1
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Lukina MV, Zhdanova PV, Koval VV. Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase. Curr Issues Mol Biol 2024; 46:4119-4132. [PMID: 38785521 PMCID: PMC11120029 DOI: 10.3390/cimb46050253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme's active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar-phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme-substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme-substrate complex.
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Affiliation(s)
- Maria V. Lukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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2
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Eckenroth BE, Bumgarner JD, Matsumoto-Elliott O, David S, Doublié S. Structural and biochemical insights into NEIL2's preference for abasic sites. Nucleic Acids Res 2023; 51:12508-12521. [PMID: 37971311 PMCID: PMC10711445 DOI: 10.1093/nar/gkad1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.
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Affiliation(s)
- Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA
| | - Joshua D Bumgarner
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Olivia Matsumoto-Elliott
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Sheila S David
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA
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3
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Dow LF, Case AM, Paustian MP, Pinkerton BR, Simeon P, Trippier PC. The evolution of small molecule enzyme activators. RSC Med Chem 2023; 14:2206-2230. [PMID: 37974956 PMCID: PMC10650962 DOI: 10.1039/d3md00399j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
There is a myriad of enzymes within the body responsible for maintaining homeostasis by providing the means to convert substrates to products as and when required. Physiological enzymes are tightly controlled by many signaling pathways and their products subsequently control other pathways. Traditionally, most drug discovery efforts focus on identifying enzyme inhibitors, due to upregulation being prevalent in many diseases and the existence of endogenous substrates that can be modified to afford inhibitor compounds. As enzyme downregulation and reduction of endogenous activators are observed in multiple diseases, the identification of small molecules with the ability to activate enzymes has recently entered the medicinal chemistry toolbox to afford chemical probes and potential therapeutics as an alternative means to intervene in diseases. In this review we highlight the progress made in the identification and advancement of non-kinase enzyme activators and their potential in treating various disease states.
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Affiliation(s)
- Louise F Dow
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Alfie M Case
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Megan P Paustian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Braeden R Pinkerton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Princess Simeon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE 68106 USA
- UNMC Center for Drug Discovery, University of Nebraska Medical Center Omaha NE 68106 USA
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4
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VRK1 Kinase Activity Modulating Histone H4K16 Acetylation Inhibited by SIRT2 and VRK-IN-1. Int J Mol Sci 2023; 24:ijms24054912. [PMID: 36902348 PMCID: PMC10003087 DOI: 10.3390/ijms24054912] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The accessibility of DNA to different cellular functions requires a dynamic regulation of chromatin organization that is mediated by different epigenetic modifications, which regulate chromatin accessibility and degree of compaction. These epigenetic modifications, particularly the acetylation of histone H4 in lysine 14 (H4K16ac), determine the degree of chromatin accessibility to different nuclear functions, as well as to DNA damage drugs. H4K16ac is regulated by the balance between two alternative histone modifications, acetylation and deacetylation, which are mediated by acetylases and deacetylases. Tip60/KAT5 acetylates, and SIRT2 deacetylates histone H4K16. However, the balance between these two epigenetic enzymes is unknown. VRK1 regulates the level of H4K16 acetylation by activating Tip60. We have shown that the VRK1 and SIRT2 are able to form a stable protein complex. For this work, we used in vitro interaction, pull-down and in vitro kinase assays. In cells, their interaction and colocalization were detected by immunoprecipitation and immunofluorescence. The kinase activity of VRK1 is inhibited by a direct interaction of its N-terminal kinase domain with SIRT2 in vitro. This interaction causes a loss of H4K16ac similarly to the effect of a novel VRK1 inhibitor (VRK-IN-1) or VRK1 depletion. The use of specific SIRT2 inhibitors in lung adenocarcinoma cells induces H4K16ac, contrary to the novel VRK-IN-1 inhibitor, which prevents H4K16ac and a correct DNA damage response. Therefore, the inhibition of SIRT2 can cooperate with VRK1 in the accessibility of drugs to chromatin in response to DNA damage caused by doxorubicin.
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5
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OGG1 in the Kidney: Beyond Base Excision Repair. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5774641. [PMID: 36620083 PMCID: PMC9822757 DOI: 10.1155/2022/5774641] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
8-Oxoguanine DNA glycosylase (OGG1) is a repair protein for 8-oxoguanine (8-oxoG) in eukaryotic atopic DNA. Through the initial base excision repair (BER) pathway, 8-oxoG is recognized and excised, and subsequently, other proteins are recruited to complete the repair. OGG1 is primarily located in the cytoplasm and can enter the nucleus and mitochondria to repair damaged DNA or to exert epigenetic regulation of gene transcription. OGG1 is involved in a wide range of physiological processes, such as DNA repair, oxidative stress, inflammation, fibrosis, and autophagy. In recent years, studies have found that OGG1 plays an important role in the progression of kidney diseases through repairing DNA, inducing inflammation, regulating autophagy and other transcriptional regulation, and governing protein interactions and functions during disease and injury. In particular, the epigenetic effects of OGG1 in kidney disease have gradually attracted widespread attention. This study reviews the structure and biological functions of OGG1 and the regulatory mechanism of OGG1 in kidney disease. In addition, the possibility of OGG1 as a potential therapeutic target in kidney disease is discussed.
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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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7
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Wang L, Jiang D, Zhang L. A thermophilic 8-oxoguanine DNA glycosylase from Thermococcus barophilus Ch5 is a new member of AGOG DNA glycosylase family. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1801-1810. [PMID: 35713316 PMCID: PMC10157611 DOI: 10.3724/abbs.2022072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
Abstract
8-Oxoguanine (8oxoG) in DNA is a major oxidized base that poses a severe threat to genome stability. To counteract the mutagenic effect generated by 8oxoG in DNA, cells have evolved 8oxoG DNA glycosylase (OGG) that can excise this oxidized base from DNA. Currently, OGG enzymes have been divided into three families: OGG1, OGG2 and AGOG (archaeal 8oxoG DNA glycosylase). Due to the limited reports, our understanding on AGOG enzymes remains incomplete. Herein, we present evidence that an AGOG from the hyperthermophilic euryarchaeon Ch5 (Tb-AGOG) excises 8oxoG from DNA at high temperature. The enzyme displays maximum efficiency at 75°C-95°C and at pH 9.0. As expected, Tb-AGOG is a bifunctional glycosylase that harbors glycosylase activity and AP (apurinic/apyrimidinic) lyase activity. Importantly, we reveal for the first time that residue D41 in Tb-AGOG is essential for 8oxoG excision and intermediate formation, but not essential for DNA binding or AP cleavage. Furthermore, residue E79 in Tb-AGOG is essential for 8oxoG excision and intermediate formation, and is partially involved in DNA binding and AP cleavage, which has not been described among the reported AGOG members to date. Overall, our work provides new insights into catalytic mechanism of AGOG enzymes.
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Affiliation(s)
- Lei Wang
- College of Environmental Science and EngineeringMarine Science & Technology InstituteYangzhou UniversityYangzhou225127China
| | - Donghao Jiang
- College of Environmental Science and EngineeringMarine Science & Technology InstituteYangzhou UniversityYangzhou225127China
| | - Likui Zhang
- College of Environmental Science and EngineeringMarine Science & Technology InstituteYangzhou UniversityYangzhou225127China
- Guangling CollegeYangzhou UniversityYangzhou225000China
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8
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OGG1 in Lung—More than Base Excision Repair. Antioxidants (Basel) 2022; 11:antiox11050933. [PMID: 35624797 PMCID: PMC9138115 DOI: 10.3390/antiox11050933] [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: 04/09/2022] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 12/04/2022] Open
Abstract
As the organ executing gas exchange and directly facing the external environment, the lungs are challenged continuously by various stimuli, causing the disequilibration of redox homeostasis and leading to pulmonary diseases. The breakdown of oxidants/antioxidants system happens when the overproduction of free radicals results in an excess over the limitation of cleaning capability, which could lead to the oxidative modification of macromolecules including nucleic acids. The most common type of oxidative base, 8-oxoG, is considered the marker of DNA oxidative damage. The appearance of 8-oxoG could lead to base mismatch and its accumulation might end up as tumorigenesis. The base 8-oxoG was corrected by base excision repair initiated by 8-oxoguanine DNA glycosylase-1 (OGG1), which recognizes 8-oxoG from the genome and excises it from the DNA double strand, generating an AP site for further processing. Aside from its function in DNA damage repairment, it has been reported that OGG1 takes part in the regulation of gene expression, derived from its DNA binding characteristic, and showed impacts on inflammation. Researchers believe that OGG1 could be the potential therapy target for relative disease. This review intends to make an overall summary of the mechanism through which OGG1 regulates gene expression and the role of OGG1 in pulmonary diseases.
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9
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Leptidis S, Papakonstantinou E, Diakou KI, Pierouli K, Mitsis T, Dragoumani K, Bacopoulou F, Sanoudou D, Chrousos GP, Vlachakis D. Epitranscriptomics of cardiovascular diseases (Review). Int J Mol Med 2022; 49:9. [PMID: 34791505 PMCID: PMC8651226 DOI: 10.3892/ijmm.2021.5064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.
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Affiliation(s)
- Stefanos Leptidis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Flora Bacopoulou
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Despina Sanoudou
- Fourth Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, Medical School, 'Attikon' Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - George P. Chrousos
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- First Department of Pediatrics, Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, Medical School, Aghia Sophia Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
- School of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
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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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11
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Trasviña-Arenas CH, Demir M, Lin WJ, David SS. Structure, function and evolution of the Helix-hairpin-Helix DNA glycosylase superfamily: Piecing together the evolutionary puzzle of DNA base damage repair mechanisms. DNA Repair (Amst) 2021; 108:103231. [PMID: 34649144 DOI: 10.1016/j.dnarep.2021.103231] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
The Base Excision Repair (BER) pathway is a highly conserved DNA repair system targeting chemical base modifications that arise from oxidation, deamination and alkylation reactions. BER features lesion-specific DNA glycosylases (DGs) which recognize and excise modified or inappropriate DNA bases to produce apurinic/apyrimidinic (AP) sites and coordinate AP-site hand-off to subsequent BER pathway enzymes. The DG superfamilies identified have evolved independently to cope with a wide variety of nucleobase chemical modifications. Most DG superfamilies recognize a distinct set of structurally related lesions. In contrast, the Helix-hairpin-Helix (HhH) DG superfamily has the remarkable ability to act upon structurally diverse sets of base modifications. The versatility in substrate recognition of the HhH-DG superfamily has been shaped by motif and domain acquisitions during evolution. In this paper, we review the structural features and catalytic mechanisms of the HhH-DG superfamily and draw a hypothetical reconstruction of the evolutionary path where these DGs developed diverse and unique enzymatic features.
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Affiliation(s)
| | - Merve Demir
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Wen-Jen Lin
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A..
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12
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Zhang L, Jiang D, Gan Q, Shi H, Miao L, Gong Y, Oger P. Identification of a novel bifunctional uracil DNA glycosylase from Thermococcus barophilus Ch5. Appl Microbiol Biotechnol 2021; 105:5449-5460. [PMID: 34223949 DOI: 10.1007/s00253-021-11422-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/22/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022]
Abstract
Genomes of hyperthermophiles are facing a severe challenge due to increased deamination rates of cytosine induced by high temperature, which could be counteracted by base excision repair mediated by uracil DNA glycosylase (UDG) or other repair pathways. Our previous work has shown that the two UDGs (Tba UDG247 and Tba UDG194) encoded by the genome of the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 can remove uracil from DNA at high temperature. Herein, we provide evidence that Tba UDG247 is a novel bifunctional glycosylase which can excise uracil from DNA and further cleave the phosphodiester bo nd of the generated apurinic/apyrimidinic (AP) site, which has never been described to date. In addition to cleaving uracil-containing DNA, Tba UDG247 can also cleave AP-containing ssDNA although at lower efficiency, thereby suggesting that the enzyme might be involved in repair of AP site in DNA. Kinetic analyses showed that Tba UDG247 displays a faster rate for uracil excision than for AP cleavage, thus suggesting that cleaving AP site by the enzyme is a rate-limiting step for its bifunctionality. Phylogenetic analysis showed that Tba UDG247 is clustered on a separate branch distant from all the reported UDGs. Overall, we designated Tba UDG247 as the prototype of a novel family of bifunctional UDGs. KEY POINTS: We first reported a novel DNA glycosylase with bifunctionality. Tba UDG247 possesses an AP lyase activity.
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Affiliation(s)
- Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China.
- Guangling College, Yangzhou University, Yangzhou, China.
| | - Donghao Jiang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Qi Gan
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Haoqiang Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Li Miao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Guangzhou, China.
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
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13
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Lebedeva NA, Rechkunova NI, Endutkin AV, Lavrik OI. Apurinic/Apyrimidinic Endonuclease 1 and Tyrosyl-DNA Phosphodiesterase 1 Prevent Suicidal Covalent DNA-Protein Crosslink at Apurinic/Apyrimidinic Site. Front Cell Dev Biol 2021; 8:617301. [PMID: 33505969 PMCID: PMC7833210 DOI: 10.3389/fcell.2020.617301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Bifunctional 8-oxoguanine-DNA glycosylase (OGG1), a crucial DNA-repair enzyme, removes from DNA 8-oxo-7,8-dihydroguanine (8-oxoG) with following cleavage of the arising apurinic/apyrimidinic (AP) site. The major enzyme in eukaryotic cells that catalyzes the cleavage of AP sites is AP endonuclease 1 (APE1). Alternatively, AP sites can be cleaved by tyrosyl-DNA phosphodiesterase 1 (TDP1) to initiate APE1-independent repair, thus expanding the ability of the base excision repair (BER) process. Poly(ADP-ribose) polymerase 1 (PARP1) is a regulatory protein of DNA repair. PARP2 is also activated in response to DNA damage and can be regarded as the BER participant. Here we analyze PARP1 and PARP2 interactions with DNA intermediates of the initial stages of the BER process (8-oxoG and AP-site containing DNA) and their interplay with the proteins recognizing and processing these DNA structures focusing on OGG1. OGG1 as well as PARP1 and PARP2 form covalent complex with AP site-containing DNA without borohydride reduction. AP site incision by APE1 or TDP1 removal of protein adducts but not proteins’ PARylation prevent DNA-protein crosslinks.
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Affiliation(s)
- Natalia A Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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14
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Jain R, Dhiman S, Grogan DW. Genetic Control of Oxidative Mutagenesis in Sulfolobus acidocaldarius. J Bacteriol 2020; 202:JB.00756-19. [PMID: 32482723 PMCID: PMC8404708 DOI: 10.1128/jb.00756-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/26/2020] [Indexed: 02/01/2023] Open
Abstract
To identify DNA-oxidation defenses of hyperthermophilic archaea, we deleted genes encoding the putative 7,8-dihydro-8-oxoguanine (oxoG)-targeted N-glycosylase of S. acidocaldarius (ogg; Saci_01367), the Y-family DNA polymerase (dbh; Saci_0554), or both, and measured the effects on cellular survival, replication accuracy, and oxoG bypass in vivo Spontaneous G:C to T:A transversions were elevated in all Δogg and Δdbh constructs, and the Δogg Δdbh double mutant lost viability at a faster rate than isogenic WT and ogg strains. The distribution of G:C to T:A transversions within mutation-detector genes suggested that reactivity of G toward oxidation and the effect on translation contribute heavily to the pattern of mutations that are recovered. An impact of the Ogg protein on overall efficiency of bypassing oxoG in transforming DNA was evident only in the absence of Dbh, and Ogg status did not affect the accuracy of bypass. Dbh function, in contrast, dramatically influenced both the efficiency and accuracy of oxoG bypass. Thus, Ogg and Dbh were found to work independently to avoid mutagenesis by oxoG, and inactivating this simple but effective defense system by deleting both genes imposed a severe mutational burden on S. acidocaldarius cells.IMPORTANCE Hyperthermophilic archaea are expected to have effective (and perhaps atypical) mechanisms to limit the genetic consequences of DNA damage, but few gene products have been demonstrated to have genome-preserving functions in vivo This study confirmed by genetic criteria that the S. acidocaldarius Ogg protein avoids the characteristic mutagenesis of G oxidation. This enzyme and the bypass polymerase Dbh have similar impacts on genome stability but work independently, and may comprise most of the DNA-oxidation defense of S. acidocaldarius The critical dependence of accurate oxoG bypass on the accessory DNA polymerase Dbh further argues that some form of polymerase exchange is important for accurate genome replication in Sulfolobus, and perhaps in related hyperthermophilic archaea.
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Affiliation(s)
- Rupal Jain
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
| | - Samuel Dhiman
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
| | - Dennis W Grogan
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
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15
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Gehring AM, Zatopek KM, Burkhart BW, Potapov V, Santangelo TJ, Gardner AF. Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis. DNA Repair (Amst) 2020; 86:102767. [PMID: 31841800 PMCID: PMC8061334 DOI: 10.1016/j.dnarep.2019.102767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022]
Abstract
Reactive oxygen species drive the oxidation of guanine to 8-oxoguanine (8oxoG), which threatens genome integrity. The repair of 8oxoG is carried out by base excision repair enzymes in Bacteria and Eukarya, however, little is known about archaeal 8oxoG repair. This study identifies a member of the Ogg-subfamily archaeal GO glycosylase (AGOG) in Thermococcus kodakarensis, an anaerobic, hyperthermophilic archaeon, and delineates its mechanism, kinetics, and substrate specificity. TkoAGOG is the major 8oxoG glycosylase in T. kodakarensis, but is non-essential. In addition to TkoAGOG, the major apurinic/apyrimidinic (AP) endonuclease (TkoEndoIV) required for archaeal base excision repair and cell viability was identified and characterized. Enzymes required for the archaeal oxidative damage base excision repair pathway were identified and the complete pathway was reconstituted. This study illustrates the conservation of oxidative damage repair across all Domains of life.
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Affiliation(s)
| | | | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
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16
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Tee JK, Yip LX, Tan ES, Santitewagun S, Prasath A, Ke PC, Ho HK, Leong DT. Nanoparticles' interactions with vasculature in diseases. Chem Soc Rev 2019; 48:5381-5407. [PMID: 31495856 DOI: 10.1039/c9cs00309f] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ever-growing use of inorganic nanoparticles (NPs) in biomedicine provides an exciting approach to develop novel imaging and drug delivery systems, owing to the ease with which these NPs can be functionalized to cater to various applications. In cancer therapeutics, nanomedicine generally relies on the enhanced permeability and retention (EPR) effect observed in tumour vasculature to deliver anti-cancer drugs across the endothelium. However, such a phenomenon is dependent on the tumour microenvironment and is not consistently observed in all tumour types, thereby limiting drug transport to the tumour site. On the other hand, there is a rise in utilizing inorganic NPs to intentionally induce endothelial leakiness, creating a window of opportunity to control drug delivery across the endothelium. While this active targeting approach creates a similar phenomenon compared to the EPR effect arising from tumour tissues, its drug delivery applications extend beyond cancer therapeutics and into other vascular-related diseases. In this review, we summarize the current findings of the EPR effect and assess its limitations in the context of anti-cancer drug delivery systems. While the EPR effect offers a possible route for drug passage, we further explore alternative uses of NPs to create controllable endothelial leakiness within short exposures, a phenomenon we coined as nanomaterial-induced endothelial leakiness (NanoEL). Furthermore, we discuss the main mechanistic features of the NanoEL effect that make it unique from conventionally established endothelial leakiness in homeostatic and pathologic conditions, as well as examine its potential applicability in vascular-related diseases, particularly cancer. Therefore, this new paradigm changes the way inorganic NPs are currently being used for biomedical applications.
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Affiliation(s)
- Jie Kai Tee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
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17
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Transcriptional Fidelity of Mitochondrial RNA Polymerase RpoTm from Arabidopsis thaliana. J Mol Biol 2019; 431:4767-4783. [PMID: 31626802 DOI: 10.1016/j.jmb.2019.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 05/30/2019] [Accepted: 08/26/2019] [Indexed: 11/21/2022]
Abstract
Fidelity of RNA synthesis is essential for the faithful transfer of information from DNA to RNA. A comprehensive analysis of the nucleotide selectivity by the mitochondrial RNA polymerase (RNAP) RpoTm, from Arabidopsis thaliana, has been carried out. The kinetic parameters for the incorporation of cognate, noncognate, and oxidized bases have been determined. The results establish high fidelity of mitochondrial transcription resembling those of replicative polymerases in the absence of repair. In addition, RpoTm incorporates oxidized nucleotides with similar efficiency compared with mismatches and is capable of extending the RNA beyond the insertion of the oxidized base. Furthermore, lesion bypass study on RpoTm demonstrates that the enzyme bypasses 8-oxo-guanine by insertion of adenine leading to C to A mutations in RNA. Homology modeling of RpoTm elongation complex allows delineation of the residues necessary for stabilizing the incoming NTP substrate and for posing the template nucleotide residue. Substitution of these residues leads to compromise in the activity of the enzyme corroborating their importance in RNA synthesis. Comparison of the data with T7 RNAPs indicates that low efficiency of misincorporation is a universal strategy used by single-subunit RNAPs for maintaining high fidelity in the absence of proofreading and repair activity in mitochondria.
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18
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Su CH, Chen JW, Chen LD, Chang JC, Liu CS, Chang CC, Wang GJ. Organic small molecule for detection and photodegradation of mitochondrial DNA mutations. J Mater Chem B 2019; 7:5947-5955. [PMID: 31517375 DOI: 10.1039/c9tb01358j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detection and degradation platform was developed to optically quantify the 6-enolate, 8-keto-dG, an important tautomer of mitochondrial mutated DNA 8-oxo-dG. We first found that 6-enolate, 8-keto-dG offers particular fluorescence emission under the conditions between pH ∼ 7 and ∼11. Thus, a mitochondria-targeting photosensitizer NV-12P was prepared to offer simultaneously photoinduced electron transfer and fluorescence resonance energy transfer (FRET) with 6-enolate, 8-keto-dG. Furthermore, NV-12P can also generate a reactive oxygen species to degrade 6-enolate, 8-keto-dG under irradiation conditions. This is the first publication about optical characterization, concentration detection and photodegradation of 6-enolate, 8-keto-dG, either in biological or in vitro applications.
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Affiliation(s)
- Chien-Hui Su
- Department of Mechanical Engineering, National Chung-Hsing University, Taichung, Taiwan
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19
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Zhang L, Li Y, Shi H, Zhang D, Yang Z, Oger P, Zheng J. Biochemical characterization and mutational studies of the 8-oxoguanine DNA glycosylase from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans. Appl Microbiol Biotechnol 2019; 103:8021-8033. [PMID: 31372707 DOI: 10.1007/s00253-019-10031-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022]
Abstract
8-oxoguanine (GO) is a major lesion found in DNA that arises from guanine oxidation. The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes an archaeal GO DNA glycosylase (Tg-AGOG). Here, we characterized biochemically Tg-AGOG and probed its GO removal mechanism by mutational studies. Tg-AGOG can remove GO from DNA at high temperature through a β-elimination reaction. The enzyme displays an optimal temperature, ca.85-95 °C, and an optimal pH, ca.7.0-8.5. In addition, Tg-AGOG activity is independent on a divalent metal ion. However, both Co2+ and Cu2+ inhibit its activity. The enzyme activity is also inhibited by NaCl. Furthermore, Tg-AGOG specifically cleaves GO-containing dsDNA in the order: GO:C, GO:T, GO:A, and GO:G. Moreover, the temperature dependence of cleavage rates of the enzyme was determined, and from this, the activation energy for GO removal from DNA was first estimated to be 16.9 ± 0.9 kcal/mol. In comparison with the wild-type Tg-AGOG, the R197A mutant has a reduced cleavage activity for GO-containing DNA, whereas both the P193A and F167A mutants exhibit similar cleavage activities for GO-containing DNA. While the mutations of P193 and F167 to Ala lead to increased binding, the mutation of R197 to Ala had no significant effect on binding. These observations suggest that residue R197 is involved in catalysis, and residues P193 and F167 are flexible for conformational change.
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Affiliation(s)
- Likui Zhang
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yuting Li
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China
| | - Haoqiang Shi
- Department of Environmental Science and Engineering Marine Science & Technology Institute, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dai Zhang
- College of Plant Protection, Agricultural University of Hebei, Baoding City, 071001, Hebei Province, China
| | - Zhihui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding City, 071001, Hebei Province, China.
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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20
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Garutti M, Pelizzari G, Bartoletti M, Malfatti MC, Gerratana L, Tell G, Puglisi F. Platinum Salts in Patients with Breast Cancer: A Focus on Predictive Factors. Int J Mol Sci 2019; 20:E3390. [PMID: 31295913 PMCID: PMC6678596 DOI: 10.3390/ijms20143390] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most frequent oncologic cause of death among women and the improvement of its treatments is compelling. Platinum salts (e.g., carboplatin, cisplatin, and oxaliplatin) are old drugs still used to treat BC, especially the triple-negative subgroup. However, only a subset of patients see a concrete benefit from these drugs, raising the question of how to select them properly. Therefore, predictive biomarkers for platinum salts in BC still represent an unmet clinical need. Here, we review clinical and preclinical works in order to summarize the current evidence about predictive or putative platinum salt biomarkers in BC. The association between BRCA1/2 gene mutations and platinum sensitivity has been largely described. However, beyond the mutations of these two genes, several other proteins belonging to the homologous recombination pathways have been linked to platinum response, defining the concept of BRCAness. Several works, here reviewed, have tried to capture BRCAness through different strategies, such as homologous recombination deficiency (HRD) score and genetic signatures. Moreover, p53 and its family members (p63 and p73) might also be used as predictors of platinum response. Finally, we describe the mounting preclinical evidence regarding base excision repair deficiency as a possible new platinum biomarker.
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Affiliation(s)
- Mattia Garutti
- U.O.C Oncologia Medica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Giacomo Pelizzari
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Michele Bartoletti
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | | | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Gianluca Tell
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy.
- Dipartimento di Oncologia Medica, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.
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21
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Lawson T, El-Kamand S, Kariawasam R, Richard DJ, Cubeddu L, Gamsjaeger R. A Structural Perspective on the Regulation of Human Single-Stranded DNA Binding Protein 1 (hSSB1, OBFC2B) Function in DNA Repair. Comput Struct Biotechnol J 2019; 17:441-446. [PMID: 30996823 PMCID: PMC6451162 DOI: 10.1016/j.csbj.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Single-stranded DNA binding (SSB) proteins are essential to protect singe-stranded DNA (ssDNA) that exists as a result of several important DNA repair pathways in living cells. In humans, besides the well-characterised Replication Protein A (RPA) we have described another SSB termed human SSB1 (hSSB1, OBFC2B) and have shown that this protein is an important player in the maintenance of the genome. In this review we define the structural and biophysical details of how hSSB1 interacts with both DNA and other essential proteins. While the presence of the oligonucleotide/oligosaccharide (OB) domain ensures ssDNA binding by hSSB1, it has also been shown to self-oligomerise as well as interact with and being modified by several proteins highlighting the versatility that hSSB1 displays in the context of DNA repair. A detailed structural understanding of these processes will likely lead to the designs of tailored hSSB1 inhibitors as anti-cancer drugs in the near future.
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Affiliation(s)
- Teegan Lawson
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Serene El-Kamand
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Derek J Richard
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland 4102, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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22
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Alnajjar KS, Sweasy JB. A new perspective on oxidation of DNA repair proteins and cancer. DNA Repair (Amst) 2019; 76:60-69. [PMID: 30818170 DOI: 10.1016/j.dnarep.2019.02.006] [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: 12/17/2018] [Revised: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Reactive oxygen and nitrogen species (RONS) are formed as byproducts of many endogenous cellular processes, in response to infections, and upon exposure to various environmental factors. An increase in RONS can saturate the antioxidation system and leads to oxidative stress. Consequently, macromolecules are targeted for oxidative modifications, including DNA and protein. The oxidation of DNA, which leads to base modification and formation of abasic sites along with single and double strand breaks, has been extensively investigated. Protein oxidation is often neglected and is only recently being recognized as an important regulatory mechanism of various DNA repair proteins. This is a review of the current state of research on the regulation of DNA repair by protein oxidation with emphasis on the correlation between inflammation and cancer.
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Affiliation(s)
- Khadijeh S Alnajjar
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, United States.
| | - Joann B Sweasy
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, United States
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23
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Lukina MV, Koval VV, Lomzov AA, Zharkov DO, Fedorova OS. Global DNA dynamics of 8-oxoguanine repair by human OGG1 revealed by stopped-flow kinetics and molecular dynamics simulation. MOLECULAR BIOSYSTEMS 2018; 13:1954-1966. [PMID: 28770925 DOI: 10.1039/c7mb00343a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The toxic action of different endogenous and exogenous agents leads to damage in genomic DNA. 8-Oxoguanine is one of the most often generated and highly mutagenic oxidative forms of damage in DNA. Normally, in human cells it is promptly removed by 8-oxoguanine-DNA-glycosylase hOGG1, the key DNA-repair enzyme. An association between the accumulation of oxidized guanine and an increased risk of harmful processes in organisms was already found. However, the detailed mechanism of damaged base recognition and removal is still unclear. To clarify the role of active site amino acids in the damaged base coordination and to reveal the elementary steps in the overall enzymatic process we investigated hOGG1 mutant forms with substituted amino acid residues in the enzyme base-binding pocket. Replacing the functional groups of the enzyme active site allowed us to change the rates of the individual steps of the enzymatic reaction. To gain further insight into the mechanism of hOGG1 catalysis a detailed pre-steady state kinetic study of this enzymatic process was carried out using the stopped-flow approach. The changes in the DNA structure after mixing with enzymes were followed by recording the FRET signal using Cy3/Cy5 labels in DNA substrates in the time range from milliseconds to hundreds of seconds. DNA duplexes containing non-damaged DNA, 8-oxoG, or an AP-site or its unreactive synthetic analogue were used as DNA-substrates. The kinetic parameters of DNA binding and damage processing were obtained for the mutant forms and for WT hOGG1. The analyses of fluorescence traces provided information about the DNA dynamics during damage recognition and removal. The kinetic study for the mutant forms revealed that all introduced substitutions reduced the efficiency of the hOGG1 activity; however, they played pivotal roles at certain elementary stages identified during the study. Taken together, our results gave the opportunity to restore the role of substituted amino acids and main "damaged base-amino acid" contacts, which provide an important link in the understanding the mechanism of the DNA repair process catalyzed by hOGG1.
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Affiliation(s)
- M V Lukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia.
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24
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Urinary levels of sirtuin-1 associated with disease activity in lupus nephritis. Clin Sci (Lond) 2018; 132:569-579. [PMID: 29440621 DOI: 10.1042/cs20171410] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/15/2018] [Accepted: 02/09/2018] [Indexed: 12/26/2022]
Abstract
Identifying new markers of disease flares in lupus nephritis (LN) that facilitate patient stratification and prognosis is important. Therefore, the aim of the present study was to analyze whether urinary SIRT1 expression was altered in LN and whether SIRT1 values in urine could be valuable biomarker of disease activity. In a cohort study, urinary pellets from 40 patients diagnosed with systemic lupus erythematosus (SLE) were analyzed. Clinical measures of lupus activity were assessed. The expression of SIRT1 was quantified by quantitative PCR (qRT-PCR) and immunoblot, then compared between patients with active lupus nephritis, in remission and healthy controls. Association with lupus activity and renal histological features was also analyzed. A significant increase in SIRT1 mRNA levels in patients with active LN was observed compared with those in remission (P=0.02) or healthy controls (P=0.009). In addition, SIRT-1 protein levels were also augmented in LN group than remission (P=0.029) and controls (P=0.001). A strong association was found between SIRT1 expression with anti-dsDNA in SLE and in patients with LN. In addition, histological features in LN biopsies were related with SIRT1, increasing its expression in proliferative forms. Finally, SIRT1 expression values showed a strong discriminatory power of renal injury in SLE. Our study demonstrated an altered urinary expression of SIRT1 and a strong association with disease activity in LN patients, being a valuable marker of renal injury. These results showed the role of the SIRT1 pathway in the SLE pathogenesis.
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Association between the 8-oxoguanine DNA glycosylase gene Ser326Cys polymorphism and age-related cataract: a systematic review and meta-analysis. Int Ophthalmol 2017. [PMID: 28631182 DOI: 10.1007/s10792-017-0606-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE To investigate the association between the 8-oxoguanine DNA glycosylase (OGG1) gene Ser326Cys (rs1052133) polymorphism and age-related cataract (ARC). METHODS MEDLINE and EMBASE were searched to identify potential studies published before May 19, 2017, investigating the association between the OGG1 gene Ser326Cys polymorphism and ARC risk. The quality of eligible studies was assessed using the Newcastle-Ottawa Scale tool. The association between the OGG1 gene Ser326Cys polymorphism and ARC was analyzed using meta-analysis. Publication bias and sensitivity analyses were also performed. RESULTS Six studies were included in this systematic review, and five of these studies with Hardy-Weinberg equilibrium were included in a meta-analysis. The sample size of the meta-analysis was 3716, including 1831 patients with cataract and 1885 controls. Odds ratios (ORs) were 0.67 (95% confidence interval (CI) 0.52-0.85), 0.90 (95% CI 0.54-1.51), 0.52 (95% CI 0.32-0.85) and 0.72 (95% CI 0.56-0.92) for recessive, dominant, additive and allele contrast models, respectively. Sensitivity analysis indicated that the results of the meta-analysis were robust. No publication bias was observed. CONCLUSIONS The OGG1 gene Ser326Cys polymorphism was associated with ARC risk.
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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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Esadze A, Rodriguez G, Cravens SL, Stivers JT. AP-Endonuclease 1 Accelerates Turnover of Human 8-Oxoguanine DNA Glycosylase by Preventing Retrograde Binding to the Abasic-Site Product. Biochemistry 2017; 56:1974-1986. [PMID: 28345889 DOI: 10.1021/acs.biochem.7b00017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A major product of oxidative DNA damage is 8-oxoguanine. In humans, 8-oxoguanine DNA glycosylase (hOGG1) facilitates removal of these lesions, producing an abasic (AP) site in the DNA that is subsequently incised by AP-endonuclease 1 (APE1). APE1 stimulates turnover of several glycosylases by accelerating rate-limiting product release. However, there have been conflicting accounts of whether hOGG1 follows a similar mechanism. In pre-steady-state kinetic measurements, we found that addition of APE1 had no effect on the rapid burst phase of 8-oxoguanine excision by hOGG1 but accelerated steady-state turnover (kcat) by ∼10-fold. The stimulation by APE1 required divalent cations, could be detected under multiple-turnover conditions using limiting concentrations of APE1, did not require flanking DNA surrounding the hOGG1 lesion site, and occurred efficiently even when the first 49 residues of APE1's N-terminus had been deleted. Stimulation by APE1 does not involve relief from product inhibition because thymine DNA glycosylase, an enzyme that binds more tightly to AP sites than hOGG1 does, could not effectively substitute for APE1. A stimulation mechanism involving stable protein-protein interactions between free APE1 and hOGG1, or the DNA-bound forms, was excluded using protein cross-linking assays. The combined results indicate a mechanism whereby dynamic excursions of hOGG1 from the AP site allow APE1 to invade the site and rapidly incise the phosphate backbone. This mechanism, which allows APE1 to access the AP site without forming specific interactions with the glycosylase, is a simple and elegant solution to passing along unstable intermediates in base excision repair.
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Affiliation(s)
- Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Gaddiel Rodriguez
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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Prakash A, Doublié S. Base Excision Repair in the Mitochondria. J Cell Biochem 2016; 116:1490-9. [PMID: 25754732 DOI: 10.1002/jcb.25103] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 01/23/2015] [Indexed: 01/01/2023]
Abstract
The 16.5 kb human mitochondrial genome encodes for 13 polypeptides, 22 tRNAs and 2 rRNAs involved in oxidative phosphorylation. Mitochondrial DNA (mtDNA), unlike its nuclear counterpart, is not packaged into nucleosomes and is more prone to the adverse effects of reactive oxygen species (ROS) generated during oxidative phosphorylation. The past few decades have witnessed an increase in the number of proteins observed to translocate to the mitochondria for the purposes of mitochondrial genome maintenance. The mtDNA damage produced by ROS, if not properly repaired, leads to instability and can ultimately manifest in mitochondrial dysfunction and disease. The base excision repair (BER) pathway is employed for the removal and consequently the repair of deaminated, oxidized, and alkylated DNA bases. Specialized enzymes called DNA glycosylases, which locate and cleave the damaged base, catalyze the first step of this highly coordinated repair pathway. This review focuses on members of the four human BER DNA glycosylase superfamilies and their subcellular localization in the mitochondria and/or the nucleus, as well as summarizes their structural features, biochemical properties, and functional role in the excision of damaged bases.
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Affiliation(s)
- Aishwarya Prakash
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont
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Lenz SAP, Kellie JL, Wetmore SD. Glycosidic Bond Cleavage in DNA Nucleosides: Effect of Nucleobase Damage and Activation on the Mechanism and Barrier. J Phys Chem B 2015; 119:15601-12. [PMID: 26618397 DOI: 10.1021/acs.jpcb.5b10337] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan A. P. Lenz
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Jennifer L. Kellie
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Kellie JL, Wilson KA, Wetmore SD. An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine–DNA Glycosylase (hOgg1). J Phys Chem B 2015; 119:8013-23. [PMID: 26018802 DOI: 10.1021/acs.jpcb.5b04051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
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Mukherjee B, Bindhani B, Saha H, Ray MR. Increased oxidative DNA damage and decreased expression of base excision repair proteins in airway epithelial cells of women who cook with biomass fuels. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 38:341-352. [PMID: 25128766 DOI: 10.1016/j.etap.2014.06.010] [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: 10/30/2013] [Revised: 05/08/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
To investigate whether biomass burning causes oxidative DNA damage and alters the expression of DNA base excision repair (BER) proteins in airway cells, sputum samples were collected from 80 premenopausal rural biomass-users and 70 age-matched control women who cooked with liquefied petroleum gas. Compared with control the airway cells of biomass-users showed increased DNA damage in alkaline comet assay. Biomass-users showed higher percentage of cells expressing oxidative DNA damage marker 8-oxoguanine and lower percentages of BER proteins OGG1 and APE1 by immunocytochemical staining. Reactive oxygen species (ROS) generation was doubled and level of superoxide dismutase was depleted significantly among biomass-users. The concentrations of particulate matters were higher in biomass-using households which positively correlated with ROS generation and negatively with BER proteins expressions. ROS generation was positively correlated with 8-oxoguanine and negatively with BER proteins suggesting cooking with biomass is a risk for genotoxicity among rural women in their child-bearing age.
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Affiliation(s)
- Bidisha Mukherjee
- Department of Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata 700 026, India
| | - Banani Bindhani
- Department of Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata 700 026, India
| | - Hirak Saha
- Department of Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata 700 026, India
| | - Manas Ranjan Ray
- Department of Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata 700 026, India.
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Akasheva DU, Plokhova EV, Strazhesko ID, Dudinskaya EN, Tkacheva ON. HEART AND AGE (PART III): MODIFYING AGEING PROCESSES. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2013. [DOI: 10.15829/1728-8800-2013-5-91-96] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Panikkanvalappil SR, Mackey MA, El-Sayed MA. Probing the Unique Dehydration-Induced Structural Modifications in Cancer Cell DNA Using Surface Enhanced Raman Spectroscopy. J Am Chem Soc 2013; 135:4815-21. [DOI: 10.1021/ja400187b] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sajanlal R. Panikkanvalappil
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Megan A. Mackey
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Mostafa A. El-Sayed
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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Oxidative Stress and DNA Damage in Human Gastric Carcinoma: 8-Oxo-7'8-dihydro-2'-deoxyguanosine (8-oxo-dG) as a Possible Tumor Marker. Int J Mol Sci 2013; 14:3467-86. [PMID: 23389043 PMCID: PMC3588053 DOI: 10.3390/ijms14023467] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/08/2013] [Accepted: 01/11/2013] [Indexed: 11/22/2022] Open
Abstract
We characterized the oxidative stress (OS) status by the levels of reduced/oxidized glutathione (GSH/GSSG), malondialdehyde (MDA) and the mutagenic base 8-oxo-7′8-dihydro-2′-deoxyguanosine (8-oxo-dG) in human gastric carcinoma (HGC) samples and compared the results with normal tissue from the same patients. We also analyzed 8-oxo-dG in peripheral mononuclear cells (PMNC) and urine from healthy control subjects and in affected patients in the basal state and one, three, six, nine and twelve months after tumor resection. The levels of DNA repair enzyme mRNA expression (hOGG1, RAD51, MUYTH and MTH1) were determined in tumor specimens and compared with normal mucosa. Tumor specimens exhibited increased levels of MDA and 8-oxo-dG compared with normal gastric tissue. GSH levels were also increased, while GSSG levels remained stable. DNA repair enzyme mRNA expression was induced in the tumor tissues. Levels of 8-oxo-dG were significantly elevated in both urine and PMNC of gastric cancer patients compared with healthy controls. After gastrectomy, the levels of the damaged base in urine and PMNC decreased progressively to values close to those found in the healthy population. The high levels of 8-oxo-dG in urine may be related to the increased induction of DNA repair activity in tumor tissue, and the changes observed after tumor resection support its potential use as a tumor marker.
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Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Recent advances in the structural mechanisms of DNA glycosylases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:247-71. [PMID: 23076011 DOI: 10.1016/j.bbapap.2012.10.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/24/2012] [Accepted: 10/05/2012] [Indexed: 02/06/2023]
Abstract
DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities.
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Affiliation(s)
- Sonja C Brooks
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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