1
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Kawada T, Kino K, Tokorodani K, Anabuki R, Morikawa M, Kobayashi T, Ohara K, Ohshima T, Miyazawa H. Analysis of nucleotide insertion opposite urea and translesion synthesis across urea by DNA polymerases. Genes Environ 2022; 44:7. [PMID: 35168664 PMCID: PMC8845263 DOI: 10.1186/s41021-022-00236-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract Urea (Ua) is produced in DNA as the result of oxidative damage to thymine and guanine. It was previously reported that Klenow fragment (Kf) exo− incorporated dATP opposite Ua, and that DNA polymerase β was blocked by Ua. We report here the following nucleotide incorporations opposite Ua by various DNA polymerases: DNA polymerase α, dATP and dGTP (dATP > dGTP); DNA polymerase δ, dATP; DNA polymerase ζ, dATP; Kf exo−, dATP; Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), dGTP and dATP (dGTP > dATP); and DNA polymerase η, dCTP, dGTP, dATP, and dTTP (dCTP > dGTP > dATP > dTTP). DNA polymerases β and ε were blocked by Ua. Elongation by DNA polymerases δ and ζ stopped after inserting dATP opposite Ua. Importantly, the elongation efficiency to full-length beyond Ua using DNA polymerase η and Dpo4 were almost the same as that of natural DNA. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s41021-022-00236-3.
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Affiliation(s)
- Taishu Kawada
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Katsuhito Kino
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan.
| | - Kyousuke Tokorodani
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Ryuto Anabuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Masayuki Morikawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Takanobu Kobayashi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Kazuaki Ohara
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Takayuki Ohshima
- Faculty of Science and Engineering, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Hiroshi Miyazawa
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
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2
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Pujari SS, Tretyakova N. Synthesis and polymerase bypass studies of DNA-peptide and DNA-protein conjugates. Methods Enzymol 2021; 661:363-405. [PMID: 34776221 PMCID: PMC10159213 DOI: 10.1016/bs.mie.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA-peptide (DpCs) and DNA-protein cross-links (DPCs) are DNA lesions formed when polypeptides and nuclear proteins become covalently trapped on DNA strands. DNA-protein cross-links are of enormous size and hence pose challenges to cell survival by blocking DNA replication, transcription, and repair. However, DPCs can undergo proteolytic degradation via various pathways to give shorter polypeptide chains (DpCs). The resulting DpC lesions are efficiently bypassed by translesion synthesis (TLS) DNA polymerases like κ, η, δ, etc., although polymerase bypass efficiency as well as correct base insertion depends heavily on size, sequence context, and position of peptides in DpCs. This chapter explores various synthetic methods to generate these lesions including detailed experimental procedures for the construction of DpCs and DPCs via reductive amination and oxime ligation. Further we describe biochemical experiments to investigate the effects of these lesions on DNA polymerase activity and fidelity.
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Affiliation(s)
- Suresh S Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.
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3
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Ghodke PP, Gonzalez-Vasquez G, Wang H, Johnson KM, Sedgeman CA, Guengerich FP. Enzymatic bypass of an N 6-deoxyadenosine DNA-ethylene dibromide-peptide cross-link by translesion DNA polymerases. J Biol Chem 2021; 296:100444. [PMID: 33617883 PMCID: PMC8024977 DOI: 10.1016/j.jbc.2021.100444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/25/2022] Open
Abstract
Unrepaired DNA-protein cross-links, due to their bulky nature, can stall replication forks and result in genome instability. Large DNA-protein cross-links can be cleaved into DNA-peptide cross-links, but the extent to which these smaller fragments disrupt normal replication is not clear. Ethylene dibromide (1,2-dibromoethane) is a known carcinogen that can cross-link the repair protein O6-alkylguanine-DNA alkyltransferase (AGT) to the N6 position of deoxyadenosine (dA) in DNA, as well as four other positions in DNA. We investigated the effect of a 15-mer peptide from the active site of AGT, cross-linked to the N6 position of dA, on DNA replication by human translesion synthesis DNA polymerases (Pols) η, ⍳, and κ. The peptide-DNA cross-link was bypassed by the three polymerases at different rates. In steady-state kinetics, the specificity constant (kcat/Km) for incorporation of the correct nucleotide opposite to the adduct decreased by 220-fold with Pol κ, tenfold with pol η, and not at all with Pol ⍳. Pol η incorporated all four nucleotides across from the lesion, with the preference dT > dC > dA > dG, while Pol ⍳ and κ only incorporated the correct nucleotide. However, LC-MS/MS analysis of the primer-template extension product revealed error-free bypass of the cross-linked 15-mer peptide by Pol η. We conclude that a bulky 15-mer peptide cross-linked to the N6 position of dA can retard polymerization and cause miscoding but that overall fidelity is not compromised because only correct pairs are extended.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Hui Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kevin M Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Carl A Sedgeman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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4
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Ji S, Fu I, Naldiga S, Shao H, Basu AK, Broyde S, Tretyakova NY. 5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells. Nucleic Acids Res 2019; 46:6455-6469. [PMID: 29905846 PMCID: PMC6061883 DOI: 10.1093/nar/gky444] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/29/2018] [Indexed: 12/24/2022] Open
Abstract
5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA–protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130–14134). We now examined the effects of 5fC mediated DPCs on DNA replication. Synthetic DNA duplexes containing site-specific DPCs between 5fC and lysine-containing proteins and peptides were subjected to primer extension experiments in the presence of human translesion synthesis DNA polymerases η and κ. We found that DPCs containing histones H2A or H4 completely inhibited DNA replication, but the replication block was removed when the proteins were subjected to proteolytic digestion. Cross-links to 11-mer or 31-mer peptides were bypassed by both polymerases in an error-prone manner, inducing targeted C→T transitions and –1 deletions. Similar types of mutations were observed when plasmids containing 5fC-peptide cross-links were replicated in human embryonic kidney (HEK) 293T cells. Molecular simulations of the 11-mer peptide-dC cross-links bound to human polymerases η and κ revealed that the peptide fits well on the DNA major groove side, and the modified dC forms a stable mismatch with incoming dATP via wobble base pairing in the polymerase active site.
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Affiliation(s)
- Shaofei Ji
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Iwen Fu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Spandana Naldiga
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Hongzhao Shao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Nakano T, Xu X, Salem AMH, Shoulkamy MI, Ide H. Radiation-induced DNA-protein cross-links: Mechanisms and biological significance. Free Radic Biol Med 2017; 107:136-145. [PMID: 27894771 DOI: 10.1016/j.freeradbiomed.2016.11.041] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Ionizing radiation produces various DNA lesions such as base damage, DNA single-strand breaks (SSBs), DNA double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, the biological significance of DPCs remains elusive. In this article, we focus on radiation-induced DPCs and review the current understanding of their induction, properties, repair, and biological consequences. When cells are irradiated, the formation of base damage, SSBs, and DSBs are promoted in the presence of oxygen. Conversely, that of DPCs is promoted in the absence of oxygen, suggesting their importance in hypoxic cells, such as those present in tumors. DNA and protein radicals generated by hydroxyl radicals (i.e., indirect effect) are responsible for DPC formation. In addition, DPCs can also be formed from guanine radical cations generated by the direct effect. Actin, histones, and other proteins have been identified as cross-linked proteins. Also, covalent linkages between DNA and protein constituents such as thymine-lysine and guanine-lysine have been identified and their structures are proposed. In irradiated cells and tissues, DPCs are repaired in a biphasic manner, consisting of fast and slow components. The half-time for the fast component is 20min-2h and that for the slow component is 2-70h. Notably, radiation-induced DPCs are repaired more slowly than DSBs. Homologous recombination plays a pivotal role in the repair of radiation-induced DPCs as well as DSBs. Recently, a novel mechanism of DPC repair mediated by a DPC protease was reported, wherein the resulting DNA-peptide cross-links were bypassed by translesion synthesis. The replication and transcription of DPC-bearing reporter plasmids are inhibited in cells, suggesting that DPCs are potentially lethal lesions. However, whether DPCs are mutagenic and induce gross chromosomal alterations remains to be determined.
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Affiliation(s)
- Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Xu Xu
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Amir M H Salem
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Pathology, Medical Research Division, National Research Centre, El-Bohouth St., Dokki, Giza 12311, Egypt
| | - Mahmoud I Shoulkamy
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Zoology, Biological Science Building, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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6
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Sedgeman CA, Su Y, Guengerich FP. Formation of S-[2-(N 6-Deoxyadenosinyl)ethyl]glutathione in DNA and Replication Past the Adduct by Translesion DNA Polymerases. Chem Res Toxicol 2017; 30:1188-1196. [PMID: 28395138 DOI: 10.1021/acs.chemrestox.7b00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1,2-Dibromoethane (DBE, ethylene dibromide) is a potent carcinogen due at least in part to its DNA cross-linking effects. DBE cross-links glutathione (GSH) to DNA, notably to sites on 2'-deoxyadenosine and 2'-deoxyguanosine ( Cmarik , J. L. , et al. ( 1991 ) J. Biol. Chem. 267 , 6672 - 6679 ). Adduction at the N6 position of 2'-deoxyadenosine (dA) had not been detected, but this is a site for the linkage of O6-alkylguanine DNA alkyltransferase ( Chowdhury , G. , et al. ( 2013 ) Angew. Chem. Int. Ed. 52 , 12879 - 12882 ). We identified and quantified a new adduct, S-[2-(N6-deoxyadenosinyl)ethyl]GSH, in calf thymus DNA using LC-MS/MS. Replication studies were performed in duplex oligonucleotides containing this adduct with human DNA polymerases (hPols) η, ι, and κ, as well as with Sulfolobus solfataricus Dpo4, Escherichia coli polymerase I Klenow fragment, and bacteriophage T7 polymerase. hPols η and ι, Dpo4, and Klenow fragment were able to bypass the adduct with only slight impedance; hPol η and ι showed increased misincorporation opposite the adduct compared to that of unmodified 2'-deoxyadenosine. LC-MS/MS analysis of full-length primer extension products by hPol η confirmed the incorporation of dC opposite S-[2-(N6-deoxyadenosinyl)ethyl]GSH and also showed the production of a -1 frameshift. These results reveal the significance of N6-dA GSH-DBE adducts in blocking replication, as well as producing mutations, by human translesion synthesis DNA polymerases.
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Affiliation(s)
- Carl A Sedgeman
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Yan Su
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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7
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Wickramaratne S, Ji S, Mukherjee S, Su Y, Pence MG, Lior-Hoffmann L, Fu I, Broyde S, Guengerich FP, Distefano M, Schärer OD, Sham YY, Tretyakova N. Bypass of DNA-Protein Cross-links Conjugated to the 7-Deazaguanine Position of DNA by Translesion Synthesis Polymerases. J Biol Chem 2016; 291:23589-23603. [PMID: 27621316 DOI: 10.1074/jbc.m116.745257] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 12/22/2022] Open
Abstract
DNA-protein cross-links (DPCs) are bulky DNA lesions that form both endogenously and following exposure to bis-electrophiles such as common antitumor agents. The structural and biological consequences of DPCs have not been fully elucidated due to the complexity of these adducts. The most common site of DPC formation in DNA following treatment with bis-electrophiles such as nitrogen mustards and cisplatin is the N7 position of guanine, but the resulting conjugates are hydrolytically labile and thus are not suitable for structural and biological studies. In this report, hydrolytically stable structural mimics of N7-guanine-conjugated DPCs were generated by reductive amination reactions between the Lys and Arg side chains of proteins/peptides and aldehyde groups linked to 7-deazaguanine residues in DNA. These model DPCs were subjected to in vitro replication in the presence of human translesion synthesis DNA polymerases. DPCs containing full-length proteins (11-28 kDa) or a 23-mer peptide blocked human polymerases η and κ. DPC conjugates to a 10-mer peptide were bypassed with nucleotide insertion efficiency 50-100-fold lower than for native G. Both human polymerase (hPol) κ and hPol η inserted the correct base (C) opposite the 10-mer peptide cross-link, although small amounts of T were added by hPol η. Molecular dynamics simulation of an hPol κ ternary complex containing a template-primer DNA with dCTP opposite the 10-mer peptide DPC revealed that this bulky lesion can be accommodated in the polymerase active site by aligning with the major groove of the adducted DNA within the ternary complex of polymerase and dCTP.
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Affiliation(s)
| | - Shaofei Ji
- From the Masonic Cancer Center and.,the Departments of Chemistry
| | | | - Yan Su
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Matthew G Pence
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Lee Lior-Hoffmann
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - Iwen Fu
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - Suse Broyde
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | | | - Orlando D Schärer
- Chemistry, Stony Brook University, Stony Brook, New York 11794.,Departments of Pharmacological Sciences and
| | | | - Natalia Tretyakova
- From the Masonic Cancer Center and .,Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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8
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Kotapati S, Wickramaratne S, Esades A, Boldry EJ, Quirk Dorr D, Pence MG, Guengerich FP, Tretyakova NY. Polymerase Bypass of N(6)-Deoxyadenosine Adducts Derived from Epoxide Metabolites of 1,3-Butadiene. Chem Res Toxicol 2015; 28:1496-507. [PMID: 26098310 DOI: 10.1021/acs.chemrestox.5b00166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine (N(6)-HB-dA I) and N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (N(6),N(6)-DHB-dA) are exocyclic DNA adducts formed upon alkylation of the N(6) position of adenine in DNA by epoxide metabolites of 1,3-butadiene (BD), a common industrial and environmental chemical classified as a human and animal carcinogen. Since the N(6)-H atom of adenine is required for Watson-Crick hydrogen bonding with thymine, N(6)-alkylation can prevent adenine from normal pairing with thymine, potentially compromising the accuracy of DNA replication. To evaluate the ability of BD-derived N(6)-alkyladenine lesions to induce mutations, synthetic oligodeoxynucleotides containing site-specific (S)-N(6)-HB-dA I and (R,R)-N(6),N(6)-DHB-dA adducts were subjected to in vitro translesion synthesis in the presence of human DNA polymerases β, η, ι, and κ. While (S)-N(6)-HB-dA I was readily bypassed by all four enzymes, only polymerases η and κ were able to carry out DNA synthesis past (R,R)-N(6),N(6)-DHB-dA. Steady-state kinetic analyses indicated that all four DNA polymerases preferentially incorporated the correct base (T) opposite (S)-N(6)-HB-dA I. In contrast, hPol β was completely blocked by (R,R)-N(6),N(6)-DHB-dA, while hPol η and κ inserted A, G, C, or T opposite the adduct with similar frequency. HPLC-ESI-MS/MS analysis of primer extension products confirmed that while translesion synthesis past (S)-N(6)-HB-dA I was mostly error-free, replication of DNA containing (R,R)-N(6),N(6)-DHB-dA induced significant numbers of A, C, and G insertions and small deletions. These results indicate that singly substituted (S)-N(6)-HB-dA I lesions are not miscoding, but that exocyclic (R,R)-N(6),N(6)-DHB-dA adducts are strongly mispairing, probably due to their inability to form stable Watson-Crick pairs with dT.
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Affiliation(s)
- Srikanth Kotapati
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Susith Wickramaratne
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Amanda Esades
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Emily J Boldry
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Danae Quirk Dorr
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew G Pence
- ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - F Peter Guengerich
- ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Natalia Y Tretyakova
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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9
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Wickramaratne S, Boldry EJ, Buehler C, Wang YC, Distefano MD, Tretyakova NY. Error-prone translesion synthesis past DNA-peptide cross-links conjugated to the major groove of DNA via C5 of thymidine. J Biol Chem 2014; 290:775-87. [PMID: 25391658 DOI: 10.1074/jbc.m114.613638] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are exceptionally bulky, structurally diverse DNA adducts formed in cells upon exposure to endogenous and exogenous bis-electrophiles, reactive oxygen species, and ionizing radiation. If not repaired, DPCs can induce toxicity and mutations. It has been proposed that the protein component of a DPC is proteolytically degraded, giving rise to smaller DNA-peptide conjugates, which can be subject to nucleotide excision repair and replication bypass. In this study, polymerase bypass of model DNA-peptide conjugates structurally analogous to the lesions induced by reactive oxygen species and DNA methyltransferase inhibitors was examined. DNA oligomers containing site-specific DNA-peptide conjugates were generated by copper-catalyzed [3 + 2] Huisgen cyclo-addition between an alkyne-functionalized C5-thymidine in DNA and an azide-containing 10-mer peptide. The resulting DNA-peptide conjugates were subjected to steady-state kinetic experiments in the presence of recombinant human lesion bypass polymerases κ and η, followed by PAGE-based assays to determine the catalytic efficiency and the misinsertion frequency opposite the lesion. We found that human polymerase κ and η can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, whereas human polymerase η preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI(-)-MS/MS sequencing of the extension products has revealed that post-lesion synthesis was highly error-prone, resulting in mutations opposite the adducted site or at the +1 position from the adduct and multiple deletions. Collectively, our results indicate that replication bypass of peptides conjugated to the C5 position of thymine by human translesion synthesis polymerases leads to large numbers of base substitution and frameshift mutations.
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Affiliation(s)
- Susith Wickramaratne
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily J Boldry
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and
| | - Charles Buehler
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Yen-Chih Wang
- Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark D Distefano
- From the Masonic Cancer Center, Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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10
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Maxwell BA, Suo Z. Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases. Biochemistry 2014; 53:2804-14. [PMID: 24716482 PMCID: PMC4018064 DOI: 10.1021/bi5000405] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
The
kinetic mechanisms by which DNA polymerases catalyze DNA replication
and repair have long been areas of active research. Recently discovered
Y-family DNA polymerases catalyze the bypass of damaged DNA bases
that would otherwise block replicative DNA polymerases and stall replication
forks. Unlike DNA polymerases from the five other families, the Y-family
DNA polymerases have flexible, solvent-accessible active sites that
are able to tolerate various types of damaged template bases and allow
for efficient lesion bypass. Their promiscuous active sites, however,
also lead to fidelities that are much lower than those observed for
other DNA polymerases and give rise to interesting mechanistic properties.
Additionally, the Y-family DNA polymerases have several other unique
structural features and undergo a set of conformational changes during
substrate binding and catalysis different from those observed for
replicative DNA polymerases. In recent years, pre-steady-state kinetic
methods have been extensively employed to reveal a wealth of information
about the catalytic properties of these fascinating noncanonical DNA
polymerases. Here, we review many of the recent findings on the kinetic
mechanisms of DNA polymerization with undamaged and damaged DNA substrates
by the Y-family DNA polymerases, and the conformational dynamics employed
by these error-prone enzymes during catalysis.
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Affiliation(s)
- Brian A Maxwell
- Ohio State Biophysics Program and ‡Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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11
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Chowdhury G, Cho SH, Pegg AE, Guengerich FP. Detection and Characterization of 1,2-Dibromoethane-Derived DNA Crosslinks Formed with O6-Alkylguanine-DNA Alkyltransferase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Cho SH, Guengerich FP. In vivo roles of conjugation with glutathione and O6-alkylguanine DNA-alkyltransferase in the mutagenicity of the bis-electrophiles 1,2-dibromoethane and 1,2,3,4-diepoxybutane in mice. Chem Res Toxicol 2013; 26:1765-74. [PMID: 24191644 PMCID: PMC3889014 DOI: 10.1021/tx4003534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Several studies with bacteria and in vitro mammalian systems have provided evidence of the roles of two thiol-based conjugation systems, glutathione (GSH) transferase and O(6)-alkylguanine DNA-alkyltransferase (AGT), in the bioactivation of the bis-electrophiles 1,2-dibromoethane and 1,2,3,4-diepoxybutane (DEB), the latter an oxidation product of 1,3-butadiene. The in vivo relevance of these conjugation reactions to biological activity in mammals has not been addressed, particularly with DEB. In this work, we used transgenic Big Blue mice, utilizing the cII gene, to examine the effects of manipulation of conjugation pathways on liver mutations arising from dibromoethane and DEB in vivo. Treatment of the mice with butathionine sulfoxime (BSO) prior to dibromoethane lowered hepatic GSH levels, dibromoethane-GSH DNA adduct levels (N(7)-guanyl), and the cII mutation frequency. Administration of O(6)-benzylguanine (O(6)-BzGua), an inhibitor of AGT, did not change the mutation frequency. Depletion of GSH (BSO) and AGT (O(6)-BzGua) lowered the mutation frequency induced by DEB, and BSO lowered the levels of GSH-DEB N(7)-guanyl and N(6)-adenyl DNA adducts. Our results provide evidence that the GSH conjugation pathway is a major in vivo factor in dibromoethane genotoxicity; both GSH conjugation and AGT conjugation are major factors in the genotoxicity of DEB. The latter findings are considered to be relevant to the carcinogenicity of 1,3-butadiene.
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Affiliation(s)
| | - F. Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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Chowdhury G, Cho SH, Pegg AE, Guengerich FP. Detection and characterization of 1,2-dibromoethane-derived DNA crosslinks formed with O(6) -alkylguanine-DNA alkyltransferase. Angew Chem Int Ed Engl 2013; 52:12879-82. [PMID: 24130045 DOI: 10.1002/anie.201307580] [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: 08/28/2013] [Indexed: 01/05/2023]
Abstract
A combination of chemical modifications and LC-tandem MS was used for the structure elucidation of various ethylene crosslinks of DNA with O(6) -alkylguanine-DNA alkyltransferase (AGT, see picture). The elucidation of the chemical structures of such DNA-protein crosslinks is necessary to understand mechanisms of mutagenesis.
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Affiliation(s)
- Goutam Chowdhury
- Department of Biochemistry, Vanderbilt University School of Medicine, 638 RRB, 2220 Pierce Ave., Nashville, TN 37232 (USA)
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