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Abstract
Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.
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Affiliation(s)
- Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Phillip Sweet
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
| | - Aparna Anantharaman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
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2
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Sun P, Dégut C, Réty S, Caissard JC, Hibrand-Saint Oyant L, Bony A, Paramita SN, Conart C, Magnard JL, Jeauffre J, Abd-El-Haliem AM, Marie-Magdelaine J, Thouroude T, Baltenweck R, Tisné C, Foucher F, Haring M, Hugueney P, Schuurink RC, Baudino S. Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:185-199. [PMID: 32639596 DOI: 10.1111/tpj.14916] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/03/2020] [Accepted: 06/24/2020] [Indexed: 05/25/2023]
Abstract
Roses use a non-canonical pathway involving a Nudix hydrolase, RhNUDX1, to synthesize their monoterpenes, especially geraniol. Here we report the characterization of another expressed NUDX1 gene from the rose cultivar Rosa x wichurana, RwNUDX1-2. In order to study the function of the RwNUDX1-2 protein, we analyzed the volatile profiles of an F1 progeny generated by crossing R. chinensis cv. 'Old Blush' with R. x wichurana. A correlation test of the volatilomes with gene expression data revealed that RwNUDX1-2 is involved in the biosynthesis of a group of sesquiterpenoids, especially E,E-farnesol, in addition to other sesquiterpenes. In vitro enzyme assays and heterologous in planta functional characterization of the RwNUDX1-2 gene corroborated this result. A quantitative trait locus (QTL) analysis was performed using the data of E,E-farnesol contents in the progeny and a genetic map was constructed based on gene markers. The RwNUDX1-2 gene co-localized with the QTL for E,E-farnesol content, thereby confirming its function in sesquiterpenoid biosynthesis in R. x wichurana. Finally, in order to understand the structural bases for the substrate specificity of rose NUDX proteins, the RhNUDX1 protein was crystallized, and its structure was refined to 1.7 Å. By molecular modeling of different rose NUDX1 protein complexes with their respective substrates, a structural basis for substrate discrimination by rose NUDX1 proteins is proposed.
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Affiliation(s)
- Pulu Sun
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Clément Dégut
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), Paris, 75005, France
| | - Stéphane Réty
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, Lyon, F-69007, France
| | - Jean-Claude Caissard
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | | | - Aurélie Bony
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Saretta N Paramita
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Corentin Conart
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Jean-Louis Magnard
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Julien Jeauffre
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Ahmed M Abd-El-Haliem
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Jordan Marie-Magdelaine
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Tatiana Thouroude
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | | | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), Paris, 75005, France
| | - Fabrice Foucher
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Michel Haring
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, Colmar, F-68000, France
| | - Robert C Schuurink
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Sylvie Baudino
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
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Andrade LDC, Santi AMM, Alves CL, Ferreira WRR, de Assis AV, Oliveira E, Machado CR, Murta SMF. The heterologous expression of Escherichia coli MutT enzyme is involved in the protection against oxidative stress in Leishmania braziliensis. Mem Inst Oswaldo Cruz 2020; 115:e190469. [PMID: 32638832 PMCID: PMC7337112 DOI: 10.1590/0074-02760190469] [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: 12/10/2019] [Accepted: 06/02/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Oxidative stress is responsible for generating DNA lesions and the 8-oxoguanine (8-oxoG) is the most commonly lesion found in DNA damage. When this base is incorporated during DNA replication, it could generate double-strand DNA breaks and cellular death. MutT enzyme hydrolyzes the 8-oxoG from the nucleotide pool, preventing its incorporation during DNA replication. OBJECTIVES To investigate the importance of 8-oxoG in Leishmania infantum and L. braziliensis, in this study we analysed the impact of heterologous expression of Escherichia coli MutT (EcMutT) enzyme in drug-resistance phenotype and defense against oxidative stress. METHODS Comparative analysis of L. braziliensis and L. infantum H2O2 tolerance and cell cycle profile were performed. Lines of L. braziliensis and L. infantum expressing EcMutT were generated and evaluated using susceptibility tests to H2O2 and SbIII, cell cycle analysis, γH2A western blotting, and BrdU native detection assay. FINDINGS Comparative analysis of tolerance to oxidative stress generated by H2O2 showed that L. infantum is more tolerant to exogenous H2O2 than L. braziliensis. In addition, cell cycle analysis showed that L. infantum, after treatment with H2O2, remains in G1 phase, returning to its normal growth rate after 72 h. In contrast, after treatment with H2O2, L. braziliensis parasites continue to move to the next stages of the cell cycle. Expression of the E. coli MutT gene in L. braziliensis and L. infantum does not interfere in parasite growth or in susceptibility to SbIII. Interestingly, we observed that L. braziliensis EcMutT-expressing clones were more tolerant to H2O2 treatment, presented lower activation of γH2A, a biomarker of genotoxic stress, and lower replication stress than its parental non-transfected parasites. In contrast, the EcMutT is not involved in protection against oxidative stress generated by H2O2 in L. infantum. MAIN CONCLUSIONS Our results showed that 8-oxoG clearance in L. braziliensis is important to avoid misincorporation during DNA replication after oxidative stress generated by H2O2.
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Affiliation(s)
| | | | - Ceres Luciana Alves
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Wesley Roger Rodrigues Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Antônio Vinícius de Assis
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Edward Oliveira
- Instituto René Rachou, Fundação Oswaldo Cruz-Fiocruz, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Oka S, Hayashi M, Taguchi K, Hidaka M, Tsuzuki T, Sekiguchi M. ROS control in human iPS cells reveals early events in spontaneous carcinogenesis. Carcinogenesis 2019; 41:36-43. [DOI: 10.1093/carcin/bgz081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/03/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sugako Oka
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Michio Hayashi
- Section of Biochemistry, Fukuoka Dental College, Fukuoka, Japan
| | - Kenichi Taguchi
- Cancer Pathology Laboratory, Department of Cancer Biology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Masumi Hidaka
- Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka, Japan
| | - Teruhisa Tsuzuki
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Mutsuo Sekiguchi
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
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Li X, Imlay JA. Improved measurements of scant hydrogen peroxide enable experiments that define its threshold of toxicity for Escherichia coli. Free Radic Biol Med 2018; 120:217-227. [PMID: 29550333 PMCID: PMC5940505 DOI: 10.1016/j.freeradbiomed.2018.03.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 01/06/2023]
Abstract
Escherichia coli is a model organism that has been exploited to reveal key details of hydrogen peroxide stress: the biomolecules that H2O2 most rapidly damages and the defensive tactics that organisms use to fend it off. Much less clear is the amount of exogenous H2O2 that is sufficient to injure the bacterium and/or to trigger its stress response. To fill this gap, we need to study the behavior of cells when they are exposed to defined amounts of H2O2 on an hours-long time scale. Such experiments are difficult because bacteria rapidly consume H2O2 that is added to test cultures. Further, lab media itself can generate H2O2, and media components interfere with the quantification of H2O2 levels. In this study we describe mechanisms by which media components interfere with H2O2 determinations, and we identify simple ways to minimize and correct for this interference. Using these techniques, it was shown that standard media generate so much H2O2 that most intracellular H2O2 derives from the medium rather than from endogenous metabolism. Indeed, bacteria spread on plates must induce their stress response or else perish. Finally, two straightforward methods were used to sustain low-micromolar steady-state concentrations of H2O2. In this way we determined that > 2 μM extracellular H2O2 is sufficient to trigger the intracellular OxyR stress response, and > 5 μM begins to impair cell growth in a minimal medium. These concentrations are orders of magnitude lower than the doses that have typically been used in lab experiments. The new approaches should enable workers to study how various organisms cope with natural levels of H2O2 stress.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, Henan 471023, China.
| | - James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave., Urbana, IL 61801, USA.
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Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proc Natl Acad Sci U S A 2017; 114:9164-9169. [PMID: 28794281 DOI: 10.1073/pnas.1707466114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Downstream metabolic events can contribute to the lethality of drugs or agents that interact with a primary cellular target. In bacteria, the production of reactive oxygen species (ROS) has been associated with the lethal effects of a variety of stresses including bactericidal antibiotics, but the relative contribution of this oxidative component to cell death depends on a variety of factors. Experimental evidence has suggested that unresolvable DNA problems caused by incorporation of oxidized nucleotides into nascent DNA followed by incomplete base excision repair contribute to the ROS-dependent component of antibiotic lethality. Expression of the chimeric periplasmic-cytoplasmic MalE-LacZ72-47 protein is an historically important lethal stress originally identified during seminal genetic experiments that defined the SecY-dependent protein translocation system. Multiple, independent lines of evidence presented here indicate that the predominant mechanism for MalE-LacZ lethality shares attributes with the ROS-dependent component of antibiotic lethality. MalE-LacZ lethality requires molecular oxygen, and its expression induces ROS production. The increased susceptibility of mutants sensitive to oxidative stress to MalE-LacZ lethality indicates that ROS contribute causally to cell death rather than simply being produced by dying cells. Observations that support the proposed mechanism of cell death include MalE-LacZ expression being bacteriostatic rather than bactericidal in cells that overexpress MutT, a nucleotide sanitizer that hydrolyzes 8-oxo-dGTP to the monophosphate, or that lack MutM and MutY, DNA glycosylases that process base pairs involving 8-oxo-dGTP. Our studies suggest stress-induced physiological changes that favor this mode of ROS-dependent death.
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Abstract
Trypanosoma cruzi is exposed to oxidative stresses during its life cycle, and amongst the strategies employed by this parasite to deal with these situations sits a peculiar trypanothione-dependent antioxidant system. Remarkably, T. cruzi's antioxidant repertoire does not include catalase. In an attempt to shed light on what are the reasons by which this parasite lacks this enzyme, a T. cruzi cell line stably expressing catalase showed an increased resistance to hydrogen peroxide (H2O2) when compared with wild-type cells. Interestingly, preconditioning carried out with low concentrations of H2O2 led untransfected parasites to be as much resistant to this oxidant as cells expressing catalase, but did not induce the same level of increased resistance in the latter ones. Also, presence of catalase decreased trypanothione reductase and increased superoxide dismutase levels in T. cruzi, resulting in higher levels of residual H2O2 after challenge with this oxidant. Although expression of catalase contributed to elevated proliferation rates of T. cruzi in Rhodnius prolixus, it failed to induce a significant increase of parasite virulence in mice. Altogether, these results indicate that the absence of a gene encoding catalase in T. cruzi has played an important role in allowing this parasite to develop a shrill capacity to sense and overcome oxidative stress.
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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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de Faria RC, Vila-Nova LG, Bitar M, Resende BC, Arantes LS, Rebelato AB, Azevedo VAC, Franco GR, Machado CR, Santos LLD, de Oliveira Lopes D. Adenine Glycosylase MutY of Corynebacterium pseudotuberculosis presents the antimutator phenotype and evidences of glycosylase/AP lyase activity in vitro. INFECTION GENETICS AND EVOLUTION 2016; 44:318-329. [PMID: 27456281 DOI: 10.1016/j.meegid.2016.07.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/07/2016] [Accepted: 07/21/2016] [Indexed: 01/30/2023]
Abstract
Corynebacterium pseudotuberculosis is the etiological agent of caseous lymphadenitis, a disease that predominantly affects small ruminants, causing significant economic losses worldwide. As a facultative intracellular pathogen, this bacterium is exposed to an environment rich in reactive oxygen species (ROS) within macrophages. To ensure its genetic stability, C. pseudotuberculosis relies on efficient DNA repair pathways for excision of oxidative damage such as 8-oxoguanine, a highly mutagenic lesion. MutY is an adenine glycosylase involved in adenine excision from 8-oxoG:A mismatches avoiding genome mutation incorporation. The purpose of this study was to characterize MutY protein from C. pseudotuberculosis and determine its involvement with DNA repair. In vivo functional complementation assay employing mutY gene deficient Escherichia coli transformed with CpmutY showed a 13.5-fold reduction in the rate of spontaneous mutation, compared to cells transformed with empty vector. Also, under oxidative stress conditions, CpMutY protein favored the growth of mutY deficient E. coli, relative to the same strain in the absence of CpMutY. To demonstrate the involvement of this enzyme in recognition and excision of 8-oxoguanine lesion, an in vitro assay was performed. CpMutY protein was capable of recognizing and excising 8-oxoG:A but not 8-oxoG:C presenting evidences of glycosylase/AP lyase activity in vitro. In silico structural characterization revealed the presence of preserved motifs related to the MutY activity on DNA repair, such as catalytic residues involved in glycosylase/AP lyase activity and structural DNA-binding elements, such as the HhH motif and the [4Fe-4S] cluster. The three-dimensional structure of CpMutY, generated by comparative modeling, exhibits a catalytic domain very similar to that of E. coli MutY. Taken together, these results indicate that the CpmutY encodes a functional protein homologous to MutY from E. coli and is involved in the prevention of mutations and the repair of oxidative DNA lesions.
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Affiliation(s)
- Rafael Cançado de Faria
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Liliane Gonçalves Vila-Nova
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Mainá Bitar
- Laboratory of Genetics and Biochemistry, Department of Biochemistry, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Bruno Carvalho Resende
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Larissa Sousa Arantes
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Arnaldo Basso Rebelato
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Vasco Ariston Carvalho Azevedo
- Laboratory of Cell and Molecular Genetics, Department of General Biology, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Glória Regina Franco
- Laboratory of Genetics and Biochemistry, Department of Biochemistry, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Carlos Renato Machado
- Laboratory of Genetics and Biochemistry, Department of Biochemistry, ICB, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Luciana Lara Dos Santos
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
| | - Débora de Oliveira Lopes
- Laboratory of Molecular Biology, Federal University of São João Del-Rei (CCO), Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG 35501-296, Brazil.
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Arantes LS, Nova LGV, Resende BC, Bitar M, Coelho IEV, Miyoshi A, Azevedo VA, Lara dos Santos L, Machado CR, de Oliveira Lopes D. The Corynebacterium pseudotuberculosis genome contains two formamidopyrimidine-DNA glycosylase enzymes, only one of which recognizes and excises 8-oxoguanine lesion. Gene 2016; 575:233-43. [DOI: 10.1016/j.gene.2015.08.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/11/2015] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
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Belenky P, Ye JD, Porter CBM, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ. Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. Cell Rep 2015; 13:968-80. [PMID: 26565910 DOI: 10.1016/j.celrep.2015.09.059] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/04/2015] [Accepted: 09/17/2015] [Indexed: 01/16/2023] Open
Abstract
Understanding how antibiotics impact bacterial metabolism may provide insight into their mechanisms of action and could lead to enhanced therapeutic methodologies. Here, we profiled the metabolome of Escherichia coli after treatment with three different classes of bactericidal antibiotics (?-lactams, aminoglycosides, quinolones). These treatments induced a similar set of metabolic changes after 30 min that then diverged into more distinct profiles at later time points. The most striking changes corresponded to elevated concentrations of central carbon metabolites, active breakdown of the nucleotide pool, reduced lipid levels, and evidence of an elevated redox state. We examined potential end-target consequences of these metabolic perturbations and found that antibiotic-treated cells exhibited cytotoxic changes indicative of oxidative stress, including higher levels of protein carbonylation, malondialdehyde adducts, nucleotide oxidation, and double-strand DNA breaks. This work shows that bactericidal antibiotics induce a complex set of metabolic changes that are correlated with the buildup of toxic metabolic by-products.
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Affiliation(s)
- Peter Belenky
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA.
| | - Jonathan D Ye
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Caroline B M Porter
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Nadia R Cohen
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Michael A Lobritz
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Saloni Jain
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting Street, Providence, RI 02912, USA
| | - Eric G Schwarz
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, 36 Cummington Mall, Boston, MA 02215, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.
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12
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Chaudhary AK, Na D, Lee EY. Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnol Adv 2015; 33:914-30. [PMID: 26027891 DOI: 10.1016/j.biotechadv.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022]
Abstract
Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea.
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Gordon AJE, Satory D, Wang M, Halliday JA, Golding I, Herman C. Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity. Nucleic Acids Res 2014; 42:12015-26. [PMID: 25294823 PMCID: PMC4231768 DOI: 10.1093/nar/gku912] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Living in an oxygen-rich environment is dangerous for a cell. Reactive oxygen species can damage DNA, RNA, protein and lipids. The MutT protein in Escherichia coli removes 8-oxo-deoxyguanosine triphosphate (8-oxo-dGTP) and 8-oxo-guanosine triphosphate (8-oxo-GTP) from the nucleotide pools precluding incorporation into DNA and RNA. While 8-oxo-dGTP incorporation into DNA is mutagenic, it is not clear if 8-oxo-GTP incorporation into RNA can have phenotypic consequences for the cell. We use a bistable epigenetic switch sensitive to transcription errors in the Escherichia coli lacI transcript to monitor transient RNA errors. We do not observe any increase in epigenetic switching in mutT cells. We revisit the original observation of partial phenotypic suppression of a lacZamber allele in a mutT background that was attributed to RNA errors. We find that Lac+ revertants can completely account for the increase in β-galactosidase levels in mutT lacZamber cultures, without invoking participation of transient transcription errors. Moreover, we observe a fluctuation type of distribution of β-galactosidase appearance in a growing culture, consistent with Lac+ DNA revertant events. We conclude that the absence of MutT produces a DNA mutator but does not equally create an RNA mutator.
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Affiliation(s)
- Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dominik Satory
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mengyu Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, 77030, USA Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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14
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Nakashima N, Miyazaki K. Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci 2014; 15:2773-93. [PMID: 24552876 PMCID: PMC3958881 DOI: 10.3390/ijms15022773] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/18/2022] Open
Abstract
Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.
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Affiliation(s)
- Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
| | - Kentaro Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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15
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Aguiar PHN, Furtado C, Repolês BM, Ribeiro GA, Mendes IC, Peloso EF, Gadelha FR, Macedo AM, Franco GR, Pena SDJ, Teixeira SMR, Vieira LQ, Guarneri AA, Andrade LO, Machado CR. Oxidative stress and DNA lesions: the role of 8-oxoguanine lesions in Trypanosoma cruzi cell viability. PLoS Negl Trop Dis 2013; 7:e2279. [PMID: 23785540 PMCID: PMC3681716 DOI: 10.1371/journal.pntd.0002279] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 04/29/2013] [Indexed: 01/09/2023] Open
Abstract
The main consequence of oxidative stress is the formation of DNA lesions, which can result in genomic instability and lead to cell death. Guanine is the base that is most susceptible to oxidation, due to its low redox potential, and 8-oxoguanine (8-oxoG) is the most common lesion. These characteristics make 8-oxoG a good cellular biomarker to indicate the extent of oxidative stress. If not repaired, 8-oxoG can pair with adenine and cause a G:C to T:A transversion. When 8-oxoG is inserted during DNA replication, it could generate double-strand breaks, which makes this lesion particularly deleterious. Trypanosoma cruzi needs to address various oxidative stress situations, such as the mammalian intracellular environment and the triatomine insect gut where it replicates. We focused on the MutT enzyme, which is responsible for removing 8-oxoG from the nucleotide pool. To investigate the importance of 8-oxoG during parasite infection of mammalian cells, we characterized the MutT gene in T. cruzi (TcMTH) and generated T. cruzi parasites heterologously expressing Escherichia coli MutT or overexpressing the TcMTH enzyme. In the epimastigote form, the recombinant and wild-type parasites displayed similar growth in normal conditions, but the MutT-expressing cells were more resistant to hydrogen peroxide treatment. The recombinant parasite also displayed significantly increased growth after 48 hours of infection in fibroblasts and macrophages when compared to wild-type cells, as well as increased parasitemia in Swiss mice. In addition, we demonstrated, using western blotting experiments, that MutT heterologous expression can influence the parasite antioxidant enzyme protein levels. These results indicate the importance of the 8-oxoG repair system for cell viability.
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Affiliation(s)
- Pedro H. N. Aguiar
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Carolina Furtado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno M. Repolês
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Grazielle A. Ribeiro
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Isabela C. Mendes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo F. Peloso
- Departamento de Bioquímica, Instituto de Biologia - UNICAMP, Campinas, Sa˜o Paulo, Brazil
| | - Fernanda R. Gadelha
- Departamento de Bioquímica, Instituto de Biologia - UNICAMP, Campinas, Sa˜o Paulo, Brazil
| | - Andrea M. Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Glória R. Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Sérgio D. J. Pena
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Leda Q. Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | | | - Luciana O. Andrade
- Departamento de Morfologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - UFMG, Belo Horizonte, Minas Gerais, Brazil
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16
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Sekiguchi T, Ito R, Hayakawa H, Sekiguchi M. Elimination and utilization of oxidized guanine nucleotides in the synthesis of RNA and its precursors. J Biol Chem 2013; 288:8128-8135. [PMID: 23376345 DOI: 10.1074/jbc.m112.418723] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reactive oxygen species are produced as side products of oxygen utilization and can lead to the oxidation of nucleic acids and their precursor nucleotides. Among the various oxidized bases, 8-oxo-7,8-dihydroguanine seems to be the most critical during the transfer of genetic information because it can pair with both cytosine and adenine. During the de novo synthesis of guanine nucleotides, GMP is formed first, and it is converted to GDP by guanylate kinase. This enzyme hardly acts on an oxidized form of GMP (8-oxo-GMP) formed by the oxidation of GMP or by the cleavage of 8-oxo-GDP and 8-oxo-GTP by MutT protein. Although the formation of 8-oxo-GDP from 8-oxo-GMP is thus prevented, 8-oxo-GDP itself may be produced by the oxidation of GDP by reactive oxygen species. The 8-oxo-GDP thus formed can be converted to 8-oxo-GTP because nucleoside-diphosphate kinase and adenylate kinase, both of which catalyze the conversion of GDP to GTP, do not discriminate 8-oxo-GDP from normal GDP. The 8-oxo-GTP produced in this way and by the oxidation of GTP can be used for RNA synthesis. This misincorporation is prevented by MutT protein, which has the potential to cleave 8-oxo-GTP as well as 8-oxo-GDP to 8-oxo-GMP. When (14)C-labeled 8-oxo-GTP was applied to CaCl2-permeabilized cells of a mutT(-) mutant strain, it could be incorporated into RNA at 4% of the rate for GTP. Escherichia coli cells appear to possess mechanisms to prevent misincorporation of 8-oxo-7,8-dihydroguanine into RNA.
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Affiliation(s)
- Takeshi Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Riyoko Ito
- Department of Biochemistry and Frontier Research Center, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | - Hiroshi Hayakawa
- Department of Biochemistry and Frontier Research Center, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | - Mutsuo Sekiguchi
- Department of Biochemistry and Frontier Research Center, Fukuoka Dental College, Fukuoka 814-0193, Japan.
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17
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McLennan AG. Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both? Cell Mol Life Sci 2013; 70:373-85. [PMID: 23184251 PMCID: PMC11113851 DOI: 10.1007/s00018-012-1210-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 12/20/2022]
Abstract
Many members of the nudix hydrolase family exhibit considerable substrate multispecificity and ambiguity, which raises significant issues when assessing their functions in vivo and gives rise to errors in database annotation. Several display low antimutator activity when expressed in bacterial tester strains as well as some degree of activity in vitro towards mutagenic, oxidized nucleotides such as 8-oxo-dGTP. However, many of these show greater activity towards other nucleotides such as ADP-ribose or diadenosine tetraphosphate (Ap(4)A). The antimutator activities have tended to gain prominence in the literature, whereas they may in fact represent the residual activity of an ancestral antimutator enzyme that has become secondary to the more recently evolved major activity after gene duplication. Whether any meaningful antimutagenic function has also been retained in vivo requires very careful assessment. Then again, other examples of substrate ambiguity may indicate as yet unexplored regulatory systems. For example, bacterial Ap(4)A hydrolases also efficiently remove pyrophosphate from the 5' termini of mRNAs, suggesting a potential role for Ap(4)A in the control of bacterial mRNA turnover, while the ability of some eukaryotic mRNA decapping enzymes to degrade IDP and dIDP or diphosphoinositol polyphosphates (DIPs) may also be indicative of new regulatory networks in RNA metabolism. DIP phosphohydrolases also degrade diadenosine polyphosphates and inorganic polyphosphates, suggesting further avenues for investigation. This article uses these and other examples to highlight the need for a greater awareness of the possible significance of substrate ambiguity among the nudix hydrolases as well as the need to exert caution when interpreting incomplete analyses.
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Affiliation(s)
- Alexander G McLennan
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown St., Liverpool, L69 7ZB, UK.
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18
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Yamada M, Shimizu M, Katafuchi A, Grúz P, Fujii S, Usui Y, Fuchs RP, Nohmi T. Escherichia coli DNA polymerase III is responsible for the high level of spontaneous mutations in mutT strains. Mol Microbiol 2012; 86:1364-75. [PMID: 23043439 PMCID: PMC3556519 DOI: 10.1111/mmi.12061] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2012] [Indexed: 01/20/2023]
Abstract
Reactive oxygen species induce oxidative damage in DNA precursors, i.e. dNTPs, leading to point mutations upon incorporation. Escherichia colimutT strains, deficient in the activity hydrolysing 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-triphosphate (8-oxo-dGTP), display more than a 100-fold higher spontaneous mutation frequency over the wild-type strain. 8-oxo-dGTP induces A to C transversions when misincorporated opposite template A. Here, we report that DNA pol III incorporates 8-oxo-dGTP ≍ 20 times more efficiently opposite template A compared with template C. Single, double or triple deletions of pol I, pol II, pol IV or pol V had modest effects on the mutT mutator phenotype. Only the deletion of all four polymerases led to a 70% reduction of the mutator phenotype. While pol III may account for nearly all 8-oxo-dGTP incorporation opposite template A, it only extends ≍ 30% of them, the remaining 70% being extended by the combined action of pol I, pol II, pol IV or pol V. The unique property of pol III, a C-family DNA polymerase present only in eubacteria, to preferentially incorporate 8-oxo-dGTP opposite template A during replication might explain the high spontaneous mutation frequency in E. colimutT compared with the mammalian counterparts lacking the 8-oxo-dGTP hydrolysing activities.
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Affiliation(s)
- Masami Yamada
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tokyo 158-8501, Japan
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