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Tomar R, Li S, Egli M, Stone MP. Replication Bypass of the N-(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase η. Biochemistry 2024; 63:754-766. [PMID: 38413007 PMCID: PMC10956437 DOI: 10.1021/acs.biochem.3c00569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/29/2024]
Abstract
Urea lesions in DNA arise from thymine glycol (Tg) or 8-oxo-dG; their genotoxicity is thought to arise in part due to their potential to accommodate the insertion of all four dNTPs during error-prone replication. Replication bypass with human DNA polymerase η (hPol η) confirmed that all four dNTPs were inserted opposite urea lesions but with purines exhibiting greater incorporation efficiency. X-ray crystal structures of ternary replication bypass complexes in the presence of Mg2+ ions with incoming dNTP analogs dAMPnPP, dCMPnPP, dGMPnPP, and dTMPnPP bound opposite urea lesions (hPol η·DNA·dNMPnPP complexes) revealed all were accommodated by hPol η. In each, the Watson-Crick face of the dNMPnPP was paired with the urea lesion, exploiting the ability of the amine and carbonyl groups of the urea to act as H-bond donors or acceptors, respectively. With incoming dAMPnPP or dGMPnPP, the distance between the imino nitrogen of urea and the N9 atoms of incoming dNMPnPP approximated the canonical distance of 9 Å in B-DNA. With incoming dCMPnPP or dTMPnPP, the corresponding distance of about 7 Å was less ideal. Improved base-stacking interactions were also observed with incoming purines vs pyrimidines. Nevertheless, in each instance, the α-phosphate of incoming dNMPnPPs was close to the 3'-hydroxyl group of the primer terminus, consistent with the catalysis of nucleotidyl transfer and the observation that all four nucleotides could be inserted opposite urea lesions. Preferential insertion of purines by hPol η may explain, in part, why the urea-directed spectrum of mutations arising from Tg vs 8-oxo-dG lesions differs.
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Affiliation(s)
- Rachana Tomar
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, and Vanderbilt Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Songlin Li
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, and Vanderbilt Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Martin Egli
- Department
of Biochemistry, School of Medicine, Vanderbilt Ingram Cancer Center,
and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, and Vanderbilt Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Kasai H, Kawai K. Formation of the mutagenic DNA lesion 1,N 2-ethenoguanine induced by heated cooking oil and identification of causative agents. Genes Environ 2023; 45:27. [PMID: 37880746 PMCID: PMC10599067 DOI: 10.1186/s41021-023-00284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The DNA-damaging compounds in heated cooking oil were identified as guanosine adducts. Heated vegetable oil was subjected to deep-frying conditions at 170 °C for 45 min, reacted with isopropylidene guanosine (ipG) at pH 7.4, and the resulting compounds were separated by high-performance liquid chromatography (HPLC). RESULTS Two adducts, 8-hydroxy-ipG and 1,N2-etheno-ipG, were identified in the reaction mixture. One of the major components in heated cooking oil, 2,4-heptadienal (HDE), efficiently produced etheno-ipG from ipG in the presence of tBuOOH. An oxidized HDE solution was fractionated using HPLC to identify causative agents, and each fraction was tested for etheno-ipG formation. In addition to the known lipid peroxidation product, 4,5-epoxy-2-heptenal, two unknown polar components with potent etheno-ipG formation activity were discovered. Based on Mass and UV spectra, their structures were identified as 6-oxo- and 6-hydroxy-2,4-HDE. Similarly, 6-oxo- and 6-hydroxy-2,4- decadienal (DDE) were formed from 2,4-DDE. Significant amounts of 6-oxo- and 6-hydroxy-2,4-alkadienal were detected in the heated cooking oil. These compounds induced the formation of 1,N2-ethenoguanine in nucleosides and DNA, especially in the presence of tBuOOH. Moreover, the formation of 6-oxo- and 6-OH-HDE from 2,4-HDE was accelerated in the presence of hemin and tBuOOH. CONCLUSION The results suggest that these compounds are not only generated during the oil heating process but also produced from 2,4-alkadienal through digestion under normal physiological conditions, especially after ingesting heme- and alkyl-OOH-containing diets. Moreover, these compounds can be formed within cells under oxidative stress, potentially linking them to gastrointestinal carcinogenesis.
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Affiliation(s)
- Hiroshi Kasai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, Fukuoka, 807-8555, Japan.
| | - Kazuaki Kawai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, Fukuoka, 807-8555, Japan
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Eichman BF. Repair and tolerance of DNA damage at the replication fork: A structural perspective. Curr Opin Struct Biol 2023; 81:102618. [PMID: 37269798 PMCID: PMC10525001 DOI: 10.1016/j.sbi.2023.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/05/2023]
Abstract
The replication machinery frequently encounters DNA damage and other structural impediments that inhibit progression of the replication fork. Replication-coupled processes that remove or bypass the barrier and restart stalled forks are essential for completion of replication and for maintenance of genome stability. Errors in replication-repair pathways lead to mutations and aberrant genetic rearrangements and are associated with human diseases. This review highlights recent structures of enzymes involved in three replication-repair pathways: translesion synthesis, template switching and fork reversal, and interstrand crosslink repair.
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Affiliation(s)
- Brandt F Eichman
- Vanderbilt University, Department of Biological Sciences and Department of Biochemistry, 5270A MRBIII, 465 21st Ave S, Nashville, TN 37232 USA.
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Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ. The peroxidation-derived DNA adduct, 6-oxo-M 1dG, is a strong block to replication by human DNA polymerase η. J Biol Chem 2023; 299:105067. [PMID: 37468099 PMCID: PMC10450521 DOI: 10.1016/j.jbc.2023.105067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
The DNA adduct 6-oxo-M1dG, (3-(2'-deoxy-β-D-erythro-pentofuranosyl)-6-oxo-pyrimido(1,2alpha)purin-10(3H)-one) is formed in the genome via oxidation of the peroxidation-derived adduct M1dG. However, the effect of 6-oxo-M1dG adducts on subsequent DNA replication is unclear. Here we investigated the ability of the human Y-family polymerase hPol η to bypass 6-oxo-M1dG. Using steady-state kinetics and analysis of DNA extension products by liquid chromatography-tandem mass spectrometry, we found hPol η preferentially inserts a dAMP or dGMP nucleotide into primer-templates across from the 6-oxo-M1dG adduct, with dGMP being slightly preferred. We also show primer-templates with a 3'-terminal dGMP or dAMP across from 6-oxo-M1dG were extended to a greater degree than primers with a dCMP or dTMP across from the adduct. In addition, we explored the structural basis for bypass of 6-oxo-M1dG by hPol η using X-ray crystallography of both an insertion-stage and an extension-stage complex. In the insertion-stage complex, we observed that the incoming dCTP opposite 6-oxo-M1dG, although present during crystallization, was not present in the active site. We found the adduct does not interact with residues in the hPol η active site but rather forms stacking interactions with the base pair immediately 3' to the adduct. In the extension-stage complex, we observed the 3' hydroxyl group of the primer strand dGMP across from 6-oxo-M1dG is not positioned correctly to form a phosphodiester bond with the incoming dCTP. Taken together, these results indicate 6-oxo-M1dG forms a strong block to DNA replication by hPol η and provide a structural basis for its blocking ability.
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Affiliation(s)
- Robyn Richie-Jannetta
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Pradeep Pallan
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Philip J Kingsley
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nikhil Kamdar
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lawrence J Marnett
- A. B. Hancock, Jr, Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Kaszubowski JD, Trakselis MA. Beyond the Lesion: Back to High Fidelity DNA Synthesis. Front Mol Biosci 2022; 8:811540. [PMID: 35071328 PMCID: PMC8766770 DOI: 10.3389/fmolb.2021.811540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
High fidelity (HiFi) DNA polymerases (Pols) perform the bulk of DNA synthesis required to duplicate genomes in all forms of life. Their structural features, enzymatic mechanisms, and inherent properties are well-described over several decades of research. HiFi Pols are so accurate that they become stalled at sites of DNA damage or lesions that are not one of the four canonical DNA bases. Once stalled, the replisome becomes compromised and vulnerable to further DNA damage. One mechanism to relieve stalling is to recruit a translesion synthesis (TLS) Pol to rapidly synthesize over and past the damage. These TLS Pols have good specificities for the lesion but are less accurate when synthesizing opposite undamaged DNA, and so, mechanisms are needed to limit TLS Pol synthesis and recruit back a HiFi Pol to reestablish the replisome. The overall TLS process can be complicated with several cellular Pols, multifaceted protein contacts, and variable nucleotide incorporation kinetics all contributing to several discrete substitution (or template hand-off) steps. In this review, we highlight the mechanistic differences between distributive equilibrium exchange events and concerted contact-dependent switching by DNA Pols for insertion, extension, and resumption of high-fidelity synthesis beyond the lesion.
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Guengerich FP, Ghodke PP. Etheno adducts: from tRNA modifications to DNA adducts and back to miscoding ribonucleotides. Genes Environ 2021; 43:24. [PMID: 34130743 PMCID: PMC8207595 DOI: 10.1186/s41021-021-00199-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/03/2021] [Indexed: 11/19/2022] Open
Abstract
Etheno (and ethano) derivatives of nucleic acid bases have an extra 5-membered ring attached. These were first noted as wyosine bases in tRNAs. Some were fluorescent, and the development of etheno derivatives of adenosine, cytosine, and guanosine led to the synthesis of fluorescent analogs of ATP, NAD+, and other cofactors for use in biochemical studies. Early studies with the carcinogen vinyl chloride revealed that these modified bases were being formed in DNA and RNA and might be responsible for mutations and cancer. The etheno bases are also derived from other carcinogenic vinyl monomers. Further work showed that endogenous etheno DNA adducts were present in animals and humans and are derived from lipid peroxidation. The chemical mechanisms of etheno adduct formation involve reactions with bis-electrophiles generated by cytochrome P450 enzymes or lipid peroxidation, which have been established in isotopic labeling studies. The mechanisms by which etheno DNA adducts miscode have been studied with several DNA polymerases, aided by the X-ray crystal structures of these polymerases in mispairing situations and in extension beyond mispairs. Repair of etheno DNA adduct damage is done primarily by glycosylases and also by the direct action of dioxygenases. Some human DNA polymerases (η, κ) can insert bases opposite etheno adducts in DNA and RNA, and the reverse transcriptase activity may be of relevance with the RNA etheno adducts. Further questions involve the extent that the etheno adducts contribute to human cancer.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, 638B Robinson Research Building, 2200 Pierce Avenue, Nashville, TN, 37232-0146, USA.
| | - Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, 638B Robinson Research Building, 2200 Pierce Avenue, Nashville, TN, 37232-0146, USA
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