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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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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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3
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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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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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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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Barbier E, Lagorce A, Hachemi A, Dutertre M, Gorlas A, Morand L, Saint-Pierre C, Ravanat JL, Douki T, Armengaud J, Gasparutto D, Confalonieri F, Breton J. Oxidative DNA Damage and Repair in the Radioresistant Archaeon Thermococcus gammatolerans. Chem Res Toxicol 2016; 29:1796-1809. [PMID: 27676238 DOI: 10.1021/acs.chemrestox.6b00128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hyperthermophilic archaeon Thermococcus gammatolerans can resist huge doses of γ-irradiation, up to 5.0 kGy, without loss of viability. The potential to withstand such harsh conditions is probably due to complementary passive and active mechanisms, including repair of damaged chromosomes. In this work, we documented the formation and repair of oxidative DNA lesions in T. gammatolerans. The basal level of the oxidized nucleoside, 8-oxo-2'-deoxyguanosine (8-oxo-dGuo), was established at 9.2 (± 0.9) 8-oxo-dGuo per 106 nucleosides, a higher level than those usually measured in eukaryotic cells or bacteria. A significant increase in oxidative damage, i.e., up to 24.2 (± 8.0) 8-oxo-dGuo/106 nucleosides, was measured for T. gammatolerans exposed to a 5.0 kGy dose of γ-rays. Surprisingly, the yield of radiation-induced modifications was lower than those previously observed for human cells exposed to doses corresponding to a few grays. One hour after irradiation, 8-oxo-dGuo levels were significantly reduced, indicating an efficient repair. Two putative base excision repair (BER) enzymes, TGAM_1277 and TGAM_1653, were demonstrated both by proteomics and transcriptomics to be present in the cells without exposure to ionizing radiation. Their transcripts were moderately upregulated after gamma irradiation. After heterologous production and purification of these enzymes, biochemical assays based on electrophoresis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry indicated that both have a β-elimination cleavage activity. TGAM_1653 repairs 8-oxo-dGuo, whereas TGAM_1277 is also able to remove lesions affecting pyrimidines (1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxyhydantoin (5-OH-dHyd) and 1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd)). This work showed that in normal growth conditions or in the presence of a strong oxidative stress, T. gammatolerans has the potential to rapidly reduce the extent of DNA oxidation, with at least these two BER enzymes as bodyguards with distinct substrate ranges.
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Affiliation(s)
- Ewa Barbier
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Arnaud Lagorce
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France.,University of Perpignan, IHPE - UMR 5244 CNRS/IFREMER/Univ. Montpellier, Montpellier, F-34095, France
| | - Amine Hachemi
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Aurore Gorlas
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Lucie Morand
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Christine Saint-Pierre
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Thierry Douki
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean Armengaud
- CEA, DSV-Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, Bagnols-sur-Cèze, F-30207, France
| | - Didier Gasparutto
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Fabrice Confalonieri
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Jean Breton
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
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Yu H, Yang M, Zhang XE, Bi L, Jiang T. Crystal structures of MBOgg1 in complex with two abasic DNA ligands. J Struct Biol 2012; 181:252-63. [PMID: 23246782 DOI: 10.1016/j.jsb.2012.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/29/2012] [Accepted: 12/02/2012] [Indexed: 11/16/2022]
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative DNA lesions. 8-oxoguanine DNA glycosylases (Oggs) detect and excise 8-oxoG through a multiple-step process. To better understand the basis for estranged base recognition, we have solved the crystal structures of MBOgg1, the 8-oxoguanine DNA glycosylase of Thermoanaerobacter tengcongensis, in complex with DNA containing a tetrahydrofuranyl site (THF, a stable abasic site analog) paired with an estranged cytosine (MBOgg1/DNA(THF:C)) or thymine (MBOgg1/DNA(THF:T)). Different states of THF (extrahelical or intrahelical) are observed in the two complexes of the ASU of MBOgg1/DNA(THF:C) structure. Analyses of their different interaction modes reveal that variable contacts on the 5' region flanking the THF abasic site are correlated with the states of the THF. Comparison of MBOgg1/DNA(THF:T) with MBOgg1/DNA(THF:C) indicates that the non-preferred estranged T may affect MBOgg1's contacts with the 5' flank of the lesion strand. Furthermore, we identified a region in MBOgg1 that is rich in positive charges and interacts with the 5' region flanking the lesion. This region is conserved only in non-eukaryotic Oggs, and additional mutagenesis and biochemical assays reveal that it may contribute to the distinct estranged base specificities between eukaryotic and non-eukaryotic Oggs.
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Affiliation(s)
- Hongjun Yu
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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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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Faucher F, Doublié S, Jia Z. 8-oxoguanine DNA glycosylases: one lesion, three subfamilies. Int J Mol Sci 2012; 13:6711-6729. [PMID: 22837659 PMCID: PMC3397491 DOI: 10.3390/ijms13066711] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/14/2012] [Accepted: 05/24/2012] [Indexed: 11/24/2022] Open
Abstract
Amongst the four bases that form DNA, guanine is the most susceptible to oxidation, and its oxidation product, 7,8-dihydro-8-oxoguanine (8-oxoG) is the most prevalent base lesion found in DNA. Fortunately, throughout evolution cells have developed repair mechanisms, such as the 8-oxoguanine DNA glycosylases (OGG), which recognize and excise 8-oxoG from DNA thereby preventing the accumulation of deleterious mutations. OGG are divided into three subfamilies, OGG1, OGG2 and AGOG, which are all involved in the base excision repair (BER) pathway. The published structures of OGG1 and AGOG, as well as the recent availability of OGG2 structures in both apo- and liganded forms, provide an excellent opportunity to compare the structural and functional properties of the three OGG subfamilies. Among the observed differences, the three-dimensional fold varies considerably between OGG1 and OGG2 members, as the latter lack the A-domain involved in 8-oxoG binding. In addition, all three OGG subfamilies bind 8-oxoG in a different manner even though the crucial interaction between the enzyme and the protonated N7 of 8-oxoG is conserved. Finally, the three OGG subfamilies differ with respect to DNA binding properties, helix-hairpin-helix motifs, and specificity for the opposite base.
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Affiliation(s)
- Frédérick Faucher
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, K7L 3N6, Canada
- Authors to whom correspondence should be addressed; E-Mails: (F.F.); (Z.J.); Tel.: +613-533-6277 (Z.J.); Fax: +613-533-2497 (Z.J.)
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, E314A Given Building, 89 Beaumont Avenue, Burlington, VT 05405, USA; E-Mail:
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, K7L 3N6, Canada
- Authors to whom correspondence should be addressed; E-Mails: (F.F.); (Z.J.); Tel.: +613-533-6277 (Z.J.); Fax: +613-533-2497 (Z.J.)
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Uracil-DNA glycosylase of Thermoplasma acidophilum directs long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and ATP/ADP, into short-patch repair. J Bacteriol 2011; 193:4495-508. [PMID: 21665970 DOI: 10.1128/jb.00233-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hydrolytic deamination of cytosine to uracil in DNA is increased in organisms adapted to high temperatures. Hitherto, the uracil base excision repair (BER) pathway has only been described in two archaeons, the crenarchaeon Pyrobaculum aerophilum and the euryarchaeon Archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. In the former the apurinic/apyrimidinic (AP) site intermediate is removed by the sequential action of a 5'-acting AP endonuclease and a 5'-deoxyribose phosphate lyase, whereas in the latter the AP site is primarily removed by a 3'-acting AP lyase, followed by a 3'-phosphodiesterase. We describe here uracil BER by a cell extract of the thermoacidophilic euryarchaeon Thermoplasma acidophilum, which prefers a similar short-patch repair mode as A. fulgidus. Importantly, T. acidophilumcell extract also efficiently executes ATP/ADP-stimulated long-patch BER in the presence of deoxynucleoside triphosphates, with a repair track of ∼15 nucleotides. Supplementation of recombinant uracil-DNA glycosylase (rTaUDG; ORF Ta0477) increased the formation of short-patch at the expense of long-patch repair intermediates, and additional supplementation of recombinant DNA ligase (rTalig; Ta1148) greatly enhanced repair product formation. TaUDG seems to recruit AP-incising and -excising functions to prepare for rapid single-nucleotide insertion and ligation, thus excluding slower and energy-costly long-patch BER.
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Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase. DNA Repair (Amst) 2009; 8:1283-9. [PMID: 19747886 DOI: 10.1016/j.dnarep.2009.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/05/2009] [Accepted: 08/10/2009] [Indexed: 11/20/2022]
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoG) is the major oxidative product of guanine and the most prevalent base lesion observed in DNA molecules. Because 8-oxoG has the capability to form a Hoogsteen pair with adenine (8-oxoG:A) in addition to a normal Watson-Crick pair with cytosine (8-oxoG:C), this lesion can lead to a G:C-->T:A transversion after replication. However, 8-oxoG is recognized and excised by the 8-oxoguanine DNA glycosylase (Ogg) of the base excision repair pathway. Members of the Ogg1 family usually display a strong preference for a C opposite the lesion. In contrast, the atypical Ogg1 from Clostridium actetobutylicum (CacOgg) can excise 8-oxoG when paired with either one of the four bases, albeit with a preference for C and A. Here we describe the first high-resolution crystal structures of CacOgg in complex with duplex DNA containing the 8-oxoG lesion paired to cytosine and to adenine. A structural comparison with human OGG1 provides a rationale for the lack of opposite base specificity displayed by the bacterial Ogg.
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