1
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Štambuk N, Konjevoda P, Brčić-Kostić K, Baković J, Štambuk A. New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group. Biosystems 2023; 233:105030. [PMID: 37717902 DOI: 10.1016/j.biosystems.2023.105030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed sequences. We present a Klein four-group algorithm (K4A) for the evolutionary analysis of nucleotide and amino acid sequences. Klein four-group set of operators consists of: identity e (U), and three elements-a = transition (C), b = transversion (G) and c = transition-transversion or complementarity (A). We generated Klein four-group based distance matrices of: 1. Cayley table (CK4), 2. Table rows (K4R), 3. Table columns (K4C), and 4. Euclidean 2D distance (K4E). The performance of the matrices was tested on a dataset of RecA proteins in bacteria, eukaryotes (Rad51 homolog) and archaea (RadA homolog). RecA and its functional homologs are found in all species, and are essential for the repair and maintenance of DNA. Consequently, they represent a good model for the study of evolutionary relationship of protein and nucleotide sequences. The ancestral relationship between the sequences was correctly classified by all K4A matrices concerning general topology. All distance matrices exhibited small variations among species, and overall results of tree classification were in agreement with the general patterns obtained by standard BLOSUM and PAM substitution matrices. During the evolution of a code there is a phase of optimization of system rules, the ambiguity of a code is eliminated, and the system starts producing specific components. Klein four-group algorithm is consistent with the concept of ambiguity reduction. It also enables the use of different genetic code table variants optimized for particular transitions in evolution based on biological specificity.
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Affiliation(s)
- Nikola Štambuk
- Centre for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Krunoslav Brčić-Kostić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Josip Baković
- University Hospital Dubrava, Department of Surgery, Avenija Gojka Šuška 6, HR-10000, Zagreb, Croatia
| | - Albert Štambuk
- Faculty of Kinesiology, University of Zagreb, Horvaćanski zavoj 15, HR-10000 Zagreb, Croatia
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2
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Chen E, Culyba MJ. Pulling the wool over a pathogen's eyes: Llama nanobody inhibitors of the bacterial SOS response. Structure 2022; 30:1467-1469. [PMID: 36332609 DOI: 10.1016/j.str.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this issue of Structure, Maso et al. (2022) discover nanobodies that inhibit the SOS response of Escherichia coli by targeting the LexA repressor-protease. High-resolution structures of the novel LexA-nanobody complexes reveal they function by stabilizing LexA in its inactive conformation and preventing co-proteolysis by RecA∗.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew J Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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3
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Mercolino J, Lo Sciuto A, Spinnato MC, Rampioni G, Imperi F. RecA and Specialized Error-Prone DNA Polymerases are not Required for Mutagenesis and Antibiotic Resistance Induced by Fluoroquinolones in Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11030325. [PMID: 35326787 PMCID: PMC8944484 DOI: 10.3390/antibiotics11030325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
To cope with stressful conditions, including antibiotic exposure, bacteria activate the SOS response, a pathway that induces error-prone DNA repair and mutagenesis mechanisms. In most bacteria, the SOS response relies on the transcriptional repressor LexA and the co-protease RecA, the latter being also involved in homologous recombination. The role of the SOS response in stress- and antibiotic-induced mutagenesis has been characterized in detail in the model organism Escherichia coli. However, its effect on antibiotic resistance in the human pathogen Pseudomonas aeruginosa is less clear. Here, we analyzed a recA deletion mutant and confirmed, by conjugation and gene expression assays, that RecA is required for homologous recombination and SOS response induction in P. aeruginosa. MIC assays demonstrated that RecA affects P. aeruginosa resistance only towards fluoroquinolones and genotoxic agents. The comparison of antibiotic-resistant mutant frequency between treated and untreated cultures revealed that, among the antibiotics tested, only fluoroquinolones induced mutagenesis in P. aeruginosa. Notably, both RecA and error-prone DNA polymerases were found to be dispensable for this process. These data demonstrate that the SOS response is not required for antibiotic-induced mutagenesis in P. aeruginosa, suggesting that RecA inhibition is not a suitable strategy to target antibiotic-induced emergence of resistance in this pathogen.
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Affiliation(s)
- Jessica Mercolino
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Alessandra Lo Sciuto
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Maria Concetta Spinnato
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
| | - Giordano Rampioni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (J.M.); (A.L.S.); (M.C.S.); (G.R.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
- Correspondence:
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4
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Kulikov M, Statsenko V, Prazdnova E, Emelyantsev S. Antioxidant, DNA-protective, and SOS inhibitory activities of Enterococcus durans metabolites. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Zhou Z, Pan Q, Lv X, Yuan J, Zhang Y, Zhang MX, Ke M, Mo XM, Xie YL, Liu Y, Chen T, Liang M, Yin F, Liu L, Zhou Y, Qiao K, Liu R, Li Z, Wong NK. Structural insights into the inhibition of bacterial RecA by naphthalene polysulfonated compounds. iScience 2021; 24:101952. [PMID: 33458611 PMCID: PMC7797525 DOI: 10.1016/j.isci.2020.101952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 10/23/2020] [Accepted: 12/14/2020] [Indexed: 02/05/2023] Open
Abstract
As a promising target for alternative antimicrobials, bacterial recombinase A (RecA) protein has attracted much attention for its roles in antibiotic-driven SOS response and mutagenesis. Naphthalene polysulfonated compounds (NPS) such as suramin have previously been explored as antibiotic adjuvants targeting RecA, although the underlying structural bases for RecA-ligand interactions remain obscure. Based on our in silico predictions and documented activity of NPS in vitro, we conclude that the analyzed NPS likely interact with Tyr103 (Y103) and other key residues in the ATPase activity center (pocket A). For validation, we generated recombinant RecA proteins (wild-type versus Y103 mutant) to determine the binding affinities for RecA protein interactions with suramin and underexamined NPS in isothermal titration calorimetry. The corresponding dissociation constants (K d) ranged from 11.5 to 18.8 μM, and Y103 was experimentally shown to be critical to RecA-NPS interactions.
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Affiliation(s)
- Ziyuan Zhou
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Qing Pan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China
| | - Xinchen Lv
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jing Yuan
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Ming-Xia Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Ming Ke
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao-Mei Mo
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yong-Li Xie
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yingxia Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Kun Qiao
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Rui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Nai-Kei Wong
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
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6
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Targeting the bacterial SOS response for new antimicrobial agents: drug targets, molecular mechanisms and inhibitors. Future Med Chem 2021; 13:143-155. [PMID: 33410707 DOI: 10.4155/fmc-2020-0310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is a pressing threat to global health, with multidrug-resistant pathogens becoming increasingly prevalent. The bacterial SOS pathway functions in response to DNA damage that occurs during infection, initiating several pro-survival and resistance mechanisms, such as DNA repair and hypermutation. This makes SOS pathway components potential targets that may combat drug-resistant pathogens and decrease resistance emergence. This review discusses the mechanism of the SOS pathway; the structure and function of potential targets AddAB, RecBCD, RecA and LexA; and efforts to develop selective small-molecule inhibitors of these proteins. These inhibitors may serve as valuable tools for target validation and provide the foundations for desperately needed novel antibacterial therapeutics.
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7
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
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8
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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: 58] [Impact Index Per Article: 11.6] [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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9
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Zinc Acetate Potentiates the Action of Tosufloxacin against Escherichia coli Biofilm Persisters. Antimicrob Agents Chemother 2019; 63:AAC.00069-19. [PMID: 30936108 DOI: 10.1128/aac.00069-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/28/2019] [Indexed: 01/31/2023] Open
Abstract
Formation of bacterial biofilms is a major health threat due to their high levels of tolerance to multiple antibiotics and the presence of persisters responsible for infection relapses. We previously showed that a combination of starvation and induction of SOS response in biofilm led to increased levels of persisters and biofilm tolerance to fluoroquinolones. In this study, we hypothesized that inhibition of the SOS response may be an effective strategy to target biofilms and fluoroquinolone persister cells. We tested the survival of Escherichia coli biofilms to different classes of antibiotics in starved and nonstarved conditions and in the presence of zinc acetate, a SOS response inhibitor. We showed that zinc acetate potentiates, albeit moderately, the activity of fluoroquinolones against E. coli persisters in starved biofilms. The efficacy of zinc acetate to increase fluoroquinolone activity, particularly that of tosufloxacin, suggests that such a combination may be a potential strategy for treating biofilm-related bacterial infections.
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10
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SOS Response Inhibitory Properties by Potential Probiotic Formulations of Bacillus amyloliquefaciens B-1895 and Bacillus subtilis KATMIRA1933 Obtained by Solid-State Fermentation. Curr Microbiol 2019; 76:312-319. [DOI: 10.1007/s00284-018-01623-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
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11
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Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP. Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response. Front Microbiol 2018; 9:2961. [PMID: 30619111 PMCID: PMC6305444 DOI: 10.3389/fmicb.2018.02961] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022] Open
Abstract
Many antibiotics, either directly or indirectly, cause DNA damage thereby activating the bacterial DNA damage (SOS) response. SOS activation results in expression of genes involved in DNA repair and mutagenesis, and the regulation of the SOS response relies on two key proteins, LexA and RecA. Genetic studies have indicated that inactivating the regulatory proteins of this response sensitizes bacteria to antibiotics and slows the appearance of resistance. However, advancement of small molecule inhibitors of the SOS response has lagged, despite their clear promise in addressing the threat of antibiotic resistance. Previously, we had addressed this deficit by performing a high throughput screen of ∼1.8 million compounds that monitored for inhibition of RecA-mediated auto-proteolysis of Escherichia coli LexA, the reaction that initiates the SOS response. In this report, the refinement of the 5-amino-1-(carbamoylmethyl)-1H-1,2,3-triazole-4-carboxamide scaffold identified in the screen is detailed. After development of a modular synthesis, a survey of key activity determinants led to the identification of an analog with improved potency and increased breadth, targeting auto-proteolysis of LexA from both E. coli and Pseudomonas aeruginosa. Comparison of the structure of this compound to those of others in the series suggests structural features that may be required for activity and cross-species breadth. In addition, the feasibility of small molecule modulation of the SOS response was demonstrated in vivo by the suppression of the appearance of resistance. These structure activity relationships thus represent an important step toward producing Drugs that Inhibit SOS Activation to Repress Mechanisms Enabling Resistance (DISARMERs).
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Affiliation(s)
- Trevor Selwood
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian J Larsen
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
| | - Charlie Y Mo
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew J Culyba
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Zachary M Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
| | - Simon D P Baugh
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
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12
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Crane JK, Cheema MB, Olyer MA, Sutton MD. Zinc Blockade of SOS Response Inhibits Horizontal Transfer of Antibiotic Resistance Genes in Enteric Bacteria. Front Cell Infect Microbiol 2018; 8:410. [PMID: 30519543 PMCID: PMC6258817 DOI: 10.3389/fcimb.2018.00410] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022] Open
Abstract
The SOS response is a conserved response to DNA damage that is found in Gram-negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate than is normally observed, which is called the SOS mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in Escherichia coli and Klebsiella pneumoniae. In this study, we demonstrate that zinc blocks the SOS-induced development of chloramphenicol resistance in Enterobacter cloacae. Zinc also blocked the transfer of an extended spectrum beta-lactamase (ESBL) gene from Enterobacter to a susceptible E. coli strain. A zinc ionophore, zinc pyrithione, was ~100-fold more potent than zinc salts in inhibition of ciprofloxacin-induced hypermutation in E. cloacae. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Electrophoretic mobility shift assays (EMSAs) revealed that zinc, but not iron or manganese, blocked the ability of the E. coli RecA protein to bind to single-stranded DNA, an important early step in the recognition of DNA damage in enteric bacteria. This suggests a mechanism for zinc's inhibitory effects on bacterial SOS responses, including hypermutation.
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Affiliation(s)
- John K Crane
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Muhammad B Cheema
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Michael A Olyer
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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13
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Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A 2018; 115:E6301-E6309. [PMID: 29915065 DOI: 10.1073/pnas.1804218115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial persisters are subpopulations of phenotypic variants in isogenic cultures that can survive lethal doses of antibiotics. Their tolerances are often attributed to reduced activities of antibiotic targets, which limit corruption and damage in persisters compared with bacteria that die from treatment. However, that model does not hold for nongrowing populations treated with ofloxacin, a fluoroquinolone, where antibiotic-induced damage is comparable between cells that live and those that die. To understand how those persisters achieve this feat, we employed a genetic system that uses orthogonal control of MazF and MazE, a toxin and its cognate antitoxin, to generate model persisters that are uniformly tolerant to ofloxacin. Despite this complete tolerance, MazF model persisters required the same DNA repair machinery (RecA, RecB, and SOS induction) to survive ofloxacin treatment as their nongrowing, WT counterparts and exhibited similar indicators of DNA damage from treatment. Further investigation revealed that, following treatment, the timing of DNA repair was critical to MazF persister survival because, when repair was delayed until after growth and DNA synthesis resumed, survival was compromised. In addition, we found that, with nongrowing, WT planktonic and biofilm populations, stalling the resumption of growth and DNA synthesis after the conclusion of fluoroquinolone treatment with a prevalent type of stress at infection sites (nutrient limitation) led to near complete survival. These findings illustrate that the timing of events, such as DNA repair, following fluoroquinolone treatment is important to persister survival and provide further evidence that knowledge of the postantibiotic recovery period is critical to understanding persistence phenotypes.
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14
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The Use of Biosensors to Explore the Potential of Probiotic Strains to Reduce the SOS Response and Mutagenesis in Bacteria. BIOSENSORS-BASEL 2018; 8:bios8010025. [PMID: 29547508 PMCID: PMC5872073 DOI: 10.3390/bios8010025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/29/2023]
Abstract
A model system based on the Escherichia coli MG1655 (pRecA-lux) Lux-biosensor was used to evaluate the ability of the fermentates of eight probiotic strains to reduce the SOS response stimulated by ciprofloxacin in bacteria and mutagenesis mediated by it. Preliminary attempts to estimate the chemical nature of active components of the fermentates were conducted.
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15
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Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM. Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. ACS Infect Dis 2018; 4:349-359. [PMID: 29275629 DOI: 10.1021/acsinfecdis.7b00122] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RecA/LexA axis of the bacterial DNA damage (SOS) response is a promising, yet nontraditional, drug target. The SOS response is initiated upon genotoxic stress, when RecA, a DNA damage sensor, induces LexA, the SOS repressor, to undergo autoproteolysis, thereby derepressing downstream genes that can mediate DNA repair and accelerate mutagenesis. As genetic inhibition of the SOS response sensitizes bacteria to DNA damaging antibiotics and decreases acquired resistance, inhibitors of the RecA/LexA axis could potentiate our current antibiotic arsenal. Compounds targeting RecA, which has many mammalian homologues, have been reported; however, small-molecules targeting LexA autoproteolysis, a reaction unique to the prokaryotic SOS response, have remained elusive. Here, we describe the logistics and accomplishments of an academic-industry partnership formed to pursue inhibitors against the RecA/LexA axis. A novel fluorescence polarization assay reporting on RecA-induced self-cleavage of LexA enabled the screening of 1.8 million compounds. Follow-up studies on select leads show distinct activity patterns in orthogonal assays, including several with activity in cell-based assays reporting on SOS activation. Mechanistic assays demonstrate that we have identified first-in-class small molecules that specifically target the LexA autoproteolysis step in SOS activation. Our efforts establish a realistic example for navigating academic-industry partnerships in pursuit of anti-infective drugs and offer starting points for dedicated lead optimization of SOS inhibitors that could act as adjuvants for current antibiotics.
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Affiliation(s)
- Charlie Y. Mo
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Matthew J. Culyba
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Trevor Selwood
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M. Kubiak
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Anthony J. Jurewicz
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul M. Keller
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Andrew J. Pope
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Amy Quinn
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jessica Schneck
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Katherine L. Widdowson
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rahul M. Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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16
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Abstract
Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.
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17
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Kulp JL, Cloudsdale IS, Kulp JL, Guarnieri F. Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS One 2017; 12:e0183327. [PMID: 28837642 PMCID: PMC5570288 DOI: 10.1371/journal.pone.0183327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/02/2017] [Indexed: 01/03/2023] Open
Abstract
Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.
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Affiliation(s)
- John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
- Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Ian S. Cloudsdale
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - Frank Guarnieri
- PAKA Pulmonary Pharmaceuticals, Acton, Massachusetts, United States of America
- * E-mail:
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18
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Bellio P, Di Pietro L, Mancini A, Piovano M, Nicoletti M, Brisdelli F, Tondi D, Cendron L, Franceschini N, Amicosante G, Perilli M, Celenza G. SOS response in bacteria: Inhibitory activity of lichen secondary metabolites against Escherichia coli RecA protein. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2017; 29:11-18. [PMID: 28515022 DOI: 10.1016/j.phymed.2017.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown. PURPOSE Twenty-seven secondary metabolites classified as anthraquinones, depsides, depsidones, dibenzofurans, diphenyl-butenolides, paraconic acids, pseudo-depsidones, triterpenes and xanthones, were investigated for their ability to inhibit RecA from Escherichia coli. They were isolated in various Chilean regions from 14 families and 19 genera of lichens. METHODS The ATP hydrolytic activity of RecA was quantified detecting the generation of free phosphate in solution. The percentage of inhibition was calculated fixing at 100µM the concentration of the compounds. Deeper investigations were reserved to those compounds showing an inhibition higher than 80%. To clarify the mechanism of inhibition, the semi-log plot of the percentage of inhibition vs. ATP and vs. ssDNA, was evaluated. RESULTS Only nine compounds showed a percentage of RecA inhibition higher than 80% (divaricatic, perlatolic, alpha-collatolic, lobaric, lichesterinic, protolichesterinic, epiphorellic acids, sphaerophorin and tumidulin). The half-inhibitory concentrations (IC50) calculated for these compounds were ranging from 14.2µM for protolichesterinic acid to 42.6µM for sphaerophorin. Investigations on the mechanism of inhibition showed that all compounds behaved as uncompetitive inhibitors for ATP binding site, with the exception of epiphorellic acid which clearly acted as non-competitive inhibitor of the ATP site. Further investigations demonstrated that epiphorellic acid competitively binds the ssDNA binding site. Kinetic data were confirmed by molecular modelling binding predictions which shows that epiphorellic acid is expected to bind the ssDNA site into the L2 loop of RecA protein. CONCLUSION In this paper the first RecA ssDNA binding site ligand is described. Our study sets epiphorellic acid as a promising hit for the development of more effective RecA inhibitors. In our drug discovery approach, natural products in general and lichen in particular, represent a successful source of active ligands and structural diversity.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Letizia Di Pietro
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Alisia Mancini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Marisa Piovano
- Department of Chemistry, Universidad Técnica Federico Santa María, Casilla 110 V, Valparaíso, 6, Chile
| | - Marcello Nicoletti
- Department of Environmental Biology, University Sapienza, P.le A. Moro, 00185, Rome, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena e Reggio Emilia, Via Campi 103, 41100, Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Nicola Franceschini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy.
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19
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Bunnell BE, Escobar JF, Bair KL, Sutton MD, Crane JK. Zinc blocks SOS-induced antibiotic resistance via inhibition of RecA in Escherichia coli. PLoS One 2017; 12:e0178303. [PMID: 28542496 PMCID: PMC5440055 DOI: 10.1371/journal.pone.0178303] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/10/2017] [Indexed: 01/22/2023] Open
Abstract
Zinc inhibits the virulence of diarrheagenic E. coli by inducing the envelope stress response and inhibiting the SOS response. The SOS response is triggered by damage to bacterial DNA. In Shiga-toxigenic E. coli, the SOS response strongly induces the production of Shiga toxins (Stx) and of the bacteriophages that encode the Stx genes. In E. coli, induction of the SOS response is accompanied by a higher mutation rate, called the mutator response, caused by a shift to error-prone DNA polymerases when DNA damage is too severe to be repaired by canonical DNA polymerases. Since zinc inhibited the other aspects of the SOS response, we hypothesized that zinc would also inhibit the mutator response, also known as hypermutation. We explored various different experimental paradigms to induce hypermutation triggered by the SOS response, and found that hypermutation was induced not just by classical inducers such as mitomycin C and the quinolone antibiotics, but also by antiviral drugs such as zidovudine and anti-cancer drugs such as 5-fluorouracil, 6-mercaptopurine, and azacytidine. Zinc salts inhibited the SOS response and the hypermutator phenomenon in E. coli as well as in Klebsiella pneumoniae, and was more effective in inhibiting the SOS response than other metals. We then attempted to determine the mechanism by which zinc, applied externally in the medium, inhibits hypermutation. Our results show that zinc interferes with the actions of RecA, and protects LexA from RecA-mediated cleavage, an early step in initiation of the SOS response. The SOS response may play a role in the development of antibiotic resistance and the effect of zinc suggests ways to prevent it.
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Affiliation(s)
- Bryan E. Bunnell
- Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY, United States of America
| | - Jillian F. Escobar
- Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY, United States of America
| | - Kirsten L. Bair
- Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY, United States of America
| | - Mark D. Sutton
- Department of Biochemistry, University at Buffalo, Buffalo, NY, United States of America
| | - John K. Crane
- Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY, United States of America
- * E-mail:
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20
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Huerta-Uribe A, Marjenberg ZR, Yamaguchi N, Fitzgerald S, Connolly JPR, Carpena N, Uvell H, Douce G, Elofsson M, Byron O, Marquez R, Gally DL, Roe AJ. Identification and Characterization of Novel Compounds Blocking Shiga Toxin Expression in Escherichia coli O157:H7. Front Microbiol 2016; 7:1930. [PMID: 27965652 PMCID: PMC5127787 DOI: 10.3389/fmicb.2016.01930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/17/2016] [Indexed: 11/23/2022] Open
Abstract
Infections caused by Shiga toxin (Stx)-producing E. coli strains constitute a health problem, as they are problematic to treat. Stx production is a key virulence factor associated with the pathogenicity of enterohaemorrhagic E. coli (EHEC) and can result in the development of haemolytic uremic syndrome in infected patients. The genes encoding Stx are located on temperate lysogenic phages integrated into the bacterial chromosome and expression of the toxin is generally coupled to phage induction through the SOS response. We aimed to find new compounds capable of blocking expression of Stx type 2 (Stx2) as this subtype of Stx is more strongly associated with human disease. High-throughput screening of a small-molecule library identified a lead compound that reduced Stx2 expression in a dose-dependent manner. We show that the optimized compound interferes with the SOS response by directly affecting the activity and oligomerization of RecA, thus limiting phage activation and Stx2 expression. Our work suggests that RecA is highly susceptible to inhibition and that targeting this protein is a viable approach to limiting production of Stx2 by EHEC. This type of approach has the potential to limit production and transfer of other phage induced and transduced determinants.
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Affiliation(s)
- Alejandro Huerta-Uribe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Zoe R Marjenberg
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Nao Yamaguchi
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh Edinburgh, UK
| | - Stephen Fitzgerald
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh Edinburgh, UK
| | - James P R Connolly
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Nuria Carpena
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Hanna Uvell
- Laboratories for Chemical Biology Umeå, Department of Chemistry, Umeå University Umeå, Sweden
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Michael Elofsson
- Laboratories for Chemical Biology Umeå, Department of Chemistry, Umeå University Umeå, Sweden
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Rudi Marquez
- Department of Chemistry, Xi'an Jiaotong-Liverpool University Suzhou, China
| | - David L Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh Edinburgh, UK
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
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21
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Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics. mSphere 2016; 1:mSphere00163-16. [PMID: 27536734 PMCID: PMC4980697 DOI: 10.1128/msphere.00163-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role in promoting survival and the evolution of resistance under antibiotic stress. As a result, targeting the SOS response has been proposed as an adjuvant strategy to revitalize our current antibiotic arsenal. However, the optimal molecular targets and partner antibiotics for such an approach remain unclear. In this study, focusing on the two key regulators of the SOS response, LexA and RecA, we provide the first comprehensive assessment of how to target the SOS response in order to increase bacterial susceptibility and reduce mutagenesis under antibiotic treatment. The bacterial SOS response is a DNA damage repair network that is strongly implicated in both survival and acquired drug resistance under antimicrobial stress. The two SOS regulators, LexA and RecA, have therefore emerged as potential targets for adjuvant therapies aimed at combating resistance, although many open questions remain. For example, it is not well understood whether SOS hyperactivation is a viable therapeutic approach or whether LexA or RecA is a better target. Furthermore, it is important to determine which antimicrobials could serve as the best treatment partners with SOS-targeting adjuvants. Here we derived Escherichia coli strains that have mutations in either lexA or recA genes in order to cover the full spectrum of possible SOS activity levels. We then systematically analyzed a wide range of antimicrobials by comparing the mean inhibitory concentrations (MICs) and induced mutation rates for each drug-strain combination. We first show that significant changes in MICs are largely confined to DNA-damaging antibiotics, with strains containing a constitutively repressed SOS response impacted to a greater extent than hyperactivated strains. Second, antibiotic-induced mutation rates were suppressed when SOS activity was reduced, and this trend was observed across a wider spectrum of antibiotics. Finally, perturbing either LexA or RecA proved to be equally viable strategies for targeting the SOS response. Our work provides support for multiple adjuvant strategies, while also suggesting that the combination of an SOS inhibitor with a DNA-damaging antibiotic could offer the best potential for lowering MICs and decreasing acquired drug resistance. IMPORTANCE Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role in promoting survival and the evolution of resistance under antibiotic stress. As a result, targeting the SOS response has been proposed as an adjuvant strategy to revitalize our current antibiotic arsenal. However, the optimal molecular targets and partner antibiotics for such an approach remain unclear. In this study, focusing on the two key regulators of the SOS response, LexA and RecA, we provide the first comprehensive assessment of how to target the SOS response in order to increase bacterial susceptibility and reduce mutagenesis under antibiotic treatment.
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22
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A role for the bacterial GATC methylome in antibiotic stress survival. Nat Genet 2016; 48:581-6. [PMID: 26998690 PMCID: PMC4848143 DOI: 10.1038/ng.3530] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance is an increasingly serious public health threat1. Understanding pathways allowing bacteria to survive antibiotic stress may unveil new therapeutic targets2–8. We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. We find that Escherichia coli survival under antibiotic pressure is severely compromised without adenine methylation at GATC sites. While the adenine methylome remains stable during drug stress, without GATC methylation, methyl-dependent mismatch repair (MMR) is deleterious, and fueled by the drug-induced error-prone polymerase PolIV, overwhelms cells with toxic DNA breaks. In multiple E. coli strains, including pathogenic and drug-resistant clinical isolates, DNA adenine methyltransferase deficiency potentiates antibiotics from the β-lactam and quinolone classes. This work indicates that the GATC methylome provides structural support for bacterial survival during antibiotics stress and suggests targeting bacterial DNA methylation as a viable approach to enhancing antibiotic activity.
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23
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Vestergaard M, Paulander W, Ingmer H. Activation of the SOS response increases the frequency of small colony variants. BMC Res Notes 2015; 8:749. [PMID: 26643526 PMCID: PMC4672542 DOI: 10.1186/s13104-015-1735-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023] Open
Abstract
Background In Staphylococcus aureus sub-populations of slow-growing cells forming small colony variants (SCVs) are associated with persistent and recurrent infections that are difficult to eradicate with antibiotic therapies. In SCVs that are resistant towards aminoglycosides, mutations have been identified in genes encoding components of the respiratory chain. Given the high frequencies of SCVs isolated clinically it is vital to understand the conditions that promote or select for SCVs. Results In this study we have examined how exposure to sub-inhibitory concentrations of antibiotics with different mechanism of action influence the formation of SCVs that are resistant to otherwise lethal concentrations of the aminoglycoside, gentamicin. We found that exposure of S. aureus to fluoroquinolones and mitomycin C increased the frequency of gentamicin resistant SCVs, while other antibiotic classes failed to do so. The higher proportion of SCVs in cultures exposed to fluoroquinolones and mitomycin C compared to un-exposed cultures correlate with an increased mutation rate monitored by rifampicin resistance and followed induction of the SOS DNA damage response. Conclusion Our observations suggest that environmental stimuli, including antimicrobials that reduce replication fidelity, increase the formation of SCVs through activation of the SOS response and thereby potentially promote persistent infections that are difficult to treat.
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Affiliation(s)
- Martin Vestergaard
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
| | - Wilhelm Paulander
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
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24
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Abstract
![]()
Bacteria
possess a remarkable ability to rapidly adapt and evolve
in response to antibiotics. Acquired antibiotic resistance can arise
by multiple mechanisms but commonly involves altering the target site
of the drug, enzymatically inactivating the drug, or preventing the
drug from accessing its target. These mechanisms involve new genetic
changes in the pathogen leading to heritable resistance. This recognition
underscores the importance of understanding how such
genetic changes can arise. Here, we review recent advances in our
understanding of the processes that contribute to the evolution of
antibiotic resistance, with a particular focus on hypermutation mediated
by the SOS pathway and horizontal gene transfer. We explore the molecular
mechanisms involved in acquired resistance and discuss their viability
as potential targets. We propose that additional studies into these
adaptive mechanisms not only can provide insights into evolution but
also can offer a strategy for potentiating our current antibiotic
arsenal.
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25
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Abstract
Microbial drug persistence is a widespread phenomenon in which a subpopulation of microorganisms is able to survive antimicrobial treatment without acquiring resistance-conferring genetic changes. Microbial persisters can cause recurrent or intractable infections, and, like resistant mutants, they carry an increasing clinical burden. In contrast to heritable drug resistance, however, the biology of persistence is only beginning to be unraveled. Persisters have traditionally been thought of as metabolically dormant, nondividing cells. As discussed in this review, increasing evidence suggests that persistence is in fact an actively maintained state, triggered and enabled by a network of intracellular stress responses that can accelerate processes of adaptive evolution. Beyond shedding light on the basis of persistence, these findings raise the possibility that persisters behave as an evolutionary reservoir from which resistant organisms can emerge. As persistence and its consequences come into clearer focus, so too does the need for clinically useful persister-eradication strategies.
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Rodríguez-Rojas A, Rodríguez-Beltrán J, Couce A, Blázquez J. Antibiotics and antibiotic resistance: a bitter fight against evolution. Int J Med Microbiol 2013; 303:293-7. [PMID: 23517688 DOI: 10.1016/j.ijmm.2013.02.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
One of the most terrible consequences of Darwinian evolution is arguably the emergence and spread of antibiotic resistance, which is becoming a serious menace to modern societies. While spontaneous mutation, recombination and horizontal gene transfer are recognized as the main causes of this notorious phenomenon; recent research has raised awareness that sub-lethal concentrations of antibiotics can also foster resistance as an undesirable side-effect. They can produce genetic changes by different ways, including a raise of free radicals within the cell, induction of error-prone DNA-polymerases mediated by SOS response, imbalanced nucleotide metabolism or affect directly DNA. In addition to certain environmental conditions, subinhibitory concentrations of antimicrobials may increase, even more, the mutagenic effect of antibiotics. Here, we review the state of knowledge on antibiotics as promoters of antibiotic resistance.
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Affiliation(s)
- Alexandro Rodríguez-Rojas
- Centro Nacional de Biotecnología CNB, Consejo Superior de Investigaciones Científicas CSIC, Darwin 3, Campus de la Universidad Autónoma, Cantoblanco-Madrid 28049, Spain
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Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii. J Bacteriol 2013; 195:1335-45. [PMID: 23316046 DOI: 10.1128/jb.02176-12] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial, opportunistic pathogen that survives desiccation and quickly acquires resistance to multiple antibiotics. Escherichia coli gains antibiotic resistances by expressing genes involved in a global response to DNA damage. Therefore, we asked whether A. baumannii does the same through a yet undetermined DNA damage response akin to the E. coli paradigm. We found that recA and all of the multiple error-prone DNA polymerase V (Pol V) genes, those organized as umuDC operons and unlinked, are induced upon DNA damage in a RecA-mediated fashion. Consequently, we found that the frequency of rifampin-resistant (Rif(r)) mutants is dramatically increased upon UV treatment, alkylation damage, and desiccation, also in a RecA-mediated manner. However, in the recA insertion knockout strain, in which we could measure the recA transcript, we found that recA was induced by DNA damage, while uvrA and one of the unlinked umuC genes were somewhat derepressed in the absence of DNA damage. Thus, the mechanism regulating the A. baumannii DNA damage response is likely different from that in E. coli. Notably, it appears that the number of DNA Pol V genes may directly contribute to desiccation-induced mutagenesis. Sequences of the rpoB gene from desiccation-induced Rif(r) mutants showed a signature that was consistent with E. coli DNA polymerase V-generated base-pair substitutions and that matched that of sequenced A. baumannii clinical Rif(r) isolates. These data strongly support an A. baumannii DNA damage-inducible response that directly contributes to antibiotic resistance acquisition, particularly in hospitals where A. baumannii desiccates and tenaciously survives on equipment and surfaces.
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Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppée JY, Ghigo JM, Beloin C. Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin. PLoS Genet 2013; 9:e1003144. [PMID: 23300476 PMCID: PMC3536669 DOI: 10.1371/journal.pgen.1003144] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 10/22/2012] [Indexed: 12/14/2022] Open
Abstract
High levels of antibiotic tolerance are a hallmark of bacterial biofilms. In contrast to well-characterized inherited antibiotic resistance, molecular mechanisms leading to reversible and transient antibiotic tolerance displayed by biofilm bacteria are still poorly understood. The physiological heterogeneity of biofilms influences the formation of transient specialized subpopulations that may be more tolerant to antibiotics. In this study, we used random transposon mutagenesis to identify biofilm-specific tolerant mutants normally exhibited by subpopulations located in specialized niches of heterogeneous biofilms. Using Escherichia coli as a model organism, we demonstrated, through identification of amino acid auxotroph mutants, that starved biofilms exhibited significantly greater tolerance towards fluoroquinolone ofloxacin than their planktonic counterparts. We demonstrated that the biofilm-associated tolerance to ofloxacin was fully dependent on a functional SOS response upon starvation to both amino acids and carbon source and partially dependent on the stringent response upon leucine starvation. However, the biofilm-specific ofloxacin increased tolerance did not involve any of the SOS-induced toxin–antitoxin systems previously associated with formation of highly tolerant persisters. We further demonstrated that ofloxacin tolerance was induced as a function of biofilm age, which was dependent on the SOS response. Our results therefore show that the SOS stress response induced in heterogeneous and nutrient-deprived biofilm microenvironments is a molecular mechanism leading to biofilm-specific high tolerance to the fluoroquinolone ofloxacin. Biofilm surface-attached communities have the capacity to tolerate high concentrations of antibiotics, and bacterial biofilms formed on indwelling medical devices are difficult to eradicate and often lead to the onset of chronic or systemic infections. The physiological heterogeneity of multicellular biofilms has been associated with development of subpopulations highly tolerant to multiple antibiotics. Here we demonstrate that, upon starvation for specific essential growth nutrients, biofilm bacteria become highly tolerant to fluoroquinolone ofloxacin. The SOS response plays a critical role in this phenomenon, while the stringent response plays only a minor role. Taken together, these results support the hypothesis that bacteria localized within nutrient-limited niches of the biofilm structure may temporarily enter a physiological state enabling them to tolerate bactericidal concentrations of antibiotics.
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Affiliation(s)
- Steve P. Bernier
- Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
| | - David Lebeaux
- Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
| | | | - Amandine Valomon
- Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
| | - Guillaume Soubigou
- Institut Pasteur, Génopole, Plate-forme 2–Transcriptome et Epigénome, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Génopole, Plate-forme 2–Transcriptome et Epigénome, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
- * E-mail:
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Abstract
Fundamental aspects of the lifestyle of Mycobacterium tuberculosis implicate DNA metabolism in bacillary survival and adaptive evolution. The environments encountered by M. tuberculosis during successive cycles of infection and transmission are genotoxic. Moreover, as an obligate pathogen, M. tuberculosis has the ability to persist for extended periods in a subclinical state, suggesting that active DNA repair is critical to maintain genome integrity and bacterial viability during prolonged infection. In this chapter, we provide an overview of the major DNA metabolic pathways identified in M. tuberculosis, and situate key recent findings within the context of mycobacterial pathogenesis. Unlike many other bacterial pathogens, M. tuberculosis is genetically secluded, and appears to rely solely on chromosomal mutagenesis to drive its microevolution within the human host. In turn, this implies that a balance between high versus relaxed fidelity mechanisms of DNA metabolism ensures the maintenance of genome integrity, while accommodating the evolutionary imperative to adapt to hostile and fluctuating environments. The inferred relationship between mycobacterial DNA repair and genome dynamics is considered in the light of emerging data from whole-genome sequencing studies of clinical M. tuberculosis isolates which have revealed the potential for considerable heterogeneity within and between different bacterial and host populations.
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Schröder W, Goerke C, Wolz C. Opposing effects of aminocoumarins and fluoroquinolones on the SOS response and adaptability in Staphylococcus aureus. J Antimicrob Chemother 2012; 68:529-38. [PMID: 23169893 DOI: 10.1093/jac/dks456] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES RecA is the key enzyme involved in DNA repair, recombination and induction of the SOS response and is central to the development of antibiotic resistance. Here we assessed the interaction of two different gyrase inhibitors, ciprofloxacin (a fluoroquinolone) and novobiocin (an aminocoumarin), on RecA activity and the SOS response in Staphylococcus aureus. METHODS The influence of different gyrase inhibitors on the SOS response of S. aureus (including recA and lexA mutants) was analysed by northern blot analysis, real-time RT-PCR, western blot analysis and promoter activity assays. Recombination as well as mutation frequencies were determined for the different antibiotic combinations. RESULTS We verified that ciprofloxacin leads to RecA activation and therefore induction of the SOS response. In contrast, novobiocin treatment resulted in an inhibition of recA transcription independent of LexA. When novobiocin and ciprofloxacin were added simultaneously, recA was reduced to the same level as with novobiocin alone. In combination, novobiocin also partially reduces the ciprofloxacin-mediated induction of the LexA target gene umuC (error-prone polymerase). Apart from reducing recA and umuC expression, novobiocin also inhibited the frequency of recombination, mutation and the formation of non-haemolytic variants. CONCLUSION In summary, aminocoumarins inhibit recA expression in S. aureus and probably delay the process of developing antibiotic resistance and gene transfer. A clinical re-evaluation of these compounds as well as designing more applicable derivatives should be considered.
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Affiliation(s)
- Wiebke Schröder
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse-6, 72076 Tübingen, Germany
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Blázquez J, Couce A, Rodríguez-Beltrán J, Rodríguez-Rojas A. Antimicrobials as promoters of genetic variation. Curr Opin Microbiol 2012; 15:561-9. [PMID: 22890188 DOI: 10.1016/j.mib.2012.07.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 12/25/2022]
Abstract
The main causes of antibiotic resistance are the selection of naturally occurring resistant variants and horizontal gene transfer processes. In recent years, the implications of antibiotic contact or treatment in drug resistance acquisition by bacteria have been gradually more evident. The ultimate source of bacterial genetic alterations to face antibiotic toxicity is mutation. All evidence points to antibiotics, especially when present at sublethal concentrations, as responsible for increasing genetic variation and therefore participating in the emergence of antibiotic resistance. Antibiotics may cause genetic changes by means of different pathways involving an increase of free radicals inside the cell or oxidative stress, by inducing error-prone polymerases mediated by SOS response, misbalancing nucleotide metabolism or acting directly on DNA. In addition, the concerted action of certain environmental conditions with subinhibitory concentrations of antimicrobials may contribute to increasing the mutagenic effect of antibiotics even more. Here we review and discuss in detail the recent advances concerning these issues and their relevance in the field of antibiotic resistance.
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Overcoming drug resistance with alginate oligosaccharides able to potentiate the action of selected antibiotics. Antimicrob Agents Chemother 2012; 56:5134-41. [PMID: 22825116 DOI: 10.1128/aac.00525-12] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The uncontrolled, often inappropriate use of antibiotics has resulted in the increasing prevalence of antibiotic-resistant pathogens, with major cost implications for both United States and European health care systems. We describe the utilization of a low-molecular-weight oligosaccharide nanomedicine (OligoG), based on the biopolymer alginate, which is able to perturb multidrug-resistant (MDR) bacteria by modulating biofilm formation and persistence and reducing resistance to antibiotic treatment, as evident using conventional and robotic MIC screening and microscopic analyses of biofilm structure. OligoG increased (up to 512-fold) the efficacy of conventional antibiotics against important MDR pathogens, including Pseudomonas, Acinetobacter, and Burkholderia spp., appearing to be effective with several classes of antibiotic (i.e., macrolides, β-lactams, and tetracyclines). Using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), increasing concentrations (2%, 6%, and 10%) of alginate oligomer were shown to have a direct effect on the quality of the biofilms produced and on the health of the cells within that biofilm. Biofilm growth was visibly weakened in the presence of 10% OligoG, as seen by decreased biomass and increased intercellular spaces, with the bacterial cells themselves becoming distorted and uneven due to apparently damaged cell membranes. This report demonstrates the feasibility of reducing the tolerance of wound biofilms to antibiotics with the use of specific alginate preparations.
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The antibiotic resistome: challenge and opportunity for therapeutic intervention. Future Med Chem 2012; 4:347-59. [PMID: 22393941 DOI: 10.4155/fmc.12.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite the relevance of infectious disease as main causes of human morbidity and mortality, the development of new antibacterials is not among the highest priorities for pharmaceutical companies. Regulatory and economic issues, together with the lack of novel targets, might justify the reduced rate of discovery of new antimicrobials. With the increasing number of antibiotic resistant pathogens, the mechanisms of resistance appear as appealing alternatives for developing new drugs. Defining the elements that contribute to the characteristic phenotype of susceptibility to antibiotics of a given bacterial species, will serve to find those targets. Recent information on the elements forming part of bacterial intrinsic resistomes and on the inhibitors of resistance currently under development are presented. The possibility of developing new therapeutic procedures based on the administration, together with antibiotics of specific metabolic intermediates capable of increasing the susceptibility to antibiotics by altering bacterial physiology, are also discussed.
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Hocquet D, Llanes C, Thouverez M, Kulasekara HD, Bertrand X, Plésiat P, Mazel D, Miller SI. Evidence for induction of integron-based antibiotic resistance by the SOS response in a clinical setting. PLoS Pathog 2012; 8:e1002778. [PMID: 22719259 PMCID: PMC3375312 DOI: 10.1371/journal.ppat.1002778] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/14/2012] [Indexed: 01/23/2023] Open
Abstract
Bacterial resistance to β-lactams may rely on acquired β-lactamases encoded by class 1 integron-borne genes. Rearrangement of integron cassette arrays is mediated by the integrase IntI1. It has been previously established that integrase expression can be activated by the SOS response in vitro, leading to speculation that this is an important clinical mechanism of acquiring resistance. Here we report the first in vivo evidence of the impact of SOS response activated by the antibiotic treatment given to a patient and its output in terms of resistance development. We identified a new mechanism of modulation of antibiotic resistance in integrons, based on the insertion of a genetic element, the gcuF1 cassette, upstream of the integron-borne cassette blaOXA-28 encoding an extended spectrum β-lactamase. This insertion creates the fused protein GCUF1-OXA-28 and modulates the transcription, the translation, and the secretion of the β-lactamase in a Pseudomonas aeruginosa isolate (S-Pae) susceptible to the third generation cephalosporin ceftazidime. We found that the metronidazole, not an anti-pseudomonal antibiotic given to the first patient infected with S-Pae, triggered the SOS response that subsequently activated the integrase IntI1 expression. This resulted in the rearrangement of the integron gene cassette array, through excision of the gcuF1 cassette, and the full expression the β-lactamase in an isolate (R-Pae) highly resistant to ceftazidime, which further spread to other patients within our hospital. Our results demonstrate that in human hosts, the antibiotic-induced SOS response in pathogens could play a pivotal role in adaptation process of the bacteria. The bacterial SOS response is a conserved regulatory network that is induced in response to DNA damage. Its activation in vitro leads to the emergence of resistance to antibiotics, leading to speculation that this is an important clinical mechanism of acquiring resistance. We found evidence here that antibiotic-induced SOS response plays a role in bacterial genome rearrangement in vivo within humans. The major classes of antibiotics can trigger the bacterial SOS response and our data raise questions about their wide use and their subsequent effect on the bacterial genetic adaptability. This suggests that emergence of antibiotic resistance during therapy could be reduced by inhibiting the bacterial SOS response. We showed that acquired resistance genes could spread latently in susceptible bacterial strains until needed. These findings could impact current policies for control of antibiotic resistance, which rely on the detection of resistant bacteria and on the assumption that resistance mechanisms have a functional cost to the bacteria. More generally, SOS response may spur changes in the behavior of bacteria and their faster adaptation to hostile environments, including humans.
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Affiliation(s)
- Didier Hocquet
- Department of Immunology, Medicine and Microbiology, University of Washington, Seattle, Washington, United States of America
- EA4266, Laboratoire de Bactériologie, Université de Franche-Comté, Besançon, France
| | - Catherine Llanes
- EA4266, Laboratoire de Bactériologie, Université de Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Laboratoire d'Hygiène Hospitalière, CHRU, Besançon, France
- UMR6249 Chrono-Environnement, Université de Franche-Comté, Besançon, France
| | - Hemantha D. Kulasekara
- Department of Immunology, Medicine and Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, CHRU, Besançon, France
- UMR6249 Chrono-Environnement, Université de Franche-Comté, Besançon, France
| | - Patrick Plésiat
- EA4266, Laboratoire de Bactériologie, Université de Franche-Comté, Besançon, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Département Génomes et Génétique, Paris, France
- * E-mail: (DM); (SIM)
| | - Samuel I. Miller
- Department of Immunology, Medicine and Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DM); (SIM)
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Du L, Luo Y. Structure of a hexameric form of RadA recombinase from Methanococcus voltae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:511-6. [PMID: 22691778 PMCID: PMC3374503 DOI: 10.1107/s1744309112010226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/07/2012] [Indexed: 11/27/2022]
Abstract
Archaeal RadA proteins are close homologues of eukaryal Rad51 and DMC1 proteins and are remote homologues of bacterial RecA proteins. For the repair of double-stranded breaks in DNA, these recombinases promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. This DNA-repair function also plays a key role in the resistance of cancer cells to chemotherapy and radiotherapy and in the resistance of bacterial cells to antibiotics. A hexameric form of a truncated Methanococcus voltae RadA protein devoid of its small N-terminal domain has been crystallized. The RadA hexamers further assemble into two-ringed assemblies. Similar assemblies can be observed in the crystals of Pyrococcus furiosus RadA and Homo sapiens DMC1. In all of these two-ringed assemblies the DNA-interacting L1 region of each protomer points inward towards the centre, creating a highly positively charged locus. The electrostatic characteristics of the central channels can be utilized in the design of novel recombinase inhibitors.
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Affiliation(s)
- Liqin Du
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
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Midon M, Gimadutdinow O, Meiss G, Friedhoff P, Pingoud A. Chemical Rescue of Active Site Mutants of S. pneumoniae Surface Endonuclease EndA and Other Nucleases of the HNH Family by Imidazole. Chembiochem 2012; 13:713-21. [DOI: 10.1002/cbic.201100775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/08/2022]
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Peterson EJR, Janzen WP, Kireev D, Singleton SF. High-throughput screening for RecA inhibitors using a transcreener adenosine 5'-O-diphosphate assay. Assay Drug Dev Technol 2011; 10:260-8. [PMID: 22192312 DOI: 10.1089/adt.2011.0409] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The activities of the bacterial RecA protein are involved in the de novo development and transmission of antibiotic resistance genes, thus allowing bacteria to overcome the metabolic stress induced by antibacterial agents. RecA is ubiquitous and highly conserved among bacteria, but has only distant homologs in human cells. Together, this evidence points to RecA as a novel and attractive antibacterial drug target. All known RecA functions require the formation of a complex formed by multiple adenosine 5'-O-triphosphate (ATP)-bound RecA monomers on single-stranded DNA. In this complex, RecA hydrolyzes ATP. Although several methods for assessing RecA's ATPase activity have been reported, these assay conditions included relatively high concentrations of enzyme and ATP and thereby restricted the RecA conformational state. Herein, we describe the validation of commercial reagents (Transcreener(®) adenosine 5'-O-diphosphate [ADP](2) fluorescence polarization assay) for the high-throughput measurement of RecA's ATPase activity with lower concentrations of ATP and RecA. Under optimized conditions, ADP detection by the Transcreener reagent provided robust and reproducible activity data (Z'=0.92). Using the Transcreener assay, we screened 113,477 small molecules against purified RecA protein. In total, 177 small molecules were identified as confirmed hits, of which 79 were characterized by IC(50) values ≤ 10 μM and 35 were active in bioassays with live bacteria. This set of compounds comprises previously unidentified scaffolds for RecA inhibition and represents tractable hit structures for efforts aimed at tuning RecA inhibitory activity in both biochemical and bacteriological assays.
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Affiliation(s)
- Eliza J R Peterson
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7568, USA
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Baquero F, Coque TM, de la Cruz F. Ecology and evolution as targets: the need for novel eco-evo drugs and strategies to fight antibiotic resistance. Antimicrob Agents Chemother 2011; 55:3649-60. [PMID: 21576439 PMCID: PMC3147629 DOI: 10.1128/aac.00013-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years, the explosive spread of antibiotic resistance determinants among pathogenic, commensal, and environmental bacteria has reached a global dimension. Classical measures trying to contain or slow locally the progress of antibiotic resistance in patients on the basis of better antibiotic prescribing policies have clearly become insufficient at the global level. Urgent measures are needed to directly confront the processes influencing antibiotic resistance pollution in the microbiosphere. Recent interdisciplinary research indicates that new eco-evo drugs and strategies, which take ecology and evolution into account, have a promising role in resistance prevention, decontamination, and the eventual restoration of antibiotic susceptibility. This minireview summarizes what is known and what should be further investigated to find drugs and strategies aiming to counteract the "four P's," penetration, promiscuity, plasticity, and persistence of rapidly spreading bacterial clones, mobile genetic elements, or resistance genes. The term "drug" is used in this eco-evo perspective as a tool to fight resistance that is able to prevent, cure, or decrease potential damage caused by antibiotic resistance, not necessarily only at the individual level (the patient) but also at the ecological and evolutionary levels. This view offers a wealth of research opportunities for science and technology and also represents a large adaptive challenge for regulatory agencies and public health officers. Eco-evo drugs and interventions constitute a new avenue for research that might influence not only antibiotic resistance but the maintenance of a healthy interaction between humans and microbial systems in a rapidly changing biosphere.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Institute Ramón and Cajal for Health Research (IRYCIS), CIBER Research Network in Epidemiology and Public Health (CIBERESP), Ramón y Cajal University Hospital, Madrid, Spain.
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Sghaier H, Satoh K, Narumi I. In silico method to predict functional similarity between two RecA orthologs. JOURNAL OF BIOMOLECULAR SCREENING 2011; 16:457-459. [PMID: 21393627 DOI: 10.1177/1087057111400909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
RecA is a highly conserved bacterial protein that plays crucial roles in many cellular processes and hence is a potential target in the chemotherapy of bacterial infections. An understanding of the functional similarity between RecA proteins from different bacterial species should yield further insights into the biochemistry of RecA protein, along with the potential for new approaches to facilitate the improvement of RecA-targeted drugs. In this technical note, the authors present an in silico method based on tri-oligonucleotide usage correlations (TOUC) to predict the functional similarity between two RecA orthologs. The TOUC values analyzed in this study are in good agreement with the available experimental results. This method should prove useful in guiding future experimental efforts aimed at furthering our understanding of the biochemistry of RecA proteins and subsequent development of new drugs that modulate RecA biological activities in bacteria.
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Affiliation(s)
- Haïtham Sghaier
- Research Unit UR04CNSTN01 Medical and Agricultural Applications of Nuclear Techniques, National Center for Nuclear Sciences and Technology, Sidi Thabet, Tunisia.
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Thi TD, Lopez E, Rodriguez-Rojas A, Rodriguez-Beltran J, Couce A, Guelfo JR, Castaneda-Garcia A, Blazquez J. Effect of recA inactivation on mutagenesis of Escherichia coli exposed to sublethal concentrations of antimicrobials. J Antimicrob Chemother 2011; 66:531-8. [DOI: 10.1093/jac/dkq496] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Petrova V, Satyshur KA, George NP, McCaslin D, Cox MM, Keck JL. X-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of RecA. J Biol Chem 2010; 285:30615-21. [PMID: 20659894 DOI: 10.1074/jbc.m110.152298] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During bacterial conjugation, genetic material from one cell is transferred to another as single-stranded DNA. The introduction of single-stranded DNA into the recipient cell would ordinarily trigger a potentially deleterious transcriptional response called SOS, which is initiated by RecA protein filaments formed on the DNA. During F plasmid conjugation, however, the SOS response is suppressed by PsiB, an F-plasmid-encoded protein that binds and sequesters free RecA to prevent filament formation. Among the many characterized RecA modulator proteins, PsiB is unique in using sequestration as an inhibitory mechanism. We describe the crystal structure of PsiB from the Escherichia coli F plasmid. The stucture of PsiB is surprisingly similar to CapZ, a eukaryotic actin filament capping protein. Structure-directed neutralization of electronegative surfaces on PsiB abrogates RecA inhibition whereas neutralization of an electropositive surface element enhances PsiB inhibition of RecA. Together, these studies provide a first molecular view of PsiB and highlight its use as a reagent in studies of RecA activity.
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Sexton JZ, Wigle TJ, He Q, Hughes MA, Smith GR, Singleton SF, Williams AL, Yeh LA. Novel Inhibitors of E. coli RecA ATPase Activity. CURRENT CHEMICAL GENOMICS 2010; 4:34-42. [PMID: 20648224 PMCID: PMC2905775 DOI: 10.2174/1875397301004010034] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/07/2009] [Accepted: 12/12/2009] [Indexed: 11/22/2022]
Abstract
The bacterial RecA protein has been implicated as a bacterial drug target not as an antimicrobial target, but as an adjuvant target with the potential to suppress the mechanism by which bacteria gain drug resistance. In order to identify small molecules that inhibit RecA/ssDNA nucleoprotein filament formation, we have adapted the phosphomolybdate-blue ATPase assay for high throughput screening to determine RecA ATPase activity against a library of 33,600 compounds, which is a selected representation of diverse structure of 350,000. Four distinct chemotypes were represented among the 40 validated hits. SAR and further chemical synthesis is underway to optimize this set of inhibitors to be used as antimicrobial adjuvant agents.
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Affiliation(s)
- Jonathan Z Sexton
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, 27707, USA
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Abstract
Antibiotic drug-target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug-target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.
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