1
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Vo KC, Sakamoto JJ, Furuta M, Tsuchido T. The impact of heat treatment on E. coli cell physiology in rich and minimal media considering oxidative secondary stress. J Appl Microbiol 2024; 135:lxae216. [PMID: 39165131 DOI: 10.1093/jambio/lxae216] [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: 04/22/2024] [Revised: 07/30/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024]
Abstract
AIMS This study investigates the cell physiology of thermally injured bacterial cells, with a specific focus on oxidative stress and the repair mechanisms associated with oxidative secondary stress. METHODS AND RESULTS We explored the effect of heat treatment on the activity of two protective enzymes, levels of intracellular reactive oxygen species, and redox potential. The findings reveal that enzyme activity slightly increased after heat treatment, gradually returning to baseline levels during subculture. The response of Escherichia coli cells to heat treatment, as assessed by the level of superoxide radicals generated and redox potential, varied based on growth conditions, namely minimal and rich media. Notably, the viability of injured cells improved when antioxidants were added to agar media, even in the presence of metabolic inhibitors. CONCLUSIONS These results suggest a complex system involved in repairing damage in heat-treated cells, particularly in rich media. While repairing membrane damage is crucial for cell regrowth and the electron transport system plays a critical role in the recovery process of injured cells under both tested conditions.
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Affiliation(s)
- Khanh C Vo
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Jin J Sakamoto
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- MPES-3 U and Faculty of Materials, Chemistry and Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Masakazu Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- Radiation Research Center, Organization for Research Promotion, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Tetsuaki Tsuchido
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
- TriBioX Laboratories Ltd., 1-125 Takano-Tamaoka-cho, Sakyo-ku, Kyoto 606-8106, Japan
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2
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Korshunov S, Imlay JA. Antioxidants are ineffective at quenching reactive oxygen species inside bacteria and should not be used to diagnose oxidative stress. Mol Microbiol 2024; 122:113-128. [PMID: 38889382 DOI: 10.1111/mmi.15286] [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: 04/19/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024]
Abstract
A wide variety of stresses have been proposed to exert killing effects upon bacteria by stimulating the intracellular formation of reactive oxygen species (ROS). A key part of the supporting evidence has often been the ability of antioxidant compounds to protect the cells. In this study, some of the most-used antioxidants-thiourea, glutathione, N-acetylcysteine, and ascorbate-have been examined. Their ability to quench superoxide and hydrogen peroxide was verified in vitro, but the rate constants were orders of magnitude too slow for them to have an impact upon superoxide and peroxide concentrations in vivo, where these species are already scavenged by highly active enzymes. Indeed, the antioxidants were unable to protect the growth and ROS-sensitive enzymes of E. coli strains experiencing authentic oxidative stress. Similar logic posits that antioxidants cannot substantially quench hydroxyl radicals inside cells, which contain abundant biomolecules that react with them at diffusion-limited rates. Indeed, antioxidants were able to protect cells from DNA damage only if they were applied at concentrations that slow metabolism and growth. This protective effect was apparent even under anoxic conditions, when ROS could not possibly be involved, and it was replicated when growth was similarly slowed by other means. Experimenters should discard the use of antioxidants as a way of detecting intracellular oxidative stress and should revisit conclusions that have been based upon such experiments. The notable exception is that these compounds can effectively degrade hydrogen peroxide from environmental sources before it enters cells.
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Affiliation(s)
- Sergey Korshunov
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
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3
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Muñoz-Villagrán C, Acevedo-Arbunic J, Härtig E, Issotta F, Mascayano C, Jahn D, Jahn M, Levicán G. The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress. Int J Mol Sci 2024; 25:6905. [PMID: 39000017 PMCID: PMC11241051 DOI: 10.3390/ijms25136905] [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: 05/06/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Extreme acidophilic bacteria like Leptospirillum sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of Leptospirillum sp. CF-1 encodes the thioredoxin-fold protein TFP2, which exhibits a high structural similarity to the thioredoxin domain of E. coli CnoX. CnoX from Escherichia coli is a chaperedoxin that protects protein substrates from oxidative stress conditions using its holdase function and a subsequent transfer to foldase chaperones for refolding. Recombinantly produced and purified Leptospirillum sp. TFP2 possesses both thioredoxin and chaperone holdase activities in vitro. It can be reduced by thioredoxin reductase (TrxR). The tfp2 gene co-locates with genes for the chaperone foldase GroES/EL on the chromosome. The "tfp2 cluster" (ctpA-groES-groEL-hyp-tfp2-recN) was found between 1.9 and 8.8-fold transcriptionally up-regulated in response to 1 mM hydrogen peroxide (H2O2). Leptospirillum sp. tfp2 heterologously expressed in E. coli wild type and cnoX mutant strains lead to an increased tolerance of these E. coli strains to H2O2 and significantly reduced intracellular protein aggregates. Finally, a proteomic analysis of protein aggregates produced in E. coli upon exposition to oxidative stress with 4 mM H2O2, showed that Leptospirillum sp. tfp2 expression caused a significant decrease in the aggregation of 124 proteins belonging to fifteen different metabolic categories. These included several known substrates of DnaK and GroEL/ES. These findings demonstrate that Leptospirillum sp. TFP2 is a chaperedoxin-like protein, acting as a key player in the control of cellular proteostasis under highly oxidative conditions that prevail in extreme acidic environments.
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Affiliation(s)
- Claudia Muñoz-Villagrán
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Javiera Acevedo-Arbunic
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
| | - Francisco Issotta
- Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago 8331150, Chile
| | - Carolina Mascayano
- Laboratorio de Simulación Computacional y Diseño Racional de Fármacos, Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
- Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (E.H.)
| | - Gloria Levicán
- Laboratorio de Microbiología Básica y Aplicada, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
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4
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Khan A, Liu G, Zhang G, Li X. Radiation-resistant bacteria in desiccated soil and their potentiality in applied sciences. Front Microbiol 2024; 15:1348758. [PMID: 38894973 PMCID: PMC11184166 DOI: 10.3389/fmicb.2024.1348758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
A rich diversity of radiation-resistant (Rr) and desiccation-resistant (Dr) bacteria has been found in arid habitats of the world. Evidence from scientific research has linked their origin to reactive oxygen species (ROS) intermediates. Rr and Dr. bacteria of arid regions have the potential to regulate imbalance radicals and evade a higher dose of radiation and oxidation than bacterial species of non-arid regions. Photochemical-activated ROS in Rr bacteria is run through photo-induction of electron transfer. A hypothetical model of the biogeochemical cycle based on solar radiation and desiccation. These selective stresses generate oxidative radicals for a short span with strong reactivity and toxic effects. Desert-inhibiting Rr bacteria efficiently evade ROS toxicity with an evolved antioxidant system and other defensive pathways. The imbalanced radicals in physiological disorders, cancer, and lung diseases could be neutralized by a self-sustaining evolved Rr bacteria antioxidant system. The direct link of evolved antioxidant system with intermediate ROS and indirect influence of radiation and desiccation provide useful insight into richness, ecological diversity, and origin of Rr bacteria capabilities. The distinguishing features of Rr bacteria in deserts present a fertile research area with promising applications in the pharmaceutical industry, genetic engineering, biological therapy, biological transformation, bioremediation, industrial biotechnology, and astrobiology.
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Affiliation(s)
- Asaf Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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5
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da Cruz Nizer WS, Adams ME, Allison KN, Montgomery MC, Mosher H, Cassol E, Overhage J. Oxidative stress responses in biofilms. Biofilm 2024; 7:100203. [PMID: 38827632 PMCID: PMC11139773 DOI: 10.1016/j.bioflm.2024.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
Oxidizing agents are low-molecular-weight molecules that oxidize other substances by accepting electrons from them. They include reactive oxygen species (ROS), such as superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (HO-), and reactive chlorine species (RCS) including sodium hypochlorite (NaOCl) and its active ingredient hypochlorous acid (HOCl), and chloramines. Bacteria encounter oxidizing agents in many different environments and from diverse sources. Among them, they can be produced endogenously by aerobic respiration or exogenously by the use of disinfectants and cleaning agents, as well as by the mammalian immune system. Furthermore, human activities like industrial effluent pollution, agricultural runoff, and environmental activities like volcanic eruptions and photosynthesis are also sources of oxidants. Despite their antimicrobial effects, bacteria have developed many mechanisms to resist the damage caused by these toxic molecules. Previous research has demonstrated that growing as a biofilm particularly enhances bacterial survival against oxidizing agents. This review aims to summarize the current knowledge on the resistance mechanisms employed by bacterial biofilms against ROS and RCS, focussing on the most important mechanisms, including the formation of biofilms in response to oxidative stressors, the biofilm matrix as a protective barrier, the importance of detoxifying enzymes, and increased protection within multi-species biofilm communities. Understanding the complexity of bacterial responses against oxidative stress will provide valuable insights for potential therapeutic interventions and biofilm control strategies in diverse bacterial species.
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Affiliation(s)
| | - Madison Elisabeth Adams
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Kira Noelle Allison
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | | | - Hailey Mosher
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
| | - Joerg Overhage
- Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, ON, Canada
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6
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [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: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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7
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Smirnova G, Tyulenev A, Sutormina L, Kalashnikova T, Muzyka N, Ushakov V, Samoilova Z, Oktyabrsky O. Regulation of Cysteine Homeostasis and Its Effect on Escherichia coli Sensitivity to Ciprofloxacin in LB Medium. Int J Mol Sci 2024; 25:4424. [PMID: 38674008 PMCID: PMC11050555 DOI: 10.3390/ijms25084424] [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: 03/28/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cysteine and its derivatives, including H2S, can influence bacterial virulence and sensitivity to antibiotics. In minimal sulfate media, H2S is generated under stress to prevent excess cysteine and, together with incorporation into glutathione and export into the medium, is a mechanism of cysteine homeostasis. Here, we studied the features of cysteine homeostasis in LB medium, where the main source of sulfur is cystine, whose import can create excess cysteine inside cells. We used mutants in the mechanisms of cysteine homeostasis and a set of microbiological and biochemical methods, including the real-time monitoring of sulfide and oxygen, the determination of cysteine and glutathione (GSH), and the expression of the Fur, OxyR, and SOS regulons genes. During normal growth, the parental strain generated H2S when switching respiration to another substrate. The mutations affected the onset time, the intensity and duration of H2S production, cysteine and glutathione levels, bacterial growth and respiration rates, and the induction of defense systems. Exposure to chloramphenicol and high doses of ciprofloxacin increased cysteine content and GSH synthesis. A high inverse relationship between log CFU/mL and bacterial growth rate before ciprofloxacin addition was revealed. The study points to the important role of maintaining cysteine homeostasis during normal growth and antibiotic exposure in LB medium.
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Affiliation(s)
- Galina Smirnova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia; (A.T.); (L.S.); (T.K.); (N.M.); (V.U.); (Z.S.); (O.O.)
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8
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Stoakes E, Chen X, Kalmar L, Baker D, Evans R, Rudder S, Grant AJ. Identification of Campylobacter jejuni and Campylobacter coli genes contributing to oxidative stress response using TraDIS analysis. BMC Microbiol 2024; 24:46. [PMID: 38302896 PMCID: PMC10832277 DOI: 10.1186/s12866-024-03201-y] [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: 09/13/2023] [Accepted: 01/21/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Campylobacter jejuni and Campylobacter coli are the major causative agents of bacterial gastroenteritis worldwide and are known obligate microaerophiles. Despite being sensitive to oxygen and its reduction products, both species are readily isolated from animal food products kept under atmospheric conditions where they face high oxygen tension levels. RESULTS In this study, Transposon Directed Insertion-site Sequencing (TraDIS) was used to investigate the ability of one C. jejuni strain and two C. coli strains to overcome oxidative stress, using H2O2 to mimic oxidative stress. Genes were identified that were required for oxidative stress resistance for each individual strain but also allowed a comparison across the three strains. Mutations in the perR and ahpC genes were found to increase Campylobacter tolerance to H2O2. The roles of these proteins in oxidative stress were previously known in C. jejuni, but this data indicates that they most likely play a similar role in C. coli. Mutation of czcD decreased Campylobacter tolerance to H2O2. The role of CzcD, which functions as a zinc exporter, has not previously been linked to oxidative stress. The TraDIS data was confirmed using defined deletions of perR and czcD in C. coli 15-537360. CONCLUSIONS This is the first study to investigate gene fitness in both C. jejuni and C. coli under oxidative stress conditions and highlights both similar roles for certain genes for both species and highlights other genes that have a role under oxidative stress.
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Affiliation(s)
- Emily Stoakes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Xuanlin Chen
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Lajos Kalmar
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Dave Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.
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9
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Gupta A, Imlay JA. How a natural antibiotic uses oxidative stress to kill oxidant-resistant bacteria. Proc Natl Acad Sci U S A 2023; 120:e2312110120. [PMID: 38109539 PMCID: PMC10756299 DOI: 10.1073/pnas.2312110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
Natural products that possess antibiotic and antitumor qualities are often suspected of working through oxidative mechanisms. In this study, two quinone-based small molecules were compared. Menadione, a classic redox-cycling compound, was confirmed to generate high levels of reactive oxygen species inside Escherichia coli. It inactivated iron-cofactored enzymes and blocked growth. However, despite the substantial levels of oxidants that it produced, it was unable to generate significant DNA damage and was not lethal. Streptonigrin, in contrast, was poorer at redox cycling and did not inactivate enzymes or block growth; however, even in low doses, it damaged DNA and killed cells. Its activity required iron and oxygen, and in vitro experiments indicated that its quinone moiety transferred electrons through the adjacent iron atom to oxygen. Additionally, in vitro experiments revealed that streptonigrin was able to damage DNA without inhibition by catalase, indicating that hydrogen peroxide was not involved. We infer that streptonigrin can reduce bound oxygen directly to a ferryl species, which then oxidizes the adjacent DNA, without release of superoxide or hydrogen peroxide intermediates. This scheme allows streptonigrin to kill a bacterial cell without interference by scavenging enzymes. Moreover, its minimal redox-cycling behavior avoids alerting either the OxyR or the SoxRS systems, which otherwise would block killing. This example highlights qualities that may be important in the design of oxidative drugs. These results also cast doubt on proposals that bacteria can be killed by stressors that merely stimulate intracellular O2- and H2O2 formation.
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Affiliation(s)
- Anshika Gupta
- Department of Microbiology, University of Illinois, Urbana, IL61801
| | - James A. Imlay
- Department of Microbiology, University of Illinois, Urbana, IL61801
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10
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Fan L, Pan Z, Zhong Y, Guo J, Liao X, Pang R, Xu Q, Ye G, Su Y. L-glutamine sensitizes Gram-positive-resistant bacteria to gentamicin killing. Microbiol Spectr 2023; 11:e0161923. [PMID: 37882580 PMCID: PMC10715002 DOI: 10.1128/spectrum.01619-23] [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: 04/18/2023] [Accepted: 08/23/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) infection severely threatens human health due to high morbidity and mortality; it is urgent to develop novel strategies to tackle this problem. Metabolites belong to antibiotic adjuvants which improve the effect of antibiotics. Despite reports of L-glutamine being applied in antibiotic adjuvant for Gram-negative bacteria, how L-glutamine affects antibiotics against Gram-positive-resistant bacteria is still unclear. In this study, L-glutamine increases the antibacterial effect of gentamicin on MRSA, and it links to membrane permeability and pH gradient (ΔpH), resulting in uptake of more gentamicin. Of great interest, reduced reactive oxygen species (ROS) by glutathione was found under L-glutamine treatment; USA300 becomes sensitive again to gentamicin. This study not only offers deep understanding on ΔpH and ROS on bacterial resistance but also provides potential treatment solutions for targeting MRSA infection.
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Affiliation(s)
- Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
| | - Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
| | - Xu Liao
- Center for Excellence in Regional Atmospheric Environment and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health,State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingqiang Xu
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
| | - Guozhu Ye
- Center for Excellence in Regional Atmospheric Environment and Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology,Jinan University, Guangzhou, China
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11
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Ghasemi S, Farokhpour F, Mortezagholi B, Movahed E, Ghaedi A, Gargari MK, Khanzadeh M, Bazrgar A, Khanzadeh S. Systematic review and meta-analysis of oxidative stress and antioxidant markers in recurrent aphthous stomatitis. BMC Oral Health 2023; 23:960. [PMID: 38042793 PMCID: PMC10693709 DOI: 10.1186/s12903-023-03636-1] [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: 04/09/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND We performed this systematic review and meta-analysis to synthesize all studies that reported the level of oxidative and antioxidative markers in recurrent aphthous stomatitis (RAS) patients compared to controls. METHODS We registered our study in PROSPERO (CRD42023431310). PubMed, ProQuest, Scopus, EMBASE, Google Scholar, and Web of Science were searched to find relevant publications up to June 5, 2023. The standardized mean differences (SMDs) with 95% confidence intervals (CIs) were calculated. We included 30 articles after multiple stags of screening. RESULTS We found that erythrocyte superoxide dismutase and Glutathione peroxidase activity were significantly lower in patients with RAS compared to healthy controls (SMD = - 1.00, 95%CI = -1.79 to -0.21, p = 0.013, and SMD = - 1.90, 95%CI = -3.43 to -0.38, p = 0.01, Respectively). However, there was not any difference between patients with RAS and healthy controls in erythrocyte Catalase (SMD = - 0.71, 95%CI = -1.56-0.14, p = 0.10). The total antioxidant status (TAS) level, in serum was significantly lower in patients than healthy controls (SMD = - 0.98, 95%CI = -1.57 to -0.39, p = 0.001). In addition, RAS patients had higher levels of serum Malondialdehyde (MDA), Serum total oxidant status, and serum oxidative stress index than healthy controls (SMD = 2.11, 95%CI = 1.43-2.79, p < 0.001, SMD = 1.53, 95%CI = 0.34-2.72, p = 0.01, and SMD = 1.25, 95%CI = 0.25-2.25, p = 0.014, Respectively); However, salivary MDA and TAS, and serum uric acid, vitamin E and C, and reduced glutathione levels of patients with RAS were not different from that of healthy controls. CONCLUSIONS The relationship between oxidative stress and RAS is well established in this meta-analysis. Although the molecular processes underlying the etiology of this pathology remain unknown, evidence indicating oxidative stress has a significant role in the pathogenesis of RAS has been revealed.
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Affiliation(s)
- Saeideh Ghasemi
- Dental school, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fataneh Farokhpour
- Department of pathology, school of medicine, Isfahan university of medical science, Isfahan, Iran
| | - Bardia Mortezagholi
- Dental Research Center, Faculty of Dentistry, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Emad Movahed
- Dental Research Center, Faculty of Dentistry, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Arshin Ghaedi
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Monireh Khanzadeh
- Geriatric & Gerontology Department, Medical School, Tehran University of medical and health sciences, Tehran, Iran
| | - Aida Bazrgar
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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12
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NajeerAhamed MJ, Soundharajan R, Srinivasan H. Antibacterial, antibiofilm, and antivirulence effects of nanoparticles synthesized from Colletotrichum gloeosporioides in pathogenic E.coli. Microb Pathog 2023; 185:106420. [PMID: 37879451 DOI: 10.1016/j.micpath.2023.106420] [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: 07/13/2023] [Revised: 10/07/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Antimicrobial resistance is a global problem and antibiotics are becoming ineffective due to the resistance developed by bacteria. In this current research, silver nanoparticles were synthesized from aqueous extract of endophytic fungi Colletotrichum gloeosporioides (CgAgNPs) and characterized by various methods. CgAgNPs efficacy was analyzed by performing antimicrobial assays in Escherichia coli ATCC 25922 and antibiotic resistant pathogenic strains. Upon treatment with CgAgNPs biofilm formation was reduced in all E.coli strains. In vitro cytotoxicity assays revealed that CgAgNPs were able to increase the membrane permeability and induced leakage of sugars and proteins. CgAgNPs induced oxidative stress in E. coli strains led to lipid peroxidation and release of malonaldehyde. The CgAgNPs were able to modulate the anti-oxidant system of cells hence there was a reduction in Glutathione reductase, Catalase and Superoxide dismutase enzymes activities. Analysis of expression of gene encoding CTX-M-15 showed the down regulation upon treatment with ampicillin and CgAgNPs. Overall, the results suggest that CgAgNPs control growth, biofilm formation in E. coli through induction of oxidative stress, interference with antioxidant enzymes, cell content leakage and finally downregulating the virulence gene by interfering with transcription and translation in E. coli. In future, CgAgNPs can be incorporated in formulations to break antibiotic resistance in antibiotic resistant pathogenic E. coli.
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Affiliation(s)
- Mohamed Juvad NajeerAhamed
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Vandalur, Chennai, 600048, India
| | - Ranjani Soundharajan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Vandalur, Chennai, 600048, India
| | - Hemalatha Srinivasan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Vandalur, Chennai, 600048, India.
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13
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Jusuf S, Dong PT. Chromophore-Targeting Precision Antimicrobial Phototherapy. Cells 2023; 12:2664. [PMID: 37998399 PMCID: PMC10670386 DOI: 10.3390/cells12222664] [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: 10/03/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023] Open
Abstract
Phototherapy, encompassing the utilization of both natural and artificial light, has emerged as a dependable and non-invasive strategy for addressing a diverse range of illnesses, diseases, and infections. This therapeutic approach, primarily known for its efficacy in treating skin infections, such as herpes and acne lesions, involves the synergistic use of specific light wavelengths and photosensitizers, like methylene blue. Photodynamic therapy, as it is termed, relies on the generation of antimicrobial reactive oxygen species (ROS) through the interaction between light and externally applied photosensitizers. Recent research, however, has highlighted the intrinsic antimicrobial properties of light itself, marking a paradigm shift in focus from exogenous agents to the inherent photosensitivity of molecules found naturally within pathogens. Chemical analyses have identified specific organic molecular structures and systems, including protoporphyrins and conjugated C=C bonds, as pivotal components in molecular photosensitivity. Given the prevalence of these systems in organic life forms, there is an urgent need to investigate the potential impact of phototherapy on individual molecules expressed within pathogens and discern their contributions to the antimicrobial effects of light. This review delves into the recently unveiled key molecular targets of phototherapy, offering insights into their potential downstream implications and therapeutic applications. By shedding light on these fundamental molecular mechanisms, we aim to advance our understanding of phototherapy's broader therapeutic potential and contribute to the development of innovative treatments for a wide array of microbial infections and diseases.
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Affiliation(s)
- Sebastian Jusuf
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Pu-Ting Dong
- Department of Microbiology, The Forsyth Institute, Boston, MA 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
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14
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Li D, Guo W, Zhai Y, Xu X, Cao X, Zhao L. The aggregated biofilm dominated by Delftia tsuruhatensis enhances the removal efficiency of 2,4-dichlorophenol in a bioelectrochemical system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122576. [PMID: 37722473 DOI: 10.1016/j.envpol.2023.122576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/03/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
Bioelectrochemical system is a prospective strategy in organic-contaminated groundwater treatment, while few studies clearly distinguish the mechanisms of adsorption or biodegradation in this process, especially when dense biofilm is formed. This study employed a single chamber microbial electrolysis cell (MEC) with two three-dimensional electrodes for removing a typical organic contaminant, 2,4-dichlorophenol (DCP) from groundwater, which inoculated with anaerobic bacteria derived from sewage treatment plant. Compared with the single biodegradation system without electrodes, the three-dimensional electrodes with a high surface enabled an increase of alpha diversity of the microbial community (increased by 52.6% in Shannon index), and provided adaptive ecological niche for more bacteria. The application of weak voltage (0.6 V) furtherly optimized the microbial community structure, and promoted the aggregation of microorganisms with the formation of dense biofilm. Desorption experiment proved that the contaminants were removed from the groundwater mainly via adsorption by the biofilm rather than biodegradation, and compared with the reactor without electricity, the bioelectrochemical system increased the adsorption capacity from 50.0% to 74.5%. The aggregated bacteria on the surface of electrodes were mainly dominated by Delftia tsuruhatensis (85.0%), which could secrete extracellular polymers and has a high adsorption capacity (0.30 mg/g electrode material) for the contaminants. We found that a bioelectrochemical system with a three-dimensional electrode could stimulate the formation of dense biofilm and remove the organic contaminants as well as their possible more toxic degradation intermediates via adsorption. This study provides important guidance for applying bioelectrochemical system in groundwater or wastewater treatment.
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Affiliation(s)
- Deping Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenbo Guo
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Zhai
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyun Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinde Cao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 201306, China
| | - Ling Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 201306, China.
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15
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Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep 2023; 42:113105. [PMID: 37713311 PMCID: PMC10591938 DOI: 10.1016/j.celrep.2023.113105] [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: 02/09/2023] [Revised: 07/09/2023] [Accepted: 08/23/2023] [Indexed: 09/17/2023] Open
Abstract
Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data analytic method for characterizing the transcriptome can simplify interpretation by grouping genes into independently modulated sets (iModulons). Here, we demonstrate how iModulons reveal deep understanding of the effects of causal mutations and metabolic rewiring. We use adaptive laboratory evolution to generate E. coli strains that tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulons, and metabolic models to elucidate six interacting stress-tolerance mechanisms: (1) modification of transport, (2) activation of ROS stress responses, (3) use of ROS-sensitive iron regulation, (4) motility, (5) broad transcriptional reallocation toward growth, and (6) metabolic rewiring to decrease NADH production. This work thus demonstrates the power of iModulon knowledge mapping for evolution analysis.
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Affiliation(s)
- Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Tan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Elsayed Tharwat Tolba Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Amitesh Anand
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra, India
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joon Ho Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Building 76, Cambridge, MA 02139, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.
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16
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Zarezadeh M, Mahmoudinezhad M, Hosseini B, Khorraminezhad L, Razaghi M, Alvandi E, Saedisomeolia A. Dietary pattern in autism increases the need for probiotic supplementation: A comprehensive narrative and systematic review on oxidative stress hypothesis. Clin Nutr 2023; 42:1330-1358. [PMID: 37418842 DOI: 10.1016/j.clnu.2023.06.014] [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: 02/28/2023] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 07/09/2023]
Abstract
Autism spectrum disorders (ASDs) are associated with specific dietary habits, including limited food selection and gastrointestinal problems, resulting in an altered gut microbiota. Autistic patients have an elevated abundance of certain gut bacteria associated with increased oxidative stress in the gastrointestinal tract. Probiotic supplementation has been shown to decrease oxidative stress in a simulated gut model, but the antioxidant effects of probiotics on the oxidative stress of the gut in autistic patients have not been directly studied. However, it is speculated that probiotic supplementation may help decrease oxidative stress in the gastrointestinal tract of autistic patients due to their specific dietary habits altering the microbiota. PubMed, Scopus and Web of Science databases and Google Scholar were searched up to May 2023. This systematic-narrative review aims to present the latest evidence regarding the changes in eating habits of autistic children which may further increase the gut microbiota induced oxidative stress. Additionally, this review will assess the available literature on the effects of probiotic supplementation on oxidative stress parameters.
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Affiliation(s)
- Meysam Zarezadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Banafshe Hosseini
- Clinical Research and Knowledge Transfer Unit on Childhood Asthma, Research Centre, Sainte-Justine University Health Centre, Montreal, QC H3T 1C5, Canada
| | - Leila Khorraminezhad
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, Québec, Canada
| | - Maryam Razaghi
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ehsan Alvandi
- School of Medicine, Western Sydney University, NSW, Australia
| | - Ahmad Saedisomeolia
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, Québec, Canada.
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17
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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18
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Lee WL, Sinha A, Lam LN, Loo HL, Liang J, Ho P, Cui L, Chan CSC, Begley T, Kline KA, Dedon P. An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis. Nat Commun 2023; 14:4093. [PMID: 37433804 DOI: 10.1038/s41467-023-39790-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N2-methyladenosine (m2A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Ameya Sinha
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Ling Ning Lam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Hooi Linn Loo
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Jiaqi Liang
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Peiying Ho
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Liang Cui
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Cheryl Siew Choo Chan
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- Critical Analytics for Manufacturing Personalized-Medicine IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Thomas Begley
- Department of Biological Sciences and The RNA Institute, University at Albany, Albany, NY, USA
| | - Kimberly Ann Kline
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Dedon
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Syed RU, Moni SS, Break MKB, Khojali WMA, Jafar M, Alshammari MD, Abdelsalam K, Taymour S, Alreshidi KSM, Elhassan Taha MM, Mohan S. Broccoli: A Multi-Faceted Vegetable for Health: An In-Depth Review of Its Nutritional Attributes, Antimicrobial Abilities, and Anti-inflammatory Properties. Antibiotics (Basel) 2023; 12:1157. [PMID: 37508253 PMCID: PMC10376324 DOI: 10.3390/antibiotics12071157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Broccoli, Brassica oleracea var. italica, has recently gained considerable attention due to its remarkable nutritional composition and numerous health benefits. In this review, the nutritional aspects of broccoli are examined, highlighting its rich nutrient content and essential bioactive compounds. The cruciferous vegetable broccoli is a rich source of several important nutrients, including fiber, vitamins (A, C, and K), minerals (calcium, potassium, and iron), and antioxidants. It has also been shown to contain bioactive compounds such as glucosinolates, sulforaphane, and indole-3-carbinol, all of which have been shown to have significant health-promoting effects. These chemicals are known to have potent antioxidant, anti-inflammatory, and anticancer effects. This review article aims to comprehensively examine the diverse spectrum of nutrients contained in broccoli and explore its medicinal potential to promote human health.
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Affiliation(s)
- Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | | | - Mohammed Khaled Bin Break
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Weam M A Khojali
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Al Khartoum 14415, Sudan
| | - Mohammed Jafar
- Department of Pharmaceutics, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 34212, Saudi Arabia
| | - Maali D Alshammari
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Karim Abdelsalam
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Soha Taymour
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | | | | | - Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai 602105, India
- School of Health Sciences, University of Petroleum and Energy Studies, Dehradun 248007, India
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20
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Gao WL, Fang JL, Zhu CY, Xu WF, Lyu ZY, Chan XA, Zhao QW, Li YQ. Identification and Characterization of a New Regulator, TagR, for Environmental Stress Resistance Based on the DNA Methylome of Streptomyces roseosporus. Microbiol Spectr 2023; 11:e0038023. [PMID: 37154757 PMCID: PMC10269677 DOI: 10.1128/spectrum.00380-23] [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: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
DNA methylation is a defense that microorganisms use against extreme environmental stress, and improving resistance against environmental stress is essential for industrial actinomycetes. However, research on strain optimization utilizing DNA methylation for breakthroughs is rare. Based on DNA methylome analysis and KEGG pathway assignment in Streptomyces roseosporus, we discovered an environmental stress resistance regulator, TagR. A series of in vivo and in vitro experiments identified TagR as a negative regulator, and it is the first reported regulator of the wall teichoic acid (WTA) ABC transport system. Further study showed that TagR had a positive self-regulatory loop and m4C methylation in the promoter improved its expression. The ΔtagR mutant exhibited better hyperosmotic resistance and higher decanoic acid tolerance than the wild type, which led to a 100% increase in the yield of daptomycin. Moreover, enhancing the expression of the WTA transporter resulted in better osmotic stress resistance in Streptomyces lividans TK24, indicating the potential for wide application of the TagR-WTA transporter regulatory pathway. This research confirmed the feasibility and effectiveness of mining regulators of environmental stress resistance based on the DNA methylome, characterized the mechanism of TagR, and improved the resistance and daptomycin yield of strains. Furthermore, this research provides a new perspective on the optimization of industrial actinomycetes. IMPORTANCE This study established a novel strategy for screening regulators of environmental stress resistance based on the DNA methylome and discovered a new regulator, TagR. The TagR-WTA transporter regulatory pathway improved the resistance and antibiotic yield of strains and has the potential for wide application. Our research provides a new perspective on the optimization and reconstruction of industrial actinomycetes.
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Affiliation(s)
- Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Jiao-Le Fang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Wei-Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Xin-Ai Chan
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
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21
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Abstract
Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.
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Affiliation(s)
- Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Phillip Sweet
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
| | - Aparna Anantharaman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
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22
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Smirnova G, Tyulenev A, Muzyka N, Ushakov V, Samoilova Z, Oktyabrsky O. Influence of Growth Medium Composition on Physiological Responses of Escherichia coli to the Action of Chloramphenicol and Ciprofloxacin. BIOTECH 2023; 12:43. [PMID: 37366791 DOI: 10.3390/biotech12020043] [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: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
The ability of hydrogen sulfide (H2S) to protect bacteria from bactericidal antibiotics has previously been described. The main source of H2S is the desulfurization of cysteine, which is either synthesized by cells from sulfate or transported from the medium, depending on its composition. Applying electrochemical sensors and a complex of biochemical and microbiological methods, changes in growth, respiration, membrane potential, SOS response, H2S production and bacterial survival under the action of bactericidal ciprofloxacin and bacteriostatic chloramphenicol in commonly used media were studied. Chloramphenicol caused a sharp inhibition of metabolism in all studied media. The physiological response of bacteria to ciprofloxacin strongly depended on its dose. In rich LB medium, cells retained metabolic activity at higher concentrations of ciprofloxacin than in minimal M9 medium. This decreased number of surviving cells (CFU) by 2-3 orders of magnitude in LB compared to M9 medium, and shifted optimal bactericidal concentration (OBC) from 0.3 µg/mL in M9 to 3 µg/mL in LB. Both drugs induced transient production of H2S in M9 medium. In media containing cystine, H2S was produced independently of antibiotics. Thus, medium composition significantly modifies physiological response of E. coli to bactericidal antibiotic, which should be taken into account when interpreting data and developing drugs.
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Affiliation(s)
- Galina Smirnova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
| | - Aleksey Tyulenev
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
| | - Nadezda Muzyka
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
| | - Vadim Ushakov
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
| | - Zoya Samoilova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
| | - Oleg Oktyabrsky
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Goleva 13, 614081 Perm, Russia
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23
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [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: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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24
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Teoh CP, Lavin P, Yusof NA, González-Aravena M, Najimudin N, Cheah YK, Wong CMVL. Transcriptomics analysis provides insights into the heat adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2023. [DOI: 10.1007/s00300-023-03115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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25
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Li Y, Ma Q, Zhang J, Meng N, Su J, Wang J. Transcriptomic profiling reveals the molecular responses of Rhodococcus aetherivorans DMU1 to skatole stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114464. [PMID: 38321683 DOI: 10.1016/j.ecoenv.2022.114464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2024]
Abstract
Skatole is a typical malodor compound in animal wastes. Several skatole-degrading bacterial strains have been obtained, whereas the molecular response of strains to skatole stress has not been well elucidated. Herein, the skatole degradation by a Gram-positive strain Rhodococcus aetherivorans DMU1 was investigated. Strain DMU1 showed high efficiency in skatole degradation under the conditions of 25-40 °C and pH 7.0-10.0. It could utilize various aromatics, including cresols, phenol, and methylindoles, as the sole carbon source for growth, implying its potential in the bioremediation application of animal wastes. Transcriptomic sequencing revealed that 328 genes were up-regulated and 640 genes were down-regulated in strain DMU1 when grown in the skatole-containing medium. Skatole increased the gene expression levels of antioxidant defense systems and heat shock proteins. The expression of ribosome-related genes was significantly inhibited which implied the growth inhibition of skatole. A rich set of oxidoreductases were changed, and a novel gene cluster containing the flavoprotein monooxygenase and ring-hydroxylating oxygenase genes was highly up-regulated, which was probably involved in skatole upstream degradation. The upregulation pattern of this gene cluster was further verified by qRT-PCR assay. Furthermore, skatole should be mainly degraded via the catechol ortho-cleavage pathway with cat25170 as the functional gene. The gene cat25170 was cloned and expressed in E. coli BL21(DE3). Pure enzyme assays showed that Cat25170 could catalyze catechol with Km 9.96 μmol/L and kcat 12.36 s-1.
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Affiliation(s)
- Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Jiaxin Zhang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; College of Life Sciences, Sichuan University, Sichuan 610064, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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26
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HslO ameliorates arrested ΔrecA polA cell growth and reduces DNA damage and oxidative stress responses. Sci Rep 2022; 12:22182. [PMID: 36564489 PMCID: PMC9789031 DOI: 10.1038/s41598-022-26703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity has been widely considered to render cells inviable, owing to deficient double-strand break repair. However, temperature-sensitive recAts polA cells grow well upon induction of DNA damage and supplementation with catalase at restrictive temperatures. These treatments reduce intracellular reactive oxygen species (ROS) levels, which suggests that recAts polA cells are susceptible to ROS, but not chronic chromosome damage. Therefore, we investigated whether polA cells can tolerate a complete lack of recombinase function. We introduced a ΔrecA allele in polA cells in the presence or absence of the hslO-encoding redox molecular chaperon Hsp33 expression plasmid. Induction of the hslO gene with IPTG resulted in increased cell viability in ΔrecA polA cells with the hslO expression plasmid. ΔrecA polA cells in the absence of the hslO expression plasmid showed rich medium sensitivity with increasing ROS levels. Adding catalase to the culture medium considerably rescued growth arrest and decreased ROS. These results suggest that hslO expression manages oxidative stress to an acceptable level in cells with oxidative damage and rescues cell growth. Overall, ROS may regulate several processes, from damage response to cell division, via ROS-sensitive cell metabolism.
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27
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Lagage V, Chen V, Uphoff S. Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress. EMBO Rep 2022; 24:e55640. [PMID: 36397732 PMCID: PMC9827559 DOI: 10.15252/embr.202255640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding the interplay between phenotypic and genetic adaptation is a focus of evolutionary biology. In bacteria, the oxidative stress response prevents mutagenesis by reactive oxygen species (ROS). We hypothesise that the stress response dynamics can therefore affect the timing of the mutation supply that fuels genetic adaptation to oxidative stress. We uncover that sudden hydrogen peroxide stress causes a burst of mutations. By developing single-molecule and single-cell microscopy methods, we determine how these mutation dynamics arise from phenotypic adaptation mechanisms. H2 O2 signalling by the transcription factor OxyR rapidly induces ROS-scavenging enzymes. However, an adaptation delay leaves cells vulnerable to the mutagenic and toxic effects of hydroxyl radicals generated by the Fenton reaction. Resulting DNA damage is counteracted by a spike in DNA repair activities during the adaptation delay. Absence of a mutation burst in cells with prior stress exposure or constitutive OxyR activation shows that the timing of phenotypic adaptation directly controls stress-induced mutagenesis. Similar observations for alkylation stress show that mutation bursts are a general phenomenon associated with adaptation delays.
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Affiliation(s)
| | - Victor Chen
- Department of BiochemistryUniversity of OxfordOxfordUK
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28
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Aribisala JO, Sabiu S. Redox Impact on Bacterial Macromolecule: A Promising Avenue for Discovery and Development of Novel Antibacterials. Biomolecules 2022; 12:1545. [PMID: 36358894 PMCID: PMC9688007 DOI: 10.3390/biom12111545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance in bacteria has remained a serious public health concern, resulting in substantial deaths and morbidity each year. Factors such as mutation and abuse of currently available antibiotics have contributed to the bulk of the menace. Hence, the introduction and implementation of new therapeutic strategies are imperative. Of these strategies, data supporting the role of reactive oxygen species (ROS) in bacterial lethality are intriguing, with several antimicrobials, including antibiotics such as fluoroquinolones, β-lactams, and aminoglycosides, as well as natural plant compounds, being remarkably implicated. Following treatment with ROS-inducing antimicrobials, ROS such as O2•-, •OH, and H2O2 generated in bacteria, which the organism is unable to detoxify, damage cellular macromolecules such as proteins, lipids, and nucleic acids and results in cell death. Despite the unique mechanism of action of ROS-inducing antibacterials and significant studies on ROS-mediated means of bacterial killing, the field remains a topical one, with contradicting viewpoints that require frequent review. Here, we appraised the antibacterial agents (antibiotics, natural and synthetic compounds) implicated in ROS generation and the safety concerns associated with their usage. Further, background information on the sources and types of ROS in bacteria, the mechanism of bacterial lethality via oxidative stress, as well as viewpoints on the ROS hypothesis undermining and solidifying this concept are discussed.
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29
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Loiseau L, Vergnes A, Ezraty B. Methionine oxidation under anaerobic conditions in Escherichia coli. Mol Microbiol 2022; 118:387-402. [PMID: 36271735 DOI: 10.1111/mmi.14971] [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: 05/08/2022] [Revised: 07/18/2022] [Accepted: 08/04/2022] [Indexed: 01/07/2023]
Abstract
Repairing oxidative-targeted macromolecules is a central mechanism necessary for living organisms to adapt to oxidative stress. Reactive oxygen and chlorine species preferentially oxidize sulfur-containing amino acids in proteins. Among these amino acids, methionine can be converted into methionine sulfoxide. This post-translational oxidation can be reversed by methionine sulfoxide reductases, Msr enzymes. In Gram-negative bacteria, the antioxidant MsrPQ system is involved in the repair of periplasmic oxidized proteins. Surprisingly, in this study, we observed in Escherichia coli that msrPQ was highly expressed in the absence of oxygen. We have demonstrated that the anaerobic induction of msrPQ was due to chlorate (ClO3 - ) contamination of the Casamino Acids. Molecular investigation led us to determine that the reduction of chlorate to the toxic oxidizing agent chlorite (ClO2 - ) by the three nitrate reductases (NarA, NarZ, and Nap) led to methionine oxidation of periplasmic proteins. In response to this stress, the E. coli HprSR two-component system was activated, leading to the over-production of MsrPQ. This study, therefore, supports the idea that methionine oxidation in proteins is part of chlorate toxicity, and that MsrPQ can be considered as an anti-chlorate/chlorite defense system in bacteria. Finally, this study challenges the traditional view of the absence of Met-oxidation during anaerobiosis.
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Affiliation(s)
- Laurent Loiseau
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
| | - Alexandra Vergnes
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
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30
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Singh A, Zhao X, Drlica K. Fluoroquinolone heteroresistance, antimicrobial tolerance, and lethality enhancement. Front Cell Infect Microbiol 2022; 12:938032. [PMID: 36250047 PMCID: PMC9559723 DOI: 10.3389/fcimb.2022.938032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
With tuberculosis, the emergence of fluoroquinolone resistance erodes the ability of treatment to interrupt the progression of MDR-TB to XDR-TB. One way to reduce the emergence of resistance is to identify heteroresistant infections in which subpopulations of resistant mutants are likely to expand and make the infections fully resistant: treatment modification can be instituted to suppress mutant enrichment. Rapid DNA-based detection methods exploit the finding that fluoroquinolone-resistant substitutions occur largely in a few codons of DNA gyrase. A second approach for restricting the emergence of resistance involves understanding fluoroquinolone lethality through studies of antimicrobial tolerance, a condition in which bacteria fail to be killed even though their growth is blocked by lethal agents. Studies with Escherichia coli guide work with Mycobacterium tuberculosis. Lethal action, which is mechanistically distinct from blocking growth, is associated with a surge in respiration and reactive oxygen species (ROS). Mutations in carbohydrate metabolism that attenuate ROS accumulation create pan-tolerance to antimicrobials, disinfectants, and environmental stressors. These observations indicate the existence of a general death pathway with respect to stressors. M. tuberculosis displays a variation on the death pathway idea, as stress-induced ROS is generated by NADH-mediated reductive stress rather than by respiration. A third approach, which emerges from lethality studies, uses a small molecule, N-acetyl cysteine, to artificially increase respiration and additional ROS accumulation. That enhances moxifloxacin lethality with M. tuberculosis in culture, during infection of cultured macrophages, and with infection of mice. Addition of ROS stimulators to fluoroquinolone treatment of tuberculosis constitutes a new direction for suppressing the transition of MDR-TB to XDR-TB.
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Affiliation(s)
- Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- *Correspondence: Amit Singh, ; Karl Drlica,
| | - Xilin Zhao
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- *Correspondence: Amit Singh, ; Karl Drlica,
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31
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Wong F, Stokes JM, Bening SC, Vidoudez C, Trauger SA, Collins JJ. Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions. Mol Cell 2022; 82:3499-3512.e10. [PMID: 35973427 PMCID: PMC10149100 DOI: 10.1016/j.molcel.2022.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/19/2022] [Accepted: 07/17/2022] [Indexed: 01/21/2023]
Abstract
Understanding how bactericidal antibiotics kill bacteria remains an open question. Previous work has proposed that primary drug-target corruption leads to increased energetic demands, resulting in the generation of reactive metabolic byproducts (RMBs), particularly reactive oxygen species, that contribute to antibiotic-induced cell death. Studies have challenged this hypothesis by pointing to antibiotic lethality under anaerobic conditions. Here, we show that treatment of Escherichia coli with bactericidal antibiotics under anaerobic conditions leads to changes in the intracellular concentrations of central carbon metabolites, as well as the production of RMBs, particularly reactive electrophilic species (RES). We show that antibiotic treatment results in DNA double-strand breaks and membrane damage and demonstrate that antibiotic lethality under anaerobic conditions can be decreased by RMB scavengers, which reduce RES accumulation and mitigate associated macromolecular damage. This work indicates that RMBs, generated in response to antibiotic-induced energetic demands, contribute in part to antibiotic lethality under anaerobic conditions.
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Affiliation(s)
- Felix Wong
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan M Stokes
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah C Bening
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charles Vidoudez
- Harvard Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Harvard Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - James J Collins
- Institute for Medical Engineering & Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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32
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Chen L, Wu Y, Zhao Q, Tang C, Pang X, Gu S, Li X. Omics analyses indicate sdhC/D act as hubs of early response of E. coli to antibiotics. Arch Microbiol 2022; 204:544. [DOI: 10.1007/s00203-022-03156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
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33
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Dandapani H, Kankaanpää P, Jones PR, Kallio P. A Plasmid-Based Fluorescence Reporter System for Monitoring Oxidative Damage in E. coli. SENSORS (BASEL, SWITZERLAND) 2022; 22:6334. [PMID: 36080791 PMCID: PMC9459809 DOI: 10.3390/s22176334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Quantitating intracellular oxidative damage caused by reactive oxygen species (ROS) is of interest in many fields of biological research. The current systems primarily rely on supplemented oxygen-sensitive substrates that penetrate the target cells, and react with ROS to produce signals that can be monitored with spectroscopic or imaging techniques. The objective here was to design a new non-invasive analytical strategy for measuring ROS-induced damage inside living cells by taking advantage of the native redox sensor system of E. coli. The developed plasmid-based sensor relies on an oxygen-sensitive transcriptional repressor IscR that controls the expression of a fluorescent marker in vivo. The system was shown to quantitatively respond to oxidative stress induced by supplemented H2O2 and lowered cultivation temperatures. Comparative analysis with fluorescence microscopy further demonstrated that the specificity of the reporter system was equivalent to the commercial chemical probe (CellROX). The strategy introduced here is not dependent on chemical probes, but instead uses a fluorescent expression system to detect enzyme-level oxidative damage in microbial cells. This provides a cheap and simple means for analysing enzyme-level oxidative damage in a biological context in E. coli.
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Affiliation(s)
- Hariharan Dandapani
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
| | - Pasi Kankaanpää
- Turku BioImaging and Turku Bioscience Centre, University of Turku, FI-20014 Turku, Finland
- Turku BioImaging and Turku Bioscience Centre, Åbo Akademi University, FI-20500 Turku, Finland
| | - Patrik R. Jones
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2BX, UK
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
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34
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Antimicrobial tolerance and its role in the development of resistance: Lessons from enterococci. Adv Microb Physiol 2022; 81:25-65. [PMID: 36167442 DOI: 10.1016/bs.ampbs.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria have developed resistance against every antimicrobial in clinical use at an alarming rate. There is a critical need for more effective use of antimicrobials to both extend their shelf life and prevent resistance from arising. Significantly, antimicrobial tolerance, i.e., the ability to survive but not proliferate during antimicrobial exposure, has been shown to precede the development of bona fide antimicrobial resistance (AMR), sparking a renewed and rapidly increasing interest in this field. As a consequence, problematic infections for the first time are now being investigated for antimicrobial tolerance, with increasing reports demonstrating in-host evolution of antimicrobial tolerance. Tolerance has been identified in a wide array of bacterial species to all bactericidal antimicrobials. Of particular interest are enterococci, which contain the opportunistic bacterial pathogens Enterococcus faecalis and Enterococcus faecium. Enterococci are one of the leading causes of hospital-acquired infection and possess intrinsic tolerance to a number of antimicrobial classes. Persistence of these infections in the clinic is of growing concern, particularly for the immunocompromised. Here, we review current known mechanisms of antimicrobial tolerance, and include an in-depth analysis of those identified in enterococci with implications for both the development and prevention of AMR.
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35
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Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Reactive oxygen species accumulation is synchronised with growth inhibition of temperature-sensitive recAts polA Escherichia coli. Arch Microbiol 2022; 204:396. [PMID: 35705748 PMCID: PMC9200703 DOI: 10.1007/s00203-022-02957-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: 02/15/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
When combined with recombinase defects, chromosome breakage and double-strand break repair deficiencies render cells inviable. However, cells are viable when an SOS response occurs in recAts polA cells in Escherichia coli. Here, we aimed to elucidate the underlying mechanisms of this process. Transposon mutagenesis revealed that the hslO gene, a redox chaperone Hsp33 involved in reactive oxidative species (ROS) metabolism, was required for the suppression of recAts polA lethality at a restricted temperature. Recently, it has been reported that lethal treatments trigger ROS accumulation. We also found that recAts polA cells accumulated ROS at the restricted temperature. A catalase addition to the medium alleviates the temperature sensitivity of recAts polA cells and decreases ROS accumulation. These results suggest that the SOS response and hslO manage oxidative insult to an acceptable level in cells with oxidative damage and rescue cell growth. Overall, ROS might regulate several cellular processes.
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Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biology, Tokai University, Sapporo, 005-8601, Japan.
| | - Noriko Ishii
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
| | - Sinngo Suzuki
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
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Zeng J, Hong Y, Zhao N, Liu Q, Zhu W, Xiao L, Wang W, Chen M, Hong S, Wu L, Xue Y, Wang D, Niu J, Drlica K, Zhao X. A broadly applicable, stress-mediated bacterial death pathway regulated by the phosphotransferase system (PTS) and the cAMP-Crp cascade. Proc Natl Acad Sci U S A 2022; 119:e2118566119. [PMID: 35648826 PMCID: PMC9191683 DOI: 10.1073/pnas.2118566119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 04/22/2022] [Indexed: 12/30/2022] Open
Abstract
Recent work indicates that killing of bacteria by diverse antimicrobial classes can involve reactive oxygen species (ROS), as if a common, self-destructive response to antibiotics occurs. However, the ROS-bacterial death theory has been challenged. To better understand stress-mediated bacterial death, we enriched spontaneous antideath mutants of Escherichia coli that survive treatment by diverse bactericidal agents that include antibiotics, disinfectants, and environmental stressors, without a priori consideration of ROS. The mutants retained bacteriostatic susceptibility, thereby ruling out resistance. Surprisingly, pan-tolerance arose from carbohydrate metabolism deficiencies in ptsI (phosphotransferase) and cyaA (adenyl cyclase); these genes displayed the activity of upstream regulators of a widely shared, stress-mediated death pathway. The antideath effect was reversed by genetic complementation, exogenous cAMP, or a Crp variant that bypasses cAMP binding for activation. Downstream events comprised a metabolic shift from the TCA cycle to glycolysis and to the pentose phosphate pathway, suppression of stress-mediated ATP surges, and reduced accumulation of ROS. These observations reveal how upstream signals from diverse stress-mediated lesions stimulate shared, late-stage, ROS-mediated events. Cultures of these stable, pan-tolerant mutants grew normally and were therefore distinct from tolerance derived from growth defects described previously. Pan-tolerance raises the potential for unrestricted disinfectant use to contribute to antibiotic tolerance and resistance. It also weakens host defenses, because three agents (hypochlorite, hydrogen peroxide, and low pH) affected by pan-tolerance are used by the immune system to fight infections. Understanding and manipulating the PtsI-CyaA-Crp–mediated death process can help better control pathogens and maintain beneficial microbiota during antimicrobial treatment.
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Affiliation(s)
- Jie Zeng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yuzhi Hong
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
- Institute of Molecular Enzymology and School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Ningqiu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Qianyu Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen 361004, China
| | - Weiwei Zhu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Lisheng Xiao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Weijie Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Miaomiao Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shouqiang Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Liwen Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yunxin Xue
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Dai Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jianjun Niu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen 361004, China
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
| | - Xilin Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103
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Polmickaitė-Smirnova E, Buchovec I, Bagdonas S, Sužiedėlienė E, Ramanavičius A, Anusevičius Ž. Photoinactivation of Salmonella enterica exposed to 5-aminolevulinic acid: Impact of sensitization conditions and irradiation time. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 231:112446. [PMID: 35487120 DOI: 10.1016/j.jphotobiol.2022.112446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
The photodynamic inactivation (PDI) represents the potential alternative to traditional antibiotic therapy, and can be applied to treat various bacterial infections, including those caused by Gram-negative bacterial strains. One of the treatment modalities is based on the capacity of bacterial cells to synthesize the excess amounts of porphyrins after exposure to an externally applied 5-aminolevulinic acid (5-ALA), which makes them photosensitive and leads to reduced survival after irradiation with an appropriately selected light source. This study focuses on the sensitization and the photoinduced inactivation of Salmonella enterica cells in PBS containing 0.5 mM 5-ALA, incubated at 37 °C for 4 h or for 20 h and afterwards irradiated with violet LED light (11.1 mW/cm2, a peak at 400 nm). It has been found that both amounts and composition of endogenous porphyrins not only depended on the incubation duration, but also were affected by externally induced photo- and chemo-oxidation reactions. The application of different sensitization conditions has revealed that the increasing amounts of endogenously produced porphyrins do not ensure the proportional reduction of bacterial cell survival numbers. The comparative investigations also demonstrated that the presence of endogenously produced porphyrins in the medium results in secondary sensitization of bacterial cells and causes a notably stronger photoinactivation effect in comparison to their externally applied standards.
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Affiliation(s)
- Evelina Polmickaitė-Smirnova
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Irina Buchovec
- Institute of Photonics and Nanotechnology, Faculty of Physics, Vilnius University, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania
| | - Saulius Bagdonas
- Laser Research Center, Faculty of Physics, Vilnius University, Saulėtekio av. 9, LT-10222 Vilnius, Lithuania
| | - Edita Sužiedėlienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Arūnas Ramanavičius
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| | - Žilvinas Anusevičius
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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de Souza AS, Ribeiro RCB, Costa DCS, Pauli FP, Pinho DR, de Moraes MG, da Silva FDC, Forezi LDSM, Ferreira VF. Menadione: a platform and a target to valuable compounds synthesis. Beilstein J Org Chem 2022; 18:381-419. [PMID: 35529893 PMCID: PMC9039524 DOI: 10.3762/bjoc.18.43] [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: 02/04/2022] [Accepted: 03/30/2022] [Indexed: 01/26/2023] Open
Abstract
Naphthoquinones are important natural or synthetic compounds belonging to the general class of quinones. Many compounds in this class have become drugs that are on the pharmaceutical market for the treatment of various diseases. A special naphthoquinone derivative is menadione, a synthetic naphthoquinone belonging to the vitamin K group. This compound can be synthesized by different methods and it has a broad range of biological and synthetic applications, which will be highlighted in this review.
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Affiliation(s)
- Acácio S de Souza
- Universidade Federal Fluminense, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, R. Dr. Mario Vianna, 523, Santa Rosa, CEP 24241-002, Niterói-RJ, Brazil
| | - Ruan Carlos B Ribeiro
- Universidade Federal Fluminense, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, R. Dr. Mario Vianna, 523, Santa Rosa, CEP 24241-002, Niterói-RJ, Brazil
| | - Dora C S Costa
- Department of Chemistry, CICECO – Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Fernanda P Pauli
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150 Niterói, RJ, Brazil
| | - David R Pinho
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150 Niterói, RJ, Brazil
| | - Matheus G de Moraes
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150 Niterói, RJ, Brazil
| | - Fernando de C da Silva
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150 Niterói, RJ, Brazil
| | - Luana da S M Forezi
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150 Niterói, RJ, Brazil
| | - Vitor F Ferreira
- Universidade Federal Fluminense, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, R. Dr. Mario Vianna, 523, Santa Rosa, CEP 24241-002, Niterói-RJ, Brazil
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Dey N, Kamatchi C, Vickram AS, Anbarasu K, Thanigaivel S, Palanivelu J, Pugazhendhi A, Ponnusamy VK. Role of nanomaterials in deactivating multiple drug resistance efflux pumps - A review. ENVIRONMENTAL RESEARCH 2022; 204:111968. [PMID: 34453898 DOI: 10.1016/j.envres.2021.111968] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The changes in lifestyle and living conditions have affected not only humans but also microorganisms. As man invents new drugs and therapies, pathogens alter themselves to survive and thrive. Multiple drug resistance (MDR) is the talk of the town for decades now. Many generations of medications have been termed useless as MDR rises among the infectious population. The surge in nanotechnology has brought a new hope in reducing this aspect of resistance in pathogens. It has been observed in several laboratory-based studies that the use of nanoparticles had a synergistic effect on the antibiotic being administered to the pathogen; several resistant strains scummed to the stress created by the nanoparticles and became susceptible to the drug. The major cause of resistance to date is the efflux system, which makes the latest generation of antibiotics ineffective without reaching the target site. If species-specific nanomaterials are used to control the activity of efflux pumps, it could revolutionize the field of medicine and make the previous generation resistant medications active once again. Therefore, the current study was devised to assess and review nanoparticles' role on efflux systems and discuss how specialized particles can be designed towards an infectious host's particular drug ejection systems.
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Affiliation(s)
- Nibedita Dey
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - C Kamatchi
- Department of Biotechnology, The Oxford College of Science, Bengaluru, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - S Thanigaivel
- Department of Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Jeyanthi Palanivelu
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, India
| | | | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry & Research Center for Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City, 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, 807, Taiwan; Program of Aquatic Science and Technology, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City, Taiwan.
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DsrA Modulates Central Carbon Metabolism and Redox Balance by Directly Repressing pflB Expression in Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0152221. [PMID: 35107349 PMCID: PMC8809350 DOI: 10.1128/spectrum.01522-21] [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: 11/23/2022] Open
Abstract
Bacterial small RNAs (sRNAs) function as vital regulators in response to various environmental stresses by base pairing with target mRNAs. The sRNA DsrA, an important posttranscriptional regulator, has been reported to play a crucial role in defense against oxidative stress in Salmonella enterica serovar Typhimurium, but its regulatory mechanism remains unclear. The transcriptome sequencing (RNA-seq) results in this study showed that the genes involved in glycolysis, pyruvate metabolism, the tricarboxylic acid (TCA) cycle, and NADH-dependent respiration exhibited significantly different expression patterns between S. Typhimurium wild type (WT) and the dsrA deletion mutant (ΔdsrA strain) before and after H2O2 treatment. This indicated the importance of DsrA in regulating central carbon metabolism (CCM) and NAD(H) homeostasis of S. Typhimurium. To reveal the direct target of DsrA action, fusion proteins of six candidate genes (acnA, srlE, tdcB, nuoH, katG, and pflB) with green fluorescent protein (GFP) were constructed, and the fluorescence analysis showed that the expression of pflB encoding pyruvate-formate lyase was repressed by DsrA. Furthermore, site-directed mutagenesis and RNase E-dependent experiments showed that the direct base pairing of DsrA with pflB mRNA could recruit RNase E to degrade pflB mRNA and reduce the stability of pflB mRNA. In addition, the NAD+/NADH ratio in WT-ppflB-pdsrA was significantly lower than that in WT-ppflB, suggesting that the repression of pflB by DsrA could contribute greatly to the redox balance in S. Typhimurium. Taken together, a novel target of DsrA was identified, and its regulatory role was clarified, which demonstrated that DsrA could modulate CCM and redox balance by directly repressing pflB expression in S. Typhimurium. IMPORTANCE Small RNA DsrA plays an important role in defending against oxidative stress in bacteria. In this study, we identified a novel target (pflB, encoding pyruvate-formate lyase) of DsrA and demonstrated its potential regulatory mechanism in S. Typhimurium by transcriptome analysis. In silico prediction revealed a direct base pairing between DsrA and pflB mRNA, which was confirmed in site-directed mutagenesis experiments. The interaction of DsrA-pflB mRNA could greatly contribute to the regulation of central carbon metabolism and intracellular redox balance in S. Typhimurium. These findings provided a better understanding of the critical roles of small RNA in central metabolism and stress responses in foodborne pathogens.
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Smirnova GV, Tyulenev AV, Muzyka NG, Oktyabrsky ON. Study of the contribution of active defense mechanisms to ciprofloxacin tolerance in Escherichia coli growing at different rates. Antonie Van Leeuwenhoek 2022; 115:233-251. [PMID: 35022927 DOI: 10.1007/s10482-021-01693-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022]
Abstract
Using rpoS, tolC, ompF, and recA knockouts, we investigated their effect on the physiological response and lethality of ciprofloxacin in E. coli growing at different rates on glucose, succinate or acetate. We have shown that, regardless of the strain, the degree of changes in respiration, membrane potential, NAD+/NADH ratio, ATP and glutathione (GSH) strongly depends on the initial growth rate and the degree of its inhibition. The deletion of the regulator of the general stress response RpoS, although it influenced the expression of antioxidant genes, did not significantly affect the tolerance to ciprofloxacin at all growth rates. The mutant lacking TolC, which is a component of many E. coli efflux pumps, showed the same sensitivity to ciprofloxacin as the parent. The absence of porin OmpF slowed down the entry of ciprofloxacin into cells, prolonged growth and shifted the optimal bactericidal concentration towards higher values. Deficiency of RecA, a regulator of the SOS response, dramatically altered the late phase of the SOS response (SOS-dependent cell death), preventing respiratory inhibition and a drop in membrane potential. The recA mutation inverted GSH fluxes across the membrane and abolished ciprofloxacin-induced H2S production. All studied mutants showed an inverse linear relationship between logCFU ml-1 and the specific growth rate. Mutations shifted the plot of this dependence relative to the parental strain according to their significance for ciprofloxacin tolerance. The crucial role of the SOS system is confirmed by dramatic shift down of this plot in the recA mutant.
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Affiliation(s)
- Galina V Smirnova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, Russia, 614081.
| | - Aleksey V Tyulenev
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, Russia, 614081
| | - Nadezda G Muzyka
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, Russia, 614081
| | - Oleg N Oktyabrsky
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, Russia, 614081
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Sharma P, Goyal D, Chudasama B. Ecotoxicity of as-synthesised copper nanoparticles on soil bacteria. IET Nanobiotechnol 2021; 15:236-245. [PMID: 34694697 PMCID: PMC8675774 DOI: 10.1049/nbt2.12039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022] Open
Abstract
Release of metallic nanoparticles in soil poses a serious threat to the ecosystem as they can affect the soil properties and impose toxicity on soil microbes that are involved in the biogeochemical cycling. In this work, in vitro ecotoxicity of as‐synthesised copper nanoparticles (CuNPs) on Bacillus subtilis (MTCC No. 441) and Pseudomonas fluorescens (MTCC No. 1749), which are commonly present in soil was investigated. Three sets of colloidal CuNPs with identical physical properties were synthesised by chemical reduction method with per batch yield of 0.2, 0.3 and 0.4 gm. Toxicity of CuNPs against these soil bacteria was investigated by MIC (minimum inhibitory concentration), MBC (minimum bactericidal concentration), cytoplasmic leakage and ROS (reactive oxygen species) assay. MIC of CuNPs were in the range of 35–60 µg/ml and 35–55 µg/ml for B. subtilis and P. fluorescens respectively, while their MBC ranged from 40–70 µg/ml and 40–60 µg/ml respectively. MIC and MBC tests reveal that Gram‐negative P. fluorescens was more sensitive to CuNPs as compared to Gram positive B. subtilis mainly due to the differences in their cell wall structure and composition. CuNPs with smaller hydrodynamic size (11.34 nm) were highly toxic as revealed by MIC, MBC tests, cytoplasmic leakage and ROS assays, which may be due to the higher active surface area of CuNPs and greater membrane penetration. Leakage of cytoplasmic components and generation of extra‐cellular oxidative stress by reactive oxygen species (ROS) causes cell death. The present study realizes in gauging the negative impact of inadvertent release of nanoparticles in the environment, however, in situ experiments to know its overall impact on soil health and soil microflora can help in finding solution to combat ecotoxicity of nanoparticles.
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Affiliation(s)
- Purnima Sharma
- Department Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India.,School of Physics and Materials Science, Thapar Institute of Engineering and Technology, Patiala, India
| | - Dinesh Goyal
- Department Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Bhupendra Chudasama
- School of Physics and Materials Science, Thapar Institute of Engineering and Technology, Patiala, India.,Thapar-VT Center of Excellence in Emerging Materials (CEEMS), Thapar Institute of Engineering and Technology, Patiala, India
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43
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Oxidative damage blocks thymineless death and trimethoprim poisoning in Escherichia coli. J Bacteriol 2021; 204:e0037021. [PMID: 34633866 DOI: 10.1128/jb.00370-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells that cannot synthesize one of the DNA precursors, dTTP, due to thyA mutation or metabolic poisoning, undergo thymineless death (TLD), - a chromosome-based phenomenon of unclear mechanisms. In E. coli, thymineless death is caused either by denying thyA mutants thymidine supplementation or by treating wild type cells with trimethoprim. Two recent reports promised a potential breakthrough in TLD understanding, suggesting significant oxidative damage during thymine starvation. Oxidative damage in vivo comes from Fenton's reaction, when hydrogen peroxide meets ferrous iron to produce hydroxyl radical. Therefore, TLD could kill via irreparable double-strand breaks behind replication forks, when starvation-caused single-strand DNA gaps are attacked by hydroxyl radicals. We tested the proposed Fenton-TLD connection, in both thyA mutants denied thymidine, as well as in trimethoprim-treated WT cells, under three conditions: 1) intracellular iron chelation; 2) mutational inactivation of hydrogen peroxide (HP) scavenging; 3) acute treatment with sublethal HP concentrations. We found that TLD kinetics are affected by neither iron chelation, nor HP stabilization in cultures, indicating no induction of oxidative damage during thymine starvation. Moreover, acute exogenous HP treatments completely block TLD, apparently by blocking cell division - which may be a novel TLD prerequisite. Separately, the acute trimethoprim sensitivity of the rffC and recBCD mutants demonstrates how bactericidal power of this antibiotic could be amplified by inhibiting the corresponding enzymes. Importance Mysterious thymineless death strikes cells that are starved for thymine and therefore replicating their chromosomal DNA without dTTP. After 67 years of experiments testing various obvious and not so obvious explanations, thymineless death is still without a mechanism. Recently, oxidative damage via in vivo Fenton's reaction was proposed as a critical contributor to the irreparable chromosome damage during thymine starvation. We have tested this idea by either blocking in vivo Fenton's reaction (expecting no thymineless death) or by amplifying oxidative damage (expecting hyper thymineless death). Instead, we found that blocking Fenton's reaction has no influence on thymineless death, while amplifying oxidative damage prevents thymineless death altogether. Thus, oxidative damage does not contribute to thymineless death, while the latter remains enigmatic.
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Zhao S, Chen X, Sun Q, Wang F, Hu C, Guo L, Bai J, Yu H. Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1. Front Microbiol 2021; 12:694874. [PMID: 34447357 PMCID: PMC8383072 DOI: 10.3389/fmicb.2021.694874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.
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Affiliation(s)
- Shuxue Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xi Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qianshu Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fei Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Hu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Mohapatra SS, Dwibedy SK, Padhy I. Polymyxins, the last-resort antibiotics: Mode of action, resistance emergence, and potential solutions. J Biosci 2021. [PMID: 34475315 PMCID: PMC8387214 DOI: 10.1007/s12038-021-00209-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infections caused by multi-drug resistant (MDR) bacterial pathogens are a leading cause of mortality and morbidity across the world. Indiscriminate use of broad-spectrum antibiotics has seriously affected this situation. With the diminishing discovery of novel antibiotics, new treatment methods are urgently required to combat MDR pathogens. Polymyxins, the cationic lipopeptide antibiotics, discovered more than half a century ago, are considered to be the last-line of antibiotics available at the moment. This antibiotic shows a great bactericidal effect against Gram-negative bacteria. Polymyxins primarily target the bacterial membrane and disrupt them, causing lethality. Because of their membrane interacting mode of action, polymyxins cause nephrotoxicity and neurotoxicity in humans, limiting their usability. However, recent modifications in their chemical structure have been able to reduce the toxic effects. The development of better dosing regimens has also helped in getting better clinical outcomes in the infections caused by MDR pathogens. Since the mid-1990s the use of polymyxins has increased manifold in clinical settings, resulting in the emergence of polymyxin-resistant strains. The risk posed by the polymyxin-resistant nosocomial pathogens such as the Enterobacteriaceae group, Pseudomonas aeruginosa, and Acinetobacter baumannii, etc. is very serious considering these pathogens are resistant to almost all available antibacterial drugs. In this review article, the mode of action of the polymyxins and the genetic regulatory mechanism responsible for the emergence of resistance are discussed. Specifically, this review aims to update our current understanding in the field and suggest possible solutions that can be pursued for future antibiotic development. As polymyxins primarily target the bacterial membranes, resistance to polymyxins arises primarily by the modification of the lipopolysaccharides (LPS) in the outer membrane (OM). The LPS modification pathways are largely regulated by the bacterial two-component signal transduction (TCS) systems. Therefore, targeting or modulating the TCS signalling mechanisms can be pursued as an alternative to treat the infections caused by polymyxin-resistant MDR pathogens. In this review article, this aspect is also highlighted.
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Affiliation(s)
- Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Indira Padhy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
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RexAB promotes the survival of Staphylococcus aureus exposed to multiple classes of antibiotics. Antimicrob Agents Chemother 2021; 65:e0059421. [PMID: 34310219 PMCID: PMC8448105 DOI: 10.1128/aac.00594-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotics inhibit essential bacterial processes, resulting in arrest of growth and, in some cases, cell death. Many antibiotics are also reported to trigger endogenous production of reactive oxygen species (ROS), which damage DNA, leading to induction of the mutagenic SOS response associated with the emergence of drug resistance. However, the type of DNA damage that arises and how this triggers the SOS response are largely unclear. We found that several different classes of antibiotic triggered dose-dependent induction of the SOS response in Staphylococcus aureus, indicative of DNA damage, including some bacteriostatic drugs. The SOS response was heterogenous and varied in magnitude between strains and antibiotics. However, in many cases, full induction of the SOS response was dependent upon the RexAB helicase/nuclease complex, which processes DNA double-strand breaks to produce single-stranded DNA and facilitate RecA nucleoprotein filament formation. The importance of RexAB in repair of DNA was confirmed by measuring bacterial survival during antibiotic exposure, with most drugs having significantly greater bactericidal activity against rexB mutants than against wild-type strains. For some, but not all, antibiotics there was no difference in bactericidal activity between wild type and rexB mutant under anaerobic conditions, indicative of a role for reactive oxygen species in mediating DNA damage. Taken together, this work confirms previous observations that several classes of antibiotics cause DNA damage in S. aureus and extends them by showing that processing of DNA double-strand breaks by RexAB is a major trigger of the mutagenic SOS response and promotes bacterial survival.
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Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation. NPJ Biofilms Microbiomes 2021; 7:56. [PMID: 34215744 PMCID: PMC8253772 DOI: 10.1038/s41522-021-00226-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Aryl polyenes (APEs) are specialized polyunsaturated carboxylic acids that were identified in silico as the product of the most widespread family of bacterial biosynthetic gene clusters (BGCs). They are present in several Gram-negative host-associated bacteria, including multidrug-resistant human pathogens. Here, we characterize a biological function of APEs, focusing on the BGC from a uropathogenic Escherichia coli (UPEC) strain. We first perform a genetic deletion analysis to identify the essential genes required for APE biosynthesis. Next, we show that APEs function as fitness factors that increase protection from oxidative stress and contribute to biofilm formation. Together, our study highlights key steps in the APE biosynthesis pathway that can be explored as potential drug targets for complementary strategies to reduce fitness and prevent biofilm formation of multi-drug resistant pathogens.
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Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants (Basel) 2021; 10:antiox10060861. [PMID: 34072091 PMCID: PMC8228696 DOI: 10.3390/antiox10060861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023] Open
Abstract
The use of oxidizing agents is one of the most favorable approaches to kill bacteria in daily life. However, bacteria have been evolving to survive in the presence of different oxidizing agents. In this study, we aimed to obtain a comprehensive list of genes whose expression can make Escherichiacoli cells resistant to different oxidizing agents. For this purpose, we utilized the ASKA library and performed a genome-wide screening of ~4200 E. coli genes. Hydrogen peroxide (H2O2) and hypochlorite (HOCl) were tested as representative oxidizing agents in this study. To further validate our screening results, we used different E. coli strains as host cells to express or inactivate selected resistance genes individually. More than 100 genes obtained in this screening were not known to associate with oxidative stress responses before. Thus, this study is expected to facilitate both basic studies on oxidative stress and the development of antibacterial agents.
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Genomics and transcriptomics analyses provide insights into the cold adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2021. [DOI: 10.1007/s00300-021-02883-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Sen A, Imlay JA. How Microbes Defend Themselves From Incoming Hydrogen Peroxide. Front Immunol 2021; 12:667343. [PMID: 33995399 PMCID: PMC8115020 DOI: 10.3389/fimmu.2021.667343] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/19/2021] [Indexed: 12/02/2022] Open
Abstract
Microbes rely upon iron as a cofactor for many enzymes in their central metabolic processes. The reactive oxygen species (ROS) superoxide and hydrogen peroxide react rapidly with iron, and inside cells they can generate both enzyme and DNA damage. ROS are formed in some bacterial habitats by abiotic processes. The vulnerability of bacteria to ROS is also apparently exploited by ROS-generating host defense systems and bacterial competitors. Phagocyte-derived O 2 - can toxify captured bacteria by damaging unidentified biomolecules on the cell surface; it is unclear whether phagocytic H2O2, which can penetrate into the cell interior, also plays a role in suppressing bacterial invasion. Both pathogenic and free-living microbes activate defensive strategies to defend themselves against incoming H2O2. Most bacteria sense the H2O2via OxyR or PerR transcription factors, whereas yeast uses the Grx3/Yap1 system. In general these regulators induce enzymes that reduce cytoplasmic H2O2 concentrations, decrease the intracellular iron pools, and repair the H2O2-mediated damage. However, individual organisms have tailored these transcription factors and their regulons to suit their particular environmental niches. Some bacteria even contain both OxyR and PerR, raising the question as to why they need both systems. In lab experiments these regulators can also respond to nitric oxide and disulfide stress, although it is unclear whether the responses are physiologically relevant. The next step is to extend these studies to natural environments, so that we can better understand the circumstances in which these systems act. In particular, it is important to probe the role they may play in enabling host infection by microbial pathogens.
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Affiliation(s)
| | - James A. Imlay
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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