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Jain K, Stanage TH, Wood EA, Cox MM. The Escherichia coli serS gene promoter region overlaps with the rarA gene. PLoS One 2022; 17:e0260282. [PMID: 35427362 PMCID: PMC9012371 DOI: 10.1371/journal.pone.0260282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflected the presence of sequences in the rarA gene that affect expression of the downstream gene, serS. The serS gene encodes the seryl aminoacyl-tRNA synthetase. Decreases in the expression of serS can trigger the stringent response. The sequences that affect serS expression are located in the last 15 nucleotides of the rarA gene.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tyler H. Stanage
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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2
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The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ. PLoS Genet 2021; 17:e1009972. [PMID: 34936656 PMCID: PMC8735627 DOI: 10.1371/journal.pgen.1009972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/06/2022] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.
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3
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Joseph AM, Daw S, Sadhir I, Badrinarayanan A. Coordination between nucleotide excision repair and specialized polymerase DnaE2 action enables DNA damage survival in non-replicating bacteria. eLife 2021; 10:e67552. [PMID: 33856342 PMCID: PMC8102061 DOI: 10.7554/elife.67552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Translesion synthesis (TLS) is a highly conserved mutagenic DNA lesion tolerance pathway, which employs specialized, low-fidelity DNA polymerases to synthesize across lesions. Current models suggest that activity of these polymerases is predominantly associated with ongoing replication, functioning either at or behind the replication fork. Here we provide evidence for DNA damage-dependent function of a specialized polymerase, DnaE2, in replication-independent conditions. We develop an assay to follow lesion repair in non-replicating Caulobacter and observe that components of the replication machinery localize on DNA in response to damage. These localizations persist in the absence of DnaE2 or if catalytic activity of this polymerase is mutated. Single-stranded DNA gaps for SSB binding and low-fidelity polymerase-mediated synthesis are generated by nucleotide excision repair (NER), as replisome components fail to localize in the absence of NER. This mechanism of gap-filling facilitates cell cycle restoration when cells are released into replication-permissive conditions. Thus, such cross-talk (between activity of NER and specialized polymerases in subsequent gap-filling) helps preserve genome integrity and enhances survival in a replication-independent manner.
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Affiliation(s)
- Asha Mary Joseph
- National Centre for Biological Sciences - Tata Institute of Fundamental ResearchBangaloreIndia
| | - Saheli Daw
- National Centre for Biological Sciences - Tata Institute of Fundamental ResearchBangaloreIndia
| | - Ismath Sadhir
- National Centre for Biological Sciences - Tata Institute of Fundamental ResearchBangaloreIndia
- Max Planck Institute for Terrestrial Microbiology, LOEWE Centre for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences - Tata Institute of Fundamental ResearchBangaloreIndia
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4
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Hanawalt P, Sweasy J. Mechanistic understanding of cellular responses to genomic stress. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:25-33. [PMID: 31793074 DOI: 10.1002/em.22349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Within the past half century we have learned of multiple pathways for repairing damaged DNA, based upon the intrinsic redundancy of information in its complementary double strands. Mechanistic details of these pathways have provided insights into environmental and endogenous threats to genomic stability. Studies on bacterial responses to ultraviolet light led to the discovery of excision repair, as well as the inducible SOS response to DNA damage. Similar responses in eukaryotes promote upregulation of error-prone translesion DNA polymerases. Recent advances in this burgeoning field include duplex DNA sequencing to provide strikingly accurate profiling of mutational signatures, analyses of gene expression patterns in single cells, CRISPR/Cas9 to generate changes at precise genomic positions, novel roles for RNA in gene expression and DNA repair, phase-separated aqueous environments for specialized cellular transactions, and DNA lesions as epigenetic signals for gene expression. The Environmental Mutagenesis and Genomics Society (EMGS), through the broad range of expertise in its membership, stands at the crossroad of basic understanding of mechanisms for genomic maintenance and the field of genetic toxicology, with the need for regulation of exposures to toxic substances. Our future challenges include devising strategies and technologies to identify individuals who are susceptible to specific genomic stresses, along with basic research on the underlying mechanisms of cellular stress responses that promote disease-causing mutations. As the science moves forward it should also be a responsibility for the EMGS to expand its outreach programs for the enlightenment and benefit of all humans and the biosphere. Environ. Mol. Mutagen. 61:25-33, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Philip Hanawalt
- Department of Biology, Stanford University, Stanford, California
| | - Joann Sweasy
- University of Arizona Cancer Center, Tucson, Arizona
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5
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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Leite WC, Penteado RF, Gomes F, Iulek J, Etto RM, Saab SC, Steffens MBR, Galvão CW. MAW point mutation impairs H. Seropedicae RecA ATP hydrolysis and DNA repair without inducing large conformational changes in its structure. PLoS One 2019; 14:e0214601. [PMID: 30998678 PMCID: PMC6472873 DOI: 10.1371/journal.pone.0214601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/17/2019] [Indexed: 11/18/2022] Open
Abstract
RecA is a multifunctional protein that plays a central role in DNA repair in bacteria. The structural Make ATP Work motif (MAW) is proposed to control the ATPase activity of RecA. In the present work, we report the biochemical activity and structural effects of the L53Q mutation at the MAW motif of the RecA protein from H. seropedicae (HsRecA L53Q). In vitro studies showed that HsRecA L53Q can bind ADP, ATP, and ssDNA, as does wild-type RecA. However, the ATPase and DNA-strand exchange activities were completely lost. In vivo studies showed that the expression of HsRecA L53Q in E. coli recA1 does not change its phenotype when cells were challenged with MMS and UV. Molecular dynamics simulations showed the L53Q point mutation did not cause large conformational changes in the HsRecA structure. However, there is a difference on dynamical cross-correlation movements of the residues involved in contacts within the ATP binding site and regions that hold the DNA binding sites. Additionally, a new hydrogen bond, formed between Q53 and T49, was hypothesized to allow an independent motion of the MAW motif from the hydrophobic core, what could explain the observed loss of activity of HsRecA L53Q.
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Affiliation(s)
- Wellington C. Leite
- Department of Physics, State University of Ponta Grossa (UEPG), Ponta Grossa,Paraná, Brazil
- * E-mail: (WCL); .(CWG)
| | - Renato F. Penteado
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Fernando Gomes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Rafael M. Etto
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Sérgio C. Saab
- Department of Physics, State University of Ponta Grossa (UEPG), Ponta Grossa,Paraná, Brazil
| | - Maria B. R. Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Carolina W. Galvão
- Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
- * E-mail: (WCL); .(CWG)
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Yakimov A, Pobegalov G, Bakhlanova I, Khodorkovskii M, Petukhov M, Baitin D. Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide. Nucleic Acids Res 2017; 45:9788-9796. [PMID: 28934502 PMCID: PMC5766188 DOI: 10.1093/nar/gkx687] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/24/2017] [Indexed: 01/19/2023] Open
Abstract
The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.
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Affiliation(s)
- Alexander Yakimov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Georgii Pobegalov
- Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Irina Bakhlanova
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | | | - Michael Petukhov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Dmitry Baitin
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
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Rojas TCG, Lobo FP, Hongo JA, Vicentini R, Verma R, Maluta RP, da Silveira WD. Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains. Foodborne Pathog Dis 2017; 14:245-252. [PMID: 28398866 DOI: 10.1089/fpd.2016.2219] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The ability to obtain bacterial genomes from the same host has allowed for comparative studies that help in the understanding of the molecular evolution of specific pathotypes. Avian pathogenic Escherichia coli (APEC) is a group of extraintestinal strains responsible for causing colibacillosis in birds. APEC is also suggested to possess a role as a zoonotic agent. Despite its importance, APEC pathogenesis still has several cryptic pathogenic processes that need to be better understood. In this work, a genome-wide survey of eight APEC strains for genes with evidence of recombination revealed that ∼14% of the homologous groups evaluated present signs of recombination. Enrichment analyses revealed that nine Gene Ontology (GO) terms were significantly more represented in recombinant genes. Among these GO terms, several were noted to be ATP-related categories. The search for positive selection in these APEC genomes revealed 32 groups of homologous genes with evidence of positive selection. Among these groups, we found several related to cell metabolism, as well as several uncharacterized genes, beyond the well-known virulence factors ompC, lamB, waaW, waaL, and fliC. A GO term enrichment test showed a prevalence of terms related to bacterial cell contact with the external environment (e.g., viral entry into host cell, detection of virus, pore complex, bacterial-type flagellum filament C, and porin activity). Finally, the genes with evidence of positive selection were retrieved from genomes of non-APEC strains and tested as were done for APEC strains. The result revealed that none of the groups of genes presented evidence of positive selection, confirming that the analysis was effective in inferring positive selection for APEC and not for E. coli in general, which means that the study of the genes with evidence of positive selection identified in this study can contribute for the better understanding of APEC pathogenesis processes.
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Affiliation(s)
- Thaís Cabrera Galvão Rojas
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Francisco Pereira Lobo
- 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil
| | - Jorge Augusto Hongo
- 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil
| | - Renato Vicentini
- 3 Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Renu Verma
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Renato Pariz Maluta
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Wanderley Dias da Silveira
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
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Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ, Schaaper RM. Suppression of the E. coli SOS response by dNTP pool changes. Nucleic Acids Res 2015; 43:4109-20. [PMID: 25824947 PMCID: PMC4417155 DOI: 10.1093/nar/gkv217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022] Open
Abstract
The Escherichia coli SOS system is a well-established model for the cellular response to DNA damage. Control of SOS depends largely on the RecA protein. When RecA is activated by single-stranded DNA in the presence of a nucleotide triphosphate cofactor, it mediates cleavage of the LexA repressor, leading to expression of the 30+-member SOS regulon. RecA activation generally requires the introduction of DNA damage. However, certain recA mutants, like recA730, bypass this requirement and display constitutive SOS expression as well as a spontaneous (SOS) mutator effect. Presently, we investigated the possible interaction between SOS and the cellular deoxynucleoside triphosphate (dNTP) pools. We found that dNTP pool changes caused by deficiencies in the ndk or dcd genes, encoding nucleoside diphosphate kinase and dCTP deaminase, respectively, had a strongly suppressive effect on constitutive SOS expression in recA730 strains. The suppression of the recA730 mutator effect was alleviated in a lexA-deficient background. Overall, the findings suggest a model in which the dNTP alterations in the ndk and dcd strains interfere with the activation of RecA, thereby preventing LexA cleavage and SOS induction.
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Affiliation(s)
- Katarzyna H Maslowska
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | | | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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