1
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Kruchinin AA, Kamzeeva PN, Zharkov DO, Aralov AV, Makarova AV. 8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals? Int J Mol Sci 2024; 25:1342. [PMID: 38279342 PMCID: PMC10816367 DOI: 10.3390/ijms25021342] [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: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.
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Affiliation(s)
- Alexander A. Kruchinin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
| | - Polina N. Kamzeeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alena V. Makarova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
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2
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Yudkina AV, Endutkin AV, Diatlova EA, Zharkov DO. A non-canonical nucleotide from viral genomes interferes with the oxidative DNA damage repair system. DNA Repair (Amst) 2024; 133:103605. [PMID: 38042029 DOI: 10.1016/j.dnarep.2023.103605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/09/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]
Abstract
Oxidative damage is a major source of genomic instability in all organisms with the aerobic metabolism. 8-Oxoguanine (8-oxoG), an abundant oxidized purine, is mutagenic and must be controlled by a dedicated DNA repair system (GO system) that prevents G:C→T:A transversions through an easily formed 8-oxoG:A mispair. In some forms, the GO system is present in nearly all cellular organisms. However, recent studies uncovered many instances of viruses possessing non-canonical nucleotides in their genomes. The features of genome damage and maintenance in such cases of alternative genetic chemistry remain barely explored. In particular, 2,6-diaminopurine (Z nucleotide) completely substitutes for A in the genomes of some bacteriophages, which have evolved pathways for dZTP synthesis and specialized polymerases that prefer dZTP over dATP. Here we address the ability of the GO system enzymes to cope with oxidative DNA damage in the presence of Z in DNA. DNA polymerases of two different structural families (Klenow fragment and RB69 polymerase) were able to incorporate dZMP opposite to 8-oxoG in the template, as well as 8-oxodGMP opposite to Z in the template. Fpg, a 8-oxoguanine-DNA glycosylase that discriminates against 8-oxoG:A mispairs, also did not remove 8-oxoG from 8-oxoG:Z mispairs. However, MutY, a DNA glycosylase that excises A from pairs with 8-oxoG, had a significantly lower activity on Z:8-oxoG mispairs. Similar preferences were observed for Fpg and MutY from different bacterial species (Escherichia coli, Staphylococcus aureus and Lactococcus lactis). Overall, the relaxed control of 8-oxoG in the presence of the Z nucleotide may be a source of additional mutagenesis in the genomes of bacteriophages or bacteria that have survived the viral invasion.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.
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3
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Balint E, Unk I. For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases. Int J Mol Sci 2023; 25:363. [PMID: 38203535 PMCID: PMC10779026 DOI: 10.3390/ijms25010363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
DNA polymerases constitute a versatile group of enzymes that not only perform the essential task of genome duplication but also participate in various genome maintenance pathways, such as base and nucleotide excision repair, non-homologous end-joining, homologous recombination, and translesion synthesis. Polymerases catalyze DNA synthesis via the stepwise addition of deoxynucleoside monophosphates to the 3' primer end in a partially double-stranded DNA. They require divalent metal cations coordinated by active site residues of the polymerase. Mg2+ is considered the likely physiological activator because of its high cellular concentration and ability to activate DNA polymerases universally. Mn2+ can also activate the known DNA polymerases, but in most cases, it causes a significant decrease in fidelity and/or processivity. Hence, Mn2+ has been considered mutagenic and irrelevant during normal cellular function. Intriguingly, a growing body of evidence indicates that Mn2+ can positively influence some DNA polymerases by conferring translesion synthesis activity or altering the substrate specificity. Here, we review the relevant literature focusing on the impact of Mn2+ on the biochemical activity of a selected set of polymerases, namely, Polβ, Polλ, and Polµ, of the X family, as well as Polι and Polη of the Y family of polymerases, where congruous data implicate the physiological relevance of Mn2+ in the cellular function of these enzymes.
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Affiliation(s)
| | - Ildiko Unk
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, H-6726 Szeged, Hungary;
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4
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Stanio S, Bacurio JHT, Yang H, Greenberg MM, Basu AK. 8-Oxo-2'-deoxyguanosine Replication in Mutational Hot Spot Sequences of the p53 Gene in Human Cells Is Less Mutagenic than That of the Corresponding Formamidopyrimidine. Chem Res Toxicol 2023; 36:782-789. [PMID: 37093780 PMCID: PMC10192040 DOI: 10.1021/acs.chemrestox.3c00069] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo) is a ubiquitous DNA damage formed by oxidation of 2'-deoxyguanosine. In this study, plasmid DNA containing 8-OxodGuo located in three mutational hot spots of human cancers, codons 248, 249, and 273 of the Tp53 tumor suppressor gene, was replicated in HEK 293T cells. 8-OxodGuo was only a weak block of replication, and the bypass was largely error-free. The mutations (1-5%) were primarily G → T transversions, and the mutation frequency was generally lower than that of the chemically related Fapy·dG. A unique 8-OxodGuo mutation spectrum was observed at each site, as reflected by replication in translesion synthesis (TLS) polymerase- or hPol λ-deficient cells. In codon 248 (CG*G) and 249 (AG*G), where G* denotes 8-OxodGuo, hPol η and hPol ζ carried out largely error-free bypass of the lesion, whereas hPol κ and hPol ι were involved mostly in error-prone TLS, resulting in G → T mutations. 8-OxodGuo bypass in codon 273 (CG*T) was unlike the other two sites, as hPol κ participated in the mostly error-free bypass of the lesion. Yet, in all three sites, including codon 273, simultaneous deficiency of hpol κ and hPol ι resulted in reduction of G → T transversions. This indicates a convincing role of these two TLS polymerases in error-prone bypass of 8-OxodGuo. Although the dominant mutation was G → T in each site, in codon 249, and to a lesser extent in codon 248, significant semi-targeted single-base deletions also occurred, which suggests that 8-OxodGuo can initiate slippage of a base near the lesion site. This study underscores the importance of sequence context in 8-OxodGuo mutagenesis in human cells. It also provides a more comprehensive comparison between 8-OxodGuo and the sister lesion, Fapy·dG. The greater mutagenicity of the latter in the same sequence contexts indicates that Fapy·dG is a biologically significant lesion and biomarker on par with 8-OxodGuo.
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Affiliation(s)
- Stephen Stanio
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | | | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ashis K. Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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5
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Franck C, Stéphane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C. Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing. Nucleic Acids Res 2022; 50:11072-11092. [PMID: 36300625 PMCID: PMC9638937 DOI: 10.1093/nar/gkac932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
8-Oxoguanine (GO) is a major purine oxidation product in DNA. Because of its highly mutagenic properties, GO absolutely must be eliminated from DNA. To do this, aerobic and anaerobic organisms from the three kingdoms of life have evolved repair mechanisms to prevent its deleterious effect on genetic integrity. The major way to remove GO is the base excision repair pathway, usually initiated by a GO-DNA glycosylase. First identified in bacteria (Fpg) and eukaryotes (OGG1), GO-DNA glycosylases were more recently identified in archaea (OGG2 and AGOG). AGOG is the less documented enzyme and its mode of damage recognition and removing remains to be clarified at the molecular and atomic levels. This study presents a complete structural characterisation of apo AGOGs from Pyrococcus abyssi (Pab) and Thermococcus gammatolerans (Tga) and the first structure of Pab-AGOG bound to lesion-containing single- or double-stranded DNA. By combining X-ray structure analysis, site directed mutagenesis and biochemistry experiments, we identified key amino acid residues of AGOGs responsible for the specific recognition of the lesion and the base opposite the lesion and for catalysis. Moreover, a unique binding mode of GO, involving double base flipping, never observed for any other DNA glycosylases, is revealed. In addition to unravelling the properties of AGOGs, our study, through comparative biochemical and structural analysis, offers new insights into the evolutionary plasticity of DNA glycosylases across all three kingdoms of life.
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Affiliation(s)
- Coste Franck
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Goffinont Stéphane
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Cros Julien
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Gaudon Virginie
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Guérin Martine
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Garnier Norbert
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Confalonieri Fabrice
- Institut de Biologie Intégrative de la cellule (I2BC), UMR 9198 Université Paris-Saclay-CNRS-CEA , Bâtiment 21, Avenue de la Terrasse , F-91190 Gif-sur-Yvette , France
| | - Flament Didier
- Université de Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds (BEEP) , F-29280 Plouzané , France
| | - Suskiewicz Marcin Josef
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
| | - Castaing Bertrand
- Centre de Biophysique Moléculaire (CBM), UPR4301 CNRS, Université d’Orléans , CS 80054, rue Charles Sadron , F-45071 Orléans cedex 02 , France
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6
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Kumari A, Yadav A, Lahiri I. Transient State Kinetics of Plasmodium falciparum Apicoplast DNA Polymerase Suggests the Involvement of Accessory Factors for Efficient and Accurate DNA Synthesis. Biochemistry 2022; 61:2319-2333. [PMID: 36251801 DOI: 10.1021/acs.biochem.2c00446] [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
Plasmodium, the causative agent of malaria, belongs to the phylum Apicomplexa. Most apicomplexans, including Plasmodium, contain an essential nonphotosynthetic plastid called the apicoplast that harbors its own genome that is replicated by a dedicated organellar replisome. This replisome employs a single DNA polymerase (apPol), which is expected to perform both replicative and translesion synthesis. Unlike other replicative polymerases, no processivity factor for apPol has been identified. While preliminary structural and biochemical studies have provided an overall characterization of apPol, the kinetic mechanism of apPol's activity remains unknown. We have used transient state methods to determine the kinetics of replicative and translesion synthesis by apPol and show that apPol has low processivity and efficiency while copying undamaged DNA. Moreover, while apPol can bypass oxidatively damaged lesions, the bypass is error-prone. Taken together, our results raise the following question─how does a polymerase with low processivity, efficiency, and fidelity (for translesion synthesis) faithfully replicate the apicoplast organellar DNA within the hostile environment of the human host? We hypothesize that interactions with putative components of the apicoplast replisome and/or an as-yet-undiscovered processivity factor transform apPol into an efficient and accurate enzyme.
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Affiliation(s)
- Anamika Kumari
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Anjali Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India.,Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
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7
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Dannenberg RL, Cardina JA, Pytko KG, Hedglin M. Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities. Nucleic Acids Res 2022; 50:9893-9908. [PMID: 36107777 PMCID: PMC9508823 DOI: 10.1093/nar/gkac745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
During DNA replication, DNA lesions in lagging strand templates are initially encountered by DNA polymerase δ (pol δ) holoenzymes comprised of pol δ and the PCNA processivity sliding clamp. These encounters are thought to stall replication of an afflicted template before the lesion, activating DNA damage tolerance (DDT) pathways that replicate the lesion and adjacent DNA sequence, allowing pol δ to resume. However, qualitative studies observed that human pol δ can replicate various DNA lesions, albeit with unknown proficiencies, which raises issues regarding the role of DDT in replicating DNA lesions. To address these issues, we re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with DNA lesions. The results indicate pol δ holoenzymes support dNTP incorporation opposite and beyond multiple lesions and the extent of these activities depends on the lesion and pol δ proofreading. Furthermore, after encountering a given DNA lesion, subsequent dissociation of pol δ is distributed around the lesion and a portion does not dissociate. The distributions of these events are dependent on the lesion and pol δ proofreading. Collectively, these results reveal complexity and heterogeneity in the replication of lagging strand DNA lesions, significantly advancing our understanding of human DDT.
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Affiliation(s)
- Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A Cardina
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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8
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Dupuy P, Ghosh S, Adefisayo O, Buglino J, Shuman S, Glickman MS. Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis. Nat Commun 2022; 13:4493. [PMID: 35918328 PMCID: PMC9346131 DOI: 10.1038/s41467-022-32022-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance of Mycobacterium tuberculosis is exclusively a consequence of chromosomal mutations. Translesion synthesis (TLS) is a widely conserved mechanism of DNA damage tolerance and mutagenesis, executed by translesion polymerases such as DinBs. In mycobacteria, DnaE2 is the only known agent of TLS and the role of DinB polymerases is unknown. Here we demonstrate that, when overexpressed, DinB1 promotes missense mutations conferring resistance to rifampicin, with a mutational signature distinct from that of DnaE2, and abets insertion and deletion frameshift mutagenesis in homo-oligonucleotide runs. DinB1 is the primary mediator of spontaneous −1 frameshift mutations in homo-oligonucleotide runs whereas DnaE2 and DinBs are redundant in DNA damage-induced −1 frameshift mutagenesis. These results highlight DinB1 and DnaE2 as drivers of mycobacterial genome diversification with relevance to antimicrobial resistance and host adaptation. This manuscript elucidates new mechanisms of mutagenesis in mycobacteria by implicating two translesion DNA polymerases in genome diversification, including creating the mutations that underlie all antibiotic resistance in these global pathogens.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Shreya Ghosh
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA
| | - John Buglino
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Michael S Glickman
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA.
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9
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Wang J, Sheng Y, Yang Y, Dai X, You C. Next-generation sequencing-based analysis of the effect of N6-methyldeoxyadenosine modification on DNA replication in human cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Bypass by Family X DNA Polymerases. Genes (Basel) 2021; 13:genes13010015. [PMID: 35052363 PMCID: PMC8774566 DOI: 10.3390/genes13010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual-coding potential it can pair both with adenine or cytidine. Therefore, it creates a challenge for DNA polymerases striving to correctly replicate and/or repair genomic or mitochondrial DNA. Numerous structural studies provide insights into the mechanistic basis of the specificity of 8OG bypass by DNA polymerases from different families. Here, we focus on how repair polymerases from Family X (Pols β, λ and µ) engage DNA substrates containing the oxidized guanine. We review structures of binary and ternary complexes for the three polymerases, which represent distinct steps in their catalytic cycles—the binding of the DNA substrate and the incoming nucleotide, followed by its insertion and extension. At each of these steps, the polymerase may favor or exclude the correct C or incorrect A, affecting the final outcome, which varies depending on the enzyme.
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11
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De Rosa M, Johnson SA, Opresko PL. Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress. Front Cell Dev Biol 2021; 9:758402. [PMID: 34869348 PMCID: PMC8640134 DOI: 10.3389/fcell.2021.758402] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 11/27/2022] Open
Abstract
Telomeres are protective nucleoprotein structures that cap linear chromosome ends and safeguard genome stability. Progressive telomere shortening at each somatic cell division eventually leads to critically short and dysfunctional telomeres, which can contribute to either cellular senescence and aging, or tumorigenesis. Human reproductive cells, some stem cells, and most cancer cells, express the enzyme telomerase to restore telomeric DNA. Numerous studies have shown that oxidative stress caused by excess reactive oxygen species is associated with accelerated telomere shortening and dysfunction. Telomeric repeat sequences are remarkably susceptible to oxidative damage and are preferred sites for the production of the mutagenic base lesion 8-oxoguanine, which can alter telomere length homeostasis and integrity. Therefore, knowledge of the repair pathways involved in the processing of 8-oxoguanine at telomeres is important for advancing understanding of the pathogenesis of degenerative diseases and cancer associated with telomere instability. The highly conserved guanine oxidation (GO) system involves three specialized enzymes that initiate distinct pathways to specifically mitigate the adverse effects of 8-oxoguanine. Here we introduce the GO system and review the studies focused on investigating how telomeric 8-oxoguanine processing affects telomere integrity and overall genome stability. We also discuss newly developed technologies that target oxidative damage selectively to telomeres to investigate roles for the GO system in telomere stability.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
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12
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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13
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Jiang T, Monari A, Dumont E, Bignon E. Molecular Mechanisms Associated with Clustered Lesion-Induced Impairment of 8-oxoG Recognition by the Human Glycosylase OGG1. Molecules 2021; 26:molecules26216465. [PMID: 34770874 PMCID: PMC8587150 DOI: 10.3390/molecules26216465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The 8-oxo-7,8-dihydroguanine, referred to as 8-oxoG, is a highly mutagenic DNA lesion that can provoke the appearance of mismatches if it escapes the DNA Damage Response. The specific recognition of its structural signature by the hOGG1 glycosylase is the first step along the Base Excision Repair pathway, which ensures the integrity of the genome by preventing the emergence of mutations. 8-oxoG formation, structural features, and repair have been matters of extensive research; more recently, this active field of research expended to the more complicated case of 8-oxoG within clustered lesions. Indeed, the presence of a second lesion within 1 or 2 helix turns can dramatically impact the repair yields of 8-oxoG by glycosylases. In this work, we use μs-range molecular dynamics simulations and machine-learning-based postanalysis to explore the molecular mechanisms associated with the recognition of 8-oxoG by hOGG1 when embedded in a multiple-lesion site with a mismatch in 5′ or 3′. We delineate the stiffening of the DNA–protein interactions upon the presence of the mismatches, and rationalize the much lower repair yields reported with a 5′ mismatch by describing the perturbation of 8-oxoG structural features upon addition of an adjacent lesion.
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Affiliation(s)
- Tao Jiang
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Université de Paris and CNRS, ITODYS, F-75006 Paris, France
| | - Elise Dumont
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
- Institut Universitaire de France, 5 rue Descartes, F-75005 Paris, France
| | - Emmanuelle Bignon
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Correspondence:
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14
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Nachtergael A, Lanterbecq D, Spanoghe M, Belayew A, Duez P. Effects of Chemopreventive Natural Compounds on the Accuracy of 8-oxo-7,8-dihydro-2'-deoxyguanosine Translesion Synthesis. PLANTA MEDICA 2021; 87:868-878. [PMID: 34237787 DOI: 10.1055/a-1527-1435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Translesion synthesis is a DNA damage tolerance mechanism that relies on a series of specialized DNA polymerases able to bypass a lesion on a DNA template strand during replication or post-repair synthesis. Specialized translesion synthesis DNA polymerases pursue replication by inserting a base opposite to this lesion, correctly or incorrectly depending on the lesion nature, involved DNA polymerase(s), sequence context, and still unknown factors. To measure the correct or mutagenic outcome of 8-oxo-7,8-dihydro-2'-deoxyguanosine bypass by translesion synthesis, a primer-extension assay was performed in vitro on a template DNA bearing this lesion in the presence of nuclear proteins extracted from human intestinal epithelial cells (FHs 74 Int cell line); the reaction products were analyzed by both denaturing capillary electrophoresis (to measure the yield of translesion elongation) and pyrosequencing (to determine the identity of the nucleotide inserted in front of the lesion). The influence of 14 natural polyphenols on the correct or mutagenic outcome of translesion synthesis through 8-oxo-7,8-dihydro-2'-deoxyguanosine was then evaluated in 2 experimental conditions by adding the polyphenol either (i) to the reaction mix during the primer extension assay; or (ii) to the culture medium, 24 h before cell harvest and nuclear proteins extraction. Most of the tested polyphenols significantly influenced the outcome of translesion synthesis, either through an error-free (apigenin, baicalein, sakuranetin, and myricetin) or a mutagenic pathway (epicatechin, chalcone, genistein, magnolol, and honokiol).
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Affiliation(s)
- Amandine Nachtergael
- Unit of Therapeutic Chemistry and Pharmacognosy, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
| | - Déborah Lanterbecq
- Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut CONDORCET, Ath, Belgium
| | - Martin Spanoghe
- Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut CONDORCET, Ath, Belgium
| | - Alexandra Belayew
- Department of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
| | - Pierre Duez
- Unit of Therapeutic Chemistry and Pharmacognosy, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
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15
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Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK. Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Nat Commun 2021; 12:4020. [PMID: 34188055 PMCID: PMC8241999 DOI: 10.1038/s41467-021-24317-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/14/2021] [Indexed: 11/30/2022] Open
Abstract
PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3′−terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3′-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells. The human DNA primase and DNA polymerase PrimPol replicates through the major oxidative DNA damage lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis in a mostly error-free manner thus suppressing oxoG-induced mutagenesis in mitochondria and the nucleus. Here, the authors present crystal structures of PrimPol in complex with an oxoG lesion in different contexts that provide mechanistic insights into how PrimPol performs predominantly accurate synthesis on oxidative-damaged DNAs in human cells.
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Affiliation(s)
- Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yogesh K Gupta
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Greehey Children's Cancer Research Institute & Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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17
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Shilkin ES, Petrova DV, Poltorachenko VA, Boldinova EO, Zharkov DO, Makarova AV. Template Properties of 5-Methyl-2'-Deoxycytidine and 5-Hydroxymethyl-2'-Deoxycytidine in Reactions with Human Translesion and Reparative DNA Polymerases. Mol Biol 2021. [DOI: 10.1134/s0026893321020138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Hoff CA, Schmidt SS, Hackert BJ, Worley TK, Courcelle J, Courcelle CT. Events associated with DNA replication disruption are not observed in hydrogen peroxide-treated Escherichia coli. G3-GENES GENOMES GENETICS 2021; 11:6137848. [PMID: 33591320 PMCID: PMC8759817 DOI: 10.1093/g3journal/jkab044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/05/2021] [Indexed: 02/05/2023]
Abstract
UV irradiation induces pyrimidine dimers that block polymerases and disrupt the replisome. Restoring replication depends on the recF pathway proteins which process and maintain the replication fork DNA to allow the lesion to be repaired before replication resumes. Oxidative DNA lesions, such as those induced by hydrogen peroxide (H2O2), are often thought to require similar processing events, yet far less is known about how cells process oxidative damage during replication. Here we show that replication is not disrupted by H2O2-induced DNA damage in vivo. Following an initial inhibition, replication resumes in the absence of either lesion removal or RecF-processing. Restoring DNA synthesis depends on the presence of manganese in the medium, which we show is required for replication, but not repair to occur. The results demonstrate that replication is enzymatically inactivated, rather than physically disrupted by H2O2-induced DNA damage; indicate that inactivation is likely caused by oxidation of an iron-dependent replication or replication-associated protein that requires manganese to restore activity and synthesis; and address a long standing paradox as to why oxidative glycosylase mutants are defective in repair, yet not hypersensitive to H2O2. The oxygen-sensitive pausing may represent an adaptation that prevents replication from occurring under potentially lethal or mutagenic conditions.
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Affiliation(s)
- Chettar A Hoff
- Department of Biology, Portland State University, Portland, OR97201, USA
| | - Sierra S Schmidt
- Department of Biology, Portland State University, Portland, OR97201, USA
| | - Brandy J Hackert
- Department of Biology, Portland State University, Portland, OR97201, USA
| | - Travis K Worley
- Department of Biology, Portland State University, Portland, OR97201, USA
| | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR97201, USA
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19
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Gorini F, Scala G, Cooke MS, Majello B, Amente S. Towards a comprehensive view of 8-oxo-7,8-dihydro-2'-deoxyguanosine: Highlighting the intertwined roles of DNA damage and epigenetics in genomic instability. DNA Repair (Amst) 2021; 97:103027. [PMID: 33285475 PMCID: PMC7926032 DOI: 10.1016/j.dnarep.2020.103027] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of DNA oxidation, is a pre-mutagenic lesion which is prone to mispair, if left unrepaired, with 2'-deoxyadenosine during DNA replication. While unrepaired or incompletely repaired 8-oxodG has classically been associated with genome instability and cancer, it has recently been reported to have a role in the epigenetic regulation of gene expression. Despite the growing collection of genome-wide 8-oxodG mapping studies that have been used to provide new insight on the functional nature of 8-oxodG within the genome, a comprehensive view that brings together the epigenetic and the mutagenic nature of the 8-oxodG is still lacking. To help address this gap, this review aims to provide (i) a description of the state-of-the-art knowledge on both the mutagenic and epigenetic roles of 8-oxodG; (ii) putative molecular models through which the 8-oxodG can cause genome instability; (iii) a possible molecular model on how 8-oxodG, acting as an epigenetic signal, could cause the translocations and deletions which are associated with cancer.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Barbara Majello
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy.
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20
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Majumdar C, McKibbin PL, Krajewski AE, Manlove AH, Lee JK, David SS. Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY. J Am Chem Soc 2020; 142:20340-20350. [PMID: 33202125 DOI: 10.1021/jacs.0c06767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediatedadenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogues of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analogue substrates with their experimental and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogues that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogues paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analogue duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogues to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analogue SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.
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Affiliation(s)
- Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Paige L McKibbin
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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21
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Wu Y, Jaremko WJ, Wilson RC, Pata JD. Heterotrimeric PCNA increases the activity and fidelity of Dbh, a Y-family translesion DNA polymerase prone to creating single-base deletion mutations. DNA Repair (Amst) 2020; 96:102967. [PMID: 32961405 DOI: 10.1016/j.dnarep.2020.102967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 11/15/2022]
Abstract
Dbh is a Y-family translesion DNA polymerase from Sulfolobus acidocaldarius, an archaeal species that grows in harsh environmental conditions. Biochemically, Dbh displays a distinctive mutational profile, creating single-base deletion mutations at extraordinarily high frequencies (up to 50 %) in specific repeat sequences. In cells, however, Dbh does not appear to contribute significantly to spontaneous frameshifts in these same sequence contexts. This suggests that either the error-prone DNA synthesis activity of Dbh is reduced in vivo and/or Dbh is restricted from replicating these sequences. Here, we test the hypothesis that the propensity for Dbh to make single base deletion mutations is reduced through interaction with the S. acidocaldarius heterotrimeric sliding clamp processivity factor, PCNA-123. We first confirm that Dbh physically interacts with PCNA-123, with the interaction requiring both the PCNA-1 subunit and the C-terminal 10 amino acids of Dbh, which contain a predicted PCNA-interaction peptide (PIP) motif. This interaction stimulates the polymerase activity of Dbh, even on short, linear primer-template DNA, by increasing the rate of nucleotide incorporation. This stimulation requires an intact PCNA-123 heterotrimer and a DNA duplex length of at least 18 basepairs, the minimal length predicted from structural data to bind to both the polymerase and the clamp. Finally, we find that PCNA-123 increases the fidelity of Dbh on a single-base deletion hotspot sequence 3-fold by promoting an increase in the rate of correct, but not incorrect, nucleotide addition and propose that PCNA-123 induces Dbh to adopt a more active conformation that is less prone to creating deletions during DNA synthesis.
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Affiliation(s)
- Yifeng Wu
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - William J Jaremko
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Ryan C Wilson
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Janice D Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States.
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22
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Rodriguez-Alvarez M, Kim D, Khobta A. EGFP Reporters for Direct and Sensitive Detection of Mutagenic Bypass of DNA Lesions. Biomolecules 2020; 10:biom10060902. [PMID: 32545792 PMCID: PMC7357151 DOI: 10.3390/biom10060902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
The sustainment of replication and transcription of damaged DNA is essential for cell survival under genotoxic stress; however, the damage tolerance of these key cellular functions comes at the expense of fidelity. Thus, translesion DNA synthesis (TLS) over damaged nucleotides is a major source of point mutations found in cancers; whereas erroneous bypass of damage by RNA polymerases may contribute to cancer and other diseases by driving accumulation of proteins with aberrant structure and function in a process termed “transcriptional mutagenesis” (TM). Here, we aimed at the generation of reporters suited for direct detection of miscoding capacities of defined types of DNA modifications during translesion DNA or RNA synthesis in human cells. We performed a systematic phenotypic screen of 25 non-synonymous base substitutions in a DNA sequence encoding a functionally important region of the enhanced green fluorescent protein (EGFP). This led to the identification of four loss-of-fluorescence mutants, in which any ulterior base substitution at the nucleotide affected by the primary mutation leads to the reversal to a functional EGFP. Finally, we incorporated highly mutagenic abasic DNA lesions at the positions of primary mutations and demonstrated a high sensitivity of detection of the mutagenic DNA TLS and TM in this system.
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Affiliation(s)
- Marta Rodriguez-Alvarez
- Unit “Responses to DNA Lesions", Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 67, 55131 Mainz, Germany;
| | - Daria Kim
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andriy Khobta
- Unit “Responses to DNA Lesions", Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 67, 55131 Mainz, Germany;
- Correspondence:
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23
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Moreno-Oñate M, Herrero-Ruiz AM, García-Dominguez M, Cortés-Ledesma F, Ruiz JF. RanBP2-Mediated SUMOylation Promotes Human DNA Polymerase Lambda Nuclear Localization and DNA Repair. J Mol Biol 2020; 432:3965-3979. [PMID: 32224012 DOI: 10.1016/j.jmb.2020.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/28/2022]
Abstract
Cellular DNA is under constant attack by a wide variety of agents, both endogenous and exogenous. To counteract DNA damage, human cells have a large collection of DNA repair factors. Among them, DNA polymerase lambda (Polλ) stands out for its versatility, as it participates in different DNA repair and damage tolerance pathways in which gap-filling DNA synthesis is required. In this work, we show that human Polλ is conjugated with Small Ubiquitin-like MOdifier (SUMO) proteins both in vitro and in vivo, with Lys27 being the main target of this covalent modification. Polλ SUMOylation takes place in the nuclear pore complex and is mediated by the E3 ligase RanBP2. This post-translational modification promotes Polλ entry into the nucleus, which is required for its recruitment to DNA lesions and stimulated by DNA damage induction. Our work represents an advance in the knowledge of molecular pathways that regulate cellular localization of human Polλ, which are essential to be able to perform its functions during repair of nuclear DNA, and that might constitute an important point for the modulation of its activity in human cells.
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Affiliation(s)
- M Moreno-Oñate
- Departamento Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Sevilla
| | - A M Herrero-Ruiz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC/Universidad Pablo Olavide/Junta de Andalucía, 41092 Sevilla, Spain
| | - M García-Dominguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC/Universidad Pablo Olavide/Junta de Andalucía, 41092 Sevilla, Spain
| | - F Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC/Universidad Pablo Olavide/Junta de Andalucía, 41092 Sevilla, Spain; Topology and DNA Breaks Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
| | - J F Ruiz
- Departamento Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Sevilla; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla/CSIC/Universidad Pablo Olavide/Junta de Andalucía, 41092 Sevilla, Spain.
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24
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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25
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Tudek A, Czerwińska J, Kosicki K, Zdżalik-Bielecka D, Shahmoradi Ghahe S, Bażlekowa-Karaban M, Borsuk EM, Speina E. DNA damage, repair and the improvement of cancer therapy - A tribute to the life and research of Barbara Tudek. Mutat Res 2020; 852:503160. [PMID: 32265045 DOI: 10.1016/j.mrgentox.2020.503160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 10/25/2022]
Abstract
Professor Barbara Tudek received the Frits Sobels Award in 2019 from the European Environmental Mutagenesis and Genomics Society (EEMGS). This article presents her outstanding character and most important lines of research. The focus of her studies covered alkylative and oxidative damage to DNA bases, in particular mutagenic and carcinogenic properties of purines with an open imidazole ring and 8-oxo-7,8-dihydroguanine (8-oxoGua). They also included analysis of mutagenic properties and pathways for the repair of DNA adducts of lipid peroxidation (LPO) products arising in large quantities during inflammation. Professor Tudek did all of this in the hope of deciphering the mechanisms of DNA damage removal, in particular by the base excision repair (BER) pathway. Some lines of research aimed at discovering factors that can modulate the activity of DNA damage repair in hope to enhance existing anti-cancer therapies. The group's ongoing research aims at deciphering the resistance mechanisms of cancer cell lines acquired following prolonged exposure to photodynamic therapy (PDT) and the possibility of re-sensitizing cells to PDT in order to increase the application of this minimally invasive therapeutic method.
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Affiliation(s)
- Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Jolanta Czerwińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Konrad Kosicki
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Daria Zdżalik-Bielecka
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Somayeh Shahmoradi Ghahe
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Milena Bażlekowa-Karaban
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland; UMR 8200 C.N.R.S., Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Ewelina M Borsuk
- Laboratory of Structural Biology, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
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Giovannini S, Weller MC, Repmann S, Moch H, Jiricny J. Synthetic lethality between BRCA1 deficiency and poly(ADP-ribose) polymerase inhibition is modulated by processing of endogenous oxidative DNA damage. Nucleic Acids Res 2019; 47:9132-9143. [PMID: 31329989 PMCID: PMC6753488 DOI: 10.1093/nar/gkz624] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/12/2019] [Indexed: 01/06/2023] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) facilitate the repair of DNA single-strand breaks (SSBs). When PARPs are inhibited, unrepaired SSBs colliding with replication forks give rise to cytotoxic double-strand breaks. These are normally rescued by homologous recombination (HR), but, in cells with suboptimal HR, PARP inhibition leads to genomic instability and cell death, a phenomenon currently exploited in the therapy of ovarian cancers in BRCA1/2 mutation carriers. In spite of their promise, resistance to PARP inhibitors (PARPis) has already emerged. In order to identify the possible underlying causes of the resistance, we set out to identify the endogenous source of DNA damage that activates PARPs. We argued that if the toxicity of PARPis is indeed caused by unrepaired SSBs, these breaks must arise spontaneously, because PARPis are used as single agents. We now show that a significant contributor to PARPi toxicity is oxygen metabolism. While BRCA1-depleted or -mutated cells were hypersensitive to the clinically approved PARPi olaparib, its toxicity was significantly attenuated by depletion of OGG1 or MYH DNA glycosylases, as well as by treatment with reactive oxygen species scavengers, growth under hypoxic conditions or chemical OGG1 inhibition. Thus, clinical resistance to PARPi therapy may emerge simply through reduced efficiency of oxidative damage repair.
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Affiliation(s)
- Sara Giovannini
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Marie-Christine Weller
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Simone Repmann
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
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McIntyre J. Polymerase iota - an odd sibling among Y family polymerases. DNA Repair (Amst) 2019; 86:102753. [PMID: 31805501 DOI: 10.1016/j.dnarep.2019.102753] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022]
Abstract
It has been two decades since the discovery of the most mutagenic human DNA polymerase, polymerase iota (Polι). Since then, the biochemical activity of this translesion synthesis (TLS) enzyme has been extensively explored, mostly through in vitro experiments, with some insight into its cellular activity. Polι is one of four members of the Y-family of polymerases, which are the best characterized DNA damage-tolerant polymerases involved in TLS. Polι shares some common Y-family features, including low catalytic efficiency and processivity, high infidelity, the ability to bypass some DNA lesions, and a deficiency in 3'→5' exonucleolytic proofreading. However, Polι exhibits numerous properties unique among the Y-family enzymes. Polι has an unusual catalytic pocket structure and prefers Hoogsteen over Watson-Crick pairing, and its replication fidelity strongly depends on the template; further, it prefers Mn2+ ions rather than Mg2+ as catalytic activators. In addition to its polymerase activity, Polι possesses also 5'-deoxyribose phosphate (dRP) lyase activity, and its ability to participate in base excision repair has been shown. As a highly error-prone polymerase, its regulation is crucial and mostly involves posttranslational modifications and protein-protein interactions. The upregulation and downregulation of Polι are correlated with different types of cancer and suggestions regarding the possible function of this polymerase have emerged from studies of various cancer lines. Nonetheless, after twenty years of research, the biological function of Polι certainly remains unresolved.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland.
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28
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Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. SCIENCE ADVANCES 2019; 5:eaaw6671. [PMID: 31579821 PMCID: PMC6760925 DOI: 10.1126/sciadv.aaw6671] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/28/2019] [Indexed: 05/22/2023]
Abstract
The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable adaptations. To reveal genomic changes that occurred during this transition, we screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We found 85 gene losses. Some of these were likely beneficial for cetaceans, for example, by reducing the risk of thrombus formation during diving (F12 and KLKB1), erroneous DNA damage repair (POLM), and oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva. Last, loss of melatonin synthesis and receptor genes (AANAT, ASMT, and MTNR1A/B) may have been a precondition for adopting unihemispheric sleep. Our findings suggest that some genes lost in ancestral cetaceans were likely involved in adapting to a fully aquatic lifestyle.
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Affiliation(s)
- Matthias Huelsmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - John Gatesy
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Corresponding author.
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Killelea T, Palud A, Akcha F, Lemor M, L'haridon S, Godfroy A, Henneke G. The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea. eLife 2019; 8:45320. [PMID: 31184586 PMCID: PMC6559790 DOI: 10.7554/elife.45320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.
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Affiliation(s)
- Tom Killelea
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Farida Akcha
- Laboratoire d'Ecotoxicologie, Ifremer, Nantes, France
| | - Mélanie Lemor
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Stephane L'haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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Abstract
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases.
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Interaction between Two Iridovirus Core Proteins and Their Effects on Ranavirus (RGV) Replication in Cells from Different Species. Viruses 2019; 11:v11050416. [PMID: 31060251 PMCID: PMC6563300 DOI: 10.3390/v11050416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/16/2022] Open
Abstract
The two putative proteins RGV-63R and RGV-91R encoded by Rana grylio virus (RGV) are DNA polymerase and proliferating cell nuclear antigen (PCNA) respectively, and are core proteins of iridoviruses. Here, the interaction between RGV-63R and RGV-91R was detected by a yeast two-hybrid (Y2H) assay and further confirmed by co-immunoprecipitation (co-IP) assays. Subsequently, RGV-63R or RGV-91R were expressed alone or co-expressed in two kinds of aquatic animal cells including amphibian Chinese giant salamander thymus cells (GSTCs) and fish Epithelioma papulosum cyprinid cells (EPCs) to investigate their localizations and effects on RGV genome replication. The results showed that their localizations in the two kinds of cells are consistent. RGV-63R localized in the cytoplasm, while RGV-91R localized in the nucleus. However, when co-expressed, RGV-63R localized in both the cytoplasm and the nucleus, and colocalized with RGV-91R in the nucleus. 91R△NLS represents the RGV-91R deleting nuclear localization signal, which is localized in the cytoplasm and colocalized with RGV-63R in the cytoplasm. qPCR analysis revealed that sole expression and co-expression of the two proteins in the cells of two species significantly promoted RGV genome replication, while varying degrees of viral genome replication levels may be linked to the cell types. This study provides novel molecular evidence for ranavirus cross-species infection and replication.
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Barnes RP, Fouquerel E, Opresko PL. The impact of oxidative DNA damage and stress on telomere homeostasis. Mech Ageing Dev 2019; 177:37-45. [PMID: 29604323 PMCID: PMC6162185 DOI: 10.1016/j.mad.2018.03.013] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Telomeres are dynamic nucleoprotein-DNA structures that cap and protect linear chromosome ends. Because telomeres shorten progressively with each replication, they impose a functional limit on the number of times a cell can divide. Critically short telomeres trigger cellular senescence in normal cells, or genomic instability in pre-malignant cells, which contribute to numerous degenerative and aging-related diseases including cancer. Therefore, a detailed understanding of the mechanisms of telomere loss and preservation is important for human health. Numerous studies have shown that oxidative stress is associated with accelerated telomere shortening and dysfunction. Oxidative stress caused by inflammation, intrinsic cell factors or environmental exposures, contributes to the pathogenesis of many degenerative diseases and cancer. Here we review the studies demonstrating associations between oxidative stress and accelerated telomere attrition in human tissue, mice and cell culture, and discuss possible mechanisms and cellular pathways that protect telomeres from oxidative damage.
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33
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Vaisman A, Woodgate R. Ribonucleotide discrimination by translesion synthesis DNA polymerases. Crit Rev Biochem Mol Biol 2018; 53:382-402. [PMID: 29972306 DOI: 10.1080/10409238.2018.1483889] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The well-being of all living organisms relies on the accurate duplication of their genomes. This is usually achieved by highly elaborate replicase complexes which ensure that this task is accomplished timely and efficiently. However, cells often must resort to the help of various additional "specialized" DNA polymerases that gain access to genomic DNA when replication fork progression is hindered. One such specialized polymerase family consists of the so-called "translesion synthesis" (TLS) polymerases; enzymes that have evolved to replicate damaged DNA. To fulfill their main cellular mission, TLS polymerases often must sacrifice precision when selecting nucleotide substrates. Low base-substitution fidelity is a well-documented inherent property of these enzymes. However, incorrect nucleotide substrates are not only those which do not comply with Watson-Crick base complementarity, but also those whose sugar moiety is incorrect. Does relaxed base-selectivity automatically mean that the TLS polymerases are unable to efficiently discriminate between ribonucleoside triphosphates and deoxyribonucleoside triphosphates that differ by only a single atom? Which strategies do TLS polymerases employ to select suitable nucleotide substrates? In this review, we will collate and summarize data accumulated over the past decade from biochemical and structural studies, which aim to answer these questions.
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Affiliation(s)
- Alexandra Vaisman
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Roger Woodgate
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
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Sihi S, Maiti S, Bakshi S, Nayak A, Chaudhuri S, Sengupta DN. Understanding the role of DNA polymerase λ gene in different growth and developmental stages of Oryza sativa L. indica rice cultivars. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:156-168. [PMID: 29031161 DOI: 10.1016/j.plaphy.2017.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
DNA polymerase λ (Pol λ) is the only member of DNA polymerase family X present in plants. The enzyme is ddNTP sensitive as it contains the conserved C-terminal Pol β domain. The 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the Pol λ gene. Comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial Pol λ gene was stable and acceptable. The alignment of both the protein models showed a RMS value of 0.783. Apart from this, expression of Pol λ and its relative activity is studied during different development stages of three different indica rice cultivars (IR29, Nonabokra and N22). Enhanced accumulation and higher activity of Pol λ during the early seedling stage was detected. Higher expression and activity were observed in the anthers, which was probably necessary for DNA repair during microspore formation. However, during the maturation stage of seed development and plant growth, expression and the activity of Pol λ decreased due to slow metabolic activity and a reduced rate of cell division respectively. Furthermore, the expression and activity of Pol λ were found to be higher in IR29 in comparison to Nonabokra and N22. IR29 is a rice cultivar susceptible to environmental stresses and hence it encounters higher DNA damages. The enhanced presence and activity of the Pol λ enzyme in IR29 with respect to the other two cultivars, which are more tolerant to the environmental stresses during various developmental stages, is therefore explainable.
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Affiliation(s)
- Sayantani Sihi
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Soumitra Maiti
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Sankar Bakshi
- Vidyasagar College for Women, 39 Sankar Ghosh Lane Kolkata 700006, India
| | - Arup Nayak
- Division of Plant Biology, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
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Markkanen E. Not breathing is not an option: How to deal with oxidative DNA damage. DNA Repair (Amst) 2017; 59:82-105. [PMID: 28963982 DOI: 10.1016/j.dnarep.2017.09.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023]
Abstract
Oxidative DNA damage constitutes a major threat to genetic integrity, and has thus been implicated in the pathogenesis of a wide variety of diseases, including cancer and neurodegeneration. 7,8-dihydro-8oxo-deoxyGuanine (8-oxo-G) is one of the best characterised oxidative DNA lesions, and it can give rise to point mutations due to its miscoding potential that instructs most DNA polymerases (Pols) to preferentially insert Adenine (A) opposite 8-oxo-G instead of the correct Cytosine (C). If uncorrected, A:8-oxo-G mispairs can give rise to C:G→A:T transversion mutations. Cells have evolved a variety of pathways to mitigate the mutational potential of 8-oxo-G that include i) mechanisms to avoid incorporation of oxidized nucleotides into DNA through nucleotide pool sanitisation enzymes (by MTH1, MTH2, MTH3 and NUDT5), ii) base excision repair (BER) of 8-oxo-G in DNA (involving MUTYH, OGG1, Pol λ, and other components of the BER machinery), and iii) faithful bypass of 8-oxo-G lesions during replication (using a switch between replicative Pols and Pol λ). In the following, the fate of 8-oxo-G in mammalian cells is reviewed in detail. The differential origins of 8-oxo-G in DNA and its consequences for genetic stability will be covered. This will be followed by a thorough discussion of the different mechanisms in place to cope with 8-oxo-G with an emphasis on Pol λ-mediated correct bypass of 8-oxo-G during MUTYH-initiated BER as well as replication across 8-oxo-G. Furthermore, the multitude of mechanisms in place to regulate key proteins involved in 8-oxo-G repair will be reviewed. Novel functions of 8-oxo-G as an epigenetic-like regulator and insights into the repair of 8-oxo-G within the cellular context will be touched upon. Finally, a discussion will outline the relevance of 8-oxo-G and the proteins involved in dealing with 8-oxo-G to human diseases with a special emphasis on cancer.
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Affiliation(s)
- Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Winterthurerstr. 260, 8057 Zürich, Switzerland.
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van Loon B, Hübscher U, Maga G. Living on the Edge: DNA Polymerase Lambda between Genome Stability and Mutagenesis. Chem Res Toxicol 2017; 30:1936-1941. [DOI: 10.1021/acs.chemrestox.7b00152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Barbara van Loon
- Department
of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Erling Skjalgssons gt 1, N-7491 Trondheim, Norway
- Department
of Pathology and Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, 7491 Trondheim, Norway
| | - Ulrich Hübscher
- Department
of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Giovanni Maga
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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Embryonic exposure to the widely-used herbicide atrazine disrupts meiosis and normal follicle formation in female mice. Sci Rep 2017; 7:3526. [PMID: 28615648 PMCID: PMC5471253 DOI: 10.1038/s41598-017-03738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/03/2017] [Indexed: 01/28/2023] Open
Abstract
The widely-used herbicide atrazine (ATZ) is detected in ground and surface water in many countries. Several studies in animals have demonstrated that ATZ has endocrine-disrupting effects on male and female reproduction in many vertebrate species. In this study, we investigated the effects of ATZ exposure on meiosis, a key step in gametogenesis in mammals. The treatment was initiated before oocyte entry into meiosis, which occurs during the embryonic period in females. We found that embryonic exposure to ATZ increases the level of 8-oxo-guanine in the nucleus of meiotic cells, reflecting oxidative stress and affecting meiotic double-strand break repair, chromosome synapsis and crossover numbers. Finally, embryonic exposure to ATZ reduces the number of primordial follicles and increases the incidence of multi-oocyte follicles in adult mice. Our data demonstrate that embryonic exposure to ATZ disrupts prophase I of meiosis and affects normal follicle formation in female mice.
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Talhaoui I, Matkarimov BT, Tchenio T, Zharkov DO, Saparbaev MK. Aberrant base excision repair pathway of oxidatively damaged DNA: Implications for degenerative diseases. Free Radic Biol Med 2017; 107:266-277. [PMID: 27890638 DOI: 10.1016/j.freeradbiomed.2016.11.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023]
Abstract
In cellular organisms composition of DNA is constrained to only four nucleobases A, G, T and C, except for minor DNA base modifications such as methylation which serves for defence against foreign DNA or gene expression regulation. Interestingly, this severe evolutionary constraint among other things demands DNA repair systems to discriminate between regular and modified bases. DNA glycosylases specifically recognize and excise damaged bases among vast majority of regular bases in the base excision repair (BER) pathway. However, the mismatched base pairs in DNA can occur from a spontaneous conversion of 5-methylcytosine to thymine and DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved special DNA repair systems that target the non-damaged DNA strand in a duplex to remove mismatched regular DNA bases. Mismatch-specific adenine- and thymine-DNA glycosylases (MutY/MUTYH and TDG/MBD4, respectively) initiated BER and mismatch repair (MMR) pathways can recognize and remove normal DNA bases in mismatched DNA duplexes. Importantly, in DNA repair deficient cells bacterial MutY, human TDG and mammalian MMR can act in the aberrant manner: MutY and TDG removes adenine and thymine opposite misincorporated 8-oxoguanine and damaged adenine, respectively, whereas MMR removes thymine opposite to O6-methylguanine. These unusual activities lead either to mutations or futile DNA repair, thus indicating that the DNA repair pathways which target non-damaged DNA strand can act in aberrant manner and introduce genome instability in the presence of unrepaired DNA lesions. Evidences accumulated showing that in addition to the accumulation of oxidatively damaged DNA in cells, the aberrant DNA repair can also contribute to cancer, brain disorders and premature senescence. For example, the aberrant BER and MMR pathways for oxidized guanine residues can lead to trinucleotide expansion that underlies Huntington's disease, a severe hereditary neurodegenerative syndrome. This review summarises the present knowledge about the aberrant DNA repair pathways for oxidized base modifications and their possible role in age-related diseases.
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Affiliation(s)
- Ibtissam Talhaoui
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Thierry Tchenio
- LBPA, UMR8113 ENSC - CNRS, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Murat K Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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Boiteux S, Coste F, Castaing B. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Free Radic Biol Med 2017; 107:179-201. [PMID: 27903453 DOI: 10.1016/j.freeradbiomed.2016.11.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/23/2023]
Abstract
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases. In prokaryotic and eukaryotic cells, 8-oxoG is primarily repaired by the base excision repair pathway (BER) initiated by a DNA N-glycosylase, Fpg and OGG1, respectively. In Escherichia coli, Fpg cooperates with MutY and MutT to prevent 8-oxoG-induced mutations, the "GO-repair system". In Saccharomyces cerevisiae, OGG1 cooperates with nucleotide excision repair (NER), mismatch repair (MMR), post-replication repair (PRR) and DNA polymerase η to prevent mutagenesis. Human and mouse cells mobilize all these pathways using OGG1, MUTYH (MutY-homolog also known as MYH), MTH1 (MutT-homolog also known as NUDT1), NER, MMR, NEILs and DNA polymerases η and λ, to prevent 8-oxoG-induced mutations. In fact, mice deficient in both OGG1 and MUTYH develop cancer in different organs at adult age, which points to the critical impact of 8-oxoG repair on genetic stability in mammals. In this review, we will focus on Fpg and OGG1 proteins, their biochemical and structural properties as well as their biological roles. Other DNA N-glycosylases able to release 8-oxoG from damaged DNA in various organisms will be discussed. Finally, we will report on the role of OGG1 in human disease and the possible use of 8-oxoG DNA N-glycosylases as therapeutic targets.
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Affiliation(s)
- Serge Boiteux
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
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41
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Matkarimov BT, Saparbaev MK. Aberrant DNA glycosylase-initiated repair pathway of free radicals in-duced DNA damage: implications for age-related diseases and natural aging. ACTA ACUST UNITED AC 2017. [DOI: 10.7124/bc.000943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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42
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Roy S. Impact of UV Radiation on Genome Stability and Human Health. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 996:207-219. [DOI: 10.1007/978-3-319-56017-5_17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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43
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Suzuki T, Kamiya H. Mutations induced by 8-hydroxyguanine (8-oxo-7,8-dihydroguanine), a representative oxidized base, in mammalian cells. Genes Environ 2016; 39:2. [PMID: 27980700 PMCID: PMC5131436 DOI: 10.1186/s41021-016-0051-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
Guanine oxidation occurs in both DNA and the cellular nucleotide pool, and one of the major products is 8-hydroxyguanine (8-oxo-7,8-dihydroguanine). The mutagenic potentials of this oxidized base have been examined in various experimental systems. In this review, we summarize the mutagenicity of the base in mammalian cells. We also describe the effects of specialized DNA polymerases, DNA repair proteins, and nucleotide pool sanitization enzymes.
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Affiliation(s)
- Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 Japan
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44
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Basu AK, Pande P, Bose A. Translesion Synthesis of 2'-Deoxyguanosine Lesions by Eukaryotic DNA Polymerases. Chem Res Toxicol 2016; 30:61-72. [PMID: 27760288 PMCID: PMC5241707 DOI: 10.1021/acs.chemrestox.6b00285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
With the discovery
of translesion synthesis DNA polymerases, great
strides have been made in the last two decades in understanding the
mode of replication of various DNA lesions in prokaryotes and eukaryotes.
A database search indicated that approximately 2000 articles on this
topic have been published in this period. This includes research involving
genetic and structural studies as well as in vitro experiments using purified DNA polymerases and accessory proteins.
It is a daunting task to comprehend this exciting and rapidly emerging
area of research. Even so, as the majority of DNA damage occurs at
2′-deoxyguanosine residues, this perspective attempts to summarize
a subset of this field, focusing on the most relevant eukaryotic DNA
polymerases responsible for their bypass.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Arindam Bose
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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45
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Krasikova YS, Rechkunova NI, Lavrik OI. Replication protein A as a major eukaryotic single-stranded DNA-binding protein and its role in DNA repair. Mol Biol 2016. [DOI: 10.1134/s0026893316030080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Nemec AA, Bush KB, Towle-Weicksel JB, Taylor BF, Schulz V, Weidhaas JB, Tuck DP, Sweasy JB. Estrogen Drives Cellular Transformation and Mutagenesis in Cells Expressing the Breast Cancer-Associated R438W DNA Polymerase Lambda Protein. Mol Cancer Res 2016; 14:1068-1077. [PMID: 27621267 DOI: 10.1158/1541-7786.mcr-16-0209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/22/2016] [Accepted: 08/30/2016] [Indexed: 11/16/2022]
Abstract
Repair of DNA damage is critical for maintaining the genomic integrity of cells. DNA polymerase lambda (POLL/Pol λ) is suggested to function in base excision repair (BER) and nonhomologous end-joining (NHEJ), and is likely to play a role in damage tolerance at the replication fork. Here, using next-generation sequencing, it was discovered that the POLL rs3730477 single-nucleotide polymorphism (SNP) encoding R438W Pol λ was significantly enriched in the germlines of breast cancer patients. Expression of R438W Pol λ in human breast epithelial cells induces cellular transformation and chromosomal aberrations. The role of estrogen was assessed as it is commonly used in hormone replacement therapies and is a known breast cancer risk factor. Interestingly, the combination of estrogen treatment and the expression of the R438W Pol λ SNP drastically accelerated the rate of transformation. Estrogen exposure produces 8-oxoguanine lesions that persist in cells expressing R438W Pol λ compared with wild-type (WT) Pol λ-expressing cells. Unlike WT Pol λ, which performs error-free bypass of 8-oxoguanine lesions, expression of R438W Pol λ leads to an increase in mutagenesis and replicative stress in cells treated with estrogen. Together, these data suggest that individuals who carry the rs3730477 POLL germline variant have an increased risk of estrogen-associated breast cancer. IMPLICATIONS The Pol λ R438W mutation can serve as a biomarker to predict cancer risk and implicates that treatment with estrogen in individuals with this mutation may further increase their risk of breast cancer. Mol Cancer Res; 14(11); 1068-77. ©2016 AACR.
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Affiliation(s)
- Antonia A Nemec
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut.
| | - Korie B Bush
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | | | - B Frazier Taylor
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut
| | - Vincent Schulz
- Department of Pediatrics, Yale University, New Haven, Connecticut
| | - Joanne B Weidhaas
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut.,Division of Molecular and Cellular Oncology, UCLA, Los Angeles, California
| | - David P Tuck
- Departmentof Pathology, Yale University, New Haven, Connecticut
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut.
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47
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Mentegari E, Kissova M, Bavagnoli L, Maga G, Crespan E. DNA Polymerases λ and β: The Double-Edged Swords of DNA Repair. Genes (Basel) 2016; 7:genes7090057. [PMID: 27589807 PMCID: PMC5042388 DOI: 10.3390/genes7090057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/30/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022] Open
Abstract
DNA is constantly exposed to both endogenous and exogenous damages. More than 10,000 DNA modifications are induced every day in each cell's genome. Maintenance of the integrity of the genome is accomplished by several DNA repair systems. The core enzymes for these pathways are the DNA polymerases. Out of 17 DNA polymerases present in a mammalian cell, at least 13 are specifically devoted to DNA repair and are often acting in different pathways. DNA polymerases β and λ are involved in base excision repair of modified DNA bases and translesion synthesis past DNA lesions. Polymerase λ also participates in non-homologous end joining of DNA double-strand breaks. However, recent data have revealed that, depending on their relative levels, the cell cycle phase, the ratio between deoxy- and ribo-nucleotide pools and the interaction with particular auxiliary proteins, the repair reactions carried out by these enzymes can be an important source of genetic instability, owing to repair mistakes. This review summarizes the most recent results on the ambivalent properties of these enzymes in limiting or promoting genetic instability in mammalian cells, as well as their potential use as targets for anticancer chemotherapy.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Miroslava Kissova
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Laura Bavagnoli
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
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48
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Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M. A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. EMBO J 2016; 35:2045-59. [PMID: 27481934 DOI: 10.15252/embj.201694332] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 11/09/2022] Open
Abstract
8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxo-dG) has high mutagenic potential as it is prone to mispair with deoxyadenine (dA). In order to maintain genomic integrity, post-replicative 8-oxo-dG:dA mispairs are removed through DNA polymerase lambda (Pol λ)-dependent MUTYH-initiated base excision repair (BER). Here, we describe seven novel crystal structures and kinetic data that fully characterize 8-oxo-dG bypass by Pol λ. We demonstrate that Pol λ has a flexible active site that can tolerate 8-oxo-dG in either the anti- or syn-conformation. Importantly, we show that discrimination against the pro-mutagenic syn-conformation occurs at the extension step and identify the residue responsible for this selectivity. This residue acts as a kinetic switch, shunting repair toward long-patch BER upon correct dCMP incorporation, thus enhancing repair efficiency. Moreover, this switch also provides a potential mechanism to increase repair fidelity of MUTYH-initiated BER.
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Affiliation(s)
- Matthew J Burak
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Kip E Guja
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elena Hambardjieva
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Burak Derkunt
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
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49
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Effects of 8-halo-7-deaza-2'-deoxyguanosine triphosphate on DNA synthesis by DNA polymerases and cell proliferation. Bioorg Med Chem 2016; 24:3856-61. [PMID: 27372838 DOI: 10.1016/j.bmc.2016.06.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 01/23/2023]
Abstract
8-OxodG (8-oxo-2'-deoxyguanosine) is representative of nucleoside damage and shows a genotoxicity. To significantly reveal the contributions of 7-NH and C8-oxygen to the mutagenic effect of 8-oxodG by DNA polymerases, we evaluated the effects of the 8-halo-7-deaza-dG (8-halogenated 7-deaza-2'-deoxyguanosine) derivatives by DNA polymerases. 8-Halo-7-deaza-dGTPs were poorly incorporated by both KF(exo(-)) and human DNA polymerase β opposite dC or dA into the template DNA. Furthermore, it was found that KF(exo(-)) was very sensitive to the introduction of the C8-halogen, while polymerase β can accommodate the C8-halogen resulting in an efficient dCTP insertion opposite the 8-halo-7-deaza-dG in the template DNA. These results indicate that strong hydrogen bonding between 7-NH in the 8-oxo-G nucleobase and 1-N in the adenine at the active site of the DNA polymerase is required for the mutagenic effects. Whereas, I-deaza-dGTP shows an antiproliferative effect for the HeLa cells, suggesting that it could become a candidate as a new antitumor agent.
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50
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Raper AT, Gadkari VV, Maxwell BA, Suo Z. Single-Molecule Investigation of Response to Oxidative DNA Damage by a Y-Family DNA Polymerase. Biochemistry 2016; 55:2187-96. [PMID: 27002236 DOI: 10.1021/acs.biochem.6b00166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Y-family DNA polymerases are known to bypass DNA lesions in vitro and in vivo and rescue stalled DNA replication machinery. Dpo4, a well-characterized model Y-family DNA polymerase, is known to catalyze translesion synthesis across a variety of DNA lesions including 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxo-dG). Our previous X-ray crystallographic, stopped-flow Förster resonance energy transfer (FRET), and computational simulation studies have revealed that Dpo4 samples a variety of global conformations as it recognizes and binds DNA. Here we employed single-molecule FRET (smFRET) techniques to investigate the kinetics and conformational dynamics of Dpo4 when it encountered 8-oxo-dG, a major oxidative lesion with high mutagenic potential. Our smFRET data indicated that Dpo4 bound the DNA substrate in multiple conformations, as suggested by three observed FRET states. An incoming correct or incorrect nucleotide affected the distribution and stability of these states with the correct nucleotide completely shifting the equilibrium toward a catalytically competent complex. Furthermore, the presence of the 8-oxo-dG lesion in the DNA stabilized both the binary and ternary complexes of Dpo4. Thus, our smFRET analysis provided a basis for the enhanced efficiency which Dpo4 is known to exhibit when replicating across from 8-oxo-dG.
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Affiliation(s)
- Austin T Raper
- Department of Chemistry and Biochemistry, †Ohio State Biochemistry Program and ‡Ohio State Biophysics Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Varun V Gadkari
- Department of Chemistry and Biochemistry, †Ohio State Biochemistry Program and ‡Ohio State Biophysics Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Brian A Maxwell
- Department of Chemistry and Biochemistry, †Ohio State Biochemistry Program and ‡Ohio State Biophysics Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, †Ohio State Biochemistry Program and ‡Ohio State Biophysics Program, The Ohio State University , Columbus, Ohio 43210, United States
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