rueda D. Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution. Chem Res Toxicol 2017; 30:1972-1983. [PMID: 29020440 DOI: 10.1021/acs.chemrestox.7b00224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.
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Affiliation(s)
- Hailey L Gahlon
- Molecular Virology, Department of Medicine, Imperial College London , Du Cane Road, London W12 0NN, U.K.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences , Du Cane Road, London W12 0NN, U.K
| | - Louis J Romano
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - David Rueda
- Molecular Virology, Department of Medicine, Imperial College London , Du Cane Road, London W12 0NN, U.K.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences , Du Cane Road, London W12 0NN, U.K
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12
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Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase. Nat Commun 2017; 8:965. [PMID: 29042535 PMCID: PMC5645340 DOI: 10.1038/s41467-017-01013-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022] Open
Abstract
Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke which, after metabolic activation, can react with the exocyclic N2 amino group of guanine to generate four stereoisomeric BP-N2-dG adducts. Rev1 is unique among translesion synthesis DNA polymerases in employing a protein-template-directed mechanism of DNA synthesis opposite undamaged and damaged guanine. Here we report high-resolution structures of yeast Rev1 with three BP-N2-dG adducts, namely the 10S (+)-trans-BP-N2-dG, 10R (+)-cis-BP-N2-dG, and 10S ( − )-cis-BP-N2-dG. Surprisingly, in all three structures, the bulky and hydrophobic BP pyrenyl residue is entirely solvent-exposed in the major groove of the DNA. This is very different from the adduct alignments hitherto observed in free or protein-bound DNA. All complexes are well poised for dCTP insertion. Our structures provide a view of cis-BP-N2-dG adducts in a DNA polymerase active site, and offer a basis for understanding error-free replication of the BP-derived stereoisomeric guanine adducts. Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke that upon metabolic activation reacts with guanine. Here, the authors present the structures of the translesion DNA synthesis polymerase Rev1 in complex with three of the four possible stereoisomeric BP-N2 -dG adducts, which gives insights how Rev1 achieves error-free replication.
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13
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Ma Z, Zhuang H. A Highly Sensitive Real-time Immuno-PCR Assay for Detecting Benzo[a]pyrene in Food Samples by Application of Biotin-Streptavidin System. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1046-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Ewa B, Danuta MŠ. Polycyclic aromatic hydrocarbons and PAH-related DNA adducts. J Appl Genet 2017; 58:321-330. [PMID: 27943120 PMCID: PMC5509823 DOI: 10.1007/s13353-016-0380-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/20/2023]
Abstract
Investigations on the impact of chemicals on the environment and human health have led to the development of an exposome concept. The exposome refers to the totality of exposures received by a person during life, including exposures to life-style factors, from the prenatal period to death. The exposure to genotoxic chemicals and their reactive metabolites can induce chemical modifications of DNA, such as, for example, DNA adducts, which have been extensively studied and which play a key role in chemically induced carcinogenesis. Development of different methods for the identification of DNA adducts has led to adopting DNA adductomic approaches. The ability to simultaneously detect multiple PAH-derived DNA adducts may allow for the improved assessment of exposure, and offer a mechanistic insight into the carcinogenic process following exposure to PAH mixtures. The major advantage of measuring chemical-specific DNA adducts is the assessment of a biologically effective dose. This review provides information about the occurrence of the polycyclic aromatic hydrocarbons (PAHs) and their influence on human exposure and biological effects, including PAH-derived DNA adduct formation and repair processes. Selected methods used for determination of DNA adducts have been presented.
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Affiliation(s)
- Błaszczyk Ewa
- Institute for Ecology of Industrial Areas, Environmental Toxicology Group, 6, Kossutha Street, 40-844, Katowice, Poland.
| | - Mielżyńska-Švach Danuta
- Witold Pilecki State School of Higher Education, 8, Maksymiliana Kolbego Street, 32-600, Oświęcim, Poland
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15
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Gowda ASP, Krzeminski J, Amin S, Suo Z, Spratt TE. Mutagenic Replication of N 2-Deoxyguanosine Benzo[a]pyrene Adducts by Escherichia coli DNA Polymerase I and Sulfolobus solfataricus DNA Polymerase IV. Chem Res Toxicol 2017; 30:1168-1176. [PMID: 28402640 DOI: 10.1021/acs.chemrestox.6b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Benzo[a]pyrene, a potent human carcinogen, is metabolized in vivo to a diol epoxide that reacts with the N2-position of guanine to produce N2-BP-dG adducts. These adducts are mutagenic causing G to T transversions. These adducts block replicative polymerases but can be bypassed by the Y-family translesion synthesis polymerases. The mechanisms by which mutagenic bypass occurs is not well-known. We have evaluated base pairing structures using atomic substitution of the dNTP with two stereoisomers, 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine and 2'-deoxy-N-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine. We have examined the kinetics of incorporation of 1-deaza-dATP, 7-deaza-dATP, 2'-deoxyinosine triphosphate, and 7-deaza-dGTP, analogues of dATP and dGTP in which single atoms are changed. Changes in rate will occur if that atom provided a critical interaction in the transition state of the reaction. We examined two polymerases, Escherichia coli DNA polymerase I (Kf) and Sulfolobus solfataricus DNA polymerase IV (Dpo4), as models of a high fidelity and TLS polymerase, respectively. We found that with Kf, substitution of the nitrogens on the Watson-Crick face of the dNTPs resulted in decreased rate of reactions. This result is consistent with a Hoogsteen base pair in which the template N2-BP-dG flipped from the anti to syn conformation. With Dpo4, while the substitution did not affect the rate of reaction, the amplitude of the reaction decreased with all substitutions. This result suggests that Dpo4 bypasses N2-BP-dG via Hoogsteen base pairs but that the flipped nucleotide can be either the dNTP or the template.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Jacek Krzeminski
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Shantu Amin
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
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16
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Nisha AR, Hazilawati H, Mohd Azmi ML, Noordin MM. DNA damage and adduct formation in immune organs of developing chicks by polycyclic aromatic hydrocarbons. Toxicol Mech Methods 2017; 27:215-222. [DOI: 10.1080/15376516.2016.1273432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- A. R. Nisha
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal sciences, Wayanad, Kerala, India
| | - H. Hazilawati
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - M. L. Mohd Azmi
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - M. M. Noordin
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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17
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Bose A, Millsap AD, DeLeon A, Rizzo C, Basu AK. Translesion Synthesis of the N(2)-2'-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1. Chem Res Toxicol 2016; 29:1549-59. [PMID: 27490094 PMCID: PMC5031085 DOI: 10.1021/acs.chemrestox.6b00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 12/18/2022]
Abstract
Translesion synthesis (TLS) of the N(2)-2'-deoxyguanosine (dG-N(2)-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5'-CG1G2CG3CC-3'). TLS efficiency was 38%, 29%, and 25% for the dG-N(2)-IQ located at G1, G2, and G3, respectively, which suggests that dG-N(2)-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8-35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N(2)-IQ bypass. Mutation frequencies (MFs) of dG-N(2)-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ( ( 2015 ) Nucleic Acids Res. 43 , 8340 - 8351 ). The major type of mutation induced by dG-N(2)-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N(2)-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N(2)-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences between the in vitro experiments using purified DNA polymerases, and the cellular results may arise from several factors including the crucial roles played by the accessory proteins in TLS.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Amy D. Millsap
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Arnie DeLeon
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carmelo
J. Rizzo
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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18
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Bose A, Surugihalli C, Pande P, Champeil E, Basu AK. Comparative Error-Free and Error-Prone Translesion Synthesis of N(2)-2'-Deoxyguanosine Adducts Formed by Mitomycin C and Its Metabolite, 2,7-Diaminomitosene, in Human Cells. Chem Res Toxicol 2016; 29:933-9. [PMID: 27082015 PMCID: PMC4871107 DOI: 10.1021/acs.chemrestox.6b00087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 11/28/2022]
Abstract
Mitomycin C (MC) is a cytotoxic and mutagenic antitumor agent that alkylates DNA upon reductive activation. 2,7-Diaminomitosene (2,7-DAM) is a major metabolite of MC in tumor cells, which also alkylates DNA. MC forms seven DNA adducts, including monoadducts and inter- and intrastrand cross-links, whereas 2,7-DAM forms two monoadducts. Herein, the biological effects of the dG-N(2) adducts formed by MC and 2,7-DAM have been compared by constructing single-stranded plasmids containing these adducts and replicating them in human embryonic kidney 293T cells. Translesion synthesis (TLS) efficiencies of dG-N(2)-MC and dG-N(2)-2,7-DAM were 38 ± 3 and 27 ± 3%, respectively, compared to that of a control plasmid. This indicates that both adducts block DNA synthesis and that dG-N(2)-2,7-DAM is a stronger replication block than dG-N(2)-MC. TLS of each adducted construct was reduced upon siRNA knockdown of pol η, pol κ, or pol ζ. For both adducts, the most significant reduction occurred with knockdown of pol κ, which suggests that pol κ plays a major role in TLS of these dG-N(2) adducts. Analysis of the progeny showed that both adducts were mutagenic, and the mutation frequencies (MF) of dG-N(2)-MC and dG-N(2)-2,7-DAM were 18 ± 3 and 10 ± 1%, respectively. For both adducts, the major type of mutation was G → T transversions. Knockdown of pol η and pol ζ reduced the MF of dG-N(2)-MC and dG-N(2)-2,7-DAM, whereas knockdown of pol κ increased the MF of these adducts. This suggests that pol κ predominantly carries out error-free TLS, whereas pol η and pol ζ are involved in error-prone TLS. The largest reduction in MF by 78 and 80%, respectively, for dG-N(2)-MC and dG-N(2)-2,7-DAM constructs occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down. This result strongly suggests that, unlike pol κ, these three TLS polymerases cooperatively perform the error-prone TLS of these adducts.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Chaitra Surugihalli
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Paritosh Pande
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Elise Champeil
- Department
of Science, John Jay College of Criminal
Justice, New York, New York 10019, United
States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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19
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Jha V, Bian C, Xing G, Ling H. Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase κ. Nucleic Acids Res 2016; 44:4957-67. [PMID: 27034468 PMCID: PMC4889944 DOI: 10.1093/nar/gkw204] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 03/16/2016] [Indexed: 01/28/2023] Open
Abstract
Benzo[a]pyrene (BP) is a well-known and frequently encountered carcinogen which generates a bulky DNA adduct (+)-trans-10S-BP-N(2)-dG (BP-dG) in cells. DNA polymerase kappa (polκ) is the only known Y-family polymerase that bypasses BP-dG accurately and thus protects cells from genotoxic BP. Here, we report the structures of human polκ in complex with DNA containing either a normal guanine (G) base or a BP-dG adduct at the active site and a correct deoxycytidine. The structures and supporting biochemical data reveal a unique mechanism for accurate replication by translesion synthesis past the major bulky adduct. The active site of polκ opens at the minor groove side of the DNA substrate to accommodate the bulky BP-dG that is attached there. More importantly, polκ stabilizes the lesion DNA substrate in the same active conformation as for regular B-form DNA substrates and the bulky BPDE ring in a 5' end pointing conformation. The BP-dG adducted DNA substrate maintains a Watson-Crick (BP-dG:dC) base pair within the active site, governing correct nucleotide insertion opposite the bulky adduct. In addition, polκ's unique N-clasp domain supports the open conformation of the enzyme and the extended conformation of the single-stranded template to allow bypass of the bulky lesion. This work illustrates the first molecular mechanism for how a bulky major adduct is replicated accurately without strand misalignment and mis-insertion.
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Affiliation(s)
- Vikash Jha
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Chuanbing Bian
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Guangxin Xing
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Hong Ling
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
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20
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Dhasmana A, Jamal QMS, Gupta R, Siddiqui MH, Kesari KK, Wadhwa G, Khan S, Haque S, Lohani M. Titanium dioxide nanoparticles provide protection against polycyclic aromatic hydrocarbon BaP and chrysene-induced perturbation of DNA repair machinery: A computational biology approach. Biotechnol Appl Biochem 2015; 63:497-513. [PMID: 25913286 DOI: 10.1002/bab.1388] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 04/18/2015] [Indexed: 01/08/2023]
Abstract
We examined the interaction of polycyclic hydrocarbons (PAHs) like benzo-α-pyrene (BaP), chrysene, and their metabolites 7,8-dihydro-7,8-dihydroxybenzo(a)pyrene,9,10-oxide (BPDE) and chrysene 1,2-diol-3,4-epoxide-2 (CDE), with the enzymes involved in DNA repair. We investigated interaction of 120 enzymes with PAHs and screened out 40 probable targets among DNA repair enzymes, on the basis of higher binding energy than positive control. Out of which, 20 enzymes lose their function in the presence of BaP, chrysene, and their metabolites, which may fetter DNA repair pathways resulting in damage accumulation and finally leading to cancer formation. We propose the use of nanoparticles as a guardian against the PAH's induced toxicity. PAHs enter the cell via aryl hydrocarbon receptor (AHR). TiO2 NP showed a much higher docking score with AHR (12,074) as compared with BaP and chrysene with AHR (4,600 and 4,186, respectively), indicating a preferential binding of TiO2 NP with the AHR. Further, docking of BaP and chrysene with the TiO2 NP bound AHR complex revealed their strong adsorption on TiO2 NP itself, and not on their original binding site (at AHR). TiO2 NPs thereby prevent the entry of PAHs into the cell via AHR and hence protect cells against the deleterious effects induced by PAHs.
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Affiliation(s)
- Anupam Dhasmana
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, India
| | - Qazi Mohd Sajid Jamal
- College of Applied Medical Sciences, Buraydah Colleges, Al Qassim-Buraydah King Abdul Aziz Road, East Qassim University, Buraydah, Kingdom of Saudi Arabia
| | - Richa Gupta
- Developmental Toxicology Division, Indian Institute of Toxicology Research, CSIR, Lucknow, India
| | - Mohd Haris Siddiqui
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, India
| | | | - Gulshan Wadhwa
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Saif Khan
- Department of Clinical Nutritions, College of Applied Medical Sciences, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Mohtashim Lohani
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, India
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21
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Mahvi A, Mardani G, Ghasemi-Dehkordi P, Saffari-Chaleshtori J, Hashemzadeh-Chaleshtori M, Allahbakhshian-Farsani M, Abdian N. Effects of Phenanthrene and Pyrene on Cytogenetic Stability of Human Dermal Fibroblasts Using Alkaline Comet Assay Technique. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40011-015-0514-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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22
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Beese L, Wang W, Hellinga H. A Unified Picture of Nucleotide Selection by a High Fidelity DNA Polymerase I. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.225.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lorena Beese
- Department of BiochemistryDuke UniversityUnited States
| | - W. Wang
- Department of BiochemistryDuke UniversityUnited States
| | - H. Hellinga
- Department of BiochemistryDuke UniversityUnited States
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23
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Ghodke PP, Harikrishna S, Pradeepkumar PI. Synthesis and Polymerase-Mediated Bypass Studies of the N2-Deoxyguanosine DNA Damage Caused by a Lucidin Analogue. J Org Chem 2015; 80:2128-38. [DOI: 10.1021/jo502627b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Pratibha P. Ghodke
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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24
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Dhasmana A, Sajid Jamal QM, Mir SS, Bhatt MLB, Rahman Q, Gupta R, Siddiqui MH, Lohani M. Titanium dioxide nanoparticles as guardian against environmental carcinogen benzo[alpha]pyrene. PLoS One 2014; 9:e107068. [PMID: 25215666 PMCID: PMC4162557 DOI: 10.1371/journal.pone.0107068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/05/2014] [Indexed: 12/03/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH), like Benzo[alpha]Pyrene (BaP) are known to cause a number of toxic manifestations including lung cancer. As Titanium dioxide Nanoparticles (TiO2 NPs) have recently been shown to adsorb a number of PAHs from soil and water, we investigated whether TiO2 NPs could provide protection against the BaP induced toxicity in biological system. A549 cells when co-exposed with BaP (25 µM, 50 µM and 75 µM) along with 0.1 µg/ml,0.5 µg/ml and 1 µg/ml of TiO2 NPs, showed significant reduction in the toxic effects of BaP, as measured by Micronucleus Assay, MTT Assay and ROS Assay. In order to explore the mechanism of protection by TiO2 NP against BaP, we performed in silico studies. BaP and other PAHs are known to enter the cell via aromatic hydrocarbon receptor (AHR). TiO2 NP showed a much higher docking score with AHR (12074) as compared to the docking score of BaP with AHR (4600). This indicates a preferential binding of TiO2 NP with the AHR, in case if both the TiO2 NP and BaP are present. Further, we have done the docking of BaP with the TiO2 NP bound AHR-complex (score 4710), and observed that BaP showed strong adsorption on TiO2 NP itself, and not at its original binding site (at AHR). TiO2 NPs thereby prevent the entry of BaP in to the cell via AHR and hence protect cells against the deleterious effects induced by BaP.
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Affiliation(s)
- Anupam Dhasmana
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Qazi Mohd. Sajid Jamal
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Snober Shabnam Mir
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Madan Lal Bramha Bhatt
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Qamar Rahman
- Science & Technology, Amity University Campus, Malhaur, Gomti Nagar, Lucknow, Uttar Pradesh, India
| | - Richa Gupta
- Developmental Toxicology Division, Indian Institute of Toxicology Research, CSIR, Qaiserbagh, Lucknow, Uttar Pradesh, India
| | - Mohd. Haris Siddiqui
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Mohtashim Lohani
- Environmental Carcinogenesis and Toxicoinformatics Laboratory, Department of Bioengineering & Biosciences, Integral University, Lucknow, Uttar Pradesh, India
- * E-mail:
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25
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Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry 2014; 53:5683-91. [PMID: 25148552 PMCID: PMC4159208 DOI: 10.1021/bi5007964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA
lesion bypass polymerases process different lesions with varying
fidelities, but the structural, dynamic, and mechanistic origins of
this phenomenon remain poorly understood. Human DNA polymerase κ
(Polκ), a member of the Y family of lesion bypass polymerases,
is specialized to bypass bulky DNA minor groove lesions in a predominantly
error-free manner, by housing them in its unique gap. We have investigated
the role of the unique Polκ gap and N-clasp structural features
in the fidelity of minor groove lesion processing with extensive molecular
modeling and molecular dynamics simulations to pinpoint their functioning
in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine,
2-acetylaminofluorene (dG-N2-AAF), that
is produced via the combustion of kerosene and diesel fuel. Our simulations
reveal how the spacious gap directionally accommodates the lesion
aromatic ring system as it transits through the stages of incorporation
of the predominant correct partner dCTP opposite the damaged guanine,
with preservation of local active site organization for nucleotidyl
transfer. Furthermore, flexibility in Polκ’s N-clasp
facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that
N-clasp flexibility depends on lesion topology, being markedly reduced
in the case of the benzo[a]pyrene-derived major adduct
to N2-dG, whose bypass by Polκ is
nearly error-free. Thus, our studies reveal how Polκ’s
unique structural and dynamic properties can regulate its bypass fidelity
of polycyclic aromatic lesions and how the fidelity is impacted by
lesion structures.
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Affiliation(s)
- Lee Lior-Hoffmann
- Department of Biology and ‡Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
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Subashchandrabose S, Krishnan K, Gratton E, Megharaj M, Naidu R. Potential of fluorescence imaging techniques to monitor mutagenic PAH uptake by microalga. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9152-9160. [PMID: 25020149 PMCID: PMC4140530 DOI: 10.1021/es500387v] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 07/14/2014] [Accepted: 07/14/2014] [Indexed: 05/30/2023]
Abstract
Benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon (PAH), is one of the major environmental pollutants that causes mutagenesis and cancer. BaP has been shown to accumulate in phytoplankton and zooplankton. We have studied the localization and aggregation of BaP in Chlorella sp., a microalga that is one of the primary producers in the food chain, using fluorescence confocal microscopy and fluorescence lifetime imaging microscopy with the phasor approach to characterize the location and the aggregation of BaP in the cell. Our results show that BaP accumulates in the lipid bodies of Chlorella sp. and that there is Förster resonance energy transfer between BaP and photosystems of Chlorella sp., indicating the close proximity of the two molecular systems. The lifetime of BaP fluorescence was measured to be 14 ns in N,N-dimethylformamide, an average of 7 ns in Bold's basal medium, and 8 ns in Chlorella cells. Number and brightness analysis suggests that BaP does not aggregate inside Chlorella sp. (average brightness = 5.330), while it aggregates in the supernatant. In Chlorella grown in sediments spiked with BaP, in 12 h the BaP uptake could be visualized using fluorescence microscopy.
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Affiliation(s)
- Suresh
Ramraj Subashchandrabose
- Centre
for Environmental Risk Assessment and Remediation, University of South Australia and CRC CARE, Mawson Lakes, Adelaide, South Australia 5095, Australia
| | - Kannan Krishnan
- Centre
for Environmental Risk Assessment and Remediation, University of South Australia and CRC CARE, Mawson Lakes, Adelaide, South Australia 5095, Australia
| | - Enrico Gratton
- Laboratory
for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Mallavarapu Megharaj
- Centre
for Environmental Risk Assessment and Remediation, University of South Australia and CRC CARE, Mawson Lakes, Adelaide, South Australia 5095, Australia
| | - Ravi Naidu
- Centre
for Environmental Risk Assessment and Remediation, University of South Australia and CRC CARE, Mawson Lakes, Adelaide, South Australia 5095, Australia
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27
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A Potential Carcinogenic Pyrene Derivative under Förster Resonance Energy Transfer to Various Energy Acceptors in Nanoscopic Environments. Chemphyschem 2013; 14:3581-93. [DOI: 10.1002/cphc.201300568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Indexed: 11/07/2022]
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28
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Kirouac KN, Basu AK, Ling H. Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase. J Mol Biol 2013; 425:4167-76. [PMID: 23876706 DOI: 10.1016/j.jmb.2013.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/10/2013] [Accepted: 07/13/2013] [Indexed: 10/26/2022]
Abstract
Polycyclic aromatic hydrocarbons and their nitro derivatives are culprits of the detrimental health effects of environmental pollution. These hydrophobic compounds metabolize to reactive species and attach to DNA producing bulky lesions, such as N-[deoxyguanosine-8-yl]-1-aminopyrene (APG), in genomic DNA. The bulky adducts block DNA replication by high-fidelity polymerases and compromise replication fidelities and efficiencies by specialized lesion bypass polymerases. Here we present three crystal structures of the DNA polymerase Dpo4, a model translesion DNA polymerase of the Y family, in complex with APG-lesion-containing DNA in pre-insertion and extension stages. APG is captured in two conformations in the pre-insertion complex; one is highly exposed to the solvent, whereas the other is harbored in a shallow cleft between the finger and unique Y family little finger domain. In contrast, APG is in a single conformation at the extension stage, in which the pyrene ring is sandwiched between the little finger domain and a base from the turning back single-stranded template strand. Strikingly, a nucleotide intercalates the DNA helix to form a quaternary complex with Dpo4, DNA, and an incoming nucleotide, which stabilizes the distorted DNA structure at the extension stage. The unique APG DNA conformations in Dpo4 inhibit DNA translocation through the polymerase active site for APG bypass. We also modeled an insertion complex that illustrates a solvent-exposed pyrene ring contributing to an unstable insertion state. The structural work combined with our lesion replication assays provides a novel structural mechanism on bypass of DNA adducts containing polycyclic aromatic hydrocarbon moieties.
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Affiliation(s)
- Kevin N Kirouac
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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Kirouac KN, Basu AK, Ling H. Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase. Nucleic Acids Res 2012; 41:2060-71. [PMID: 23268450 PMCID: PMC3561991 DOI: 10.1093/nar/gks1296] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene–derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. Polι maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson–Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polη prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer.
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Affiliation(s)
- Kevin N Kirouac
- Department of Biochemistry, Medical Sciences Building 334, University of Western Ontario, London, ON N6A 5C1, Canada
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30
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Wang W, Wu EY, Hellinga HW, Beese LS. Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J Biol Chem 2012; 287:28215-26. [PMID: 22648417 PMCID: PMC3436578 DOI: 10.1074/jbc.m112.366609] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/15/2012] [Indexed: 12/20/2022] Open
Abstract
In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2'-hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base pair discrimination.
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Affiliation(s)
- Weina Wang
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Eugene Y. Wu
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Homme W. Hellinga
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Lorena S. Beese
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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31
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Vaidyanathan VG, Cho BP. Sequence Effects on Translesion Synthesis of an Aminofluorene–DNA Adduct: Conformational, Thermodynamic, and Primer Extension Kinetic Studies. Biochemistry 2012; 51:1983-95. [DOI: 10.1021/bi2017443] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. G. Vaidyanathan
- Department of Biomedical and Pharmaceutical
Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Bongsup P. Cho
- Department of Biomedical and Pharmaceutical
Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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32
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Tommasi S, Kim SI, Zhong X, Wu X, Pfeifer GP, Besaratinia A. Investigating the epigenetic effects of a prototype smoke-derived carcinogen in human cells. PLoS One 2010; 5:e10594. [PMID: 20485678 PMCID: PMC2868871 DOI: 10.1371/journal.pone.0010594] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 04/20/2010] [Indexed: 12/11/2022] Open
Abstract
Global loss of DNA methylation and locus/gene-specific gain of DNA methylation are two distinct hallmarks of carcinogenesis. Aberrant DNA methylation is implicated in smoking-related lung cancer. In this study, we have comprehensively investigated the modulation of DNA methylation consequent to chronic exposure to a prototype smoke-derived carcinogen, benzo[a]pyrene diol epoxide (B[a]PDE), in genomic regions of significance in lung cancer, in normal human cells. We have used a pulldown assay for enrichment of the CpG methylated fraction of cellular DNA combined with microarray platforms, followed by extensive validation through conventional bisulfite-based analysis. Here, we demonstrate strikingly similar patterns of DNA methylation in non-transformed B[a]PDE-treated cells vs control using high-throughput microarray-based DNA methylation profiling confirmed by conventional bisulfite-based DNA methylation analysis. The absence of aberrant DNA methylation in our model system within a timeframe that precedes cellular transformation suggests that following carcinogen exposure, other as yet unknown factors (secondary to carcinogen treatment) may help initiate global loss of DNA methylation and region-specific gain of DNA methylation, which can, in turn, contribute to lung cancer development. Unveiling the initiating events that cause aberrant DNA methylation in lung cancer has tremendous public health relevance, as it can help define future strategies for early detection and prevention of this highly lethal disease.
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Affiliation(s)
- Stella Tommasi
- Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
| | - Sang-in Kim
- Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
| | - Xueyan Zhong
- Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
| | - Xiwei Wu
- Division of Information Sciences, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
| | - Gerd P. Pfeifer
- Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
| | - Ahmad Besaratinia
- Department of Cancer Biology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail:
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Lily MK, Bahuguna A, Dangwal K, Garg V. Optimization of an inducible, chromosomally encoded benzo [a] pyrene (BaP) degradation pathway in Bacillus subtilis BMT4i (MTCC 9447). ANN MICROBIOL 2010. [DOI: 10.1007/s13213-009-0010-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Lily MK, Bahuguna A, Dangwal K, Garg V. Degradation of Benzo [a] Pyrene by a novel strain Bacillus subtilis BMT4i (MTCC 9447). Braz J Microbiol 2009; 40:884-92. [PMID: 24031437 PMCID: PMC3768576 DOI: 10.1590/s1517-838220090004000020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 11/04/2008] [Accepted: 05/15/2009] [Indexed: 03/24/2024] Open
Abstract
Benzo [a] Pyrene (BaP) is a highly recalcitrant, polycyclic aromatic hydrocarbon (PAH) with high genotoxicity and carcinogenicity. It is formed and released into the environment due to incomplete combustion of fossil fuel and various anthropogenic activities including cigarette smoke and automobile exhausts. The aim of present study is to isolate bacteria which can degrade BaP as a sole source of carbon and energy. We have isolated a novel strain BMT4i (MTCC 9447) of Bacillus subtilis from automobile contaminated soil using BaP (50 g /ml) as the sole source of carbon and energy in basal salt mineral (BSM) medium. The growth kinetics of BMT4i was studied using CFU method which revealed that BMT4i is able to survive in BaP-BSM medium up to 40 days attaining its peak growth (10(29) fold increase in cell number) on 7 days of incubation. The BaP degradation kinetics of BMT4i was studied using High Performance Liquid Chromatography (HPLC) analysis of BaP biodegradation products. BMT4i started degrading BaP after 24 hours and continued up to 28 days achieving maximum degradation of approximately 84.66 %. The above findings inferred that BMT4i is a very efficient degrader of BaP. To our best of knowledge, this is the first report showing utilization of BaP as a sole source of carbon and energy by bacteria. In addition, BMT4i can degrade a wide range of PAHs including naphthalene, anthracene, and dibenzothiophene therefore, it could serve as a better candidate for bioremediation of PAHs contaminated sites.
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Affiliation(s)
- Madhuri Kaushish Lily
- Department of Biotechnology, Modern Institute of Technology (MIT), Dhalwala, Rishikesh-249201, Uttarakhand, India
| | - Ashutosh Bahuguna
- Department of Biotechnology, Modern Institute of Technology (MIT), Dhalwala, Rishikesh-249201, Uttarakhand, India
| | - Koushalya Dangwal
- Department of Biotechnology, Modern Institute of Technology (MIT), Dhalwala, Rishikesh-249201, Uttarakhand, India
| | - Veena Garg
- Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India
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35
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Affiliation(s)
- Anthony J Berdis
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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36
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Christian TD, Romano LJ. Monitoring the conformation of benzo[a]pyrene adducts in the polymerase active site using fluorescence resonance energy transfer. Biochemistry 2009; 48:5382-8. [PMID: 19435285 DOI: 10.1021/bi900148t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Benzo[a]pyrene (B[a]P) is a potent environmental carcinogen that is metabolized into diol epoxides that react with exocyclic amines in DNA. These DNA adducts have been shown to block DNA replication by high-fidelity polymerases and induce both base substitution and frame-shift mutations. To improve our understanding of the molecular mechanism of B[a]P-induced mutagenesis, a fluorescence resonance energy transfer (FRET) method was developed in which the (+)- or (-)-trans-anti-B[a]P-N(2)-dG adducts, positioned in the active site of DNA polymerase I (Klenow fragment), serve as donor fluorophores to an acceptor molecule positioned on the DNA primer strand. FRET was measured for a primer that ended one nucleotide before the adduct position and one that ended across from the adduct and used to estimate the distances between the two fluorophores. These estimates are consistent with prior studies that suggest the adducts are positioned in the minor groove. A comparison of the FRET for the (+)- and (-)-trans-B[a]P adducts in the Klenow active site suggested that the (+)-trans adduct is positioned approximately 2 A farther from the acceptor, consistent with the structural differences observed in duplex DNA where it has been shown that the (+)-trans adduct is oriented toward the 5'-end of the template strand while the (-)-trans adduct lies toward the 3'-end. Surprisingly, the adduct position did not change significantly when the primer was one nucleotide longer. The addition of either a correct (dCTP) or incorrect nucleotides showed only minor differences in FRET, suggesting that the adduct did not undergo a large change in the position within the polymerase active site, as expected if the adduct inhibited the polymerase conformational change.
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Affiliation(s)
- Thomas D Christian
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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37
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Xu P, Oum L, Lee YC, Geacintov NE, Broyde S. Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. Biochemistry 2009; 48:4677-90. [PMID: 19364137 DOI: 10.1021/bi802363f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding how DNA polymerases process lesions remains fundamental to determining the molecular origins of mutagenic translesion bypass. We have investigated how a benzo[a]pyrene-derived N(2)-dG adduct, 10S-(+)-trans-anti-[BP]-N(2)-dG ([BP]G*), is processed in Dpo4, the well-characterized Y-family bypass DNA polymerase. This polymerase has a slippage-prone spacious active site region. Experimental results in a 5'-C[BP]G*G-3' sequence context reveal significant selectivity for dGTP insertion that predominantly yields -1 deletion extension products. A less pronounced error-prone nonslippage pathway that leads to full extension products with insertion of A > C > G opposite the lesion is also observed. Molecular modeling and dynamics simulations follow the bypass of [BP]G* through an entire replication cycle for the first time in Dpo4, providing structural interpretations for the experimental observations. The preference for dGTP insertion is explained by a 5'-slippage pattern in which the unmodified G rather than G* is skipped, the incoming dGTP pairs with the C on the 5'-side of G*, and the -1 deletion is produced upon further primer extension which is more facile than nucleotide insertion. In addition, the simulations suggest that the [BP]G* may undergo an anti/syn conformational rearrangement during the stages of the replication cycle. In the minor nonslippage pathway, the nucleotide insertion preferences opposite the lesion are explained by relative distortions to the active site region. These structural insights, provided by the modeling and dynamics studies, augment kinetic and limited available crystallographic investigations with bulky lesions, by providing molecular explanations for lesion bypass activities over an entire replication cycle.
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Affiliation(s)
- Pingna Xu
- Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, New York 10003, USA
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38
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Crystal structure analysis of DNA lesion repair and tolerance mechanisms. Curr Opin Struct Biol 2009; 19:87-95. [DOI: 10.1016/j.sbi.2009.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/12/2009] [Accepted: 01/16/2009] [Indexed: 12/16/2022]
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Jia L, Geacintov NE, Broyde S. The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions. Nucleic Acids Res 2008; 36:6571-84. [PMID: 18931375 PMCID: PMC2582633 DOI: 10.1093/nar/gkn719] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 01/10/2023] Open
Abstract
DNA bypass polymerases are utilized to transit bulky DNA lesions during replication, but the process frequently causes mutations. The structural origins of mutagenic versus high fidelity replication in lesion bypass is therefore of fundamental interest. As model systems, we investigated the molecular basis of the experimentally observed essentially faithful bypass of the guanine 10S-(+)-trans-anti-benzo[a]pyrene-N(2)-dG adduct by the Y-family human DNA polymerase kappa, and the observed blockage of pol kappa produced by the adenine 10S-(+)-trans-anti-benzo[a]pyrene-N(2)-dA adduct. These lesions are derived from the most tumorigenic metabolite of the ubiquitous cancer-causing pollutant, benzo[a]pyrene. We compare our results for the dG adduct with our earlier studies for the pol kappa archaeal homolog Dpo4, which processes the same lesion in an error-prone manner. Molecular modeling, molecular mechanics calculations and molecular dynamics simulations were utilized. Our results show that the pol kappa N-clasp is a key structural feature that accounts for the dA adduct blockage and the near-error-free bypass of the dG lesion. Absence of the N-clasp in Dpo4 explains the error-prone processing of the same lesion by this enzyme. Thus, our studies elucidate structure-function relationships in the fidelity of lesion bypass.
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Affiliation(s)
- Lei Jia
- Department of Biology and Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Nicholas E. Geacintov
- Department of Biology and Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology and Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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40
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Wang Y, Schnetz-Boutaud NC, Kroth H, Yagi H, Sayer JM, Kumar S, Jerina DM, Stone MP. 3'-Intercalation of a N2-dG 1R-trans-anti-benzo[c]phenanthrene DNA adduct in an iterated (CG)3 repeat. Chem Res Toxicol 2008; 21:1348-58. [PMID: 18549249 PMCID: PMC2755548 DOI: 10.1021/tx7004103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformation of the 1 R,2 S,3 R,4 S-benzo[ c]phenanthrene- N (2)-dG adduct, arising from trans opening of the (+)-1 S,2 R,3 R,4 S- anti-benzo[ c]phenanthrene diol epoxide, was examined in 5'- d(ATCGC XCGGCATG)-3'.5'-d(CATGCCG CGCGAT)-3', where X = 1 R,2 S,3 R,4 S-B[ c]P- N (2)-dG. This duplex, derived from the hisD3052 frameshift tester strain of Salmonella typhimurium, contains a (CG) 3 iterated repeat, a hotspot for frameshift mutagenesis. NMR experiments showed a disconnection in sequential NOE connectivity between X (4) and C (5), and in the complementary strand, they showed another disconnection between G (18) and C (19). In the imino region of the (1)H NMR spectrum, a resonance was observed at the adducted base pair X (4) x C (19). The X (4) N1H and G (18) N1H resonances shifted upfield as compared to the other guanine imino proton resonances. NOEs were observed between X (4) N1H and C (19) N (4)H and between C (5) N (4)H and G (18) N1H, indicating that base pairs X (4) x C (19) and C (5) x G (18) maintained Watson-Crick hydrogen bonding. No NOE connectivity was observed between X (4) and G (18) in the imino region of the spectrum. Chemical shift perturbations of greater than 0.1 ppm were localized at nucleotides X (4) and C (5) in the modified strand and G (18) and C (19) in the complementary strand. A total of 13 NOEs between the protons of the 1 R-B[ c]Ph moiety and the DNA were observed between B[ c]Ph and major groove aromatic or amine protons at base pairs X (4) x C (19) and 3'-neighbor C (5) x G (18). Structural refinement was achieved using molecular dynamics calculations restrained by interproton distances and torsion angle restraints obtained from NMR data. The B[ c]Ph moiety intercalated on the 3'-face of the X (4) x C (19) base pair such that the terminal ring of 1 R-B[ c]Ph threaded the duplex and faced into the major groove. The torsion angle alpha' [X (4)]-N3-C2-N2-B[ c]Ph]-C1 was calculated to be -177 degrees, maintaining an orientation in which the X (4) exocyclic amine remained in plane with the purine. The torsion angle beta' [X (4)]-C2-N2-[B[ c]Ph]-C1-C2 was calculated to be 75 degrees. This value governed the 3'-orientation of the B[ c]Ph moiety with respect to X (4). The helical rise between base pairs X (4) x C (19) and C (5) x G (18) increased and resulted in unwinding of the right-handed helix. The aromatic rings of the B[ c]Ph moiety were below the Watson-Crick hydrogen-bonding face of the modified base pair X (4) x C (19). The B[c]Ph moiety was stacked above nucleotide G (18), in the complementary strand.
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Affiliation(s)
- Yazhen Wang
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Nathalie C. Schnetz-Boutaud
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Heiko Kroth
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Haruhiko Yagi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Jane M. Sayer
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Subodh Kumar
- Environmental Toxicology and Chemistry Laboratory, Great Lakes Center, State University of New York College at Buffalo, Buffalo, New York 14222
| | - Donald M. Jerina
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
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41
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Venkatramani R, Radhakrishnan R. Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus. Proteins 2008; 71:1360-72. [PMID: 18058909 PMCID: PMC3023110 DOI: 10.1002/prot.21824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We study the effect of the oxidative lesion 8-oxoguanine (8oxoG) on the preorganization of the active site for DNA replication in the closed (active) state of the Bacillus fragment (BF), a Klenow analog from Bacillus stearothermophilus. Our molecular dynamics and free energy simulations of explicitly solvated model ternary complexes of BF bound to correct dCTP/incorrect dATP opposite guanine (G) and 8oxoG bases in DNA suggest that the lesion introduces structural and energetic changes at the catalytic site to favor dATP insertion. Despite the formation of a stable Watson-Crick pairing in the 8oxoG:dCTP system, the catalytic geometry is severely distorted to possibly slow down catalysis. Indeed, our calculated free energy landscapes associated with active site preorganization suggest additional barriers to assemble an efficient catalytic site, which need to be overcome during dCTP incorporation opposite 8oxoG relative to that opposite undamaged G. In contrast, the catalytic geometry for the Hoogsteen pairing in the 8oxoG:dATP system is highly organized and poised for efficient nucleotide incorporation via the "two-metal-ion" catalyzed phosphoryl transfer mechanism. However, the free energy calculations suggest that the catalytic geometry during dATP incorporation opposite 8oxoG is considerably less plastic than that during dCTP incorporation opposite G despite a very similar, well organized catalytic site for both systems. A correlation analysis of the dynamics trajectories suggests the presence of significant coupling between motions of the polymerase fingers and the primary distance for nucleophilic attack (i.e., between the terminal primer O3' and the dNTP P(alpha.) atoms) during correct dCTP incorporation opposite undamaged G. This coupling is shown to be disrupted during nucleotide incorporation by the polymerase with oxidatively damaged DNA/dNTP substrates. We also suggest that the lesion affects DNA interactions with key polymerase residues, thereby affecting the enzymes ability to discriminate against non-complementary DNA/dNTP substrates. Taken together, our results provide a unified structural, energetic, and dynamic platform to rationalize experimentally observed relative nucleotide incorporation rates for correct dCTP/incorrect dATP insertion opposite an undamaged/oxidatively damaged template G by BF.
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Affiliation(s)
- Ravindra Venkatramani
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Department Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Department Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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42
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Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Trends Biochem Sci 2008; 33:209-19. [PMID: 18407502 DOI: 10.1016/j.tibs.2008.02.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 02/08/2008] [Accepted: 02/12/2008] [Indexed: 12/18/2022]
Abstract
When a high-fidelity DNA polymerase encounters certain DNA-damage sites, its progress can be stalled and one or more lesion-bypass polymerases are recruited to transit the lesion. Here, we consider two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine (8-oxoG), a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene, in the high-fidelity DNA polymerase Bacillus fragment (BF) from Bacillus stearothermophilus and in the lesion-bypass DNA polymerase IV (Dpo4) from Sulfolobus solfataricus. The tight fit of the BF polymerase around the nascent base pair contrasts with the more spacious, solvent-exposed active site of Dpo4, and these differences in architecture result in distinctions in their respective functions: one-step versus stepwise polymerase translocation, mutagenic versus accurate bypass of 8-oxoG, and polymerase stalling versus mutagenic bypass at bulky benzo[a]pyrene-derived lesions.
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Delaney JC, Essigmann JM. Biological properties of single chemical-DNA adducts: a twenty year perspective. Chem Res Toxicol 2008; 21:232-52. [PMID: 18072751 PMCID: PMC2821157 DOI: 10.1021/tx700292a] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The genome and its nucleotide precursor pool are under sustained attack by radiation, reactive oxygen and nitrogen species, chemical carcinogens, hydrolytic reactions, and certain drugs. As a result, a large and heterogeneous population of damaged nucleotides forms in all cells. Some of the lesions are repaired, but for those that remain, there can be serious biological consequences. For example, lesions that form in DNA can lead to altered gene expression, mutation, and death. This perspective examines systems developed over the past 20 years to study the biological properties of single DNA lesions.
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Affiliation(s)
- James C. Delaney
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - John M. Essigmann
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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Broyde S, Wang L, Zhang L, Rechkoblit O, Geacintov NE, Patel DJ. DNA adduct structure-function relationships: comparing solution with polymerase structures. Chem Res Toxicol 2007; 21:45-52. [PMID: 18052109 DOI: 10.1021/tx700193x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It has now been nearly two decades since the first solution structures of DNA duplexes covalently damaged by metabolically activated polycyclic aromatic hydrocarbons and amines were determined by NMR. Dozens of such high-resolution structures are now available, and some broad structural themes have been uncovered. It has been hypothesized that the solution structures are relevant to the biochemical processing of the adducts. The structural features of the adducts are considered to determine their mutational properties in DNA polymerases and their repair susceptibilities. In recent years, a number of crystal structures of DNA adducts of interest to our work have been determined in DNA polymerases. Accordingly, it is now timely to consider how NMR solution structures relate to structures within DNA polymerases. The NMR solution structural themes for polycyclic aromatic adducts are often observed in polymerase crystal structures. While the polymerase interactions can on occasion override the solution preferences, intrinsic adduct conformations favored in solution are often manifested within polymerases and likely play a significant role in lesion processing.
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Affiliation(s)
- Suse Broyde
- Department of Biology, New York University, New York NY 10003, USA.
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Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H. A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment. Proc Natl Acad Sci U S A 2007; 104:14905-10. [PMID: 17848527 PMCID: PMC1986586 DOI: 10.1073/pnas.0700717104] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-N(2)-deoxyguanosine (BP-dG), was placed at a template-primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a -1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5' to the adduct to serve as the template, resulting in a -1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and -1 frameshift mutations.
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Affiliation(s)
- Jacob Bauer
- Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1; and
| | - Guangxin Xing
- Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1; and
| | - Haruhiko Yagi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Jane M. Sayer
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Donald M. Jerina
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Hong Ling
- Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1; and
- To whom correspondence should be addressed. E-mail:
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46
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Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Nucleic Acids Res 2007; 35:4275-88. [PMID: 17576677 PMCID: PMC1934992 DOI: 10.1093/nar/gkm416] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We have investigated how a benzo[a]pyrene-derived N2-dG adduct, 10S(+)-trans-anti-[BP]-N2-dG ([BP]G*), is processed in a well-characterized Pol I family model replicative DNA polymerase, Bacillus fragment (BF). Experimental results are presented that reveal relatively facile nucleotide incorporation opposite the lesion, but very inefficient further extension. Computational studies follow the possible bypass of [BP]G* through the pre-insertion, insertion and post-insertion sites as BF alternates between open and closed conformations. With dG* in the normal B-DNA anti conformation, BP seriously disturbs the polymerase structure, positioning itself either deeply in the pre-insertion site or on the crowded evolving minor groove side of the modified template, consistent with a polymerase-blocking conformation. With dG* in the less prevalent syn conformation, BP causes less distortion: it is either out of the pre-insertion site or in the major groove open pocket of the polymerase. Thus, the syn conformation can account for the observed relatively easy incorporation of nucleotides, with mutagenic purines favored, opposite the [BP]G* adduct. However, with the lesion in the BF post-insertion site, more serious distortions caused by the adduct even in the syn conformation explain the very inefficient extension observed experimentally. In vivo, a switch to a potentially error-prone bypass polymerase likely dominates translesion bypass.
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Affiliation(s)
- Pingna Xu
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lida Oum
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lorena S. Beese
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Nicholas E. Geacintov
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Suse Broyde
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- *To whom correspondence should be addressed. (212)998-8231(212)995-4015
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47
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Garcia-Diaz M, Bebenek K. Multiple functions of DNA polymerases. CRITICAL REVIEWS IN PLANT SCIENCES 2007; 26:105-122. [PMID: 18496613 PMCID: PMC2391090 DOI: 10.1080/07352680701252817] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The primary role of DNA polymerases is to accurately and efficiently replicate the genome in order to ensure the maintenance of the genetic information and its faithful transmission through generations. This is not a simple task considering the size of the genome and its constant exposure to endogenous and environmental DNA damaging agents. Thus, a number of DNA repair pathways operate in cells to protect the integrity of the genome. In addition to their role in replication, DNA polymerases play a central role in most of these pathways. Given the multitude and the complexity of DNA transactions that depend on DNA polymerase activity, it is not surprising that cells in all organisms contain multiple highly specialized DNA polymerases, the majority of which have only recently been discovered. Five DNA polymerases are now recognized in Escherichia coli, 8 in Saccharomyces cerevisiae, and at least 15 in humans. While polymerases in bacteria, yeast and mammalian cells have been extensively studied much less is known about their counterparts in plants. For example, the plant model organism Arabidopsis thaliana is thought to contain 12 DNA polymerases, whose functions are mostly unknown. Here we review the properties and functions of DNA polymerases focusing on yeast and mammalian cells but paying special attention to the plant enzymes and the special circumstances of replication and repair in plant cells.
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Affiliation(s)
- Miguel Garcia-Diaz
- Laboratory of Structural Biology and Laboratory of Molecular Genetics NIEHS, NIH, DHHS, Research Triangle Park, North Carolina 27709
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48
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Rodríguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context. Nucleic Acids Res 2007; 35:1555-68. [PMID: 17287290 PMCID: PMC1865068 DOI: 10.1093/nar/gkm022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5′- ··· GG ··· dinucleotide sequences, but their origins are poorly understood. Here we used high resolution NMR and molecular dynamics simulations to investigate differences in G* adduct conformations in 5′- ··· CG*GC ··· and 5′- ··· CGG* C··· sequence contexts in otherwise identical 12-mer duplexes. The BP rings are positioned 5′ along the modified strand in the minor groove in both cases. However, subtle orientational differences cause strong distinctions in structural distortions of the DNA duplexes, because the exocyclic amino groups of flanking guanines on both strands compete for space with the BP rings in the minor groove, acting as guideposts for placement of the BP. In the 5′- ··· CGG* C ··· case, the 5′-flanking G · C base pair is severely untwisted, concomitant with a bend deduced from electrophoretic mobility. In the 5′- ··· CG*GC ··· context, there is no untwisting, but there is significant destabilization of the 5′-flanking Watson–Crick base pair. The minor groove width opens near the lesion in both cases, but more for 5′- ··· CGG*C···. Differential sequence-dependent removal rates of this lesion result and may contribute to the mutation hotspot phenomenon.
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Affiliation(s)
- Fabián A. Rodríguez
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yuqin Cai
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Chin Lin
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yijin Tang
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Alexander Kolbanovskiy
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Shantu Amin
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Dinshaw J. Patel
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Suse Broyde
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Nicholas E. Geacintov
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- *To whom correspondence should be addressed. +1 212 998 8407+1 212 998 8421
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49
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Warren JJ, Forsberg LJ, Beese LS. The structural basis for the mutagenicity of O(6)-methyl-guanine lesions. Proc Natl Acad Sci U S A 2006; 103:19701-6. [PMID: 17179038 PMCID: PMC1750904 DOI: 10.1073/pnas.0609580103] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Indexed: 11/18/2022] Open
Abstract
Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine with similar efficiency opposite O(6)-methyl-guanine (O6MeG). We combined pre-steady-state kinetic analysis and a series of nine x-ray crystal structures to contrast the reaction pathways of accurate and mutagenic replication of O6MeG in a high-fidelity DNA polymerase from Bacillus stearothermophilus. Polymerases achieve substrate specificity by selecting for nucleotides with shape and hydrogen-bonding patterns that complement a canonical DNA template. Our structures reveal that both thymine and cytosine O6MeG base pairs evade proofreading by mimicking the essential molecular features of canonical substrates. The steric mimicry depends on stabilization of a rare cytosine tautomer in C.O6MeG-polymerase complexes. An unusual electrostatic interaction between O-methyl protons and a thymine carbonyl oxygen helps stabilize T.O6MeG pairs bound to DNA polymerase. Because DNA methylators constitute an important class of chemotherapeutic agents, the molecular mechanisms of replication of these DNA lesions are important for our understanding of both the genesis and treatment of cancer.
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Affiliation(s)
- Joshua J. Warren
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
| | - Lawrence J. Forsberg
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
| | - Lorena S. Beese
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710
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50
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Meneni S, Liang F, Cho BP. Examination of the long-range effects of aminofluorene-induced conformational heterogeneity and its relevance to the mechanism of translesional DNA synthesis. J Mol Biol 2006; 366:1387-400. [PMID: 17217958 PMCID: PMC1850230 DOI: 10.1016/j.jmb.2006.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 12/06/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Adduct-induced conformational heterogeneity complicates the understanding of how DNA adducts exert mutation. A case in point is the N-deacetylated AF lesion [N-(2'-deoxyguanosin-8-yl)-2-aminofluorene], the major adduct derived from the strong liver carcinogen N-acetyl-2-aminofluorene. Three conformational families have been previously characterized and are dependent on the positioning of the aminofluorene rings: B is in the "B-DNA" major groove, S is "stacked" into the helix with base-displacement, and W is "wedged" into the minor groove. Here, we conducted (19)F NMR, CD, T(m), and modeling experiments at various primer positions with respect to a template modified by a fluorine tagged AF-adduct (FAF). In the first set, the FAF-G was paired with C and in the second set it was paired with A. The FAF-G:C oligonucleotides were found to preferentially adopt the B or S-conformers while the FAF-G:A mismatch ones preferred the B and W-conformers. The conformational preferences of both series were dependent on temperature and complementary strand length; the largest differences in conformation were displayed at lower temperatures. The CD and T(m) results are in general agreement with the NMR data. Molecular modeling indicated that the aminofluorene moiety in the minor groove of the W-conformer would impose a steric clash with the tight-packing amino acid residues on the DNA binding area of the Bacillus fragment (BF), a replicative DNA polymerase. In the case of the B-type conformer, the carcinogenic moiety resides in the solvent-exposed major groove throughout the replication/translocation process. The present dynamic NMR results, combined with previous primer extension kinetic data by Miller & Grollman, support a model in which adduct-induced conformational heterogeneities at positions remote from the replication fork affect polymerase function through a long-range DNA-protein interaction.
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Affiliation(s)
| | | | - Bongsup P. Cho
- *Address correspondence to: Bongsup P. Cho, Dept. of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, Rhode Island 02881, Tel. 401-874-5024; Fax. 401-874-5766;
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