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Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [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: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
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Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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2
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Pleiotropic actions of phenothiazine drugs are detrimental to Gram-negative bacterial persister cells. Commun Biol 2022; 5:217. [PMID: 35264714 PMCID: PMC8907348 DOI: 10.1038/s42003-022-03172-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/15/2022] [Indexed: 12/28/2022] Open
Abstract
Bacterial persister cells are temporarily tolerant to bactericidal antibiotics but are not necessarily dormant and may exhibit physiological activities leading to cell damage. Based on the link between fluoroquinolone-mediated SOS responses and persister cell recovery, we screened chemicals that target fluoroquinolone persisters. Metabolic inhibitors (e.g., phenothiazines) combined with ofloxacin (OFX) perturbed persister levels in metabolically active cell populations. When metabolically stimulated, intrinsically tolerant stationary phase cells also became OFX-sensitive in the presence of phenothiazines. The effects of phenothiazines on cell metabolism and physiology are highly pleiotropic: at sublethal concentrations, phenothiazines reduce cellular metabolic, transcriptional, and translational activities; impair cell repair and recovery mechanisms; transiently perturb membrane integrity; and disrupt proton motive force by dissipating the proton concentration gradient across the cell membrane. Screening a subset of mutant strains lacking membrane-bound proteins revealed the pleiotropic effects of phenothiazines potentially rely on their ability to inhibit a wide range of critical metabolic proteins. Altogether, our study further highlights the complex roles of metabolism in persister cell formation, survival and recovery, and suggests metabolic inhibitors such as phenothiazines can be selectively detrimental to persister cells.
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Mohiuddin SG, Massahi A, Orman MA. High-Throughput Screening of a Promoter Library Reveals New Persister Mechanisms in Escherichia Coli. Microbiol Spectr 2022; 10:e0225321. [PMID: 35196813 PMCID: PMC8865558 DOI: 10.1128/spectrum.02253-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/31/2022] [Indexed: 11/23/2022] Open
Abstract
Persister cells are a small subpopulation of phenotypic variants that survive high concentrations of bactericidal antibiotics. Their survival mechanisms are not heritable and can be formed stochastically or triggered by environmental stresses such as antibiotic treatment. In this study, high-throughput screening of an Escherichia coli promoter library and subsequent validation experiments identified several genes whose expression was upregulated by antibiotic treatment. Among the identified genes, waaG, guaA, and guaB were found to be important in persister cell formation in E. coli as their deletion significantly enhanced the sensitivity of cells to various antibiotics. The GuaA and GuaB enzymes form the upstream reactions of ppGpp (a global persister molecule) biosynthesis, and the deletion of guaA and guaB drastically perturbs the ppGpp regulon in E. coli. WaaG, a lipopolysaccharide glucosyltransferase, plays an important role in shaping the outer membrane structure, and the deletion of waaG dissipates the proton gradient (ΔpH) component of cellular proton motive force (PMF), perturbs cellular ATP production, and reduces type I persister formation in stationary phase. Active respiration in the stationary phase, which drives the PMF, was previously shown to play a critical role in type I persister formation, and our results associated with the waaG deficient strain further corroborate these findings. IMPORTANCE Persistence is a nonheritable trait by which normal growing cells switch phenotypically to antibiotic tolerant persister cells. This transient state enables persister cells to recover and grow into an antibiotic-sensitive population. Persister cells have been observed in many pathogenic and nonpathogenic bacteria. Previous studies highlight the complexity and diversity of bacterial persister-cell mechanisms, many of which still remain to be elucidated. Here, using promoter and knockout cell libraries in Escherichia coli, we have identified genes that reveal novel persister mechanisms. As persistence is a critical survival strategy that evolved in many bacteria, our study will enhance the current molecular-level understanding of this conserved mechanism.
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Affiliation(s)
- Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Aslan Massahi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
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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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5
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Wainwright J, Hobbs G, Nakouti I. Persister cells: formation, resuscitation and combative therapies. Arch Microbiol 2021; 203:5899-5906. [PMID: 34739553 PMCID: PMC8590677 DOI: 10.1007/s00203-021-02585-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022]
Abstract
Persister cells, or superfits, have been strongly implicated in the recalcitrance and recurrence of chronic bacterial infection through the dormant (metabolically reduced) phenotype they display and the tolerance to antimicrobial agents this dormancy grants them. The complex biochemical events that lead to the formation of persister cells are not completely understood, though much research has linked the degradation of type II toxin/antitoxin systems and reduced cellular ATP levels to the rise in stress response molecules (where (p)ppGpp is of particular interest), which induce this dormant state. The equally complex mechanism of resuscitation is initiated by the cells’ ability to sense nutrient availability via chemotaxis systems. Levels of secondary messenger proteins (i.e., cAMP) within the cell are reduced to allow the resuscitation of ribosomes, by ribosomal resuscitation factor HflX, to reinstate protein synthesis and, therefore, growth to re-populate. Techniques of superfit eradication utilise one, or more, of three approaches (i) direct killing, (ii) re-sensitising persister cells to conventional antimicrobials, or (iii) prevention of persister formation though few laboratory findings have been translated to clinical practice. This work will outline current findings in the field with a critical approach, where possible.
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Affiliation(s)
- Jack Wainwright
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Glyn Hobbs
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Ismini Nakouti
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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6
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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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Abstract
Persister cells are defined as a small fraction of phenotypic variants in a cell population that are temporarily tolerant to bactericidal antibiotics. Persisters are not mutant cells; they generally survive lethal concentrations of antibiotics due to their transient nongrowing state. Persister cells have the ability to resuscitate after the end of antibiotic treatment. Despite significant advancements in the understanding of the molecular mechanisms underlying persister formation, we still have little information about their resuscitation mechanisms. In this chapter, we describe a method to detect and monitor persister resuscitation at the single-cell level using flow cytometry analysis. This method enables us to not only assess the resuscitation characteristics of persisters but also determine and quantify various subpopulations in antibiotic-treated cultures, including viable but nonculturable (VBNC) and dead cells.
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Affiliation(s)
- Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Mehmet A Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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Yin W, Xu S, Wang Y, Zhang Y, Chou SH, Galperin MY, He J. Ways to control harmful biofilms: prevention, inhibition, and eradication. Crit Rev Microbiol 2020; 47:57-78. [PMID: 33356690 DOI: 10.1080/1040841x.2020.1842325] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Biofilms are complex microbial architectures that encase microbial cells in a matrix comprising self-produced extracellular polymeric substances. Microorganisms living in biofilms are much more resistant to hostile environments than their planktonic counterparts and exhibit enhanced resistance against the microbicides. From the human perspective, biofilms can be classified into beneficial, neutral, and harmful. Harmful biofilms impact food safety, cause plant and animal diseases, and threaten medical fields, making it urgent to develop effective and robust strategies to control harmful biofilms. In this review, we discuss various strategies to control biofilm formation on infected tissues, implants, and medical devices. We classify the current strategies into three main categories: (i) changing the properties of susceptible surfaces to prevent biofilm formation; (ii) regulating signalling pathways to inhibit biofilm formation; (iii) applying external forces to eradicate the biofilm. We hope this review would motivate the development of innovative and effective strategies for controlling harmful biofilms.
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Affiliation(s)
- Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Siyang Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Yiting Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Yuling Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
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Wang M, Chan EWC, Yang C, Chen K, So PK, Chen S. N-Acetyl-D-Glucosamine Acts as Adjuvant that Re-Sensitizes Starvation-Induced Antibiotic-Tolerant Population of E. Coli to β-Lactam. iScience 2020; 23:101740. [PMID: 33225246 PMCID: PMC7662850 DOI: 10.1016/j.isci.2020.101740] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial tolerance to antibiotics causes reduction in efficacy in antimicrobial treatment of chronic and recurrent infections. Nutrient availability is one major factor that determines the degree of phenotypic antibiotic tolerance. In an attempt to test if specific nutrients can reverse phenotypic tolerance, we identified N-acetyl-D-glucosamine (GlcNAc) as a potent tolerance-suppressing agent and showed that it could strongly re-sensitize a tolerant population of E. coli to ampicillin. Such re-sensitization effect was attributable to two physiology-modulating effects of GlcNAc. First, uptake of GlcNAc by the tolerant population triggers formation of the peptidoglycan precursor UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) and subsequently re-activates the peptidoglycan biosynthesis process, rendering the organism susceptible to β-lactam antibiotics. Second, activation of glycolysis by-products of GlcNAc catabolism drives the re-sensitization process. Our findings imply that GlcNAc may serve as a non-toxic β-lactam adjuvant that enhances the efficacy of treatment of otherwise hard-to-treat bacterial infections due to phenotypic antibiotic tolerance.
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Affiliation(s)
- Miaomiao Wang
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Chen Yang
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Pui-kin So
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Corresponding author
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Martins D, McKay GA, English AM, Nguyen D. Sublethal Paraquat Confers Multidrug Tolerance in Pseudomonas aeruginosa by Inducing Superoxide Dismutase Activity and Lowering Envelope Permeability. Front Microbiol 2020; 11:576708. [PMID: 33101252 PMCID: PMC7546422 DOI: 10.3389/fmicb.2020.576708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Stressors and environmental cues shape the physiological state of bacteria, and thus how they subsequently respond to antibiotic toxicity. To understand how superoxide stress can modulate survival to bactericidal antibiotics, we examined the effect of intracellular superoxide generators, paraquat and menadione, on stationary-phase antibiotic tolerance of the opportunistic pathogen, Pseudomonas aeruginosa. We tested how pre-challenge with sublethal paraquat and menadione alters the tolerance to ofloxacin and meropenem in wild-type P. aeruginosa and mutants lacking superoxide dismutase (SOD) activity (sodAB), the paraquat responsive regulator soxR, (p)ppGpp signaling (relA spoT mutant), or the alternative sigma factor rpoS. We confirmed that loss of SOD activity impairs ofloxacin and meropenem tolerance in stationary phase cells, and found that sublethal superoxide generators induce drug tolerance by stimulating SOD activity. This response is rapid, requires de novo protein synthesis, and is RpoS-dependent but does not require (p)ppGpp signaling nor SoxR. We further showed that pre-challenge with sublethal paraquat induces a SOD-dependent reduction in cell-envelope permeability and ofloxacin penetration. Our results highlight a novel mechanism of hormetic protection by superoxide generators, which may have important implications for stress-induced antibiotic tolerance in P. aeruginosa cells.
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Affiliation(s)
- Dorival Martins
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Geoffrey A McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
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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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12
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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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13
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Investigating the Effects of Osmolytes and Environmental pH on Bacterial Persisters. Antimicrob Agents Chemother 2020; 64:AAC.02393-19. [PMID: 32094133 DOI: 10.1128/aac.02393-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/14/2020] [Indexed: 01/21/2023] Open
Abstract
Bacterial persisters are phenotypic variants that temporarily demonstrate an extraordinary tolerance toward antibiotics. Persisters have been linked to the recalcitrance of biofilm-related infections; hence, a complete understanding of their physiology can lead to improvement of therapeutic strategies for such infections. Mechanisms pertaining to persister formation are thought to be associated with stress response pathways triggered by intra- or extracellular stress factors. Unfortunately, studies demonstrating the effects of osmolyte- and/or pH-induced stresses on bacterial persistence are largely missing. To fill this knowledge gap within the field, we studied the effects of various osmolytes and pH conditions on Escherichia coli persistence with the use of phenotype microarrays and antibiotic tolerance assays. Although we found that a number of chemicals and pH environments, including urea, sodium nitrite, and acidic pH, significantly reduced persister formation in E. coli compared to no-osmolyte/no-buffer controls, this reduction in persister levels was less pronounced in late-stationary-phase cultures. Our results further demonstrated a positive correlation between cell growth and persister formation, which challenges the general notion in the field that slow-growing cultures have more persister cells than fast-growing cultures.
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Mohiuddin SG, Hoang T, Saba A, Karki P, Orman MA. Identifying Metabolic Inhibitors to Reduce Bacterial Persistence. Front Microbiol 2020; 11:472. [PMID: 32292393 PMCID: PMC7118205 DOI: 10.3389/fmicb.2020.00472] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial persisters are rare phenotypic variants that are temporarily tolerant to high concentrations of antibiotics. We have previously discovered that stationary-phase-cell subpopulations exhibiting high redox activities were less capable of producing proteins and resuming growth upon their dilution into fresh media. The redox activities of these cells were maintained by endogenous protein and RNA degradation, resulting in self-inflicted damage that transiently repressed the cellular functions targeted by antibiotics. Here, we showed that pretreatment of stationary-phase cells with an ATP synthase inhibitor, chlorpromazine hydrochloride (CPZ), significantly reduced stationary-phase-redox activities and protein degradation, and yielded cells that were more susceptible to cell death when exposed to antibiotics in fresh media. Leveraging this knowledge, we developed an assay integrating a degradable fluorescent protein system and a small library, containing FDA-approved drugs and antibiotics, to detect medically relevant drugs that potentially target persister metabolism. We identified a subset of chemical inhibitors, including polymyxin B, poly-L-lysine and phenothiazine anti-psychotic drugs, that were able to reduce the persistence phenotype in Escherichia coli. These chemical inhibitors also reduced Pseudomonas aeruginosa persistence, potentially verifying the existence of similar mechanisms in a medically relevant organism.
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Affiliation(s)
- Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Thuy Hoang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Adesola Saba
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Prashant Karki
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Mehmet A Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
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15
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Prasetyoputri A, Jarrad AM, Cooper MA, Blaskovich MA. The Eagle Effect and Antibiotic-Induced Persistence: Two Sides of the Same Coin? Trends Microbiol 2019; 27:339-354. [DOI: 10.1016/j.tim.2018.10.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/21/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022]
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16
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Smith A, Kaczmar A, Bamford RA, Smith C, Frustaci S, Kovacs-Simon A, O'Neill P, Moore K, Paszkiewicz K, Titball RW, Pagliara S. The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli. Front Microbiol 2018; 9:1739. [PMID: 30158905 PMCID: PMC6104134 DOI: 10.3389/fmicb.2018.01739] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.
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Affiliation(s)
- Ashley Smith
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kaczmar
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Simona Frustaci
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
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17
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Abstract
Urinary tract infection (UTI) is one of the most common bacterial infections in humans, and the majority are caused by uropathogenic Escherichia coli (UPEC). The rising antibiotic resistance among UPEC and the frequent failure of antibiotics to effectively treat recurrent UTI and catheter-associated UTI motivate research on alternative ways of managing UTI. Abundant evidence indicates that the toxic radical nitric oxide (NO), formed by activation of the inducible nitric oxide synthase, plays an important role in host defence to bacterial infections, including UTI. The major source of NO production during UTI is from inflammatory cells, especially neutrophils, and from the uroepithelial cells that are known to orchestrate the innate immune response during UTI. NO and reactive nitrogen species have a wide range of antibacterial targets, including DNA, heme proteins, iron-sulfur clusters, and protein thiol groups. However, UPEC have acquired a variety of defence mechanisms for protection against NO, such as the NO-detoxifying enzyme flavohemoglobin and the NO-tolerant cytochrome bd-I respiratory oxidase. The cytotoxicity of NO-derived intermediates is nonspecific and may be detrimental to host cells, and a balanced NO production is crucial to maintain the tissue integrity of the urinary tract. In this review, we will give an overview of how NO production from host cells in the urinary tract is activated and regulated, the effect of NO on UPEC growth and colonization, and the ability of UPEC to protect themselves against NO. We also discuss the attempts that have been made to develop NO-based therapeutics for UTI treatment.
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18
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Fighting bacterial persistence: Current and emerging anti-persister strategies and therapeutics. Drug Resist Updat 2018; 38:12-26. [DOI: 10.1016/j.drup.2018.03.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/07/2018] [Accepted: 03/25/2018] [Indexed: 01/13/2023]
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19
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Tkachenko AG. Stress Responses of Bacterial Cells as Mechanism of Development of Antibiotic Tolerance (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020114] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Bactericidal activity of alpha-bromocinnamaldehyde against persisters in Escherichia coli. PLoS One 2017; 12:e0182122. [PMID: 28750057 PMCID: PMC5531548 DOI: 10.1371/journal.pone.0182122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/12/2017] [Indexed: 12/18/2022] Open
Abstract
Persisters are tolerant to multiple antibiotics, and widely distributed in bacteria, fungi, parasites, and even cancerous human cell populations, leading to recurrent infections and relapse after therapy. In this study, we investigated the potential of cinnamaldehyde and its derivatives to eradicate persisters in Escherichia coli. The results showed that 200 μg/ml of alpha-bromocinnamaldehyde (Br-CA) was capable of killing all E. coli cells during the exponential phase. Considering the heterogeneous nature of persisters, multiple types of persisters were induced and exposed to Br-CA. Our results indicated that no cells in the ppGpp-overproducing strain or TisB-overexpressing strain survived the treatment of Br-CA although considerable amounts of persisters to ampicillin (Amp) and ciprofloxacin (Cip) were induced. Chemical induction by carbonyl cyanide m-chlorophenylhydrazone (CCCP) led to the formation of more than 10% persister to Amp and Cip in the entire population, and Br-CA still completely eradicated them. In addition, the cells in the stationary phase, which are usually highly recalcitrant to antibiotics treatment, were also completely eradicated by 400 μg/ml of Br-CA. Further studies showed that neither thiourea (hydroxyl-radical scavenger) nor DPTA (Fe3+ chelator to block the hydroxyl-radical) affected the bactericidal efficiency of the Br-CA to kill E. coli, indicating a ROS-independent bactericidal mechanism. Taken together, we concluded that Br-CA compound has a novel bactericidal mechanism and the potential to mitigate antibiotics resistance crisis.
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21
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Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev 2017; 41:219-251. [DOI: 10.1093/femsre/fux001] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
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22
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Levin-Reisman I, Ronin I, Gefen O, Braniss I, Shoresh N, Balaban NQ. Antibiotic tolerance facilitates the
evolution of resistance. Science 2017; 355:826-830. [DOI: 10.1126/science.aaj2191] [Citation(s) in RCA: 634] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/16/2017] [Indexed: 12/24/2022]
Abstract
Controlled experimental evolution during
antibiotic treatment can help to explain the
processes leading to antibiotic resistance in
bacteria. Recently, intermittent antibiotic
exposures have been shown to lead rapidly to the
evolution of tolerance—that is, the ability to
survive under treatment without developing
resistance. However, whether tolerance delays or
promotes the eventual emergence of resistance is
unclear. Here we used in vitro evolution
experiments to explore this question. We found
that in all cases, tolerance preceded resistance.
A mathematical population-genetics model showed
how tolerance boosts the chances for resistance
mutations to spread in the population. Thus,
tolerance mutations pave the way for the rapid
subsequent evolution of resistance. Preventing the
evolution of tolerance may offer a new strategy
for delaying the emergence of resistance.
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Affiliation(s)
- Irit Levin-Reisman
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Irine Ronin
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Orit Gefen
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ilan Braniss
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Shoresh
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nathalie Q. Balaban
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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23
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Van den Bergh B, Michiels JE, Fauvart M, Michiels J. Should we develop screens for multi-drug antibiotic tolerance? Expert Rev Anti Infect Ther 2016; 14:613-6. [DOI: 10.1080/14787210.2016.1194754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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24
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Gowers GOF, Robinson JL, Brynildsen MP. Starved Escherichia coli preserve reducing power under nitric oxide stress. Biochem Biophys Res Commun 2016; 476:29-34. [PMID: 27207837 DOI: 10.1016/j.bbrc.2016.05.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/16/2016] [Indexed: 01/15/2023]
Abstract
Nitric oxide (NO) detoxification enzymes, such as NO dioxygenase (NOD) and NO reductase (NOR), are important to the virulence of numerous bacteria. Pathogens use these defense systems to ward off immune-generated NO, and they do so in environments that contain additional stressors, such as reactive oxygen species, nutrient deprivation, and acid stress. NOD and NOR both use reducing equivalents to metabolically deactivate NO, which suggests that nutrient deprivation could negatively impact their functionality. To explore the relationship between NO detoxification and nutrient deprivation, we examined the ability of Escherichia coli to detoxify NO under different levels of carbon source availability in aerobic cultures. We observed failure of NO detoxification under both carbon source limitation and starvation, and those failures could have arisen from inabilities to synthesize Hmp (NOD of E. coli) and/or supply it with sufficient NADH (preferred electron donor). We found that when limited quantities of carbon source were provided, NO detoxification failed due to insufficient NADH, whereas starvation prevented Hmp synthesis, which enabled cells to maintain their NADH levels. This maintenance of NADH levels under starvation was confirmed to be dependent on the absence of Hmp. Intriguingly, these data show that under NO stress, carbon-starved E. coli are better positioned with regard to reducing power to cope with other stresses than cells that had consumed an exhaustible amount of carbon.
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Affiliation(s)
| | - Jonathan L Robinson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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