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Sett A, Dubey V, Bhowmik S, Pathania R. Decoding Bacterial Persistence: Mechanisms and Strategies for Effective Eradication. ACS Infect Dis 2024. [PMID: 38940498 DOI: 10.1021/acsinfecdis.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The ability of pathogenic bacteria to evade antibiotic treatment is an intricate and multifaceted phenomenon. Over the years, treatment failure among patients due to determinants of antimicrobial resistance (AMR) has been the focal point for the research and development of new therapeutic agents. However, the survival of bacteria by persisting under antibiotic stress has largely been overlooked. Bacterial persisters are a subpopulation of sensitive bacterial cells exhibiting a noninheritable drug-tolerant phenotype. They are linked to the recalcitrance of infections in healthcare settings, in turn giving rise to AMR variants. The importance of bacterial persistence in recurring infections has been firmly recognized. Fundamental work over the past decade has highlighted numerous unique tolerance factors contributing to the persister phenotype in many clinically relevant pathogens. This review summarizes contributing factors that could aid in developing new strategies against bacterial antibiotic persisters.
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Affiliation(s)
- Abhiroop Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Vineet Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Somok Bhowmik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
- Centre of Excellence in Disaster Mitigation and Management, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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Hossain A, Gnanagobal H, Cao T, Chakraborty S, Chukwu-Osazuwa J, Soto-Dávila M, Vasquez I, Santander J. Role of cold shock proteins B and D in Aeromonas salmonicida subsp. salmonicida physiology and virulence in lumpfish ( Cyclopterus lumpus). Infect Immun 2024:e0001124. [PMID: 38920386 DOI: 10.1128/iai.00011-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Cold shock proteins (Csp) are pivotal nucleic acid binding proteins known for their crucial roles in the physiology and virulence of various bacterial pathogens affecting plant, insect, and mammalian hosts. However, their significance in bacterial pathogens of teleost fish remains unexplored. Aeromonas salmonicida subsp. salmonicida (hereafter A. salmonicida) is a psychrotrophic pathogen and the causative agent of furunculosis in marine and freshwater fish. Four csp genes (cspB, cspD, cspA, and cspC) have been identified in the genome of A. salmonicida J223 (wild type). Here, we evaluated the role of DNA binding proteins, CspB and CspD, in A. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus). A. salmonicida ΔcspB, ΔcspD, and the double ΔcspBΔcspD mutants were constructed and characterized. A. salmonicida ΔcspB and ΔcspBΔcspD mutants showed a faster growth at 28°C, and reduced virulence in lumpfish. A. salmonicida ΔcspD showed a slower growth at 28°C, biofilm formation, lower survival in low temperatures and freezing conditions (-20°C, 0°C, and 4°C), deficient in lipopolysaccharide synthesis, and low virulence in lumpfish. Additionally, ΔcspBΔcspD mutants showed less survival in the presence of bile compared to the wild type. Transcriptome analysis revealed that 200, 37, and 921 genes were differentially expressed in ΔcspB, ΔcspD, and ΔcspBΔcspD, respectively. In ΔcspB and ΔcspBΔcspD virulence genes in the chromosome and virulence plasmid were downregulated. Our analysis indicates that CspB and CspD mostly act as a transcriptional activator, influencing cell division (e.g., treB), virulence factors (e.g., aexT), and ultimately virulence.
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Affiliation(s)
- Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Joy Chukwu-Osazuwa
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Manuel Soto-Dávila
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
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Bustamante P, Ramos-Corominas MN, Martinez-Medina M. Contribution of Toxin-Antitoxin Systems to Adherent-Invasive E. coli Pathogenesis. Microorganisms 2024; 12:1158. [PMID: 38930540 PMCID: PMC11205521 DOI: 10.3390/microorganisms12061158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Pathobionts have been implicated in various chronic diseases, including Crohn's disease (CD), a multifactorial chronic inflammatory condition that primarily affects the gastrointestinal tract, causing inflammation and damage to the digestive system. While the exact cause of CD remains unclear, adherent-invasive Escherichia coli (AIEC) strains have emerged as key contributors to its pathogenesis. AIEC are characterized by their ability to adhere to and invade intestinal epithelial cells and survive and replicate inside macrophages. However, the mechanisms underlying the virulence and persistence of AIEC within their host remain the subject of intensive research. Toxin-antitoxin systems (TAs) play a potential role in AIEC pathogenesis and may be therapeutic targets. These systems generally consist of two components: a toxin harmful to the cell and an antitoxin that neutralizes the toxin's effects. They contribute to bacterial survival in adverse conditions and regulate bacterial growth and behavior, affecting various cellular processes in bacterial pathogens. This review focuses on the current information available to determine the roles of TAs in the pathogenicity of AIEC. Their contribution to the AIEC stress response, biofilm formation, phage inhibition, the maintenance of mobile genetic elements, and host lifestyles is discussed.
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Affiliation(s)
- Paula Bustamante
- Molecular and Cellular Microbiology Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - María Núria Ramos-Corominas
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, 17003 Girona, Spain; (M.N.R.-C.); (M.M.-M.)
| | - Margarita Martinez-Medina
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, 17003 Girona, Spain; (M.N.R.-C.); (M.M.-M.)
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Fernández-García L, Gao X, Kirigo J, Song S, Battisti ME, Garcia-Contreras R, Tomas M, Guo Y, Wang X, Wood TK. Single-cell analysis reveals that cryptic prophage protease LfgB protects Escherichia coli during oxidative stress by cleaving antitoxin MqsA. Microbiol Spectr 2024; 12:e0347123. [PMID: 38206055 PMCID: PMC10846083 DOI: 10.1128/spectrum.03471-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Although toxin/antitoxin (TA) systems are ubiquitous, beyond phage inhibition and mobile element stabilization, their role in host metabolism is obscure. One of the best-characterized TA systems is MqsR/MqsA of Escherichia coli, which has been linked previously to protecting gastrointestinal species during the stress it encounters from the bile salt deoxycholate as it colonizes humans. However, some recent whole-population studies have challenged the role of toxins such as MqsR in bacterial physiology since the mqsRA locus is induced over a hundred-fold during stress, but a phenotype was not found upon its deletion. Here, we investigate further the role of MqsR/MqsA by utilizing single cells and demonstrate that upon oxidative stress, the TA system MqsR/MqsA has a heterogeneous effect on the transcriptome of single cells. Furthermore, we discovered that MqsR activation leads to induction of the poorly characterized yfjXY ypjJ yfjZF operon of cryptic prophage CP4-57. Moreover, deletion of yfjY makes the cells sensitive to H2O2, acid, and heat stress, and this phenotype was complemented. Hence, we recommend yfjY be renamed to lfgB (less fatality gene B). Critically, MqsA represses lfgB by binding the operon promoter, and LfgB is a protease that degrades MqsA to derepress rpoS and facilitate the stress response. Therefore, the MqsR/MqsA TA system facilitates the stress response through cryptic phage protease LfgB.IMPORTANCEThe roles of toxin/antitoxin systems in cell physiology are few and include phage inhibition and stabilization of genetic elements; yet, to date, there are no single-transcriptome studies for toxin/antitoxin systems and few insights for prokaryotes from this novel technique. Therefore, our results with this technique are important since we discover and characterize a cryptic prophage protease that is regulated by the MqsR/MqsA toxin/antitoxin system in order to regulate the host response to oxidative stress.
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Affiliation(s)
- Laura Fernández-García
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Microbiology Department, Hospital A Coruña (HUAC), A Coruña, Spain
- Microbiology Translational and Multidisciplinary (MicroTM)‐Research Institute Biomedical A Coruña (INIBIC) and Microbiology, University of A Coruña (UDC), A Coruña, Spain
| | - Xinyu Gao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Guangdong Key Laboratory of Marine Materia Medica, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea, Chinese Academy of Sciences, China, Nansha,, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Joy Kirigo
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Animal Science, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
| | - Michael E. Battisti
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rodolfo Garcia-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Maria Tomas
- Microbiology Department, Hospital A Coruña (HUAC), A Coruña, Spain
- Microbiology Translational and Multidisciplinary (MicroTM)‐Research Institute Biomedical A Coruña (INIBIC) and Microbiology, University of A Coruña (UDC), A Coruña, Spain
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Guangdong Key Laboratory of Marine Materia Medica, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea, Chinese Academy of Sciences, China, Nansha,, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
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Cardoza E, Singh H. From Stress Tolerance to Virulence: Recognizing the Roles of Csps in Pathogenicity and Food Contamination. Pathogens 2024; 13:69. [PMID: 38251376 PMCID: PMC10819108 DOI: 10.3390/pathogens13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Be it for lab studies or real-life situations, bacteria are constantly exposed to a myriad of physical or chemical stresses that selectively allow the tolerant to survive and thrive. In response to environmental fluctuations, the expression of cold shock domain family proteins (Csps) significantly increases to counteract and help cells deal with the harmful effects of stresses. Csps are, therefore, considered stress adaptation proteins. The primary functions of Csps include chaperoning nucleic acids and regulating global gene expression. In this review, we focus on the phenotypic effects of Csps in pathogenic bacteria and explore their involvement in bacterial pathogenesis. Current studies of csp deletions among pathogenic strains indicate their involvement in motility, host invasion and stress tolerance, proliferation, cell adhesion, and biofilm formation. Through their RNA chaperone activity, Csps regulate virulence-associated genes and thereby contribute to bacterial pathogenicity. Additionally, we outline their involvement in food contamination and discuss how foodborne pathogens utilize the stress tolerance roles of Csps against preservation and sanitation strategies. Furthermore, we highlight how Csps positively and negatively impact pathogens and the host. Overall, Csps are involved in regulatory networks that influence the expression of genes central to stress tolerance and virulence.
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Affiliation(s)
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University, Vile Parle West, Mumbai 400056, India
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Pont CL, Bernay B, Gérard M, Dhalluin A, Gravey F, Giard JC. Proteomic characterization of persisters in Enterococcus faecium. BMC Microbiol 2024; 24:9. [PMID: 38172710 PMCID: PMC10765921 DOI: 10.1186/s12866-023-03162-8] [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: 09/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Enterococcus faecium is a Gram-positive bacterium, naturally present in the human intestinal microbiota, but is also an opportunistic pathogen responsible for healthcare-associated infections. Persisters are individuals of a subpopulation able to survive by arrest of growth coping with conditions that are lethal for the rest of the population. These persistent cells can grow again when the stress disappears from their environment and can cause relapses. RESULTS In this study, we highlighted that ciprofloxacin (10-fold the MIC) led to the formation of persister cells of E. faecium. The kill curve was typically biphasic with an initial drop of survival (more than 2 orders of magnitude reduction) followed by a constant bacterial count. Growth curves and antimicrobial susceptibility tests of these persisters were similar to those of the original cells. In addition, by genomic analyses, we confirmed that the persisters were genotypically identical to the wild type. Comparative proteomic analysis revealed that 56 proteins have significantly different abundances in persisters compared to cells harvested before the addition of stressing agent. Most of them were related to energetic metabolisms, some polypeptides were involved in transcription regulation, and seven were stress proteins like CspA, PrsA, ClpX and particularly enzymes linked to the oxidative stress response. CONCLUSIONS This work provided evidences that the pathogen E. faecium was able to enter a state of persister that may have an impact in chronic infections and relapses. Moreover, putative key effectors of this phenotypical behavior were identified by proteomic approach.
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Affiliation(s)
- Charlotte Le Pont
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Benoît Bernay
- Plateforme Proteogen SFR ICORE 4206, Université de Caen Normandie, Caen, 14000, France
| | - Mattéo Gérard
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Anne Dhalluin
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - François Gravey
- Department of infectious agents, UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, CHU Caen, Caen, F-14000, France
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Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023; 24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.
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Affiliation(s)
- Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Elizaveta Semenova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
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Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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9
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Bhatia RP, Kirit HA, Lewis CM, Sankaranarayanan K, Bollback JP. Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella. Evol Lett 2023; 7:227-239. [PMID: 37475746 PMCID: PMC10355182 DOI: 10.1093/evlett/qrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 07/22/2023] Open
Abstract
Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.
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Affiliation(s)
- Rama P Bhatia
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Hande Acar Kirit
- Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Anthropology, University of Oklahoma, Norman, OK, United States
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jonathan P Bollback
- Corresponding author: Institute of Infection, Veterinary, and Ecological Sciences, Department of Evolution, Ecology, and Behaviour, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
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10
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Sonika S, Singh S, Mishra S, Verma S. Toxin-antitoxin systems in bacterial pathogenesis. Heliyon 2023; 9:e14220. [PMID: 37101643 PMCID: PMC10123168 DOI: 10.1016/j.heliyon.2023.e14220] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Toxin-Antitoxin (TA) systems are abundant in prokaryotes and play an important role in various biological processes such as plasmid maintenance, phage inhibition, stress response, biofilm formation, and dormant persister cell generation. TA loci are abundant in pathogenic intracellular micro-organisms and help in their adaptation to the harsh host environment such as nutrient deprivation, oxidation, immune response, and antimicrobials. Several studies have reported the involvement of TA loci in establishing successful infection, intracellular survival, better colonization, adaptation to host stresses, and chronic infection. Overall, the TA loci play a crucial role in bacterial virulence and pathogenesis. Nonetheless, there are some controversies about the role of TA system in stress response, biofilm and persister formation. In this review, we describe the role of the TA systems in bacterial virulence. We discuss the important features of each type of TA system and the recent discoveries identifying key contributions of TA loci in bacterial pathogenesis.
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11
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Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states. Cell 2023; 186:877-891.e14. [PMID: 36708705 PMCID: PMC10014032 DOI: 10.1016/j.cell.2023.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023]
Abstract
We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA sequencing that has overcome many challenges hindering the development of scRNA-seq in bacteria. BacDrop can be applied to thousands to millions of cells from both gram-negative and gram-positive species. It features universal ribosomal RNA depletion and combinatorial barcodes that enable multiplexing and massively parallel sequencing. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and to elucidate their heterogeneous responses to antibiotic stress. In an unperturbed population presumed to be homogeneous, we found within-population heterogeneity largely driven by the expression of mobile genetic elements that promote the evolution of antibiotic resistance. Under antibiotic perturbation, BacDrop revealed transcriptionally distinct subpopulations associated with different phenotypic outcomes including antibiotic persistence. BacDrop thus can capture cellular states that cannot be detected by bulk RNA-seq, which will unlock new microbiological insights into bacterial responses to perturbations and larger bacterial communities such as the microbiome.
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Affiliation(s)
- Peijun Ma
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Haley M Amemiya
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lorrie L He
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shivam J Gandhi
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert Nicol
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roby P Bhattacharyya
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Smillie
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Deborah T Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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12
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Pourhajibagher M, Parker S, Pourakbari B, Valian NK, Raoofian R, Bahador A. Enhancement of hypericin nanoparticle-mediated sonoinduced disruption of biofilm and persister cells of Streptococcus mutans by dermcidin-derived peptide DCD-1L. Photodiagnosis Photodyn Ther 2023; 41:103308. [PMID: 36709017 DOI: 10.1016/j.pdpdt.2023.103308] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/28/2022] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND Streptococcus mutans is considered a major significant contributor to dental caries and its effective removal is difficult due to the formation of biofilm. Therefore, the development of adjuvant therapeutic strategies with anti-biofilm properties is a promising approach. In the present study, we examined the effect of dermcidin-derived peptide DCD-1 L on the antibacterial activity of hypericin nanoparticle (HypNP)-mediated antimicrobial sonodynamic therapy (aSDT) against persister cells growing- and biofilm cultures of S. mutans. MATERIALS AND METHODS Following synthesis and confirmation of HypNP, the fractional inhibitory concentration (FIC) index of HypNP and DCD-1 L was determined by checkerboard assay. Cellular uptake of HypNP-DCD-1 L and generation of endogenous reactive oxygen species (ROS) were assessed and followed by the determination of antimicrobial sonoactivity of HypNP-DCD-1 L against persister cells growing- and biofilm cultures of S. mutans. The water-insoluble extracellular polysaccharide (EPS) and expression of the gtfD, comDE, and smuT genes were then evaluated in persister cells growing- and biofilm cultures of S. mutans. RESULTS There was a synergistic activity in the combination of HypNP and DCD-1 L against S. mutans with an FIC index value of 0.37. The HypNP-DCD-1L-mediated aSDT also displayed the highest cellular uptake and endogenous ROS generation by bacterial cells. When biofilm and persister cells of S. mutans were treated with HypNP-DCD-1 L and subsequently exposed to ultrasound waves, 5.1 log and 3.8 log reductions, respectively, in bacterial numbers were observed (P<0.05). According to the data, EPS in both persister cells growing- and biofilm cultures of S. mutans were significantly decreased after exposure to the HypNP-DCD-1L-mediated aSDT (P<0.05). In addition, the quantitative real-time PCR data illustrated the high level of similarities in very low-expression profiles of the gtfD before and after all treated groups for persister cells. While, following HypNP-DCD-1L-mediated aSDT treatment, the expression levels of gtfD, comDE, and smuT were significantly lower in treated persister cells growing- and biofilm cultures of S. mutans in comparison with control groups (P<0.05). CONCLUSIONS Combined, the results of this study indicate that ultrasound waves-activated HypNP-DCD-1 L can sonoinactivate S. mutans biofilms and persister cells, as well as reduce effectively pathogenicity potency of S. mutans. Hence, HypNP-DCD-1L-mediated aSDT may be proposed as a promising adjunctive therapeutic approach for dental caries.
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Affiliation(s)
- Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Steven Parker
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, United Kingdom.
| | - Babak Pourakbari
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran; Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Nasrin Keshavarz Valian
- Department of Periodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran.
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Fellowship in Clinical Laboratory Sciences, BioHealth Lab, Tehran, Iran.
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13
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Kim H, Kim JH, Cho H, Ko KS. Overexpression of a DNA Methyltransferase Increases Persister Cell Formation in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0265522. [PMID: 36416541 PMCID: PMC9769888 DOI: 10.1128/spectrum.02655-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
Many mechanisms have been proposed to be involved in the formation of bacterial persister cells. In this study, we investigated the impact of dam encoding DNA methylation on persister cell formation in Acinetobacter. We constructed plasmids overexpressing dam encoding DNA-(adenine N6)-methyltransferase and four genes as possibly involved in persistence and introduced them into three A. baumannii strains. For persister cell formation assays, bacteria were exposed to ciprofloxacin, imipenem, cefotaxime, and rifampin, and the transcription levels of the genes were measured by qRT-PCR. In addition, growth curves of strains were determined. We found that all five genes were upregulated following antibiotic exposure. Dam overexpression increased persister cell formation rates and activated the four persister cell-involved genes. Among the four persister cell-involved genes, only RecC overexpression increase persister cell formation rates. While recC-overexpressing strains showed higher growth rates, dam-overexpressing strains showed decreased growth rates. In this study, we revealed that a DNA methyltransferase may regulate persister cell formation in A. baumannii, while RecC seems to mediate epigenetic regulation of persister cell formation. However, Dam and RecC may act at different persister cell formation states. IMPORTANCE Bacterial persister cells are not killed by high concentration of antibiotics, despite its antibiotic susceptibility. It has been known that they may cause antibiotic treatment failure and contribute to the evolution of antibiotic resistance. Although many mechanisms have been suggested and verified for persister cell formation, many remains to be uncovered. In this study, we report that DNA methyltransferase leads to an increase in persister cell formation, through transcriptional activation of several regulatory genes. Our results suggest that DNA methyltransferases could be target proteins to prevent formation of persister cells.
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Affiliation(s)
- Hyunkeun Kim
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jee Hong Kim
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hongbaek Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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14
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Dawan J, Ahn J. Variability in Adaptive Resistance of Salmonella Typhimurium to Sublethal Levels of Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11121725. [PMID: 36551382 PMCID: PMC9774383 DOI: 10.3390/antibiotics11121725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
This study was designed to evaluate the adaptive resistance of Salmonella Typhimurium under continuous sublethal selective pressure. Salmonella Typhimurium ATCC 19585 (STATCC) and S. Typhimurium CCARM 8009 (STCCARM) were sequentially cultured for 3 days at 37 °C in trypticase soy broth containing 1/2 × MICs of cefotaxime (CEF1/2), chloramphenicol (CHL1/2), gentamicin (GEN1/2), and polymyxin B (POL1/2). The STATCC and STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were evaluated using antibiotic susceptibility, cross-resistance, and relative fitness. The susceptibilities of STATCC exposed to GEN1/2 and POL1/2 were increased by a 2-fold (gentamicin) and 8-fold (polymyxin B) increase in minimum inhibitory concentration (MIC) values, respectively. The MIC values of STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were increased by 4-fold (cefotaxime), 2-fold (chloramphenicol), 2-fold (gentamicin), and 8-fold (polymyxin B). The highest heterogeneous fractions were observed for the STATCC exposed to CEF1/2 (38%) and POL1/2 (82%). The STCCARM exposed to GEN1/2 was cross-resistant to cefotaxime (p < 0.05), chloramphenicol (p < 0.01), and polymyxin B (p < 0.05). The highest relative fitness levels were 0.92 and 0.96, respectively, in STATCC exposed to CEF1/2 and STCCARM exposed to POL1/2. This study provides new insight into the fate of persistent cells and also guidance for antibiotic use.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Correspondence: ; Tel.: +82-33-250-6564
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15
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Shi X, Zarkan A. Bacterial survivors: evaluating the mechanisms of antibiotic persistence. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748698 DOI: 10.1099/mic.0.001266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria withstand antibiotic onslaughts by employing a variety of strategies, one of which is persistence. Persistence occurs in a bacterial population where a subpopulation of cells (persisters) survives antibiotic treatment and can regrow in a drug-free environment. Persisters may cause the recalcitrance of infectious diseases and can be a stepping stone to antibiotic resistance, so understanding persistence mechanisms is critical for therapeutic applications. However, current understanding of persistence is pervaded by paradoxes that stymie research progress, and many aspects of this cellular state remain elusive. In this review, we summarize the putative persister mechanisms, including toxin-antitoxin modules, quorum sensing, indole signalling and epigenetics, as well as the reasons behind the inconsistent body of evidence. We highlight present limitations in the field and underscore a clinical context that is frequently neglected, in the hope of supporting future researchers in examining clinically important persister mechanisms.
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Affiliation(s)
- Xiaoyi Shi
- Cambridge Centre for International Research, Cambridge CB4 0PZ, UK
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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16
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17
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Berkvens A, Chauhan P, Bruggeman FJ. Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220129. [PMID: 36099930 PMCID: PMC9470271 DOI: 10.1098/rsif.2022.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbial populations often contain persister cells, which reduce the extinction risk upon sudden stresses. Persister cell formation is deeply intertwined with physiology. Due to this complexity, it cannot be satisfactorily understood by focusing only on mechanistic, physiological or evolutionary aspects. In this review, we take an integrative biology perspective to identify common principles of persister cell formation, which might be applicable across evolutionary-distinct microbes. Persister cells probably evolved to cope with a fundamental trade-off between cellular stress and growth tasks, as any biosynthetic resource investment in growth-supporting proteins is at the expense of stress tasks and vice versa. Natural selection probably favours persister cell subpopulation formation over a single-phenotype strategy, where each cell is prepared for growth and stress to a suboptimal extent, since persister cells can withstand harsher environments and their coexistence with growing cells leads to a higher fitness. The formation of coexisting phenotypes requires bistable molecular circuitry. Bistability probably emerges from growth-modulated, positive feedback loops in the cell's growth versus stress control network, involving interactions between sigma factors, guanosine pentaphosphate and toxin-antitoxin (TA) systems. We conclude that persister cell formation is most likely a response to a sudden reduction in growth rate, which can be achieved by antibiotic addition, nutrient starvation, sudden stresses, nutrient transitions or activation of a TA system.
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Affiliation(s)
- Alicia Berkvens
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Priyanka Chauhan
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
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18
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Qiu J, Zhai Y, Wei M, Zheng C, Jiao X. Toxin–antitoxin systems: Classification, biological roles, and applications. Microbiol Res 2022; 264:127159. [DOI: 10.1016/j.micres.2022.127159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
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19
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Kaushik V, Tiwari M, Tiwari V. Interaction of RecA mediated SOS response with bacterial persistence, biofilm formation, and host response. Int J Biol Macromol 2022; 217:931-943. [PMID: 35905765 DOI: 10.1016/j.ijbiomac.2022.07.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Antibiotics have a primary mode of actions, and most of them have a common secondary mode of action via reactive species (ROS and RNS) mediated DNA damage. Bacteria have been able to tolerate this DNA damage by SOS (Save-Our-Soul) response. RecA is the universal essential key protein of the DNA damage mediated SOS repair in various bacteria including ESKAPE pathogens. In addition, antibiotics also triggers activation of various other bacterial mechanisms such as biofilm formation, host dependent responses, persister subpopulation formation. These supporting the survival of bacteria in unfriendly natural conditions i.e. antibiotic presence. This review highlights the detailed mechanism of RecA mediated SOS response as well as role of RecA-LexA interaction in SOS response. The review also focuses on inter-connection between DNA damage repair pathway (like SOS response) with other survival mechanisms of bacteria such as host mediated RecA induction, persister-SOS interplay, and biofilm-SOS interplay. This understanding of inter-connection of SOS response with different other survival mechanisms will prove beneficial in targeting the SOS response for prevention and development of therapeutics against recalcitrant bacterial infections. The review also covers the significance of RecA as a promising potent therapeutic target for hindering bacterial SOS response in prevailing successful treatments of bacterial infections and enhancing the conventional antibiotic efficiency.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India.
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20
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Dawan J, Ahn J. Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10071385. [PMID: 35889104 PMCID: PMC9322497 DOI: 10.3390/microorganisms10071385] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Korea
- Correspondence: ; Tel.: +82-33-250-6564
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21
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Schmidt F, Zimmermann J, Tanna T, Farouni R, Conway T, Macpherson AJ, Platt RJ. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 2022; 376:eabm6038. [PMID: 35549411 PMCID: PMC11163514 DOI: 10.1126/science.abm6038] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.
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Affiliation(s)
- Florian Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Tanmay Tanna
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, 8092 Zurich, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Andrew J. Macpherson
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
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22
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de Souza-Neto RR, Carvalho IGB, Martins PMM, Picchi SC, Tomaz JP, Caserta R, Takita MA, de Souza AA. MqsR toxin as a biotechnological tool for plant pathogen bacterial control. Sci Rep 2022; 12:2794. [PMID: 35181693 PMCID: PMC8857320 DOI: 10.1038/s41598-022-06690-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacteria and are involved in important cell features, such as cell growth inhibition and antimicrobial tolerance, through the induction of persister cells. Overall, these characteristics are associated with bacterial survival under stress conditions and represent a significant genetic mechanism to be explored for antibacterial molecules. We verified that even though Xylella fastidiosa and Xanthomonas citri subsp. citri share closely related genomes, they have different Type II TA system contents. One important difference is the absence of mqsRA in X. citri. The toxin component of this TA system has been shown to inhibit the growth of X. fastidiosa. Thus, the absence of mqsRA in X. citri led us to explore the possibility of using the MqsR toxin to impair X. citri growth. We purified MqsR and confirmed that the toxin was able to inhibit X. citri. Subsequently, transgenic citrus plants producing MqsR showed a significant reduction in citrus canker and citrus variegated chlorosis symptoms caused, respectively, by X. citri and X. fastidiosa. This study demonstrates that the use of toxins from TA systems is a promising strategy to be explored aiming bacterial control.
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Affiliation(s)
- Reinaldo Rodrigues de Souza-Neto
- Citrus Research Center, Agronomic Institute - IAC, Cordeirópolis, SP, Brazil.,Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | | | | | | | - Juarez Pires Tomaz
- Rural Development Institute of Parana - IAPAR-EMATER, Londrina, PR, Brazil
| | - Raquel Caserta
- Citrus Research Center, Agronomic Institute - IAC, Cordeirópolis, SP, Brazil
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23
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Veetilvalappil VV, Aranjani JM, Mahammad FS, Joseph A. Awakening sleeper cells: a narrative review on bacterial magic spot synthetases as potential drug targets to overcome persistence. Curr Genet 2022; 68:49-60. [PMID: 34787710 PMCID: PMC8801413 DOI: 10.1007/s00294-021-01221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 10/29/2022]
Abstract
Magic spot synthetases are emerging targets to overcome persistence caused by stringent response. The 'stringent response' is a bacterial stress survival mechanism, which results in the accumulation of alarmones (also called Magic spots) leading to the formation of dormant persister cells. These 'sleeper cells' evade antibiotic treatment and could result in relapse of infection. This review broadly investigates the phenomenon of stringent response and persistence, and specifically discusses the distribution, classification, and nomenclature of proteins such as Rel/SpoT homologs (RSH), responsible for alarmone synthesis. The authors further explain the relevance of RSH as potential drug targets to break the dormancy of persister cells commonly seen in biofilms. One of the significant factors that initiate alarmone synthesis is nutrient deficiency. In a starved condition, ribosome-associated RSH detects deacylated tRNA and initiates alarmone synthesis. Accumulation of alarmones has a considerable effect on bacterial physiology, virulence, biofilm formation, and persister cell formation. Preventing alarmone synthesis by inhibiting RSH responsible for alarmone synthesis will prevent or reduce persister cells' formation. Magic spot synthetases are thus potential targets that could be explored to overcome persistence seen in biofilms.
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Affiliation(s)
- Vimal Venu Veetilvalappil
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India.
| | - Fayaz Shaik Mahammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
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Kaushik V, Sharma S, Tiwari M, Tiwari V. Anti-persister strategies against stress induced bacterial persistence. Microb Pathog 2022; 164:105423. [PMID: 35092834 DOI: 10.1016/j.micpath.2022.105423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 01/22/2023]
Abstract
The increase in antibiotic non-responsive bacteria is the leading concern in current research-oriented to eliminate pathogens. Nowadays, the excess use of antibiotics without specifically understanding the potentiality of killing pathogens and bacterial survival patterns has helped bacteria emerge indefatigably. Bacteria use various mechanisms such as resistance, persistence, and tolerance to ensure survival. Among these, persistence is a mechanism by which bacteria reside in their dormant state, bypassing the effects of treatments, making it crucial for bacterial survival. Persistent bacterial cells arise from the normal bacterial population as a slow-growing subset of bacteria with no metabolic flux. This behavior renders it to survive for a longer duration and at higher concentrations of antibiotics. They are one of the underlying causes of recurrence of bacterial infections. The present article explains the detailed molecular mechanisms and strategies of bacterial persistence, including the toxin-antitoxin modules, DNA damage, the formation of inactive ribosomal complexes, (p)ppGpp network, antibiotic-induced persistence, which are triggered by drug-induced stress. The article also comprehensively covers the epigenetic memory of persistence in bacteria, and anti-persistent therapeutics like antimicrobial molecules, synthetic peptides, acyldepsipeptide antibiotics, and endolysin therapy to reduce persister cell formation and control their frequency. These strategies could be utilized in combating the pathogenic bacteria undergoing persistence.
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Affiliation(s)
- Vaishali Kaushik
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Saroj Sharma
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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25
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Margalit A, Carolan JC, Walsh F. Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin. J Glob Antimicrob Resist 2021; 28:90-96. [PMID: 34922055 DOI: 10.1016/j.jgar.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES This study compared the proteomics of Escherichia coli containing the multi-drug resistance pEK499 plasmid under antimicrobial stress and no antimicrobial. METHODS We utilised mass spectrometry-based proteomics to compare the proteomes of the bacteria and plasmid under antimicrobial stress and no antimicrobial. RESULTS Our analysis identified statistically significant differentially abundant proteins common to groups exposed to the β-lactam antimicrobials but not ciprofloxacin, indicating a β-lactam stress response to exposure from this class of drugs, irrespective of β-lactam resistance or susceptibility. Data arising from comparisons of the proteomes of ciprofloxacin-treated E. coli and controls detected an increase in the relative abundance of proteins associated with ribosomes, translation, the TCA-cycle and several proteins associated with detoxification and a decrease in the relative abundances of proteins associated with stress response, including oxidative stress. We identified changes in proteins associated with persister formation in the presence of ciprofloxacin but not the β-lactams. The plasmid proteome differed across each treatment and did not follow the pattern of antimicrobial - AMR protein associations: a relative increase in the amount of blaCTX-M-15 in the presence of cefotaxime and ciprofloxacin but not the other β-lactams, suggesting regulation of the blaCTX-M-15 protein production. CONCLUSIONS The proteomic data from the this study provided novel insights into the proteins produced from the chromosome and plasmid under different antimicrobial stresses. These data also identified novel proteins not previously associated with AMR or antimicrobials responses in pathogens, which may well represent potential targets of AMR inhibition.
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Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - James C Carolan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Co. Kildare, Ireland.
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Sindeldecker D, Stoodley P. The many antibiotic resistance and tolerance strategies of Pseudomonas aeruginosa. Biofilm 2021; 3:100056. [PMID: 34471871 PMCID: PMC8387898 DOI: 10.1016/j.bioflm.2021.100056] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a bacterial pathogen associated with a wide range of infections and utilizes several strategies to establish and maintain infection including biofilm production, multidrug resistance, and antibiotic tolerance. Multidrug resistance in P. aeruginosa, as well as in all other bacterial pathogens, is a growing concern. Aminoglycoside resistance, in particular, is a major concern in P. aeruginosa infections and must be better understood in order to maintain effective clinical treatment. In this review, the various antibiotic resistance and tolerance mechanisms of Pseudomonas are explored including: classic mutation driven resistance, adaptive resistance, persister cells, small colony variants, phoenix colonies, and biofilms. It is important to further characterize each of these phenotypes and continue to evaluate antibiotic surviving isolates for novel driving mechanisms, so that we are better prepared to combat the rising number of recurrent and recalcitrant infections.
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Affiliation(s)
- Devin Sindeldecker
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Department of Orthopaedics, The Ohio State University, Columbus, OH, USA
- National Center for Advanced Tribology at Southampton (nCATS), Mechanical Engineering, University of Southampton, Southampton, UK
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Mohiuddin SG, Ghosh S, Ngo HG, Sensenbach S, Karki P, Dewangan NK, Angardi V, Orman MA. Cellular Self-Digestion and Persistence in Bacteria. Microorganisms 2021; 9:2269. [PMID: 34835393 PMCID: PMC8626048 DOI: 10.3390/microorganisms9112269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.
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Affiliation(s)
| | | | | | | | | | | | | | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; (S.G.M.); (S.G.); (H.G.N.); (S.S.); (P.K.); (N.K.D.); (V.A.)
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28
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Carvalho IGB, Merfa MV, Teixeira-Silva NS, Martins PMM, Takita MA, de Souza AA. Overexpression of mqsR in Xylella fastidiosa Leads to a Priming Effect of Cells to Copper Stress Tolerance. Front Microbiol 2021; 12:712564. [PMID: 34616378 PMCID: PMC8488296 DOI: 10.3389/fmicb.2021.712564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Copper-based compounds are widely used in agriculture as a chemical strategy to limit the spread of multiple plant diseases; however, the continuous use of this heavy metal has caused environmental damage as well as the development of copper-resistant strains. Thus, it is important to understand how the bacterial phytopathogens evolve to manage with this metal in the field. The MqsRA Toxin-Antitoxin system has been recently described for its function in biofilm formation and copper tolerance in Xylella fastidiosa, a plant-pathogen bacterium responsible for economic damage in several crops worldwide. Here we identified differentially regulated genes by X. fastidiosa MqsRA by assessing changes in global gene expression with and without copper. Results show that mqsR overexpression led to changes in the pattern of cell aggregation, culminating in a global phenotypic heterogeneity, indicative of persister cell formation. This phenotype was also observed in wild-type cells but only in the presence of copper. This suggests that MqsR regulates genes that alter cell behavior in order to prime them to respond to copper stress, which is supported by RNA-Seq analysis. To increase cellular tolerance, proteolysis and efflux pumps and regulator related to multidrug resistance are induced in the presence of copper, in an MqsR-independent response. In this study we show a network of genes modulated by MqsR that is associated with induction of persistence in X. fastidiosa. Persistence in plant-pathogenic bacteria is an important genetic tolerance mechanism still neglected for management of phytopathogens in agriculture, for which this work expands the current knowledge and opens new perspectives for studies aiming for a more efficient control in the field.
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Affiliation(s)
| | - Marcus Vinicius Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | | | | | - Marco Aurélio Takita
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico, Cordeirópolis, Brazil
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29
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Karimaei S, Kazem Aghamir SM, Foroushani AR, Pourmand MR. Antibiotic tolerance in biofilm persister cells of Staphylococcus aureus and expression of toxin-antitoxin system genes. Microb Pathog 2021; 159:105126. [PMID: 34384900 DOI: 10.1016/j.micpath.2021.105126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/04/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022]
Abstract
The ability of Staphylococcus aureus to form biofilm and persister cells is the main cause of recurrent infections. This study aimed to evaluate the expression of toxin-antitoxin (TA) systems in persister cells within S. aureus biofilms. Time-dependent variation in the persister population present in biofilms of S. aureus was examined after treatment with bactericidal antibiotics. Then, the relative expression level of type II TA system (mazF, relE1, and relE2), type I TA system (sprG), and clpP protease genes in S. aureus strains were assessed by Real _Time PCR. Among the sixteen isolates, two isolates were found to be the strongest biofilm producers. The established biofilm of these isolates showed a comparable biphasic pattern at the lethal dose of the antibiotics. The expression level of TA system genes was increased and strain-specific expression patterns were observed under antibiotics stress conditions. Persisters within a biofilm may establish a reservoir for relapsing infection and could contribute to treatment failures. Hence, the possible role of the TA systems should be considered in biofilm and persister cell formation.
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Affiliation(s)
- Samira Karimaei
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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30
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Abstract
Escherichia coli was one of the first species to have its genome sequenced and remains one of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies have shown that a substantial number of genes have been overlooked. Genes encoding more than 140 small proteins, defined as those containing 50 or fewer amino acids, have been identified in E. coli in the past 10 years, and there is substantial evidence indicating that many more remain to be discovered. This review covers the methods that have been successful in identifying small proteins and the short open reading frames that encode them. The small proteins that have been functionally characterized to date in this model organism are also discussed. It is hoped that the review, along with the associated databases of known as well as predicted but undetected small proteins, will aid in and provide a roadmap for the continued identification and characterization of these proteins in E. coli as well as other bacteria.
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31
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Evaluation of Antibiotic Tolerance in Pseudomonas aeruginosa for Aminoglycosides and Its Predicted Gene Regulations through In-Silico Transcriptomic Analysis. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12030045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas aeruginosa causes chronic infections, such as cystic fibrosis, endocarditis, bacteremia, and sepsis, which are life-threatening and difficult to treat. The lack of antibiotic response in P. aeruginosa is due to adaptive resistance mechanism, which prevents the entry of antibiotics into the cytosol of the cell to achieve tolerance. Among the different groups of antibiotics, aminoglycosides are used as a parenteral antibiotic for the treatment of P. aeruginosa. This study aimed to determine the kinetics of antibiotic tolerance and gene expression changes in P. aeruginosa exposed to amikacin, gentamicin, and tobramycin. These antibiotics were exposed to P. aeruginosa at their MICs and the experimental setup was monitored for 72 h, followed by the measurement of optical density every 12 h. The growth of P. aeruginosa in the MICs of antibiotics represented the kinetics of antibiotic tolerance in amikacin, gentamicin, and tobramycin. The transcriptomic profile of antibiotic exposed P. aeruginosa PA14 was taken from the Gene Expression Omnibus (GEO), NCBI as microarray datasets. The gene expressions of two datasets were compared by test versus control. Tobramycin-exposed P. aeruginosa failed to develop tolerance in MICs of 0.5 µg/mL, 1 µg/mL, and 1.5 µg/mL, whereas amikacin- and gentamicin-treated P. aeruginosa developed tolerance. This illustrated the superior in vitro response of tobramycin over gentamicin and amikacin. Further, in silico transcriptomic analysis of tobramycin-treated P. aeruginosa resulted in differentially expressed genes (DEGs), enriched in 16s rRNA methyltransferase E, B, and L, alginate biosynthesis genes, and several proteins of the type II secretion system (T2SS) and type III secretion system (T3SS). The regulation of mucA in alginate biosynthesis, and gidB in RNA methyltransferases, suggested an increased antibiotic response and a low probability of developing resistance during tobramycin treatment. The use of tobramycin as a parenteral antibiotic with its synergistic combination might combat P. aeruginosa with increased response.
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Johnston RD, Woodall BM, Harrison J, Campagna SR, Fozo EM. Removal of peptidoglycan and inhibition of active cellular processes leads to daptomycin tolerance in Enterococcus faecalis. PLoS One 2021; 16:e0254796. [PMID: 34297729 PMCID: PMC8301656 DOI: 10.1371/journal.pone.0254796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/04/2021] [Indexed: 11/19/2022] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic used in the clinic for treatment of severe enterococcal infections. Recent reports indicate that daptomycin targets active cellular processes, specifically, peptidoglycan biosynthesis. Within, we examined the efficacy of daptomycin against Enterococcus faecalis under a range of environmental growth conditions including inhibitors that target active cellular processes. Daptomycin was far less effective against cells in late stationary phase compared to cells in exponential phase, and this was independent of cellular ATP levels. Further, the addition of either the de novo protein synthesis inhibitor chloramphenicol or the fatty acid biosynthesis inhibitor cerulenin induced survival against daptomycin far better than controls. Alterations in metabolites associated with peptidoglycan synthesis correlated with protection against daptomycin. This was further supported as removal of peptidoglycan induced physiological daptomycin tolerance, a synergistic relation between daptomycin and fosfomycin, an inhibitor of the fist committed step peptidoglycan synthesis, was observed, as well as an additive effect when daptomycin was combined with ampicillin, which targets crosslinking of peptidoglycan strands. Removal of the peptidoglycan of Enterococcus faecium, Staphylococcus aureus, and Bacillus subtilis also resulted in significant protection against daptomycin in comparison to whole cells with intact cell walls. Based on these observations, we conclude that bacterial growth phase and metabolic activity, as well as the presence/absence of peptidoglycan are major contributors to the efficacy of daptomycin.
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Affiliation(s)
- Rachel D. Johnston
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States of America
| | - Brittni M. Woodall
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States of America
| | - Johnathan Harrison
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States of America
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN, United States of America
| | - Elizabeth M. Fozo
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
- * E-mail:
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The RNA Chaperone Hfq Participates in Persistence to Multiple Antibiotics in the Fish Pathogen Yersinia ruckeri. Microorganisms 2021; 9:microorganisms9071404. [PMID: 34209738 PMCID: PMC8308036 DOI: 10.3390/microorganisms9071404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Yersinia ruckeri causes outbreaks of enteric redmouth disease in salmon aquaculture all over the world. The transient antibiotic tolerance exhibited by bacterial persisters is commonly thought to be responsible for outbreaks; however, the molecular factors underlying this behavior have not been explored in Y. ruckeri. In this study, we investigated the participation of the RNA chaperone Hfq from Y. ruckeri in antibiotic persistence. Cultures of the hfq-knockout mutant (Δhfq) exhibited faster replication, increased ATP levels and a more reductive environment than the wild type. The growth curves of bacteria exposed to sublethal concentrations of ampicillin, oxolinic acid, ciprofloxacin and polymyxin B revealed a greater susceptibility for the Δhfq strain. The time-kill curves of bacteria treated with the antibiotics mentioned above and florfenicol, using inoculums from exponential, stationary and biofilm cultures, demonstrated that the Δhfq strain has significant defects in persister cells production. To shed more light on the role of Hfq in antibiotic persistence, we analyzed its dependence on the (p)ppGpp synthetase RelA by determining the persister cells production in the absence of the relA gene. The ΔrelA and ΔrelAΔhfq strains displayed similar defects in persister cells formation, but higher than Δhfq strain. Similarly, stationary cultures of the ΔrelA and ΔrelAΔhfq strains exhibited comparable levels of ATP but higher than that of the Δhfq strain, indicating that relA is epistatic over hfq. Taken together, our findings provide valuable information on antibiotic persistence in Y. ruckeri, shedding light on the participation of Hfq in the persistence phenomenon.
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34
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Kamruzzaman M, Wu AY, Iredell JR. Biological Functions of Type II Toxin-Antitoxin Systems in Bacteria. Microorganisms 2021; 9:microorganisms9061276. [PMID: 34208120 PMCID: PMC8230891 DOI: 10.3390/microorganisms9061276] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
After the first discovery in the 1980s in F-plasmids as a plasmid maintenance system, a myriad of toxin-antitoxin (TA) systems has been identified in bacterial chromosomes and mobile genetic elements (MGEs), including plasmids and bacteriophages. TA systems are small genetic modules that encode a toxin and its antidote and can be divided into seven types based on the nature of the antitoxin molecules and their mechanism of action to neutralise toxins. Among them, type II TA systems are widely distributed in chromosomes and plasmids and the best studied so far. Maintaining genetic material may be the major function of type II TA systems associated with MGEs, but the chromosomal TA systems contribute largely to functions associated with bacterial physiology, including the management of different stresses, virulence and pathogenesis. Due to growing interest in TA research, extensive work has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules. However, there are still controversies about some of the functions associated with different TA systems. This review will discuss the most current findings and the bona fide functions of bacterial type II TA systems.
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Affiliation(s)
- Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
- Correspondence: (M.K.); (J.R.I.)
| | - Alma Y. Wu
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
- Westmead Hospital, Westmead, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
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35
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Wilmaerts D, De Loose PJ, Vercauteren S, De Smedt S, Verstraeten N, Michiels J. Functional analysis of cysteine residues of the Hok/Gef type I toxins in Escherichia coli. FEMS Microbiol Lett 2021; 368:6296419. [PMID: 34114031 DOI: 10.1093/femsle/fnab069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
The Hok/Gef family consists of structurally similar, single-span membrane peptides that all contain a positively charged N-terminal domain, an α-helix and a periplasmic C-terminal domain. Hok/Gef peptides have previously been described to play distinct physiological roles. Indeed, while HokB has been implicated in bacterial persistence, other members of the Hok/Gef family are known to induce cell lysis. However, the generalizability of previously published studies is problematic, as they have all used different expression systems. Therefore, we conducted a systematic study of the nine Hok/Gef peptides of Escherichia coli. We observed rapid cell death following expression of hokA, hokC, hokD, hokE, pndA1, hok or srnB, while expression of hokB or pndA2 does not result in cell lysis. A remarkable feature of Hok/Gef peptides is the presence of conserved periplasmic tyrosine and/or cysteine residues. For the HokB peptide, one of these residues has previously been implicated in intermolecular dimerization, which is essential for HokB to exert its role in persistence. To assess the role of the periplasmic cysteine and tyrosine residues in other Hok/Gef peptides and to decipher whether these residues determine peptide toxicity, an array of substitution mutants were constructed. We found that these residues are important activators of toxicity for Hok, HokA and HokE peptides. Despite the loss of the cell killing phenotype in HokS31_Y48, HokAS29_S46 and HokES29_Y46, these peptides do not exert a persister phenotype. More research is needed to fully comprehend why HokB is the sole peptide of the Hok/Gef family that mediates persistence.
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Affiliation(s)
- Dorien Wilmaerts
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Pieter-Jan De Loose
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Silke Vercauteren
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Sandrien De Smedt
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Natalie Verstraeten
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Jan Michiels
- KU Leuven Centre of Microbial and Plant Genetics, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
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Hossain T, Deter HS, Peters EJ, Butzin NC. Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B. iScience 2021; 24:102391. [PMID: 33997676 PMCID: PMC8091054 DOI: 10.1016/j.isci.2021.102391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/01/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance is a growing problem, but bacteria can evade antibiotic treatment via tolerance and persistence. Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. Hence, persistence is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. Here, we used the synthetically developed minimal cell Mycoplasma mycoides JCVI-Syn3B to examine essential mechanisms of antibiotic survival. The minimal cell contains only 473 genes, and most genes are essential. Its reduced complexity helps to reveal hidden phenomenon and fundamental biological principles can be explored because of less redundancy and feedback between systems compared to natural cells. We found that Syn3B evolves antibiotic resistance to different types of antibiotics expeditiously. The minimal cell also tolerates and persists against multiple antibiotics. It contains a few already identified persister-related genes, although lacking many systems previously linked to persistence (e.g. toxin-antitoxin systems, ribosome hibernation genes).
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Affiliation(s)
- Tahmina Hossain
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Heather S. Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Eliza J. Peters
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
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Ray S, Da Costa R, Thakur S, Nandi D. Salmonella Typhimurium encoded cold shock protein E is essential for motility and biofilm formation. MICROBIOLOGY-SGM 2021; 166:460-473. [PMID: 32159509 DOI: 10.1099/mic.0.000900] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability of bacteria to form biofilms increases their survival under adverse environmental conditions. Biofilms have enormous medical and environmental impact; consequently, the factors that influence biofilm formation are an important area of study. In this investigation, the roles of two cold shock proteins (CSP) during biofilm formation were investigated in Salmonella Typhimurium, which is a major foodborne pathogen. Among all CSP transcripts studied, the expression of cspE (STM14_0732) was higher during biofilm growth. The cspE deletion strain (ΔcspE) did not form biofilms on a cholesterol coated glass surface; however, complementation with WT cspE, but not the F30V mutant, was able to rescue this phenotype. Transcript levels of other CSPs demonstrated up-regulation of cspA (STM14_4399) in ΔcspE. The cspA deletion strain (ΔcspA) did not affect biofilm formation; however, ΔcspEΔcspA exhibited higher biofilm formation compared to ΔcspE. Most likely, the higher cspA amounts in ΔcspE reduced biofilm formation, which was corroborated using cspA over-expression studies. Further functional studies revealed that ΔcspE and ΔcspEΔcspA exhibited slow swimming but no swarming motility. Although cspA over-expression did not affect motility, cspE complementation restored the swarming motility of ΔcspE. The transcript levels of the major genes involved in motility in ΔcspE demonstrated lower expression of the class III (fliC, motA, cheY), but not class I (flhD) or class II (fliA, fliL), flagellar regulon genes. Overall, this study has identified the interplay of two CSPs in regulating two biological processes: CspE is essential for motility in a CspA-independent manner whereas biofilm formation is CspA-dependent.
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Affiliation(s)
- Semanti Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Rochelle Da Costa
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Samriddhi Thakur
- Department of Undergraduate Studies, Indian Insitute of Science, Bangalore-560012, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
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Ma D, Gu H, Shi Y, Huang H, Sun D, Hu Y. Edwardsiella piscicida YefM-YoeB: A Type II Toxin-Antitoxin System That Is Related to Antibiotic Resistance, Biofilm Formation, Serum Survival, and Host Infection. Front Microbiol 2021; 12:646299. [PMID: 33732226 PMCID: PMC7957083 DOI: 10.3389/fmicb.2021.646299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
The emergence of drug resistant bacteria is a tricky and confronted problem in modern medicine, and one of important reasons is the widespread of toxin-antitoxin (TA) systems in pathogenic bacteria. Edwardsiella piscicida (also known as E. tarda) is the leading pathogen threatening worldwide fresh and seawater aquaculture industries and has been considered as a model organism for studying intracellular and systemic infections. However, the role of type II TA systems are completely unknown in aquatic pathogenic bacteria. In this study, we identified and characterized a type II TA system, YefM-YoeB, of E. piscicida, where YefM is the antitoxin and YoeB is the toxin. yefM and yoeB are co-expressed in a bicistronic operon. When expressed in E. coli, YoeB cause bacterial growth arrest, which was restored by the addition of YefM. To investigate the biological role of the TA system, two markerless yoeB and yefM-yoeB in-frame mutant strains, TX01ΔyoeB and TX01ΔyefM-yoeB, were constructed, respectively. Compared to the wild strain TX01, TX01ΔyefM-yoeB exhibited markedly reduced resistance against oxidative stress and antibiotic, and markedly reduced ability to form persistent bacteria. The deletion of yefM-yoeB enhanced the bacterial ability of high temperature tolerance, biofilm formation, and host serum resistance, which is the first study about the relationship between type II TA system and serum resistance. In vitro infection experiment showed that the inactivation of yefM-yoeB greatly enhanced bacterial capability of adhesion in host cells. Consistently, in vivo experiment suggested that the yefM-yoeB mutation had an obvious positive effect on bacteria dissemination of fish tissues and general virulence. Introduction of a trans-expressed yefM-yoeB restored the virulence of TX01ΔyefM-yoeB. These findings suggest that YefM-YoeB is involved in responding adverse circumstance and pathogenicity of E. piscicida. In addition, we found that YefM-YoeB negatively autoregulated the expression of yefM-yoeB and YefM could directly bind with own promoter. This study provides first insights into the biological activity of type II TA system YefM-YoeB in aquatic pathogenic bacteria and contributes to understand the pathogenesis of E. piscicida.
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Affiliation(s)
- Dongmei Ma
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China.,Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, China
| | - Yanjie Shi
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, China
| | - Huiqin Huang
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, China
| | - Dongmei Sun
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, China
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39
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Srivastava A, Pati S, Kaushik H, Singh S, Garg LC. Toxin-antitoxin systems and their medical applications: current status and future perspective. Appl Microbiol Biotechnol 2021; 105:1803-1821. [PMID: 33582835 DOI: 10.1007/s00253-021-11134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Almost all bacteria synthesize two types of toxins-one for its survival by regulating different cellular processes and another as a strategy to interact with host cells for pathogenesis. Usually, "bacterial toxins" are contemplated as virulence factors that harm the host organism. However, toxins produced by bacteria, as a survival strategy against the host, also hamper its cellular processes. To overcome this, the bacteria have evolved with the production of a molecule, referred to as antitoxin, to negate the deleterious effect of the toxin against itself. The toxin and antitoxins are encoded by a two-component toxin-antitoxin (TA) system. The antitoxin, a protein or RNA, sequesters the toxins of the TA system for neutralization within the bacterial cell. In this review, we have described different TA systems of bacteria and their potential medical and biotechnological applications. It is of interest to note that while bacterial toxin-antitoxin systems have been well studied, the TA system in unicellular eukaryotes, though predicted by the investigators, have never been paid the desired attention. In the present review, we have also touched upon the TA system of eukaryotes identified to date. KEY POINTS: Bacterial toxins harm the host and also affect the bacterial cellular processes. The antitoxin produced by bacteria protect it from the toxin's harmful effects. The toxin-antitoxin systems can be targeted for various medical applications.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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40
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Abstract
Bacterial endoribonuclease toxins belong to a protein family that inhibits bacterial growth by degrading mRNA or rRNA sequences. The toxin genes are organized in pairs with its cognate antitoxins in the chromosome and thus the activities of the toxins are antagonized by antitoxin proteins or RNAs during active translation. In response to a variety of cellular stresses, the endoribonuclease toxins appear to be released from antitoxin molecules via proteolytic cleavage of antitoxin proteins or preferential degradation of antitoxin RNAs and cleave a diverse range of mRNA or rRNA sequences in a sequence-specific or codon-specific manner, resulting in various biological phenomena such as antibiotic tolerance and persister cell formation. Given that substrate specificity of each endoribonuclease toxin is determined by its structure and the composition of active site residues, we summarize the biology, structure, and substrate specificity of the updated bacterial endoribonuclease toxins.
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Affiliation(s)
- Yoontak Han
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul 02481, Korea
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41
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Ropelewska M, Gross MH, Konieczny I. DNA and Polyphosphate in Directed Proteolysis for DNA Replication Control. Front Microbiol 2020; 11:585717. [PMID: 33123115 PMCID: PMC7566177 DOI: 10.3389/fmicb.2020.585717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/10/2020] [Indexed: 12/03/2022] Open
Abstract
The strict control of bacterial cell proliferation by proteolysis is vital to coordinate cell cycle processes and to adapt to environmental changes. ATP-dependent proteases of the AAA + family are molecular machineries that contribute to cellular proteostasis. Their activity is important to control the level of various proteins, including those that are essential for the regulation of DNA replication. Since the process of proteolysis is irreversible, the protease activity must be tightly regulated and directed toward a specific substrate at the exact time and space in a cell. In our mini review, we discuss the impact of phosphate-containing molecules like DNA and inorganic polyphosphate (PolyP), accumulated during stress, on protease activities. We describe how the directed proteolysis of essential replication proteins contributes to the regulation of DNA replication under normal and stress conditions in bacteria.
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Affiliation(s)
- Malgorzata Ropelewska
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Marta H Gross
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Igor Konieczny
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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MazEF-rifampicin interaction suggests a mechanism for rifampicin induced inhibition of persisters. BMC Mol Cell Biol 2020; 21:73. [PMID: 33109090 PMCID: PMC7590665 DOI: 10.1186/s12860-020-00316-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Persistence is a natural phenomenon whereby a subset of a population of isogenic bacteria either grow slow or become dormant conferring them with the ability to withstand various stresses including antibiotics. In a clinical setting bacterial persistence often leads to the recalcitrance of various infections increasing the treatment time and cost. Additionally, some studies also indicate that persistence can also pave way for the emergence of resistant strains. In a laboratory setting this persistent phenotype is enriched in nutritionally deprived environments. Consequently, in a batch culture the late stationary phase is enriched with persistent bacteria. The mechanism of persister cell formation and its regulation is not well understood. Toxin-antitoxin (TA) systems have been implicated to be responsible for bacterial persistence and rifampicin is used to treat highly persistent bacterial strains. The current study tries to explore a possible interaction between rifampicin and the MazEF TA system that furthers the former’s success rate in treating persistent bacteria. Results In the current study we found that the population of bacteria in the death phase of a batch culture consists of metabolically inactive live cells resembling persisters, which showed higher membrane depolarization as compared to the log phase bacteria. We also observed an increase in the expression of the MazEF TA modules in this phase. Since rifampicin is used to kill the persisters, we assessed the interaction of rifampicin with MazEF complex. We showed that rifampicin moderately interacts with MazEF complex with 1:1 stoichiometry. Conclusion Our study suggests that the interaction of rifampicin with MazEF complex might play an important role in inhibition of persisters. Supplementary information The online version contains supplementary material available at 10.1186/s12860-020-00316-8.
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Wang X, Rai N, Merchel Piovesan Pereira B, Eetemadi A, Tagkopoulos I. Accelerated knowledge discovery from omics data by optimal experimental design. Nat Commun 2020; 11:5026. [PMID: 33024104 PMCID: PMC7538421 DOI: 10.1038/s41467-020-18785-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. We present an optimal experimental design method (coined OPEX) to identify informative omics experiments using machine learning models for both experimental space exploration and model training. OPEX-guided exploration of Escherichia coli’s populations exposed to biocide and antibiotic combinations lead to more accurate predictive models of gene expression with 44% less data. Analysis of the proposed experiments shows that broad exploration of the experimental space followed by fine-tuning emerges as the optimal strategy. Additionally, analysis of the experimental data reveals 29 cases of cross-stress protection and 4 cases of cross-stress vulnerability. Further validation reveals the central role of chaperones, stress response proteins and transport pumps in cross-stress exposure. This work demonstrates how active learning can be used to guide omics data collection for training predictive models, making evidence-driven decisions and accelerating knowledge discovery in life sciences. How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. Here, the authors present OPEX, an optimal experimental design method to identify informative omics experiments for both experimental space exploration and model training.
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Affiliation(s)
- Xiaokang Wang
- Department of Biomedical Engineering, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA
| | - Navneet Rai
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Computer Science, University of California, Davis, CA, 95616, USA
| | - Beatriz Merchel Piovesan Pereira
- Genome Center, University of California, Davis, CA, 95616, USA.,Microbiology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Ameen Eetemadi
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Computer Science, University of California, Davis, CA, 95616, USA
| | - Ilias Tagkopoulos
- Genome Center, University of California, Davis, CA, 95616, USA. .,Department of Computer Science, University of California, Davis, CA, 95616, USA.
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Khan F, Pham DTN, Tabassum N, Oloketuyi SF, Kim YM. Treatment strategies targeting persister cell formation in bacterial pathogens. Crit Rev Microbiol 2020; 46:665-688. [DOI: 10.1080/1040841x.2020.1822278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Korea
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45
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Salcedo-Sora JE, Kell DB. A Quantitative Survey of Bacterial Persistence in the Presence of Antibiotics: Towards Antipersister Antimicrobial Discovery. Antibiotics (Basel) 2020; 9:E508. [PMID: 32823501 PMCID: PMC7460088 DOI: 10.3390/antibiotics9080508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Bacterial persistence to antibiotics relates to the phenotypic ability to survive lethal concentrations of otherwise bactericidal antibiotics. The quantitative nature of the time-kill assay, which is the sector's standard for the study of antibiotic bacterial persistence, is an invaluable asset for global, unbiased, and cross-species analyses. Methods: We compiled the results of antibiotic persistence from antibiotic-sensitive bacteria during planktonic growth. The data were extracted from a sample of 187 publications over the last 50 years. The antibiotics used in this compilation were also compared in terms of structural similarity to fluorescent molecules known to accumulate in Escherichia coli. Results: We reviewed in detail data from 54 antibiotics and 36 bacterial species. Persistence varies widely as a function of the type of antibiotic (membrane-active antibiotics admit the fewest), the nature of the growth phase and medium (persistence is less common in exponential phase and rich media), and the Gram staining of the target organism (persistence is more common in Gram positives). Some antibiotics bear strong structural similarity to fluorophores known to be taken up by E. coli, potentially allowing competitive assays. Some antibiotics also, paradoxically, seem to allow more persisters at higher antibiotic concentrations. Conclusions: We consolidated an actionable knowledge base to support a rational development of antipersister antimicrobials. Persistence is seen as a step on the pathway to antimicrobial resistance, and we found no organisms that failed to exhibit it. Novel antibiotics need to have antipersister activity. Discovery strategies should include persister-specific approaches that could find antibiotics that preferably target the membrane structure and permeability of slow-growing cells.
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Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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46
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Song S, Wood TK. A Primary Physiological Role of Toxin/Antitoxin Systems Is Phage Inhibition. Front Microbiol 2020; 11:1895. [PMID: 32903830 PMCID: PMC7438911 DOI: 10.3389/fmicb.2020.01895] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022] Open
Abstract
Toxin/antitoxin (TA) systems are present in most prokaryote genomes. Toxins are almost exclusively proteins that reduce metabolism (but do not cause cell death), and antitoxins are either RNA or proteins that counteract the toxin or the RNA that encodes it. Although TA systems clearly stabilize mobile genetic elements, after four decades of research, the physiological roles of chromosomal TA systems are less clear. For example, recent reports have challenged the notion of TA systems as stress-response elements, including a role in creating the dormant state known as persistence. Here, we present evidence that a primary physiological role of chromosomally encoded TA systems is phage inhibition, a role that is also played by some plasmid-based TA systems. This includes results that show some CRISPR-Cas system elements are derived from TA systems and that some CRISPR-Cas systems mimic the host growth inhibition invoked by TA systems to inhibit phage propagation.
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Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju-si, South Korea
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
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Abstract
Antibiotics constitute one of the cornerstones of modern medicine. However, individuals may succumb to a bacterial infection if a pathogen survives exposure to antibiotics. The ability of bacteria to survive bactericidal antibiotics results from genetic changes in the preexisting bacterial genome, from the acquisition of genes from other organisms, and from nonheritable phenomena that give rise to antibiotic tolerance. Nonheritable antibiotic tolerance can be exhibited by a large fraction of the bacterial population or by a small subpopulation referred to as persisters. Nonheritable resistance to antibiotics has been ascribed to the activity of toxins that are part of toxin-antitoxin modules, to the universal energy currency ATP, and to the signaling molecule guanosine (penta) tetraphosphate. However, these molecules are dispensable for nonheritable resistance to antibiotics in many organisms. By contrast, nutrient limitation, treatment with bacteriostatic antibiotics, or expression of genes that slow bacterial growth invariably promote nonheritable resistance. We posit that antibiotic persistence results from conditions promoting feedback inhibition among core cellular processes, resulting phenotypically in a slowdown or halt in bacterial growth.
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48
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Gollan B, Grabe G, Michaux C, Helaine S. Bacterial Persisters and Infection: Past, Present, and Progressing. Annu Rev Microbiol 2020; 73:359-385. [PMID: 31500532 DOI: 10.1146/annurev-micro-020518-115650] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Persisters are nongrowing, transiently antibiotic-tolerant bacteria within a clonal population of otherwise susceptible cells. Their formation is triggered by environmental cues and involves the main bacterial stress response pathways that allow persisters to survive many harsh conditions, including antibiotic exposure. During infection, bacterial pathogens are exposed to a vast array of stresses in the host and form nongrowing persisters that survive both antibiotics and host immune responses, thereby most likely contributing to the relapse of many infections. While antibiotic persisters have been extensively studied over the last decade, the bulk of the work has focused on how these bacteria survive exposure to drugs in vitro. The ability of persisters to survive their interaction with a host is important yet underinvestigated. In order to tackle the problem of persistence of infections that contribute to the worldwide antibiotic resistance crisis, efforts should be made by scientific communities to understand and merge these two fields of research: antibiotic persisters and host-pathogen interactions. Here we give an overview of the history of the field of antibiotic persistence, report evidence for the importance of persisters in infection, and highlight studies that bridge the two areas.
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Affiliation(s)
- Bridget Gollan
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom; , , ,
| | - Grzegorz Grabe
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom; , , ,
| | - Charlotte Michaux
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom; , , ,
| | - Sophie Helaine
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom; , , ,
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Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. Genes (Basel) 2020; 11:genes11020231. [PMID: 32098200 PMCID: PMC7074383 DOI: 10.3390/genes11020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms like Escherichia coli, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the Burkholderia cepacia complex (Bcc). Bcc is a group of bacterial species associated with a poor clinical prognosis in cystic fibrosis patients. These species have some of the largest bacterial genomes, and except for the presence of two-distinct Hfq-like proteins, their RBP repertoire has not been analyzed so far. Using in silico approaches, we identified 186 conventional putative RBPs in Burkholderia cenocepacia J2315, an epidemic and multidrug resistant pathogen of cystic fibrosis patients. Here we describe the comparative genomics and phylogenetic analysis of RBPs present in multiple copies and predicted to play a role in transcription, protein synthesis, and RNA decay in Bcc bacteria. In addition to the two different Hfq chaperones, five cold shock proteins phylogenetically close to E. coli CspD protein and three distinct RhlE-like helicases could be found in the B. cenocepacia J2315 genome. No RhlB, SrmB, or DeaD helicases could be found in the genomes of these bacteria. These results, together with the multiple copies of other proteins generally involved in RNA degradation, suggest the existence, in B. cenocepacia and in other Bcc bacteria, of some extra and unexplored functions for the mentioned RBPs, as well as of alternative mechanisms involved in RNA regulation and metabolism in these bacteria.
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Song S, Wood TK. Toxin/Antitoxin System Paradigms: Toxins Bound to Antitoxins Are Not Likely Activated by Preferential Antitoxin Degradation. ACTA ACUST UNITED AC 2020; 4:e1900290. [PMID: 32293143 DOI: 10.1002/adbi.201900290] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Indexed: 12/28/2022]
Abstract
Periodically, a scientific field should examine its early premises. For ubiquitous toxin/antitoxin (TA) systems, several initial paradigms require adjustment based on accumulated data. For example, it is now clear that under physiological conditions, there is little evidence that toxins of TA systems cause cell death and little evidence that TA systems cause persistence. Instead, TA systems are utilized to reduce metabolism during stress, inhibit phages, stabilize genetic elements, and influence biofilm formation (bacterial cells attached via an extracellular matrix). In this essay, it is argued that toxins bound to antitoxins are not likely to become activated by preferential antitoxin degradation but instead, de novo toxin synthesis in the absence of stoichiometric amounts of antitoxin activates toxins.
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Affiliation(s)
- Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
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