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Miao X, Han X, Liu C, Bai X. Intrinsic chlorine resistance of bacteria modulated by glutaminyl-tRNA biosynthesis in drinking water supply systems. CHEMOSPHERE 2022; 308:136322. [PMID: 36084827 DOI: 10.1016/j.chemosphere.2022.136322] [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: 06/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The existence of chlorine-resistant bacteria (CRB) in drinking water supply systems (DWSSs) results in significant challenges to the biological security of drinking water. However, little is known about the intrinsic chlorine-resistant molecular metabolic mechanism of bacteria in DWSSs. This research explored the microbial interactions and the key metabolic pathways that modulate the chlorine resistance of bacteria in full-scale chloraminated DWSSs. The dominant CRB, including Bdellovibrio, Bradyrhizobium, Peredibacter, Sphingomonas, and Hydrogenophaga, strongly interacted with each other to maintain basic metabolism. A total of 4.21% of the bacterial metabolic pathways were key and specific to chlorine-resistant bacteria. Glutaminyl-tRNA biosynthesis was the dominant metabolic pathway of CRB in the target DWSSs. After chloramine disinfection, the relative abundance of glutamate-tRNA ligase (GlnRS) and the related orthologous genes increased by 10.11% and 14.58%, respectively. The inactivation rate of the GlnRS overexpression strain (81.40%) was lower than that of the wild-type strain (90.11%) after exposure to chloramine. Meanwhile, the growth rate of the GlnRS overexpression strain was higher than that of the wild-type strain. Glutaminyl-tRNA biosynthesis can enhance chlorine resistance in DWSSs.
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Affiliation(s)
- Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xue Han
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Chenxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Gene Networks and Pathways Involved in Escherichia coli Response to Multiple Stressors. Microorganisms 2022; 10:microorganisms10091793. [PMID: 36144394 PMCID: PMC9501238 DOI: 10.3390/microorganisms10091793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Stress response helps microorganisms survive extreme environmental conditions and host immunity, making them more virulent or drug resistant. Although both reductionist approaches investigating specific genes and systems approaches analyzing individual stress conditions are being used, less is known about gene networks involved in multiple stress responses. Here, using a systems biology approach, we mined hundreds of transcriptomic data sets for key genes and pathways involved in the tolerance of the model microorganism Escherichia coli to multiple stressors. Specifically, we investigated the E. coli K-12 MG1655 transcriptome under five stresses: heat, cold, oxidative stress, nitrosative stress, and antibiotic treatment. Overlaps of transcriptional changes between studies of each stress factor and between different stressors were determined: energy-requiring metabolic pathways, transport, and motility are typically downregulated to conserve energy, while genes related to survival, bona fide stress response, biofilm formation, and DNA repair are mainly upregulated. The transcription of 15 genes with uncharacterized functions is higher in response to multiple stressors, which suggests they may play pivotal roles in stress response. In conclusion, using rank normalization of transcriptomic data, we identified a set of E. coli stress response genes and pathways, which could be potential targets to overcome antibiotic tolerance or multidrug resistance.
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Analysis of the Metabolic Response of Planktonic Cells and Biofilms of Klebsiella pneumoniae to Sublethal Disinfection with Sodium Hypochlorite Measured by NMR. Microorganisms 2022; 10:microorganisms10071323. [PMID: 35889041 PMCID: PMC9323045 DOI: 10.3390/microorganisms10071323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is a pathogenic agent able to form biofilms on water storage tanks and pipe walls. This opportunistic pathogen can generate a thick layer as one of its essential virulence factors, enabling the bacteria to survive disinfection processes and thus develop drug resistance. Understanding the metabolic differences between biofilm and planktonic cells of the K. pneumoniae response to NaClO is key to developing strategies to control its spread. In this study, we performed an NMR metabolic profile analysis to compare the response to a sublethal concentration of sodium hypochlorite of biofilm and planktonic cells of K. pneumoniae cultured inside silicone tubing. Metabolic profiles revealed changes in the metabolism of planktonic cells after a contact time of 10 min with 7 mg L−1 of sodium hypochlorite. A decrease in the production of metabolites such as lactate, acetate, ethanol, and succinate in this cell type was observed, thus indicating a disruption of glucose intake. In contrast, the biofilms displayed a high metabolic heterogeneity, and the treatment did not affect their metabolic signature.
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Abstract
Metabolomics is a powerful tool that can systematically describe global changes in the metabolome of microbes, thus improving our understanding of the mechanisms of action of antibiotics and facilitating the development of next-generation antibacterial therapies. However, current sample preparation methods are not efficient or reliable for studying the effects of antibiotics on microbes. In the present study, we reported a novel sample preparation approach using cold methanol/ethylene glycol for quenching Escherichia coli, thus overcoming the loss of intracellular metabolites caused by cell membrane damage. After evaluating the extraction efficiency of several extraction methods, we employed the optimized workflow to profile the metabolome of E. coli exposed to cephalexin. In doing so, we proved the utility of the proposed approach and provided insights into the comprehensive metabolic alterations associated with antibiotic treatment. IMPORTANCE The emergence and global spread of multidrug-resistant bacteria and genes are a global problem. It is critical to understand the interactions between antibiotics and bacteria and find alternative treatments for infections when we are moving closer to a postantibiotic era. It has been demonstrated that the bacterial metabolic environment plays an important role in the modulation of antibiotic susceptibility and efficacy. In the present study, we proposed a novel metabolomic approach for intracellular metabolite profiling of E. coli, which can be used to investigate the metabolite alterations of bacteria caused by antibiotic treatment. Further understanding of antibiotic-induced perturbations of bacterial metabolism would facilitate the discovery of new therapeutic targets and pathways.
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Pan Y, Cheng JH, Sun DW. Metabolomic analyses on microbial primary and secondary oxidative stress responses. Compr Rev Food Sci Food Saf 2021; 20:5675-5697. [PMID: 34601780 DOI: 10.1111/1541-4337.12835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/20/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Food safety is veryimportant in our daily life. In food processing or disinfection, microorganisms are commonly exposed to oxidative stress perturbations. However, microorganisms can adapt and respond to physicochemical interventions, leading to difficulty and complexity for food safety assurance. Therefore, understanding the response mechanisms of microbes and providing an overview of the responses under oxidative stress conditions are beneficial for ensuring food safety for the industry. The current review takes the metabolomics approach to reveal small metabolite signatures and key pathway alterations during oxidative stress at the molecular and technical levels. These alterations are involved in primary oxidative stress responses due to inactivation treatments such as using hypochlorite (HOCl), hydrogen peroxide (H2 O2 ), electrolyzed water (EW), irradiation, pulsed light (PL), electron beam (EB), and secondary oxidative stress responses due to exposures to excessive conditions such as heat, pressure, acid, and alkaline. Details on the putative origin of exogenous or endogenous reactive oxygen species (ROS) are discussed, with particular attention paid to their effects on lipid, amino acid, nucleotide, and carbohydrate metabolism. In addition, mechanisms on counteracting oxidative stresses, stabilization of cell osmolality as well as energy provision for microbes to survive are also discussed.
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Affiliation(s)
- Yuanyuan Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Jun-Hu Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin, Ireland
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Khan H, Liu M, Kayani MUR, Ahmad S, Liang J, Bai X. DNA phosphorothioate modification facilitates the dissemination of mcr-1 and bla NDM-1 in drinking water supply systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115799. [PMID: 33162214 DOI: 10.1016/j.envpol.2020.115799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
The mechanism driving the dissemination of antibiotic resistance genes (ARGs) in drinking water supply systems (DWSSs) with multiple barriers remains poorly understood despite several recent efforts. Phosphorothioate (PT) modifications, governed by dndABCDE genes, occur naturally in various bacteria and involve the incorporation of sulfur into the DNA backbone. PT is regarded as a mild antioxidant in vivo and is known to provide protection against bacterial genomes. We combined quantitative polymerase chain reaction, metagenomic, and network analyses for the water treatment process and laboratory-scale experiments for chlorine treatment using model strains to determine if DNA PT modification occurred in DWSS and facilitated the dissemination of mobilized colistin resistance-1 (mcr-1) and New Delhi metallo-β-lactamase-1 (blaNDM-1) in DWSS. Our results indicated that the relative abundance of dndB increased in the effluent, compared with the influent, in the water treatment plants. Presence of dndB copies had a positive correlation with the concentration of chloramine disinfectant. Network analysis revealed Bdellovibrio as a potential host for MCR genes, NDM genes, and dndB in the DWSS. E. coli DH10B (Wild-type with the dndABCDE gene cluster and ΔdndB) model strains were used to investigate resistance to chlorine treatment at the concentration range of 0.5-3 mg/L. The resistance of the wild-type strain increased with increasing concentration of chlorine. DNA PT modification protected MCR- and NDM-carrying bacteria from chloramine disinfection during the water treatment process. The higher relative abundance of ARGs in the effluent of the water treatment plants may be due to the resistance of DNA PT modification to chloramine disinfection, thereby causing the enrichment of genera carrying MCR, NDM, and dndB. This study provides a new understanding on the mechanism of ARG dissemination in DWSS, which will help to improve the performance of drinking water treatment to control the risk associated with antibiotic-resistant bacteria.
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Affiliation(s)
- Hira Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Mingkun Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Masood Ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, PR China
| | - Shakeel Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Azevedo AS, Gerola GP, Baptista J, Almeida C, Peres J, Mergulhão FJ, Azevedo NF. Increased Intraspecies Diversity in Escherichia coli Biofilms Promotes Cellular Growth at the Expense of Matrix Production. Antibiotics (Basel) 2020; 9:antibiotics9110818. [PMID: 33212939 PMCID: PMC7698454 DOI: 10.3390/antibiotics9110818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 11/30/2022] Open
Abstract
Intraspecies diversity in biofilm communities is associated with enhanced survival and growth of the individual biofilm populations. Studies on the subject are scarce, namely, when more than three strains are present. Hence, in this study, the influence of intraspecies diversity in biofilm populations composed of up to six different Escherichia coli strains isolated from urine was evaluated in conditions mimicking the ones observed in urinary tract infections and catheter-associated urinary tract infections. In general, with the increasing number of strains in a biofilm, an increase in cell cultivability and a decrease in matrix production were observed. For instance, single-strain biofilms produced an average of 73.1 µg·cm−2 of extracellular polymeric substances (EPS), while six strains biofilms produced 19.9 µg·cm−2. Hence, it appears that increased genotypic diversity in a biofilm leads E. coli to direct energy towards the production of its offspring, in detriment of the production of public goods (i.e., matrix components). Apart from ecological implications, these results can be explored as another strategy to reduce the biofilm burden, as a decrease in EPS matrix production may render these intraspecies biofilms more sensitive to antimicrobial agents.
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Affiliation(s)
- Andreia S. Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga, 4710-057 Braga, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2250-8158; Fax: +351-225-081-449
| | - Gislaine P. Gerola
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
| | - João Baptista
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
| | - Carina Almeida
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga, 4710-057 Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal
| | - Joana Peres
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
| | - Filipe J. Mergulhão
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
| | - Nuno F. Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; (G.P.G.); (J.B.); (C.A.); (J.P.); (F.J.M.); (N.F.A.)
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8
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Paley EL. Discovery of Gut Bacteria Specific to Alzheimer's Associated Diseases is a Clue to Understanding Disease Etiology: Meta-Analysis of Population-Based Data on Human Gut Metagenomics and Metabolomics. J Alzheimers Dis 2020; 72:319-355. [PMID: 31561379 DOI: 10.3233/jad-190873] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD)-associated sequence (ADAS) of cultured fecal bacteria was discovered in human gut targeted screening. This study provides important information to expand our current understanding of the structure/activity relationship of ADAS and putative inhibitors/activators that are potentially involved in ADAS appearance/disappearance. The NCBI database analysis revealed that ADAS presents at a large proportion in American Indian Oklahoman (C&A) with a high prevalence of obesity/diabetes and in colorectal cancer (CRC) patients from the US and China. An Oklahoman non-native group (NNI) showed no ADAS. Comparison of two large US populations reveals that ADAS is more frequent in individuals aged ≥66 and in females. Prevalence and levels of fecal metabolites are altered in the C&A and CRC groups versus controls. Biogenic amines (histamine, tryptamine, tyramine, phenylethylamine, cadaverine, putrescine, agmatine, spermidine) that present in food and are produced by gut microbiota are significantly higher in C&A (e.g., histamine/histidine 95-fold) versus NNI (histamine/histidine 16-fold). The majority of these bio-amines are cytotoxic at concentrations found in food. Inositol phosphate signaling implicated in AD is altered in C&A and CRC. Tryptamine stimulated accumulation of inositol phosphate. The seizure-eliciting tryptamine induced cytoplasmic vacuolization and vesiculation with cell fragmentation. Present additions of ADAS-carriers at different ages including infants led to an ADAS-comprising human sample size of 2,830 from 27 studies from four continents (North America, Australia, Asia, Europe). Levels of food-derived monoamine oxidase inhibitors and anti-bacterial compounds, the potential modulators of ADAS-bacteria growth and biogenic amine production, were altered in C&A versus NNI. ADAS is attributable to potentially modifiable risk factors of AD associated diseases.
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Affiliation(s)
- Elena L Paley
- Expert Biomed, Inc., Miami, FL, USA.,Stop Alzheimers Corp, Miami, FL, USA
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9
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Pardo-Esté C, Castro-Severyn J, Krüger GI, Cabezas CE, Briones AC, Aguirre C, Morales N, Baquedano MS, Sulbaran YN, Hidalgo AA, Meneses C, Poblete-Castro I, Castro-Nallar E, Valvano MA, Saavedra CP. The Transcription Factor ArcA Modulates Salmonella's Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress. Front Microbiol 2019; 10:2754. [PMID: 31866961 PMCID: PMC6906141 DOI: 10.3389/fmicb.2019.02754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 01/03/2023] Open
Abstract
Salmonella Typhimurium, a bacterial pathogen with high metabolic plasticity, can adapt to different environmental conditions; these traits enhance its virulence by enabling bacterial survival. Neutrophils play important roles in the innate immune response, including the production of microbicidal reactive oxygen species (ROS). In addition, the myeloperoxidase in neutrophils catalyzes the formation of hypochlorous acid (HOCl), a highly toxic molecule that reacts with essential biomolecules, causing oxidative damage including lipid peroxidation and protein carbonylation. The bacterial response regulator ArcA regulates adaptive responses to oxygen levels and influences the survival of Salmonella inside phagocytic cells. Here, we demonstrate by whole transcriptomic analyses that ArcA regulates genes related to various metabolic pathways, enabling bacterial survival during HOCl-stress in vitro. Also, inside neutrophils, ArcA controls the transcription of several metabolic pathways by downregulating the expression of genes related to fatty acid degradation, lysine degradation, and arginine, proline, pyruvate, and propanoate metabolism. ArcA also upregulates genes encoding components of the oxidative pathway. These results underscore the importance of ArcA in ATP generation inside the neutrophil phagosome and its participation in bacterial metabolic adaptations during HOCl stress.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Gabriel I Krüger
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Elizabeth Cabezas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alan Cristóbal Briones
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Camila Aguirre
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Maria Soledad Baquedano
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Yoelvis Noe Sulbaran
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alejandro A Hidalgo
- Laboratorio de Patogenesis Bacteriana, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Poblete-Castro
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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10
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Sublethal Injury Caused to Listeria monocytogenes by Natural Plant Extracts: Case Study on Grape Seed Extract and Garlic Extract. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Natural antimicrobials, such as grape seed extract (GSE) and garlic extract (GE), are often used as (a part of) novel food preservation technologies, especially due to their antilisterial effect. However, little is known on the extent of sublethal injury (SI) these extracts cause to Listeria monocytogenes, possibly leading to overestimated efficacies for such novel technologies. The influence of both extracts on the sublethal injury of L. monocytogenes strain LMG23775 was investigated, also using propidium iodide staining to investigate the nature of the injury. Minimum inhibitory concentrations were 500 mg gallic acid equivalents (GAE)/L and 7.5 μg allicin/mL for GSE and GE, respectively. These concentrations slowed down the growth of L. monocytogenes, while only causing a significant amount of SI for GSE. Pure extracts caused inactivation of the cells, with GSE being the most effective. Sublethal injury from pure GSE was mainly caused by membrane damage. In pure GE, a significant amount of SI, not caused by membrane damage, was also present, albeit less pronounced than in pure GSE. In conclusion, both extracts cause a significant amount of sublethal injury to L. monocytogenes, which is not taken into account in relevant studies investigating novel food preservation applications involving natural plant extracts.
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11
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Noster J, Persicke M, Chao TC, Krone L, Heppner B, Hensel M, Hansmeier N. Impact of ROS-Induced Damage of TCA Cycle Enzymes on Metabolism and Virulence of Salmonella enterica serovar Typhimurium. Front Microbiol 2019; 10:762. [PMID: 31105651 PMCID: PMC6491894 DOI: 10.3389/fmicb.2019.00762] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/26/2019] [Indexed: 01/10/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (STM) is exposed to reactive oxygen species (ROS) originating from aerobic respiration, antibiotic treatment, and the oxidative burst occurring inside the Salmonella-containing vacuole (SCV) within host cells. ROS damage cellular compounds, thereby impairing bacterial viability and inducing cell death. Proteins containing iron–sulfur (Fe–S) clusters are particularly sensitive and become non-functional upon oxidation. Comprising five enzymes with Fe–S clusters, the TCA cycle is a pathway most sensitive toward ROS. To test the impact of ROS-mediated metabolic perturbations on bacterial physiology, we analyzed the proteomic and metabolic profile of STM deficient in both cytosolic superoxide dismutases (ΔsodAB). Incapable of detoxifying superoxide anions (SOA), endogenously generated SOA accumulate during growth. ΔsodAB showed reduced abundance of aconitases, leading to a metabolic profile similar to that of an aconitase-deficient strain (ΔacnAB). Furthermore, we determined a decreased expression of acnA in STM ΔsodAB. While intracellular proliferation in RAW264.7 macrophages and survival of methyl viologen treatment were not reduced for STM ΔacnAB, proteomic profiling revealed enhanced stress response. We conclude that ROS-mediated reduced expression and damage of aconitase does not impair bacterial viability or virulence, but might increase ROS amounts in STM, which reinforces the bactericidal effects of antibiotic treatment and immune responses of the host.
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Affiliation(s)
- Janina Noster
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tzu-Chiao Chao
- Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada
| | - Lena Krone
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Bianca Heppner
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Nicole Hansmeier
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany.,Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada.,Luther College, University of Regina, Regina, SK, Canada
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12
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Metabolome analysis of Escherichia coli ATCC25922 cells treated with high hydrostatic pressure at 400 and 600 MPa. J Biosci Bioeng 2018; 126:611-616. [PMID: 29853298 DOI: 10.1016/j.jbiosc.2018.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 11/21/2022]
Abstract
Escherichia coli cells were treated with high hydrostatic pressure (HHP) at 400 and 600 MPa. Metabolites (70-1027 m/z) extracted from HHP-treated cells were analyzed using capillary electrophoresis-time-of-flight mass spectrometry and were compared with those extracted from control cells (not treated with HHP). A total of 133 metabolites were identified and mapped to metabolic pathways, and many of these (42.1%) decreased due to the HHP treatment, including NAD+, NADP+, ATP, and substrates for DNA synthesis. Principal component analysis suggested that the central sugar and nucleic acid metabolic pathways were strongly influenced by HHP. A bottleneck in the central sugar metabolic pathway was observed in HHP-treated cells, which created a metabolic imbalance; metabolites mapped upstream (glucose 6-phosphate, fructose 6-phosphate, and fructose 1,6-diphosphate) were accumulated and those downstream (3-phosphoglycerate, 2-phosphoglycerate, and phosphoenolpyruvate) were depleted. Ribonucleotides were decreased, but the reduction was moderate compared with that of substrates for DNA synthesis; the exception was ATP, which also substantially decreased. The bottleneck in the glycolytic pathway partly explained the exhaustion of ATP. NAD+/NADH ratio of HHP treated cells was comparable with that of untreated control cells.
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Miguez AM, McNerney MP, Styczynski MP. Metabolomics Analysis of the Toxic Effects of the Production of Lycopene and Its Precursors. Front Microbiol 2018; 9:760. [PMID: 29774011 PMCID: PMC5944366 DOI: 10.3389/fmicb.2018.00760] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/04/2018] [Indexed: 01/01/2023] Open
Abstract
Using cells as microbial factories enables highly specific production of chemicals with many advantages over chemical syntheses. A number of exciting new applications of this approach are in the area of precision metabolic engineering, which focuses on improving the specificity of target production. In recent work, we have used precision metabolic engineering to design lycopene-producing Escherichia coli for use as a low-cost diagnostic biosensor. To increase precursor availability and thus the rate of lycopene production, we heterologously expressed the mevalonate pathway. We found that simultaneous induction of these pathways increases lycopene production, but induction of the mevalonate pathway before induction of the lycopene pathway decreases both lycopene production and growth rate. Here, we aim to characterize the metabolic changes the cells may be undergoing during expression of either or both of these heterologous pathways. After establishing an improved method for quenching E. coli for metabolomics analysis, we used two-dimensional gas chromatography coupled to mass spectrometry (GCxGC-MS) to characterize the metabolomic profile of our lycopene-producing strains in growth conditions characteristic of our biosensor application. We found that the metabolic impacts of producing low, non-toxic levels of lycopene are of much smaller magnitude than the typical metabolic changes inherent to batch growth. We then used metabolomics to study differences in metabolism caused by the time of mevalonate pathway induction and the presence of the lycopene biosynthesis genes. We found that overnight induction of the mevalonate pathway was toxic to cells, but that the cells could recover if the lycopene pathway was not also heterologously expressed. The two pathways appeared to have an antagonistic metabolic effect that was clearly reflected in the cells’ metabolic profiles. The metabolites homocysteine and homoserine exhibited particularly interesting behaviors and may be linked to the growth inhibition seen when the mevalonate pathway is induced overnight, suggesting potential future work that may be useful in engineering increased lycopene biosynthesis.
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Affiliation(s)
- April M Miguez
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Monica P McNerney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
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Schatschneider S, Abdelrazig S, Safo L, Henstra AM, Millat T, Kim DH, Winzer K, Minton NP, Barrett DA. Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in Clostridium autoethanogenum with Uniformly 13C-Labeled Standards Derived from Spirulina. Anal Chem 2018. [PMID: 29533656 DOI: 10.1021/acs.analchem.7b04758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have investigated the applicability of commercially available lyophilized spirulina ( Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze-thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves ( R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood-Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation.
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Affiliation(s)
- Sarah Schatschneider
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Laudina Safo
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anne M Henstra
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Thomas Millat
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Klaus Winzer
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Nigel P Minton
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
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15
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Kellner S, DeMott MS, Cheng CP, Russell BS, Cao B, You D, Dedon PC. Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol 2017; 13:888-894. [PMID: 28604692 PMCID: PMC5577368 DOI: 10.1038/nchembio.2407] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/30/2017] [Indexed: 12/12/2022]
Abstract
Genomic modification with sulfur as phosphorothioate (PT) is widespread among prokaryotes, including human pathogens. Apart from its physiological functions, the redox and nucleophilic properties of PT sulfur suggest effects on bacterial fitness in stressful environments. Here we show that PTs are dynamic and labile DNA modifications that cause genomic instability during oxidative stress. Using coupled isotopic labeling-mass spectrometry, we observed sulfur replacement in PTs at a rate of ~2%/h in unstressed Escherichia coli and Salmonella enterica. While PT levels were unaffected by exposure to hydrogen peroxide (H2O2) or hypochlorous acid (HOCl), PT turnover increased to 3.8–10%/h for HOCl and was unchanged for H2O2, consistent with repair of HOCl-induced sulfur damage. PT-dependent HOCl sensitivity extended to cytotoxicity and DNA strand-breaks, which occurred at orders-of-magnitude lower doses of HOCl than H2O2. The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during human infections.
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Affiliation(s)
- Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ching Pin Cheng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Brandon S Russell
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bo Cao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Delin You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Singapore
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Khan S, Beattie TK, Knapp CW. The use of minimum selectable concentrations (MSCs) for determining the selection of antimicrobial resistant bacteria. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:283-292. [PMID: 28155034 PMCID: PMC5318476 DOI: 10.1007/s10646-017-1762-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 05/25/2023]
Abstract
The use of antimicrobial compounds is indispensable in many industries, especially drinking water production, to eradicate microorganisms. However, bacterial growth is not unusual in the presence of disinfectant concentrations that would be typically lethal, as bacterial populations can develop resistance. The common metric of population resistance has been based on the Minimum Inhibitory Concentration (MIC), which is based on bacteria lethality. However, sub-lethal concentrations may also select for resistant bacteria due to the differences in bacterial growth rates. This study determined the Minimal Selective Concentrations (MSCs) of bacterial populations exposed to free chlorine and monochloramine, representing a metric that possibly better reflects the selective pressures occurring at lower disinfectant levels than MIC. Pairs of phylogenetically similar bacteria were challenged to a range of concentrations of disinfectants. The MSCs of free chlorine and monochloramine were found to range between 0.021 and 0.39 mg L-1, which were concentrations 1/250 to 1/5 than the MICs of susceptible bacteria (MIC susc ). This study indicates that sub-lethal concentrations of disinfectants could result in the selection of resistant bacterial populations, and MSCs would be a more sensitive indicator of selective pressure, especially in environmental systems.
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Affiliation(s)
- Sadia Khan
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK.
- Department of Environmental Engineering, NED University of Engineering and Technology, University Road, Karachi, 75270, Pakistan.
| | - Tara K Beattie
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, Scotland, G1 1XJ, UK
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Cossu A, Le P, Young GM, Nitin N. Assessment of sanitation efficacy against Escherichia coli O157:H7 by rapid measurement of intracellular oxidative stress, membrane damage or glucose active uptake. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Patejko M, Jacyna J, Markuszewski MJ. Sample preparation procedures utilized in microbial metabolomics: An overview. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1043:150-157. [PMID: 27693061 DOI: 10.1016/j.jchromb.2016.09.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/17/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
Abstract
Bacteria are remarkably diverse in terms of their size, structure and biochemical properties. Due to this fact, it is hard to develop a universal method for handling bacteria cultures during metabolomic analysis. The choice of suitable processing methods constitutes a key element in any analysis, because only appropriate selection of procedures may provide accurate results, leading to reliable conclusions. Because of that, every analytical experiment concerning bacteria requires individually and very carefully planned research methodology. Although every study varies in terms of sample preparation, there are few general steps to follow while planning experiment, like sampling, separation of cells from growth medium, stopping their metabolism and extraction. As a result of extraction, all intracellular metabolites should be washed out from cell environment. What is more, extraction method utilized cannot cause any chemical decomposition or degradation of the metabolome. Furthermore, chosen extraction method should correlate with analytical technique, so it will not disturb or prolong following sample preparation steps. For those reasons, we observe a need to summarize sample preparation procedures currently utilized in microbial metabolomic studies. In the presented overview, papers concerning analysis of extra- and intracellular metabolites, published over the last decade, have been discussed. Presented work gives some basic guidelines that might be useful while planning experiments in microbial metabolomics.
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Affiliation(s)
- Małgorzata Patejko
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Julia Jacyna
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Michał J Markuszewski
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland.
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