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Fuentes-León F, Quintero-Ruiz N, Fernández-Silva FS, Munford V, Vernhes Tamayo M, Menck CFM, Galhardo RS, Sánchez-Lamar A. Genotoxicity of ultraviolet light and sunlight in the bacterium Caulobacter crescentus: Wavelength-dependence. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 894:503727. [PMID: 38432774 DOI: 10.1016/j.mrgentox.2024.503727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 03/05/2024]
Abstract
The ultraviolet (UV) component of sunlight can damage DNA. Although most solar UV is absorbed by the ozone layer, wavelengths > 300 nm (UVA and UVB bands) can reach the Earth's surface. It is essential to understand the genotoxic effects of UV light, particularly in natural environments. Caulobacter crescentus, a bacterium widely employed as a model for cell cycle studies, was selected for this study. Strains proficient and deficient in DNA repair (uvrA-) were used to concurrently investigate three genotoxic endpoints: cytotoxicity, SOS induction, and gene mutation, using colony-formation, the SOS chromotest, and RifR mutagenesis, respectively. Our findings underscore the distinct impacts of individual UV bands and the full spectrum of sunlight itself in C. crescentus. UVC light was highly genotoxic, especially for the repair-deficient strain. A UVB dose equivalent to 20 min sunlight exposure also affected the cells. UVA exposure caused a significant response only at high doses, likely due to activation of photorepair. Exposure to solar irradiation resulted in reduced levels of SOS induction, possibly due to decreased cell survival. However, mutagenicity is increased, particularly in uvrA- deficient cells.
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Affiliation(s)
- Fabiana Fuentes-León
- Laboratorio de Genotoxicología, Facultad de Biología, Universidad de La Habana, Calle 25 # 455 e\ J e I, Vedado, 10400 La Habana, Cuba; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil.
| | - Nathalia Quintero-Ruiz
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil
| | - Frank S Fernández-Silva
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil
| | - Veridiana Munford
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil
| | - Marioly Vernhes Tamayo
- Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear (CEADEN), Calle 5ta # 502 e/ 5ta Avenida y7ma, Miramar, Playa, La Habana, Cuba
| | - Carlos Frederico Martins Menck
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil
| | - Rodrigo S Galhardo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, Ed. Biomédicas 2, São Paulo 05508-900, São Paulo, Brazil
| | - Angel Sánchez-Lamar
- Laboratorio de Genotoxicología, Facultad de Biología, Universidad de La Habana, Calle 25 # 455 e\ J e I, Vedado, 10400 La Habana, Cuba.
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Alves IR, Vêncio RZ, Galhardo RS. Whole genome analysis of UV-induced mutagenesis in Caulobacter crescentus. Mutat Res 2022; 825:111787. [PMID: 35691139 DOI: 10.1016/j.mrfmmm.2022.111787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
UV-induced mutagenesis is, to greater extent, a phenomenon dependent on translesion synthesis (TLS) and regulated by the SOS response in bacteria. Caulobacter crescentus, like many bacterial species, employs the ImuABC (ImuAB DnaE2) pathway in TLS. To have a better understanding of the characteristics of UV-induced mutagenesis in this organism, we performed a whole genome analysis of mutations present in survivors after an acute UVC exposure (300 J/m2). We found an average of 3.2 mutations/genome in irradiated samples, distributed in a mutational spectrum consisting exclusively of base substitutions, including tandem mutations. Although limited in conclusions by the small number of mutations identified, our study points to the feasibility of using whole-genome sequencing to study mutagenesis occurring in experiments involving a single acute exposure to genotoxic agents.
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Affiliation(s)
- Ingrid R Alves
- Institute of Biomedical Sciences, Department of Microbiology, University of São Paulo, São Paulo, Brazil
| | - Ricardo Z Vêncio
- Department of Computing and Mathematics FFCLRP, Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Rodrigo S Galhardo
- Institute of Biomedical Sciences, Department of Microbiology, University of São Paulo, São Paulo, Brazil.
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Ely B. Genomic GC content drifts downward in most bacterial genomes. PLoS One 2021; 16:e0244163. [PMID: 34038432 PMCID: PMC8153448 DOI: 10.1371/journal.pone.0244163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail:
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Chai T, Terrettaz C, Collier J. Spatial coupling between DNA replication and mismatch repair in Caulobacter crescentus. Nucleic Acids Res 2021; 49:3308-3321. [PMID: 33677508 PMCID: PMC8034640 DOI: 10.1093/nar/gkab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
The DNA mismatch repair (MMR) process detects and corrects replication errors in organisms ranging from bacteria to humans. In most bacteria, it is initiated by MutS detecting mismatches and MutL nicking the mismatch-containing DNA strand. Here, we show that MMR reduces the appearance of rifampicin resistances more than a 100-fold in the Caulobacter crescentus Alphaproteobacterium. Using fluorescently-tagged and functional MutS and MutL proteins, live cell microscopy experiments showed that MutS is usually associated with the replisome during the whole S-phase of the C. crescentus cell cycle, while MutL molecules may display a more dynamic association with the replisome. Thus, MMR components appear to use a 1D-scanning mode to search for rare mismatches, although the spatial association between MutS and the replisome is dispensible under standard growth conditions. Conversely, the spatial association of MutL with the replisome appears as critical for MMR in C. crescentus, suggesting a model where the β-sliding clamp licences the endonuclease activity of MutL right behind the replication fork where mismatches are generated. The spatial association between MMR and replisome components may also play a role in speeding up MMR and/or in recognizing which strand needs to be repaired in a variety of Alphaproteobacteria.
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Affiliation(s)
- Tiancong Chai
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH-1015, Switzerland
| | - Céline Terrettaz
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH-1015, Switzerland
| | - Justine Collier
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH-1015, Switzerland
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Joseph AM, Badrinarayanan A. Visualizing mutagenic repair: novel insights into bacterial translesion synthesis. FEMS Microbiol Rev 2020; 44:572-582. [PMID: 32556198 PMCID: PMC7476773 DOI: 10.1093/femsre/fuaa023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
DNA repair is essential for cell survival. In all domains of life, error-prone and error-free repair pathways ensure maintenance of genome integrity under stress. Mutagenic, low-fidelity repair mechanisms help avoid potential lethality associated with unrepaired damage, thus making them important for genome maintenance and, in some cases, the preferred mode of repair. However, cells carefully regulate pathway choice to restrict activity of these pathways to only certain conditions. One such repair mechanism is translesion synthesis (TLS), where a low-fidelity DNA polymerase is employed to synthesize across a lesion. In bacteria, TLS is a potent source of stress-induced mutagenesis, with potential implications in cellular adaptation as well as antibiotic resistance. Extensive genetic and biochemical studies, predominantly in Escherichia coli, have established a central role for TLS in bypassing bulky DNA lesions associated with ongoing replication, either at or behind the replication fork. More recently, imaging-based approaches have been applied to understand the molecular mechanisms of TLS and how its function is regulated. Together, these studies have highlighted replication-independent roles for TLS as well. In this review, we discuss the current status of research on bacterial TLS, with emphasis on recent insights gained mostly through microscopy at the single-cell and single-molecule level.
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Affiliation(s)
- Asha Mary Joseph
- National Centre for Biological Sciences (Tata Institute of Fundamental Research), Bangalore, Karnataka 560065, India
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences (Tata Institute of Fundamental Research), Bangalore, Karnataka 560065, India
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Valencia AO, Braz VS, Magalhães M, Galhardo RS. Role of error-prone DNA polymerases in spontaneous mutagenesis in Caulobacter crescentus. Genet Mol Biol 2020; 43:e20180283. [PMID: 31479094 PMCID: PMC7198004 DOI: 10.1590/1678-4685-gmb-2018-0283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/04/2019] [Indexed: 11/22/2022] Open
Abstract
Spontaneous mutations are important players in evolution. Nevertheless, there is a paucity of information about the mutagenic processes operating in most bacterial species. In this work, we implemented two forward mutational markers for studies in Caulobacter crescentus. We confirmed previous results in which A:T → G:C transitions are the most prevalent type of spontaneous base substitutions in this organism, although there is considerable deviation from this trend in one of the loci analyzed. We also investigated the role of dinB and imuC, encoding error-prone DNA polymerases, in spontaneous mutagenesis in this GC-rich organism. Both dinB and imuC mutant strains show comparable mutation rates to the parental strain. Nevertheless, both strains show differences in the base substitution patterns, and the dinB mutant strain shows a striking reduction in the number of spontaneous -1 deletions and an increase in C:G → T:A transitions in both assays.
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Affiliation(s)
- Alexy O Valencia
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Vânia S Braz
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Magna Magalhães
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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Fernández-Silva FS, Schulz ML, Alves IR, Freitas RR, da Rocha RP, Lopes-Kulishev CO, Medeiros MHG, Galhardo RS. Contribution of GO System Glycosylases to Mutation Prevention in Caulobacter crescentus. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:246-255. [PMID: 31569269 DOI: 10.1002/em.22335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/29/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
8-oxo-7,8-dihydroguanine, commonly referred to as 8-oxoG, is considered one of the most predominant oxidative lesions formed in DNA. Due to its ability to pair with adenines in its syn configuration, this lesion has a strong mutagenic potential in both eukaryotes and prokaryotes. Escherichia coli cells are endowed with the GO system, which protects them from the mutagenic properties of this lesion when formed both in cellular DNA and the nucleotide pool. MutY and MutM (Fpg) DNA glycosylases are crucial components of the GO system. A strong mutator phenotype of the Escherichia coli mutM mutY double mutant underscores the importance of 8-oxoG repair for genomic stability. Here, we report that in Caulobacter crescentus, a widely studied alpha-proteobacterium with a GC-rich genome, the combined lack of MutM and MutY glycosylases produces a more modest mutator phenotype when compared to E. coli. Genetic analysis indicates that other glycosylases and other repair pathways do not act synergistically with the GO system for spontaneous mutation prevention. We also show that there is not a statistically significant difference in the spontaneous levels 8-oxodGuo in E. coli and C. crescentus, suggesting that other yet to be identified differences in repair or replication probably account for the differential importance of the GO system between these two species. Environ. Mol. Mutagen. 61:246-255, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Frank S Fernández-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Mariane L Schulz
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Ingrid Reale Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rubia R Freitas
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Raquel Paes da Rocha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carina O Lopes-Kulishev
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marisa H G Medeiros
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Rodrigo S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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