1
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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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2
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Zhang H. Mechanisms of mutagenesis induced by DNA lesions: multiple factors affect mutations in translesion DNA synthesis. Crit Rev Biochem Mol Biol 2020; 55:219-251. [PMID: 32448001 DOI: 10.1080/10409238.2020.1768205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental mutagens lead to mutagenesis. However, the mechanisms are very complicated and not fully understood. Environmental mutagens produce various DNA lesions, including base-damaged or sugar-modified DNA lesions, as well as epigenetically modified DNA. DNA polymerases produce mutation spectra in translesion DNA synthesis (TLS) through misincorporation of incorrect nucleotides, frameshift deletions, blockage of DNA replication, imbalance of leading- and lagging-strand DNA synthesis, and genome instability. Motif or subunit in DNA polymerases further affects the mutations in TLS. Moreover, protein interactions and accessory proteins in DNA replisome also alter mutations in TLS, demonstrated by several representative DNA replisomes. Finally, in cells, multiple DNA polymerases or cellular proteins collaborate in TLS and reduce in vivo mutagenesis. Summaries and perspectives were listed. This review shows mechanisms of mutagenesis induced by DNA lesions and the effects of multiple factors on mutations in TLS in vitro and in vivo.
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Affiliation(s)
- Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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3
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Abstract
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Pd-catalyzed
cross-coupling reactions that form C–N bonds
have become useful methods to synthesize anilines and aniline derivatives,
an important class of compounds throughout chemical research. A key
factor in the widespread adoption of these methods has been the continued
development of reliable and versatile catalysts that function under
operationally simple, user-friendly conditions. This review provides
an overview of Pd-catalyzed N-arylation reactions found in both basic
and applied chemical research from 2008 to the present. Selected examples
of C–N cross-coupling reactions between nine classes of nitrogen-based
coupling partners and (pseudo)aryl halides are described for the synthesis
of heterocycles, medicinally relevant compounds, natural products,
organic materials, and catalysts.
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Affiliation(s)
- Paula Ruiz-Castillo
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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4
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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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5
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Bose A, Pande P, Jasti VP, Millsap AD, Hawkins EK, Rizzo CJ, Basu AK. DNA polymerases κ and ζ cooperatively perform mutagenic translesion synthesis of the C8-2'-deoxyguanosine adduct of the dietary mutagen IQ in human cells. Nucleic Acids Res 2015. [PMID: 26220181 PMCID: PMC4787813 DOI: 10.1093/nar/gkv750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8-2'-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G1-, G2- or G3-positions of the NarI site (5'-G1G2CG3CC-3') were replicated in HEK293T cells. Fifty percent of the progeny from the G3 construct were mutants, largely G→T, compared to 18% and 24% from the G1 and G2 constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38-67% upon siRNA knockdown of pol κ, whereas it was increased by 10-24% in pol η knockdown cells. When pol κ and pol ζ were simultaneously knocked down, MF of the G1 and G3 constructs was reduced from 18% and 50%, respectively, to <3%, whereas it was reduced from 24% to <1% in the G2 construct. In vitro TLS using yeast pol ζ showed that it can extend G3*:A pair more efficiently than G3*:C pair, but it is inefficient at nucleotide incorporation opposite dG-C8-IQ. We conclude that pol κ and pol ζ cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol η is involved primarily in its error-free bypass.
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Affiliation(s)
- Arindam Bose
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Vijay P Jasti
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Amy D Millsap
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Edward K Hawkins
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Carmelo J Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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Jain V, Vaidyanathan VG, Patnaik S, Gopal S, Cho BP. Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, surface plasmon resonance, and primer kinetic studies. Biochemistry 2014; 53:4059-71. [PMID: 24915610 PMCID: PMC4075988 DOI: 10.1021/bi5003212] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Adduct-induced DNA damage can affect
transcription efficiency and
DNA replication and repair. We previously investigated the effects
of the 3′-next flanking base (G*CT vs G*CA; G*, FABP, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl;
FAF, N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene)
on the conformation of arylamine-DNA lesions in relation to E. coli nucleotide excision repair (JainV., HiltonB., LinB., PatnaikS., LiangF., DarianE., ZouY., MackerellA. D.Jr., and ChoB. P. (2013) , 41, 869−88023180767). Here,
we report the differential effects of the same pair of sequences on
DNA replication in vitro by the polymerases exofree
Klenow fragment (Kf-exo–) and Dpo4. We obtained
dynamic 19F NMR spectra for two 19-mer modified templates
during primer elongation: G*CA [d(5′-CTTACCATCG*CAACCATTC-3′)]
and G*CT [d(5′-CTTACCATCG*CTACCATTC-3′)].
We found that lesion stacking is favored in the G*CT sequence compared to the G*CA counterpart. Surface
plasmon resonance binding results showed consistently weaker affinities
for the modified DNA with the binding strength in the order of FABP
> FAF and G*CA > G*CT. Primer extension was stalled at
(n) and near (n – 1 and n + 1) the lesion site, and the extent of blockage and the extension
rates across the lesion were influenced by not only the DNA sequences
but also the nature of the adduct’s chemical structure (FAF
vs FABP) and the polymerase employed (Kf-exo– vs
Dpo4). Steady-state kinetics analysis with Kf-exo– revealed the most dramatic sequence and lesion effects at the lesion
(n) and postinsertion (n + 1) sites,
respectively. Taken together, these results provide insights into
the important role of lesion-induced conformational heterogeneity
in modulating translesion DNA synthesis.
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Affiliation(s)
- Vipin Jain
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity. Future Med Chem 2012; 4:1981-2007. [PMID: 23088278 DOI: 10.4155/fmc.12.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.
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Shamovsky I, Ripa L, Blomberg N, Eriksson LA, Hansen P, Mee C, Tyrchan C, O'Donovan M, Sjö P. Theoretical Studies of Chemical Reactivity of Metabolically Activated Forms of Aromatic Amines toward DNA. Chem Res Toxicol 2012; 25:2236-52. [DOI: 10.1021/tx300313b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Lena Ripa
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Niklas Blomberg
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Leif A. Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-412 96 Göteborg, Sweden
| | - Peter Hansen
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Christine Mee
- Genetic Toxicology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Christian Tyrchan
- Department of Medicinal Chemistry, CVGI iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Mike O'Donovan
- Genetic Toxicology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Peter Sjö
- Department of Medicinal Chemistry, R&I iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
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