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Stobbe MD, Thun GA, Diéguez-Docampo A, Oliva M, Whalley JP, Raineri E, Gut IG. Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer. PLoS Comput Biol 2019; 15:e1007496. [PMID: 31765368 PMCID: PMC6901237 DOI: 10.1371/journal.pcbi.1007496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 12/09/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
The sheer size of the human genome makes it improbable that identical somatic mutations at the exact same position are observed in multiple tumours solely by chance. The scarcity of cancer driver mutations also precludes positive selection as the sole explanation. Therefore, recurrent mutations may be highly informative of characteristics of mutational processes. To explore the potential, we use recurrence as a starting point to cluster >2,500 whole genomes of a pan-cancer cohort. We describe each genome with 13 recurrence-based and 29 general mutational features. Using principal component analysis we reduce the dimensionality and create independent features. We apply hierarchical clustering to the first 18 principal components followed by k-means clustering. We show that the resulting 16 clusters capture clinically relevant cancer phenotypes. High levels of recurrent substitutions separate the clusters that we link to UV-light exposure and deregulated activity of POLE from the one representing defective mismatch repair, which shows high levels of recurrent insertions/deletions. Recurrence of both mutation types characterizes cancer genomes with somatic hypermutation of immunoglobulin genes and the cluster of genomes exposed to gastric acid. Low levels of recurrence are observed for the cluster where tobacco-smoke exposure induces mutagenesis and the one linked to increased activity of cytidine deaminases. Notably, the majority of substitutions are recurrent in a single tumour type, while recurrent insertions/deletions point to shared processes between tumour types. Recurrence also reveals susceptible sequence motifs, including TT[C>A]TTT and AAC[T>G]T for the POLE and 'gastric-acid exposure' clusters, respectively. Moreover, we refine knowledge of mutagenesis, including increased C/G deletion levels in general for lung tumours and specifically in midsize homopolymer sequence contexts for microsatellite instable tumours. Our findings are an important step towards the development of a generic cancer diagnostic test for clinical practice based on whole-genome sequencing that could replace multiple diagnostics currently in use.
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Affiliation(s)
- Miranda D. Stobbe
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gian A. Thun
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Diéguez-Docampo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Meritxell Oliva
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Justin P. Whalley
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivo G. Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Pezzotti G, Horiguchi S, Boschetto F, Adachi T, Marin E, Zhu W, Yamamoto T, Kanamura N, Ohgitani E, Mazda O. Raman Imaging of Individual Membrane Lipids and Deoxynucleoside Triphosphates in Living Neuronal Cells during Neurite Outgrowth. ACS Chem Neurosci 2018; 9:3038-3048. [PMID: 30024146 DOI: 10.1021/acschemneuro.8b00235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Recent developments in Raman imaging at the microscopic scale were exploited here with the specific purpose of locating spectral fingerprints of individual membrane lipids and deoxynucleoside triphosphates during neuronal cell networking and separation. After carefully screening the Raman spectra of isolated lipid components, we located an in situ mapped specific Raman fingerprints from individual phospholipids at the micrometric level in comparison with the total lipid distribution within single living cells. We concurrently examined silent zones of lipid emissions and exploited those peculiar spectral ranges for mapping both abundance and localization of individual DNA nucleoside triphosphates. This work represents a first step toward label-free/molecular-selective Raman patterning with high spectral resolution of the relevant chemical species involved with the functionality of neuronal cells.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
- Department of Orthopedic Surgery, Tokyo Medical University,6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, Yamadaoka, Suita, 565-0871 Osaka, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
| | - Satoshi Horiguchi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, 606-8585 Kyoto, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku, 465 Kajii-cho, Kawaramachi dori 602-0841 Kyoto, Japan
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3
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Tomkova M, Tomek J, Kriaucionis S, Schuster-Böckler B. Mutational signature distribution varies with DNA replication timing and strand asymmetry. Genome Biol 2018; 19:129. [PMID: 30201020 PMCID: PMC6130095 DOI: 10.1186/s13059-018-1509-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. CONCLUSIONS Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jakub Tomek
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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4
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Mathews CK. Oxidized deoxyribonucleotides, mutagenesis, and cancer. FASEB J 2016; 31:11-13. [PMID: 27729413 DOI: 10.1096/fj.201601100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Christopher K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
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Abstract
Cancer was recognized as a genetic disease at least four decades ago, with the realization that the spontaneous mutation rate must increase early in tumorigenesis to account for the many mutations in tumour cells compared with their progenitor pre-malignant cells. Abnormalities in the deoxyribonucleotide pool have long been recognized as determinants of DNA replication fidelity, and hence may contribute to mutagenic processes that are involved in carcinogenesis. In addition, many anticancer agents antagonize deoxyribonucleotide metabolism. Here, we consider the extent to which aspects of deoxyribonucleotide metabolism contribute to our understanding of both carcinogenesis and to the effective use of anticancer agents.
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Affiliation(s)
- Christopher K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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Kamiya H, Yamazaki D, Nakamura E, Makino T, Kobayashi M, Matsuoka I, Harashima H. Action-at-a-Distance Mutagenesis Induced by Oxidized Guanine in Werner Syndrome Protein-Reduced Human Cells. Chem Res Toxicol 2015; 28:621-8. [DOI: 10.1021/tx500418m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hiroyuki Kamiya
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
- Graduate
School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Daiki Yamazaki
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Eri Nakamura
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
| | - Tetsuaki Makino
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
- Graduate
School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Miwako Kobayashi
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Ichiro Matsuoka
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Hideyoshi Harashima
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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7
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Kamiya H, Suzuki T, Harashima H. Suppression of Short Tract Gene Conversion in Episomal DNA by p53 Reduction. Genes Environ 2014. [DOI: 10.3123/jemsge.2014.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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8
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Kamiya H, Kurokawa M. DNA Polymerase ^|^lambda; Promotes Mutagenesis Induced by 8-Oxo-7,8-dihydroguanine (8-hydroxyguanine) Paired with Adenine. Genes Environ 2013. [DOI: 10.3123/jemsge.2013.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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9
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Nagira K, Tamura S, Kawano S, Ikeda S. Ascorbic Acid and Thiol Antioxidants Suppress Spontaneous Mutagenesis in a Cu,Zn-superoxide Dismutase-deficient Mutant of Saccharomyces cerevisiae. Genes Environ 2013. [DOI: 10.3123/jemsge.2013.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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10
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Kamiya H, Kurokawa M. Mutagenic bypass of 8-oxo-7,8-dihydroguanine (8-hydroxyguanine) by DNA polymerase κ in human cells. Chem Res Toxicol 2012; 25:1771-6. [PMID: 22804710 DOI: 10.1021/tx300259x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of 8-oxo-7,8-dihydroguanine (G(O), 8-hydroxyguanine) in DNA and in the nucleotide pool results in G:C→T:A and A:T→C:G substitution mutations, respectively, since G(O) can pair with both C and A. In this study, the role of DNA polymerase κ in the mutagenicity of G(O) was investigated, using a supF shuttle plasmid propagated in human U2OS cells. This translesion synthesis DNA polymerase was knocked down by siRNA, and plasmid DNAs containing G(O):C and G(O):A pairs were transfected into the knock-down cells. The supF plasmid DNAs replicated in the cells were then introduced into Escherichia coli. Mutation analyses indicated that the knock-down of DNA polymerase κ by siRNA decreased the frequency of G:C→T:A mutation caused by G(O):C, although no effects of the DNA polymerase κ reduction were observed for the A:T→C:G substitution induced by G(O):A. These results suggested that DNA polymerase κ is involved in the mutagenic bypass of G(O) in living human cells, when the damaged base is generated by direct DNA oxidation.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan.
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11
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Hori M, Suzuki T, Minakawa N, Matsuda A, Harashima H, Kamiya H. Mutagenicity of secondary oxidation products of 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate (8-hydroxy-2'- deoxyguanosine 5'-triphosphate). Mutat Res 2011; 714:11-6. [PMID: 21704046 DOI: 10.1016/j.mrfmmm.2011.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 05/20/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
Abstract
8-Oxo-7,8-dihydroguanine (8-hydroxyguanine) is oxidized more easily than normal nucleobases, which can produce spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). These secondary oxidation products of 8-oxo-7,8-dihydroguanine are highly mutagenic when formed within DNA. To evaluate the mutagenicity of the corresponding oxidation products of 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate (8-hydroxy-2'- deoxyguanosine 5'-triphosphate) in the nucleotide pool, Escherichia coli cells deficient in the mutT gene were treated with H(2)O(2), and the induced mutations were analyzed. Moreover, the 2'-deoxyriboside 5'-triphosphate derivatives of Sp and Gh were also introduced into competent E. coli cells. The H(2)O(2) treatment of mutT E. coli cells resulted in increase of G:C → T:A and A:T → T:A mutations. However, the incorporation of exogenous Sp and Gh 2'-deoxyribonucleotides did not significantly increase the mutation frequency. These results suggested that the oxidation product(s) of 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate induces G:C → T:A and A:T → T:A mutations, and that the 2'-deoxyriboside 5'-triphosphate derivatives of Sp and Gh exhibit quite weak mutagenicity, in contrast to the bases in DNA.
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Affiliation(s)
- Mika Hori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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12
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Kamiya H. Mutagenicity of oxidized DNA precursors in living cells: Roles of nucleotide pool sanitization and DNA repair enzymes, and translesion synthesis DNA polymerases. Mutat Res 2010; 703:32-6. [PMID: 20542139 DOI: 10.1016/j.mrgentox.2010.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 06/04/2010] [Indexed: 10/19/2022]
Abstract
The base moieties of DNA precursors in the nucleotide pool are subjected to oxidative damage, and the formation of damaged DNA precursors is an important source of mutagenesis. 8-Hydroxy-2'-deoxyguanosine 5'-triphosphate, also known by the name of its keto-enol tautomer as 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate, and 2-hydroxy-2'-deoxyadenosine 5'-triphosphate have been identified as the major products of in vitro oxidation reactions. The mutagenicities of these damaged precursors in living cells will be summarized in this review. In addition, the roles of the nucleotide pool sanitization and DNA repair enzymes, and the translesion synthesis DNA polymerases will be described.
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Affiliation(s)
- Hiroyuki Kamiya
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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13
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Kamiya H, Hori M, Arimori T, Sekiguchi M, Yamagata Y, Harashima H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 2009; 8:1250-4. [PMID: 19699693 DOI: 10.1016/j.dnarep.2009.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/22/2009] [Accepted: 07/27/2009] [Indexed: 01/22/2023]
Abstract
The human NUDT5 protein catalyzes the hydrolysis of 8-hydroxy-dGDP. To examine its substrate specificity, four oxidized deoxyribonucleotides (2-hydroxy-dADP, 8-hydroxy-dADP, 5-formyl-dUDP, and 5-hydroxy-dCDP) were incubated with the NUDT5 protein. Interestingly, all of the nucleotides, except for 5-hydroxy-dCDP, were hydrolyzed with various efficiencies. The kinetic parameters indicated that 8-hydroxy-dADP was hydrolyzed as efficiently as 8-hydroxy-dGDP. The hydrolyzing activities for their triphosphate counterparts were quite weak. These results suggest that the NUDT5 protein eliminates various oxidized deoxyribonucleoside diphosphates from the nucleotide pool and prevents their toxic effects.
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Satou K, Hori M, Kawai K, Kasai H, Harashima H, Kamiya H. Involvement of specialized DNA polymerases in mutagenesis by 8-hydroxy-dGTP in human cells. DNA Repair (Amst) 2009; 8:637-42. [PMID: 19179121 DOI: 10.1016/j.dnarep.2008.12.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/17/2022]
Abstract
The mutagenicity of an oxidized form of dGTP, 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (8-OH-dGTP), was examined using human 293T cells. Shuttle plasmid DNA containing the supF gene was first transfected into the cells, and then 8-OH-dGTP was introduced by means of osmotic pressure. The DNAs replicated in the cells were recovered and then transfected into Escherichia coli. 8-OH-dGTP induced A:T-->C:G substitution mutations in the cells. The knock-downs of DNA polymerases eta and zeta, and REV1 by siRNAs reduced the A:T-->C:G substitution mutations, suggesting that these DNA polymerases are involved in the misincorporation of 8-OH-dGTP opposite A in human cells. In contrast, the knock-down of DNA polymerase iota did not affect the 8-OH-dGTP-induced mutations. The decrease in the induced mutation frequency was more evident by double knock-downs of DNA pols eta plus zeta and REV1 plus DNA pol zeta (but not by that of DNA pol eta plus REV1), suggesting that REV1-DNA pol eta and DNA pol zeta work in different steps. These results indicate that specialized DNA polymerases are involved in the mutagenesis induced by the oxidized dGTP.
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Affiliation(s)
- Kazuya Satou
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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15
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Kamiya H, Suzuki A, Yamaguchi Y, Handa H, Harashima H. Incorporation of 8-hydroxyguanosine (8-oxo-7,8-dihydroguanosine) 5'-triphosphate by bacterial and human RNA polymerases. Free Radic Biol Med 2009; 46:1703-7. [PMID: 19362141 DOI: 10.1016/j.freeradbiomed.2009.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 03/24/2009] [Accepted: 04/04/2009] [Indexed: 10/20/2022]
Abstract
Oxidized RNA precursors formed in the nucleotide pool may be incorporated into RNA. In this study, the incorporation of 8-hydroxyguanosine 5'-triphosphate (8-OH-GTP; 8-oxo-7,8-dihydroguanosine 5'-triphosphate) into RNA by Escherichia coli RNA polymerase was examined in vitro, using a primer RNA and a template DNA with defined sequences. 8-OH-GTP was incorporated opposite C and A in the template DNA. Surprisingly, 8-OH-GTP was quite efficiently incorporated by the bacterial RNA polymerase, in contrast to the incorporation of the 2'-deoxyribo counterpart by DNA polymerases, as indicated by the kinetic parameters. The primer was further extended by the addition of a ribonucleotide complementary to the nucleobase adjacent to C or A (the nucleobase opposite which 8-OH-GTP was inserted). Thus, the incorporation of 8-OH-GTP did not completely inhibit further RNA chain elongation. 8-OH-GTP was also incorporated opposite C and A by human RNA polymerase II. These results suggest that 8-OH-GTP in the nucleotide pool can cause the formation of oxidized RNA and disturb the transmittance of genetic information.
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Affiliation(s)
- Hiroyuki Kamiya
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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