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Zhu L, Wang Z, Gao L, Chen X. Unraveling the Potential of γ-Aminobutyric Acid: Insights into Its Biosynthesis and Biotechnological Applications. Nutrients 2024; 16:2760. [PMID: 39203897 PMCID: PMC11357613 DOI: 10.3390/nu16162760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/09/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
γ-Aminobutyric acid (GABA) is a widely distributed non-protein amino acid that serves as a crucial inhibitory neurotransmitter in the brain, regulating various physiological functions. As a result of its potential benefits, GABA has gained substantial interest in the functional food and pharmaceutical industries. The enzyme responsible for GABA production is glutamic acid decarboxylase (GAD), which catalyzes the irreversible decarboxylation of glutamate. Understanding the crystal structure and catalytic mechanism of GAD is pivotal in advancing our knowledge of GABA production. This article provides an overview of GAD's sources, structure, and catalytic mechanism, and explores strategies for enhancing GABA production through fermentation optimization, metabolic engineering, and genetic engineering. Furthermore, the effects of GABA on the physiological functions of animal organisms are also discussed. To meet the increasing demand for GABA, various strategies have been investigated to enhance its production, including optimizing fermentation conditions to facilitate GAD activity. Additionally, metabolic engineering techniques have been employed to increase the availability of glutamate as a precursor for GABA biosynthesis. By fine-tuning fermentation conditions and utilizing metabolic and genetic engineering techniques, it is possible to achieve higher yields of GABA, thus opening up new avenues for its application in functional foods and pharmaceuticals. Continuous research in this field holds immense promise for harnessing the potential of GABA in addressing various health-related challenges.
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Affiliation(s)
- Lei Zhu
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China;
| | - Zhefeng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China;
| | - Le Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China;
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China;
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2
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Dubois Q, Brual T, Oriol C, Mandin P, Condemine G, Gueguen E. Function and mechanism of action of the small regulatory RNA ArcZ in Enterobacterales. RNA (NEW YORK, N.Y.) 2024; 30:1107-1121. [PMID: 38839110 PMCID: PMC11331407 DOI: 10.1261/rna.080010.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
ArcZ is a small regulatory RNA conserved in Enterobacterales It is an Hfq-dependent RNA that is cleaved by RNase E in a processed form of 55-60 nucleotides. This processed form is highly conserved for controlling the expression of target mRNAs. ArcZ expression is induced by abundant oxygen levels and reaches its peak during the stationary growth phase. This control is mediated by the oxygen-responsive two-component system ArcAB, leading to the repression of arcZ transcription under low-oxygen conditions in most bacteria in which it has been studied. ArcZ displays multiple targets, and it can control up to 10% of a genome and interact directly with more than 300 mRNAs in Escherichia coli and Salmonella enterica ArcZ displays a multifaceted ability to regulate its targets through diverse mechanisms such as RNase recruitment, modulation of ribosome accessibility on the mRNA, and interaction with translational enhancing regions. By influencing stress response, motility, and virulence through the regulation of master regulators such as FlhDC or RpoS, ArcZ emerges as a major orchestrator of cell physiology within Enterobacterales.
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Affiliation(s)
- Quentin Dubois
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, UMR5240 MAP Lyon, France
| | - Typhaine Brual
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, UMR5240 MAP Lyon, France
| | - Charlotte Oriol
- CNRS, Aix-Marseille Université, Laboratoire de Chimie Bactérienne, UMR7283, IMM, IM2B, F-13009 Marseille, France
| | - Pierre Mandin
- CNRS, Aix-Marseille Université, Laboratoire de Chimie Bactérienne, UMR7283, IMM, IM2B, F-13009 Marseille, France
| | - Guy Condemine
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, UMR5240 MAP Lyon, France
| | - Erwan Gueguen
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, UMR5240 MAP Lyon, France
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3
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Muehler D, Morini S, Geißert J, Engesser C, Hiller KA, Widbiller M, Maisch T, Buchalla W, Cieplik F. Stress response in Escherichia coli following sublethal phenalene-1-one mediated antimicrobial photodynamic therapy: an RNA-Seq study. Photochem Photobiol Sci 2024; 23:1573-1586. [PMID: 39103724 DOI: 10.1007/s43630-024-00617-3] [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: 01/22/2024] [Accepted: 07/20/2024] [Indexed: 08/07/2024]
Abstract
Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq). Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. After treatment, RNA was extracted, and RNA-Seq was performed on the Illumina NextSeq 500. Differentially expressed genes were analyzed and validated by qRT-PCR. Furthermore, expression of specific stress response proteins was investigated using Western blot analysis.The analysis of the differential gene expression following pathway enrichment analysis revealed a considerable number of genes and pathways significantly up- or down-regulated in E. coli after sublethal treatment with aPDT. Expression of 1018 genes was up-regulated and of 648 genes was down-regulated after sublethal treatment with aPDT as compared to irradiated controls. Analysis of differentially expressed genes and significantly de-regulated pathways showed regulation of genes involved in oxidative stress response and bacterial membrane damage. In conclusion, the results show a transcriptomic stress response in E. coli upon exposure to aPDT using SAPYR and give an insight into potential molecular mechanisms that may result in development of adaptation.
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Affiliation(s)
- Denise Muehler
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Silvia Morini
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Janina Geißert
- NGS-Competence Center Tübingen, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Christina Engesser
- NGS-Competence Center Tübingen, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Karl-Anton Hiller
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Matthias Widbiller
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Tim Maisch
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Wolfgang Buchalla
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany.
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
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4
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Pilati GVT, Salles GBC, Savi BP, Dahmer M, Muniz EC, Filho VB, Elois MA, Souza DSM, Fongaro G. Isolation and Characterization of Escherichia coli from Brazilian Broilers. Microorganisms 2024; 12:1463. [PMID: 39065231 PMCID: PMC11279037 DOI: 10.3390/microorganisms12071463] [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: 06/19/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis, one of the main diseases leading to economic losses in industrial poultry farming due to high morbidity and mortality and its role in the condemnation of chicken carcasses. This study aimed to isolate and characterize APEC obtained from necropsied chickens on Brazilian poultry farms. Samples from birds already necropsied by routine inspection were collected from 100 batches of broiler chickens from six Brazilian states between August and November 2021. Three femurs were collected per batch, and characteristic E. coli colonies were isolated on MacConkey agar and characterized by qualitative PCR for minimal predictive APEC genes, antimicrobial susceptibility testing, and whole genome sequencing to identify species, serogroups, virulence genes, and resistance genes. Phenotypic resistance indices revealed significant resistance to several antibiotics from different antimicrobial classes. The isolates harbored virulence genes linked to APEC pathogenicity, including adhesion, iron acquisition, serum resistance, and toxins. Aminoglycoside resistance genes were detected in 79.36% of isolates, 74.6% had sulfonamide resistance genes, 63.49% showed β-lactam resistance genes, and 49.2% possessed at least one tetracycline resistance gene. This study found a 58% prevalence of avian pathogenic E. coli in Brazilian poultry, with strains showing notable antimicrobial resistance to commonly used antibiotics.
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Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil;
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | | | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Doris Sobral Marques Souza
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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6
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Matta T, Bhatia R, Joshi SR, Bishnoi M, Chopra K, Kondepudi KK. GABA synthesizing lactic acid bacteria and genomic analysis of Levilactobacillus brevis LAB6. 3 Biotech 2024; 14:62. [PMID: 38344283 PMCID: PMC10850046 DOI: 10.1007/s13205-024-03918-7] [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: 06/07/2023] [Accepted: 01/03/2024] [Indexed: 03/10/2024] Open
Abstract
This study was conducted to investigate the γ-aminobutyric acid (GABA) production ability of 20 Lactobacillus and 25 Bifidobacterium strains which were previously isolated in our laboratory. Effect of initial pH, incubation time, monosodium glutamate (MSG), and pyridoxal-5'-phosphate (PLP) concentration for highest GABA production by two potent bacterial strains, Levilactobacillus brevis LAB6 and Limosilactobacillus fermentum LAB19 were optimized in the MRS media. A threefold increase in GABA production at an initial pH 4.0, incubation time of 120 h in medium supplemented with 3% MSG and 400 μM of PLP for LAB6 and 300 μM for LAB19 lead to the production of 19.67 ± 0.28 and 20.77 ± 0.14 g/L of GABA, respectively. Coculturing both strains under optimized conditions led to a GABA yield of 20.02 ± 0.17 g/L. Owing to potent anti-inflammatory activity in-vitro, as reported previously, and highest GABA production ability of LAB6 (MTCC 25662), its whole-genome sequencing and bioinformatics analysis was carried out for mining genes related to GABA metabolism. LAB6 harbored a complete glutamate decarboxylase (GAD) gene system comprising gadA, gadB, and gadC as well as genes responsible for the beneficial probiotic traits, such as for acid and bile tolerance and host adhesion. Comparative genomic analysis of LAB6 with 28 completely sequenced Levilactobacillus brevis strains revealed the presence of 95 strain-specific genes-families that was significantly higher than most other L. brevis strains. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03918-7.
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Affiliation(s)
- Tushar Matta
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Pharmacology Research Laboratory, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014 India
| | - Ruchika Bhatia
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Santa Ram Joshi
- Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya 793022 India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
- Regional Centre of Biotechnology, Faridabad, India
| | - Kanwaljit Chopra
- Pharmacology Research Laboratory, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014 India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
- Regional Centre of Biotechnology, Faridabad, India
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7
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Saint Martin C, Caccia N, Darsonval M, Gregoire M, Combeau A, Jubelin G, Dubois-Brissonnet F, Leroy S, Briandet R, Desvaux M. Spatially localised expression of the glutamate decarboxylase gadB in Escherichia coli O157:H7 microcolonies in hydrogel matrices. NPJ Sci Food 2023; 7:55. [PMID: 37838796 PMCID: PMC10576782 DOI: 10.1038/s41538-023-00229-8] [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: 02/28/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Functional diversity within isogenic spatially organised bacterial populations has been shown to trigger emergent community properties such as stress tolerance. Considering gadB gene encoding a key glutamate decarboxylase involved in E. coli tolerance to acidic conditions, we investigated its expression in hydrogels mimicking the texture of some structured food matrices (such as minced meat or soft cheese). Taking advantage of confocal laser scanning microscopy combined with a genetically-engineered dual fluorescent reporter system, it was possible to visualise the spatial patterns of bacterial gene expression from in-gel microcolonies. In E. coli O157:H7 microcolonies, gadB showed radically different expression patterns between neutral (pH 7) or acidic (pH 5) hydrogels. Differential spatial expression was determined in acidic hydrogels with a strong expression of gadB at the microcolony periphery. Strikingly, very similar spatial patterns of gadB expression were further observed for E. coli O157:H7 grown in the presence of L. lactis. Considering the ingestion of contaminated foodstuff, survival of E. coli O157:H7 to acidic stomachal stress (pH 2) was significantly increased for bacterial cells grown in microcolonies in acidic hydrogels compared to planktonic cells. These findings have significant implications for risk assessment and public health as they highlight inherent differences in bacterial physiology and virulence between liquid and structured food products. The contrasting characteristics observed underscore the need to consider the distinct challenges posed by these food types, thereby emphasising the importance of tailored risk mitigation strategies.
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Affiliation(s)
- Cédric Saint Martin
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Nelly Caccia
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Maud Darsonval
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | - Marina Gregoire
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | - Arthur Combeau
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France
| | | | | | - Sabine Leroy
- INRAE, UCA, UMR0454 MEDIS, 63000, Clermont-Ferrand, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350, Jouy-en-Josas, France.
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8
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Wang B, Lin AE, Yuan J, Novak KE, Koch MD, Wingreen NS, Adamson B, Gitai Z. Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection. Nat Microbiol 2023; 8:1846-1862. [PMID: 37653008 PMCID: PMC10522482 DOI: 10.1038/s41564-023-01462-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/31/2023] [Indexed: 09/02/2023]
Abstract
Bacterial populations are highly adaptive. They can respond to stress and survive in shifting environments. How the behaviours of individual bacteria vary during stress, however, is poorly understood. To identify and characterize rare bacterial subpopulations, technologies for single-cell transcriptional profiling have been developed. Existing approaches show some degree of limitation, for example, in terms of number of cells or transcripts that can be profiled. Due in part to these limitations, few conditions have been studied with these tools. Here we develop massively-parallel, multiplexed, microbial sequencing (M3-seq)-a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We show that M3-seq can profile bacterial cells from different species under a range of conditions in single experiments. We then apply M3-seq to hundreds of thousands of cells, revealing rare populations and insights into bet-hedging associated with stress responses and characterizing phage infection.
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Affiliation(s)
- Bruce Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Aaron E Lin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jiayi Yuan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Katherine E Novak
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthias D Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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9
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Niu H, Li T, Du Y, Lv Z, Cao Q, Zhang Y. Glutamate Transporters GltS, GltP and GltI Are Involved in Escherichia coli Tolerance In Vitro and Pathogenicity in Mouse Urinary Tract Infections. Microorganisms 2023; 11:1173. [PMID: 37317147 DOI: 10.3390/microorganisms11051173] [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: 02/08/2023] [Revised: 04/02/2023] [Accepted: 04/09/2023] [Indexed: 06/16/2023] Open
Abstract
To verify the roles of GltS, GltP, and GltI in E. coli tolerance and pathogenicity, we quantified and compared the relative abundance of gltS, gltP, and gltI in log-phase and stationary-phase E. coli and constructed their knockout mutant strains in E. coli BW25113 and uropathogenic E. coli (UPEC) separately, followed by analysis of their abilities to tolerate antibiotics and stressors, their capacity for adhesion to and invasion of human bladder epithelial cells, and their survival ability in mouse urinary tracts. Our results showed that gltS, gltP, and gltI transcripts were higher in stationary phase E. coli than in log-phase incubation. Furthermore, deletion of gltS, gltP, and gltI genes in E. coli BW25113 results in decreased tolerance to antibiotics (levofloxacin and ofloxacin) and stressors (acid pH, hyperosmosis, and heat), and loss of gltS, gltP, and gltI in uropathogenic E. coli UTI89 caused attenuated adhesion and invasion in human bladder epithelial cells and markedly reduced survival in mice. The results showed the important roles of the glutamate transporter genes gltI, gltP, and gltS in E. coli tolerance to antibiotics (levofloxacin and ofloxacin) and stressors (acid pH, hyperosmosis, and heat) in vitro and in pathogenicity in mouse urinary tracts and human bladder epithelial cells, as shown by reduced survival and colonization, which improves our understanding of the molecular mechanisms of bacterial tolerance and pathogenicity.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tuodi Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yunjie Du
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhuoxuan Lv
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Qianqian Cao
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ying Zhang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310053, China
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10
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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11
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Nakatani Y, Fukaya T, Kishino S, Ogawa J. Production of GABA-enriched tomato juice by Lactiplantibacillus plantarum KB1253. J Biosci Bioeng 2022; 134:424-431. [PMID: 36137895 DOI: 10.1016/j.jbiosc.2022.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
To produce tomato juice with health-promoting functions, lactic acid bacteria (LAB) capable of converting l-glutamic acid in tomatoes into γ-aminobutyric acid (GABA) was screened from LAB stocks isolated from Japanese pickles. Lactiplantibacillus plantarum KB1253 was selected as the highest GABA producer among 74 strains of LAB stocks. gad gene expression and glutamic acid decarboxylation activity increased at low pH (3.0-3.5), whereas the growth decreased. Under optimal reaction conditions using resting cells as catalysts, this strain produced 245.8 ± 3.4 mM GABA. Furthermore, this strain produced 41.0 ± 1.1 mM GABA from l-glutamic acid in tomato juice under optimal fermentation conditions (pH 4.0, 20°Bx). This study may provide the basis for developing health-promoting functional foods rich in GABA from tomatoes and other agricultural products.
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Affiliation(s)
- Yuki Nakatani
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Product Development Division, Kagome Co., Ltd., 1-24-11 Nihonbashi-Kakigaracho, Chuo-ku, Tokyo 103-0014, Japan
| | - Tetsuya Fukaya
- Niigata-Agro Food University, 2416, Hiranedai, Tainai, Niigata 959-2702, Japan; International Business Division, Kagome Co., Ltd., 3-21-1 Nihonbashi-Hamacho, Chuo-ku, Tokyo 103-8461, Japan
| | - Shigenobu Kishino
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
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12
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Gelalcha BD, Brown SM, Crocker HE, Agga GE, Kerro Dego O. Regulation Mechanisms of Virulence Genes in Enterohemorrhagic Escherichia coli. Foodborne Pathog Dis 2022; 19:598-612. [PMID: 35921067 DOI: 10.1089/fpd.2021.0103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is one of the most common E. coli pathotypes reported to cause several outbreaks of foodborne illnesses. EHEC is a zoonotic pathogen, and ruminants, especially cattle, are considered important reservoirs for the most common EHEC serotype, E. coli O157:H7. Humans are infected indirectly through the consumption of food (milk, meat, leafy vegetables, and fruits) and water contaminated by animal feces or direct contact with carrier animals or humans. E. coli O157:H7 is one of the most frequently reported causes of foodborne illnesses in developed countries. It employs two essential virulence mechanisms to trigger damage to the host. These are the development of attaching and effacing (AE) phenotypes on the intestinal mucosa of the host and the production of Shiga toxin (Stx) that causes hemorrhagic colitis and hemolytic uremic syndrome. The AE phenotype is controlled by the pathogenicity island, the locus of enterocyte effacement (LEE). The induction of both AE and Stx is under strict and highly complex regulatory mechanisms. Thus, a good understanding of these mechanisms, major proteins expressed, and environmental cues involved in the regulation of the expression of the virulence genes is vital to finding a method to control the colonization of reservoir hosts, especially cattle, and disease development in humans. This review is a concise account of the current state of knowledge of virulence gene regulation in the LEE-positive EHEC.
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Affiliation(s)
- Benti D Gelalcha
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Selina M Brown
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Hannah E Crocker
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Getahun E Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture, Bowling Green, Kentucky, USA
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
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13
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Kim Y, Lee S, Park K, Yoon H. Cooperative Interaction between Acid and Copper Resistance in Escherichia coli. J Microbiol Biotechnol 2022; 32:602-611. [PMID: 35283428 PMCID: PMC9628877 DOI: 10.4014/jmb.2201.01034] [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: 01/27/2022] [Revised: 02/22/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022]
Abstract
The persistence of pathogenic Escherichia coli under acidic conditions poses a serious risk to food safety, especially in acidic foods such as kimchi. To identify the bacterial factors required for acid resistance, transcriptomic analysis was conducted on an acid-resistant enterotoxigenic E. coli strain and the genes with significant changes in their expression under acidic pH were selected as putative resistance factors against acid stress. These genes included those associated with a glutamatedependent acid resistance (GDAR) system and copper resistance. E. coli strains lacking GadA, GadB, or YbaST, the components of the GDAR system, exhibited significantly attenuated growth and survival under acidic stress conditions. Accordantly, the inhibition of the GDAR system by 3-mercaptopropionic acid and aminooxyacetic acid abolished bacterial adaptation and survival under acidic conditions, indicating the indispensable role of a GDAR system in acid resistance. Intriguingly, the lack of cueR encoding a transcriptional regulator for copper resistance genes markedly impaired bacterial resistance to acid stress as well as copper. Conversely, the absence of YbaST severely compromised bacterial resistance against copper, suggesting an interplay between acid and copper resistance. These results suggest that a GDAR system can be a promising target for developing control measures to prevent E. coli resistance to acid and copper treatments.
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Affiliation(s)
- Yeeun Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Seohyeon Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Kyungah Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea,Corresponding author Phone: +82-31-219-2450 Fax: +82-31-219-1610 E-mail:
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14
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The Retrospective on Atypical Brucella Species Leads to Novel Definitions. Microorganisms 2022; 10:microorganisms10040813. [PMID: 35456863 PMCID: PMC9025488 DOI: 10.3390/microorganisms10040813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.
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15
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Vashishtha K, Shukla S, Mahadevan S. Involvement of BglG in Lipopolysaccharides (LPS) Synthesis and Transport in Stationary Phase in E. coli. Curr Microbiol 2022; 79:153. [PMID: 35397010 DOI: 10.1007/s00284-022-02837-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
BglG, an RNA binding regulatory protein encoded by the β-glucoside (bgl) operon of E. coli is known to be involved in the regulation of several metabolic functions in stationary phase. A genome-wide comparative transcriptome analysis performed earlier between a ∆bglG strain and its isogenic WT counterpart revealed that genes involved in lipopolysaccharide (LPS) biosynthesis and transport were significantly down-regulated in the absence of BglG in stationary phase, suggesting a role for BglG in their regulation. We have investigated the involvement of BglG in LPS biosynthesis and transport. Consistent with the down-regulation of LPS synthesis and transport genes, the ∆bglG strain showed a loss of permeability barrier specifically in stationary phase, which could be rescued by introduction of wild type bglG on a plasmid. A search for a putative transcription factor involved in the regulation mediated by BglG led to the identification of GadE, which is one of the primary positive regulators of pH homeostasis and LPS core biosynthesis. Using RNA mobility shift and stability assays, we show that BglG binds specifically to gadE mRNA and enhances its stability. Consistent with this, loss of gadE leads to a partial defect in permeability. Based on our findings, we propose a model for the molecular mechanism involved in the regulation on LPS synthesis and transport by BglG.
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Affiliation(s)
- Kartika Vashishtha
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Shambhavi Shukla
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Subramony Mahadevan
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore, 560012, India.
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16
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Division of labor and collective functionality in Escherichia coli under acid stress. Commun Biol 2022; 5:327. [PMID: 35393532 PMCID: PMC8989999 DOI: 10.1038/s42003-022-03281-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
The acid stress response is an important factor influencing the transmission of intestinal microbes such as the enterobacterium Escherichia coli. E. coli activates three inducible acid resistance systems - the glutamate decarboxylase, arginine decarboxylase, and lysine decarboxylase systems to counteract acid stress. Each system relies on the activity of a proton-consuming reaction catalyzed by a specific amino acid decarboxylase and a corresponding antiporter. Activation of these three systems is tightly regulated by a sophisticated interplay of membrane-integrated and soluble regulators. Using a fluorescent triple reporter strain, we quantitatively illuminated the cellular individuality during activation of each of the three acid resistance (AR) systems under consecutively increasing acid stress. Our studies highlight the advantages of E. coli in possessing three AR systems that enable division of labor in the population, which ensures survival over a wide range of low pH values.
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17
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Meng Q, Wu M, Shang Z, Zhang Z, Zhang R. Responsive gadolinium(III) complex-based small molecule magnetic resonance imaging probes: Design, mechanism and application. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Acidic Neutralization by Indigenous Bacteria Isolated from Abandoned Mine Areas. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil acidification has been a serious problem in abandoned mine areas, and could be exacerbated by acid deposition with the release of mine wastes. In this study, three different indigenous bacterial consortia were isolated from abandoned mines in South Korea, from which the potential for acid neutralization of microorganisms was evaluated. They were all able to neutralize acidity within 24 h in the liquid nutrient medium. Moreover, a strong positive correlation (R = +0.922, p < 0.05) was established between the ammonium ion (NH4+) production yield and the resulting pH, indicating that NH4+ served as an important metabolite for biological neutralization. Serratialiquefaciens, Citrobacter youngae, Pseudescherichia vulneris, and Serratia grimesii had higher acid neutralization ability to generate NH4+ by the metabolism of nitrogen compounds such as carboxylation and urea hydrolysis. Therefore, acidic soils can be expected to be ameliorated by indigenous microorganisms through in situ biostimulation with the adequate introduction of nitrogenous substances into the soil environments.
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19
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Yang D, Jiang F, Huang X, Li G, Cai W. Transcriptomic and Metabolomic Profiling Reveals That KguR Broadly Impacts the Physiology of Uropathogenic Escherichia coli Under in vivo Relevant Conditions. Front Microbiol 2022; 12:793391. [PMID: 34975816 PMCID: PMC8716947 DOI: 10.3389/fmicb.2021.793391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Urinary tract infections are primarily caused by uropathogenic Escherichia coli (UPEC). In contrast to the intestinal E. coli strains that reside in nutrient-rich gut environment, UPEC encounter distinct niches, for instance human urine, which is an oxygen- and nutrient-limited environment. Alpha-ketoglutarate (KG) is an abundant metabolite in renal proximal tubule cells; and previously we showed that two-component signaling system (TCS) KguS/KguR contributes to UPEC colonization of murine urinary tract by promoting the utilization of KG as a carbon source under anaerobic conditions. However, knowledge about the KguR regulon and its impact on UPEC fitness is lacking. In this work, we analyzed transcriptomic and metabolomic changes caused by kguR deletion under anaerobiosis when KG is present. Our results indicated that 620 genes were differentially expressed in the ΔkguR mutant, as compared to the wild type; of these genes, 513 genes were downregulated and 107 genes were upregulated. Genes with substantial changes in expression involve KG utilization, acid resistance, iron uptake, amino acid metabolism, capsule biosynthesis, sulfur metabolism, among others. In line with the transcriptomics data, several amino acids (glutamate, lysine, etc.) and uridine 5′-diphosphogalactose (involved in capsule biosynthesis) were significantly less abundant in the ΔkguR mutant. We then confirmed that the ΔkguR mutant, indeed, was more sensitive to acid stress than the wild type, presumably due to downregulation of genes belonging to the glutamate-dependent acid resistance system. Furthermore, using gene expression and electrophoretic mobility shift assays (EMSAs), we demonstrate that KguR autoregulates its own expression by binding to the kguSR promoter region. Lastly, we performed a genome-wide search of KguR binding sites, and this search yielded an output of at least 22 potential binding sites. Taken together, our data establish that in the presence of KG, KguR broadly impacts the physiology of UPEC under anaerobiosis. These findings greatly further our understanding of KguS/KguR system as well as UPEC pathobiology.
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Affiliation(s)
- Dawei Yang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fengwei Jiang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinxin Huang
- Technical Centre for Animal, Plant, and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Ganwu Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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20
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Bessaiah H, Anamalé C, Sung J, Dozois CM. What Flips the Switch? Signals and Stress Regulating Extraintestinal Pathogenic Escherichia coli Type 1 Fimbriae (Pili). Microorganisms 2021; 10:5. [PMID: 35056454 PMCID: PMC8777976 DOI: 10.3390/microorganisms10010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
Pathogens are exposed to a multitude of harmful conditions imposed by the environment of the host. Bacterial responses against these stresses are pivotal for successful host colonization and pathogenesis. In the case of many E. coli strains, type 1 fimbriae (pili) are an important colonization factor that can contribute to diseases such as urinary tract infections and neonatal meningitis. Production of type 1 fimbriae in E. coli is dependent on an invertible promoter element, fimS, which serves as a phase variation switch determining whether or not a bacterial cell will produce type 1 fimbriae. In this review, we present aspects of signaling and stress involved in mediating regulation of type 1 fimbriae in extraintestinal E. coli; in particular, how certain regulatory mechanisms, some of which are linked to stress response, can influence production of fimbriae and influence bacterial colonization and infection. We suggest that regulation of type 1 fimbriae is potentially linked to environmental stress responses, providing a perspective for how environmental cues in the host and bacterial stress response during infection both play an important role in regulating extraintestinal pathogenic E. coli colonization and virulence.
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Affiliation(s)
- Hicham Bessaiah
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 0B1, Canada
| | - Carole Anamalé
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
| | - Jacqueline Sung
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 0B1, Canada
| | - Charles M. Dozois
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (H.B.); (C.A.); (J.S.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
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21
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The hdeD Gene Represses the Expression of Flagella Biosynthesis via LrhA in Escherichia coli K-12. J Bacteriol 2021; 204:e0042021. [PMID: 34694904 DOI: 10.1128/jb.00420-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli survives under acid stress conditions by the glutamic acid-dependent acid resistance (GAD) system, which enzymatically decreases intracellular protons. We found a linkage between GAD and flagellar systems in E. coli. The hdeD gene, one of the GAD cluster genes, encodes an uncharacterized membrane protein. A reporter assay showed that the hdeD promoter was induced in a GadE-dependent manner when grown in the M9 glycerol medium. Transcriptome analysis revealed that most of the transcripts were from genes involved in flagella synthesis, and cell motility increased not only in the hdeD-deficient mutant but also in the gadE-deficient mutant. Defects in both the hdeD and gadE increased the intracellular level of FliA, an alternative sigma factor for flagella synthesis, activated by the master regulator FlhDC. The promoter activity of the lrhA gene, which encodes repressor for the flhDC operon, was found to decrease in both the hdeD- and gadE-deficient mutants. Transmission electron microscopy showed that the number of flagellar filaments on the hdeD-, gadE-, and lrhA-deficient cells increased, and all three mutants showed higher motility than the parent strain. Thus, HdeD in the GAD system activates the lrhA promoter, resulting in a decrease in flagellar filaments in E. coli cells. We speculated that the synthesis of HdeD, stimulated in E. coli exposed to acid stress, could control the flagella biosynthesis by sensing slight changes in pH at the cytoplasmic membrane. This could help in saving energy through termination of flagella biosynthesis and improve bacterial survival efficiency within the animal digestive system. IMPORTANCE E. coli cells encounter various environments from the mouth down to the intestines within the host animals. The pH of gastric juice is lower than 2.0, and the bacterial must quickly respond and adapt to the following environmental changes before reaching the intestines. The quick response plays a role in cellular survival in the population, whereas adaptation may contribute to species survival. The GAD and flagella systems are important for response to low pH in E. coli. Here, we identified the novel inner membrane regulator HdeD, encoding in the GAD cluster, to repress the synthesis of flagella. These insights provide a deeper understanding of how the bacteria enter the animal digestive system, survive, and form colonies in the intestines.
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22
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Gu X, Zhao J, Zhang R, Yu R, Guo T, Kong J. Molecular Analysis of Glutamate Decarboxylases in Enterococcus avium. Front Microbiol 2021; 12:691968. [PMID: 34566904 PMCID: PMC8461050 DOI: 10.3389/fmicb.2021.691968] [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: 04/07/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Enterococcus avium (E. avium) is a common bacterium inhabiting the intestines of humans and other animals. Most strains of this species can produce gamma-aminobutyric acid (GABA) via the glutamate decarboxylase (GAD) system, but the presence and genetic organization of their GAD systems are poorly characterized. In this study, our bioinformatics analyses showed that the GAD system in E. avium strains was generally encoded by three gadB genes (gadB1, gadB2, and gadB3), together with an antiporter gene (gadC) and regulator gene (gadR), and these genes are organized in a cluster. This finding contrasts with that for other lactic acid bacteria. E. avium SDMCC050406, a GABA producer isolated from human feces, was employed to investigate the contribution of the three gadB genes to GABA biosynthesis. The results showed that the relative expression level of gadB3 was higher than those of gadB1 and gadB2 in the exponential growth and stationary phases, and this was accompanied by the synchronous transcription of gadC. After heterologous expression of the three gadB genes in Escherichia coli BL21 (DE3), the Km value of the purified GAD3 was 4.26 ± 0.48 mM, a value lower than those of the purified GAD1 and GAD2. Moreover, gadB3 gene inactivation caused decreased GABA production, accompanied by a reduction in resistance to acid stress. These results indicated that gadB3 plays a crucial role in GABA biosynthesis and this property endowed the strain with acid tolerance. Our findings provided insights into how E. avium strains survive the acidic environments of fermented foods and throughout transit through the stomach and gut while maintaining cell viability.
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Affiliation(s)
- Xinyi Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jiancun Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rongling Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruohan Yu
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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23
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Du C, Huo X, Gu H, Wu D, Hu Y. Acid resistance system CadBA is implicated in acid tolerance and biofilm formation and is identified as a new virulence factor of Edwardsiella tarda. Vet Res 2021; 52:117. [PMID: 34521475 PMCID: PMC8438976 DOI: 10.1186/s13567-021-00987-x] [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: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
Edwardsiella tarda is a facultative intracellular pathogen in humans and animals. The Gram-negative bacterium is widely considered a potentially important bacterial pathogen. Adaptation to acid stress is important for the transmission of intestinal microbes, so the acid-resistance (AR) system is essential. However, the AR systems of E. tarda are totally unknown. In this study, a lysine-dependent acid resistance (LDAR) system in E. tarda, CadBA, was characterized and identified. CadB is a membrane protein and shares high homology with the lysine/cadaverine antiporter. CadA contains a PLP-binding core domain and a pyridoxal phosphate-binding motif. It shares high homology with lysine decarboxylase. cadB and cadA are co-transcribed under one operon. To study the function of the cadBA operon, isogenic cadA, cadB and cadBA deletion mutant strains TX01ΔcadA, TX01ΔcadB and TX01ΔcadBA were constructed. When cultured under normal conditions, the wild type strain and three mutants exhibited the same growth performance. However, when cultured under acid conditions, the growth of three mutants, especially TX01ΔcadA, were obviously retarded, compared to the wild strain TX01, which indicates the important involvement of the cadBA operon in acid resistance. The deletion of cadB or cadA, especially cadBA, significantly attenuated bacterial activity of lysine decarboxylase, suggesting the vital participation of cadBA operon in lysine metabolism, which is closely related to acid resistance. The mutations of cadBA operon enhanced bacterial biofilm formation, especially under acid conditions. The deletions of the cadBA operon reduced bacterial adhesion and invasion to Hela cells. Consistently, the deficiency of cadBA operon abated bacterial survival and replication in macrophages, and decreased bacterial dissemination in fish tissues. Our results also show that the expression of cadBA operon and regulator cadC were up-regulated upon acid stress, and CadC rigorously regulated the expression of cadBA operon, especially under acid conditions. These findings demonstrate that the AR CadBA system was a requisite for the resistance of E. tarda against acid stress, and played a critical role in bacterial infection of host cells and in host tissues. This is the first study about the acid resistance system of E. tarda and provides new insights into the acid-resistance mechanism and pathogenesis of E. tarda.
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Affiliation(s)
- Chunmei Du
- College of Basic Medicine, Jiamusi University, 154007, Jiamusi, China.,Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,College of Life Science, Jiamusi University, 154007, Jiamusi, China
| | - Xiaoping Huo
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,College of Life Science, Jiamusi University, 154007, Jiamusi, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, 571101, Haikou, China
| | - Dongmei Wu
- College of Basic Medicine, Jiamusi University, 154007, Jiamusi, China. .,Heilongjiang Provincial Key Laboratory of New Drug Development and Evaluation of the Efficacy of Toxicology, 154007, Jiamusi, China.
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266071, Qingdao, China. .,College of Life Science, Jiamusi University, 154007, Jiamusi, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, 571101, Haikou, China.
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Wu D, Qi W, Nie W, Lu Z, Ye Y, Li J, Sun T, Zhu Y, Cheng H, Wang X. BacFlash signals acid-resistance gene expression in bacteria. Cell Res 2021; 31:703-712. [PMID: 33159153 PMCID: PMC8169942 DOI: 10.1038/s41422-020-00431-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/14/2020] [Indexed: 11/08/2022] Open
Abstract
Intracellular pH (pHi) homeostasis is crucial for cellular functions and signal transduction across all kingdoms of life. In particular, bacterial pHi homeostasis is important for physiology, ecology, and pathogenesis. Here we report an exquisite bacterial acid-resistance (AR) mechanism in which proton leak elicits a pre-emptive AR response. A single bacterial cell undergoes quantal electrochemical excitation, termed "BacFlash", which consists of membrane depolarization, transient pHi rise, and bursting production of reactive oxygen species. BacFlash ignition is dictated by acid stress in the form of proton leak across the plasma membrane and the rate of BacFlash occurrence is reversely correlated with the pHi buffering capacity. Through genome-wide screening, we further identify the ATP synthase Fo complex subunit a as the putative proton sensor for BacFlash biogenesis. Importantly, persistent BacFlash hyperactivity activates transcription of a panel of key AR genes and predisposes the cells to survive imminent extreme acid stress. These findings demonstrate a prototypical coupling between electrochemical excitation and nucleoid gene expression in prokaryotes.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Wenfeng Qi
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Wei Nie
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Zhengyuan Lu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Yongxin Ye
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Jinghang Li
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Tao Sun
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Yufei Zhu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China.
| | - Xianhua Wang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China.
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Characterization and comparative genomic analysis of gamma-aminobutyric acid (GABA)-producing lactic acid bacteria from Thai fermented foods. Biotechnol Lett 2021; 43:1637-1648. [PMID: 33999363 DOI: 10.1007/s10529-021-03140-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/23/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to screen, characterize, and annotate the genome along with the comparison of GABA synthesis genes presented in lactic acid bacteria (LAB). RESULTS Thirty-five LAB isolates from fermented foods were screened for GABA production using thin-layer chromatography (TLC). Fifteen isolates produced GABA ranging from 0.07 to 22.94 g/L. Based on their GTG5 profiles, phenotypic, and genotypic characteristics, isolates LSI1-1, LSI1-5, LSI2-1, LSI2-2, LSI2-3, LSI2-5, and LSM3-1-4 were identified as Lactobacillus plantarum subsp. plantarum; isolate LSM1-4 was Lactobacillus argentoratensis; isolates CAB1-2, CAB1-5, CAB1-7, and LSI1-4 were Lactobacillus pentosus; and CAB1-1, LSM3-1-1 and LSM3-2-3 were Lactobacillus fermentum. Strains LSI2-1 and CAB1-7 from pickled vegetables were selected for genome analysis. The gadA gene (1410 bp, 470aa) was encountered in GABA production of both strains and no other glutamate decarboxylase (GAD) genes were found in the genomes when compared with other LAB strains. The presence of gadA is evidence for GABA production. Strains LSI2-1 and CAB1-7 produced 22.94 g/L and 11.59 g/L of GABA in GYP broth supplemented with 3% (w/v) MSG at 30 °C for 72 h, respectively. CONCLUSIONS Our report highlights the characterization of LAB and GABA production of L. plantarum LSI2-1 strain with its GABA synthesis gene. GABA production of strains LSI2-1 and CAB1-7 in GYP broth with 3% (w/v) MSG and comparative GAD genes.
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Sheikh SW, Ali A, Ahsan A, Shakoor S, Shang F, Xue T. Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli. Antibiotics (Basel) 2021; 10:522. [PMID: 34063307 PMCID: PMC8147483 DOI: 10.3390/antibiotics10050522] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.
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Affiliation(s)
- Salma Waheed Sheikh
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Asma Ahsan
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Punjab, Pakistan;
| | - Sidra Shakoor
- Station de Neucfchateau, CIRAD, 97130 Sainte-Marie, Capesterre Belle Eau, Guadeloupe, France;
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
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27
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Lauxen AI, Kobauri P, Wegener M, Hansen MJ, Galenkamp NS, Maglia G, Szymanski W, Feringa BL, Kuipers OP. Mechanism of Resistance Development in E. coli against TCAT, a Trimethoprim-Based Photoswitchable Antibiotic. Pharmaceuticals (Basel) 2021; 14:ph14050392. [PMID: 33919397 PMCID: PMC8143356 DOI: 10.3390/ph14050392] [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: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
During the last decades, a continuous rise of multi-drug resistant pathogens has threatened antibiotic efficacy. To tackle this key challenge, novel antimicrobial therapies are needed with increased specificity for the site of infection. Photopharmacology could enable such specificity by allowing for the control of antibiotic activity with light, as exemplified by trans/cis-tetra-ortho-chloroazobenzene-trimethoprim (TCAT) conjugates. Resistance development against the on (irradiated, TCATa) and off (thermally adapted, TCATd) states of TCAT were compared to that of trimethoprim (TMP) in Escherichia coli mutant strain CS1562. Genomics and transcriptomics were used to explore the acquired resistance. Although TCAT shows TMP-like dihydrofolate reductase (DHFR) inhibition in vitro, transcriptome analyses show different responses in acquired resistance. Resistance against TCATa (on) relies on the production of exopolysaccharides and overexpression of TolC. While resistance against TCATd (off) follows a slightly different gene expression profile, both indicate hampering the entrance of the molecule into the cell. Conversely, resistance against TMP is based on alterations in cell metabolism towards a more persister-like phenotype, as well as alteration of expression levels of enzymes involved in the folate biosynthesis. This study provides a deeper understanding of the development of new therapeutic strategies and the consequences on resistance development against photopharmacological drugs.
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Affiliation(s)
- Anna I. Lauxen
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
| | - Piermichele Kobauri
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Michael Wegener
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Mickel J. Hansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Nicole S. Galenkamp
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Giovanni Maglia
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Medical Imaging Center, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
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28
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Laroute V, Mazzoli R, Loubière P, Pessione E, Cocaign-Bousquet M. Environmental Conditions Affecting GABA Production in Lactococcus lactis NCDO 2118. Microorganisms 2021; 9:microorganisms9010122. [PMID: 33430203 PMCID: PMC7825684 DOI: 10.3390/microorganisms9010122] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/19/2023] Open
Abstract
GABA (γ-aminobutyric acid) production has been widely described as an adaptive response to abiotic stress, allowing bacteria to survive in harsh environments. This work aimed to clarify and understand the relationship between GABA production and bacterial growth conditions, with particular reference to osmolarity. For this purpose, Lactococcus lactis NCDO 2118, a GABA-producing strain, was grown in glucose-supplemented chemically defined medium containing 34 mM L-glutamic acid, and different concentrations of salts (chloride, sulfate or phosphate ions) or polyols (sorbitol, glycerol). Unexpectedly, our data demonstrated that GABA production was not directly related to osmolarity. Chloride ions were the most significant factor influencing GABA yield in response to acidic stress while sulfate ions did not enhance GABA production. We demonstrated that the addition of chloride ions increased the glutamic acid decarboxylase (GAD) synthesis and the expression of the gadBC genes. Finally, under fed-batch conditions in a complex medium supplemented with 0.3 M NaCl and after a pH shift to 4.6, L. lactis NCDO 2118 was able to produce up to 413 mM GABA from 441 mM L-glutamic acid after only 56 h of culture, revealing the potential of L. lactis strains for intensive production of this bioactive molecule.
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Affiliation(s)
- Valérie Laroute
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France;
- Correspondence: (V.L.); (M.C.-B.)
| | - Roberto Mazzoli
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.M.); (E.P.)
| | - Pascal Loubière
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France;
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; (R.M.); (E.P.)
| | - Muriel Cocaign-Bousquet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France;
- Correspondence: (V.L.); (M.C.-B.)
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29
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Arcari T, Feger ML, Guerreiro DN, Wu J, O’Byrne CP. Comparative Review of the Responses of Listeria monocytogenes and Escherichia coli to Low pH Stress. Genes (Basel) 2020; 11:genes11111330. [PMID: 33187233 PMCID: PMC7698193 DOI: 10.3390/genes11111330] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Acidity is one of the principal physicochemical factors that influence the behavior of microorganisms in any environment, and their response to it often determines their ability to grow and survive. Preventing the growth and survival of pathogenic bacteria or, conversely, promoting the growth of bacteria that are useful (in biotechnology and food production, for example), might be improved considerably by a deeper understanding of the protective responses that these microorganisms deploy in the face of acid stress. In this review, we survey the molecular mechanisms used by two unrelated bacterial species in their response to low pH stress. We chose to focus on two well-studied bacteria, Escherichia coli (phylum Proteobacteria) and Listeria monocytogenes (phylum Firmicutes), that have both evolved to be able to survive in the mammalian gastrointestinal tract. We review the mechanisms that these species use to maintain a functional intracellular pH as well as the protective mechanisms that they deploy to prevent acid damage to macromolecules in the cells. We discuss the mechanisms used to sense acid in the environment and the regulatory processes that are activated when acid is encountered. We also highlight the specific challenges presented by organic acids. Common themes emerge from this comparison as well as unique strategies that each species uses to cope with acid stress. We highlight some of the important research questions that still need to be addressed in this fascinating field.
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30
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Insights on the genetic features of endometrial pathogenic Escherichia coli strains from pyometra in companion animals: Improving the knowledge about pathogenesis. INFECTION GENETICS AND EVOLUTION 2020; 85:104453. [DOI: 10.1016/j.meegid.2020.104453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/11/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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31
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RNase E-dependent degradation of tnaA mRNA encoding tryptophanase is prerequisite for the induction of acid resistance in Escherichia coli. Sci Rep 2020; 10:7128. [PMID: 32346014 PMCID: PMC7188888 DOI: 10.1038/s41598-020-63981-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/09/2020] [Indexed: 01/25/2023] Open
Abstract
Acid-resistance systems are essential for pathogenic Escherichia coli to survive in the strongly acidic environment of the human stomach (pH < 2.5). Among these, the glutamic acid decarboxylase (GAD) system is the most effective. However, the precise mechanism of GAD induction is unknown. We previously reported that a tolC mutant lacking the TolC outer membrane channel was defective in GAD induction. Here, we show that indole, a substrate of TolC-dependent efflux pumps and produced by the tryptophanase encoded by the tnaA gene, negatively regulates GAD expression. GAD expression was restored by deleting tnaA in the tolC mutant; in wild-type E. coli, it was suppressed by adding indole to the growth medium. RNA-sequencing revealed that tnaA mRNA levels drastically decreased upon exposure to moderately acidic conditions (pH 5.5). This decrease was suppressed by RNase E deficiency. Collectively, our results demonstrate that the RNase E-dependent degradation of tnaA mRNA is accelerated upon acid exposure, which decreases intracellular indole concentrations and triggers GAD induction.
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32
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An acid-tolerance response system protecting exponentially growing Escherichia coli. Nat Commun 2020; 11:1496. [PMID: 32198415 PMCID: PMC7083825 DOI: 10.1038/s41467-020-15350-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 03/05/2020] [Indexed: 01/05/2023] Open
Abstract
The ability to grow at moderate acidic conditions (pH 4.0–5.0) is important to Escherichia coli colonization of the host’s intestine. Several regulatory systems are known to control acid resistance in E. coli, enabling the bacteria to survive under acidic conditions without growth. Here, we characterize an acid-tolerance response (ATR) system and its regulatory circuit, required for E. coli exponential growth at pH 4.2. A two-component system CpxRA directly senses acidification through protonation of CpxA periplasmic histidine residues, and upregulates the fabA and fabB genes, leading to increased production of unsaturated fatty acids. Changes in lipid composition decrease membrane fluidity, F0F1-ATPase activity, and improve intracellular pH homeostasis. The ATR system is important for E. coli survival in the mouse intestine and for production of higher level of 3-hydroxypropionate during fermentation. Furthermore, this ATR system appears to be conserved in other Gram-negative bacteria. The ability to grow at acidic pH is crucial for E. coli colonization of the host’s intestine. Here, the authors identify an acid-tolerance response system that is important for E. coli exponential growth at pH 4.2, survival in the mouse intestine, and production of 3-hydroxypropionate during fermentation.
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33
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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34
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López-Santiago R, Sánchez-Argáez AB, De Alba-Núñez LG, Baltierra-Uribe SL, Moreno-Lafont MC. Immune Response to Mucosal Brucella Infection. Front Immunol 2019; 10:1759. [PMID: 31481953 PMCID: PMC6710357 DOI: 10.3389/fimmu.2019.01759] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/11/2019] [Indexed: 01/18/2023] Open
Abstract
Brucellosis is one of the most prevalent bacterial zoonosis of worldwide distribution. The disease is caused by Brucella spp., facultative intracellular pathogens. Brucellosis in animals results in abortion of fetuses, while in humans, it frequently manifests flu-like symptoms and a typical undulant fever, being osteoarthritis a common complication of the chronic infection. The two most common ways to acquire the infection in humans are through the ingestion of contaminated dairy products or by inhalation of contaminated aerosols. Brucella spp. enter the body mainly through the gastrointestinal and respiratory mucosa; however, most studies of immune response to Brucella spp. are performed analyzing models of systemic immunity. It is necessary to better understand the mucosal immune response induced by Brucella infection since this is the main entry site for the bacterium. In this review, some virulence factors and the mechanisms needed for pathogen invasion and persistence are discussed. Furthermore, some aspects of local immune responses induced during Brucella infection will be reviewed. With this knowledge, better vaccines can be designed focused on inducing protective mucosal immune response.
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Affiliation(s)
- Rubén López-Santiago
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ana Beatriz Sánchez-Argáez
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Liliana Gabriela De Alba-Núñez
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - Martha Cecilia Moreno-Lafont
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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35
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Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
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36
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Retnoningrum DS, Santika IWM, Kesuma S, Ekowati SA, Riani C. Construction and Characterization of a Medium Copy Number Expression Vector Carrying Auto-Inducible dps Promoter to Overproduce a Bacterial Superoxide Dismutase in Escherichia coli. Mol Biotechnol 2019; 61:231-240. [PMID: 30721405 DOI: 10.1007/s12033-018-00151-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Medium copy number expression vector and auto-inducible promoter could be a solution for producing recombinant therapeutic proteins in industrial scale regarding plasmid stability, cost, and product quality. This work aimed to construct a medium copy number pBR322-based expression vector carrying auto-inducible promoter, determine its ability to express heterologous gene, and study its segregational stability. Three stationary-phase promoters of Escherichia coli genes (gadA, dps and sbmC) were used to produce a superoxide dismutase from Staphylococcus equorum (rMnSODSeq) coding region from pBR322Δtet (pBR322-mini). Four plasmids were constructed with different promoters, i.e., T7 (pBMsod), gadA (pMCDsod), dps (pCADsod), and sbmC (pCDSsod) using pBR322-mini as backbone. Results showed that rMnSODSeq expression from pBMsod was significantly higher than that from pJExpress414sod (high copy number plasmid). Meanwhile, rMnSODSeq from pCADsod (auto-inducible promoter) was as high as from pBMsod (IPTG-inducible T7 promoter). rMnSODSeq expressed from pCADsod when bacterial cells entered stationary phase appeared as an active protein band of 23.5 kDa when analyzed by zymography and SDS-PAGE. pCADsod displayed the highest stability compared with pBMsod and pJEXpress414sod by plasmid retention assay. We demonstrate the use of an auto-inducible dps promoter to express high level of heterologous protein, an SOD of S. equorum, from a stable expression vector with medium copy number.
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Affiliation(s)
- Debbie Soefie Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | - I Wayan Martadi Santika
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Suryanata Kesuma
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Syahdu Ayu Ekowati
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Catur Riani
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, 40132, Indonesia
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37
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Krammer EM, Prévost M. Function and Regulation of Acid Resistance Antiporters. J Membr Biol 2019; 252:465-481. [DOI: 10.1007/s00232-019-00073-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/08/2019] [Indexed: 01/07/2023]
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38
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Xu J, Li T, Gao Y, Deng J, Gu J. MgrB affects the acid stress response of Escherichia coli by modulating the expression of iraM. FEMS Microbiol Lett 2019; 366:fnz123. [PMID: 31158277 DOI: 10.1093/femsle/fnz123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/01/2019] [Indexed: 10/18/2023] Open
Abstract
Although MgrB is established to be a feedback inhibitor of the PhoP/Q system in Escherichia coli, the biological functions of MgrB remain largely unknown. To explore new functions of MgrB, a comparative transcriptome analysis was performed (E. coli K-12 W3110 ΔmgrB vs E. coli K-12 W3110). The results showed that many genes involved in acid stress are upregulated, suggesting that MgrB is related to acid sensitivity in E. coli. The survival rates under acid stress of the ΔmgrB mutant and wild-type showed that deletion of mgrB resulted in acid resistance. According to previous research, we deleted phoP, phoQ and iraM in the ΔmgrB mutant, and found that further deletion of phoP/phoQ only partially restored acid sensitivity. Additionally, we found that deletion of mgrB resulted in increased accumulation of RpoS during the exponential growth phase, which could be blocked by further deletion of iraM. Mutation of iraM or rpoS completely suppressed the effect of mgrB mutation on acid resistance. Taken together, the data suggest that MgrB affects the acid resistance of E. coli by modulating the expression of iraM, but not completely through PhoP/Q. This indicates that MgrB may have other protein interactors aside from PhoQ, which merits further investigation.
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Affiliation(s)
- Jintian Xu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ting Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yunrong Gao
- The Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou 510623, China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan Institude of Industrial Technology, Chinese Academic of Sciences, Foshan 528000, China
| | - Jing Gu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Wang D, Li H, Ma X, Tang Y, Tang H, Hu X, Liu Z. Small RNA AvrA Regulates IscR to Increase the Stress Tolerances in SmpB Deficiency of Aeromonas veronii. Front Cell Infect Microbiol 2019; 9:142. [PMID: 31192158 PMCID: PMC6517841 DOI: 10.3389/fcimb.2019.00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
The superbacteria Aeromonas veronii displays not only a strong pathogenicity but also the resistance to nine kinds of antibiotics, resulting in the economic losses and health hazards. Small Protein B (SmpB) plays an important role in protein quality control, virulence, and stress reactions. Transcriptomic data revealed that expressions of the type IV pilus assembly and type VI secretion system (T6SS) proteins were downregulated in SmpB deficiency, indicating that the virulence of A. veronii might be attenuated. Although SmpB deletion decreased colonization in the mouse spleen and liver, LD50 of the smpB mutant was not altered as expected, compared with the wild type. Further, the transcriptomic and quantitative RT-PCR analyses showed that the combination of the downregulated AvrA and the upregulated iron-sulfur protein activator IscR, mediated the oxidative tolerance in smpB deletion. Next a reporter plasmid was constructed in which the promoter of iscR was applied to control the expression of the enhanced green fluorescent protein (eGFP) gene. When the reporter plasmid was co-expressed with the AvrA expression into E. coli, the relative fluorescence intensity was decreased significantly, suggesting that AvrA bound to iscR mRNA by base pairing, which in turn relieved the inhibition of iscR and intensified the downstream iron-sulfur proteins. Collectively, the smpB mutant exhibited an attenuated virulence in mice and enhanced tolerances to oxidative stress. This study demonstrates the complexity of gene regulation networks mediated by sRNA in systems biology, and also reflects the strong adaptability of superbacteria A. veronii in the process of evolution.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hongqian Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xinwen Hu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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40
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Establishment of Listeria monocytogenes in the Gastrointestinal Tract. Microorganisms 2019; 7:microorganisms7030075. [PMID: 30857361 PMCID: PMC6463042 DOI: 10.3390/microorganisms7030075] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes is a Gram positive foodborne pathogen that can colonize the gastrointestinal tract of a number of hosts, including humans. These environments contain numerous stressors such as bile, low oxygen and acidic pH, which may impact the level of colonization and persistence of this organism within the GI tract. The ability of L. monocytogenes to establish infections and colonize the gastrointestinal tract is directly related to its ability to overcome these stressors, which is mediated by the efficient expression of several stress response mechanisms during its passage. This review will focus upon how and when this occurs and how this impacts the outcome of foodborne disease.
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Chakraborty S, Kenney LJ. A New Role of OmpR in Acid and Osmotic Stress in Salmonella and E. coli. Front Microbiol 2018; 9:2656. [PMID: 30524381 PMCID: PMC6262077 DOI: 10.3389/fmicb.2018.02656] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022] Open
Abstract
Bacteria survive and respond to diverse environmental conditions and during infection inside the host by systematic regulation of stress response genes. E. coli and S. Typhimurium can undergo large changes in intracellular osmolality (up to 1.8 Osmol/kg) and can tolerate cytoplasmic acidification to at least pHi 5.6. Recent analyses of single cells challenged a long held view that bacteria respond to extracellular acid stress by rapid acidification followed by a rapid recovery. It is now appreciated that both S. Typhimurium and E. coli maintain an acidic cytoplasm through the actions of the outer membrane protein regulator OmpR via its regulation of distinct signaling pathways. However, a comprehensive comparison of OmpR regulons between S. Typhimurium and E. coli is lacking. In this study, we examined the expression profiles of wild-type and ompR null strains of the intracellular pathogen S. Typhimurium and a commensal E. coli in response to acid and osmotic stress. Herein, we classify distinct OmpR regulons and also identify shared OmpR regulatory pathways between S. Typhimurium and E. coli in response to acid and osmotic stress. Our study establishes OmpR as a key regulator of bacterial virulence, growth and metabolism, in addition to its role in regulating outer membrane proteins.
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Affiliation(s)
- Smarajit Chakraborty
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Linda J. Kenney
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- Departments of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, United States
- Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
- Jesse Brown Veterans Administration Medical Center, Chicago, IL, United States
- *Correspondence: Linda J. Kenney,
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Pennacchietti E, D'Alonzo C, Freddi L, Occhialini A, De Biase D. The Glutaminase-Dependent Acid Resistance System: Qualitative and Quantitative Assays and Analysis of Its Distribution in Enteric Bacteria. Front Microbiol 2018; 9:2869. [PMID: 30498489 PMCID: PMC6250119 DOI: 10.3389/fmicb.2018.02869] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/08/2018] [Indexed: 12/22/2022] Open
Abstract
Neutralophilic bacteria have developed several strategies to overcome the deleterious effects of acid stress. In particular, the amino acid-dependent systems are widespread, with their activities overlapping, covering a rather large pH range, from 6 to <2. Recent reports showed that an acid resistance (AR) system relying on the amino acid glutamine (AR2_Q), the most readily available amino acid in the free form, is operative in Escherichia coli, Lactobacillus reuteri, and some Brucella species. This system requires a glutaminase active at acidic pH and the antiporter GadC to import L-glutamine and export either glutamate (the glutamine deamination product) or GABA. The latter occurs when the deamination of glutamine to glutamate, via acid-glutaminase (YbaS/GlsA), is coupled to the decarboxylation of glutamate to GABA, via glutamate decarboxylase (GadB), a structural component of the glutamate-dependent AR (AR2) system, together with GadC. Taking into account that AR2_Q could be widespread in bacteria and that until now assays based on ammonium ion detection were typically employed, this work was undertaken with the aim to develop assays that allow a straightforward identification of the acid-glutaminase activity in permeabilized bacterial cells (qualitative assay) as well as a sensitive method (quantitative assay) to monitor in the pH range 2.5-4.0 the transport of the relevant amino acids in vivo. The qualitative assay is colorimetric, rapid and reliable and provides several additional information, such as co-occurrence of AR2 and AR2_Q in the same bacterial species and assessment of the growth conditions that support maximal expression of glutaminase at acidic pH. The quantitative assay is HPLC-based and allows to concomitantly measure the uptake of glutamine and the export of glutamate and/or GABA via GadC in vivo and depending on the external pH. Finally, an extensive bioinformatic genome analysis shows that the gene encoding the glutaminase involved in AR2_Q is often nearby or in operon arrangement with the genes coding for GadC and GadB. Overall, our results indicate that AR2_Q is likely to be of prominent importance in the AR of enteric bacteria and that it modulates the enzymatic as well as antiport activities depending on the imposed acidic stress.
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Affiliation(s)
- Eugenia Pennacchietti
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Chiara D'Alonzo
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Luca Freddi
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Alessandra Occhialini
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory Affiliated to the Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
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Cardoso MH, de Almeida KC, Cândido ES, Fernandes GDR, Dias SC, de Alencar SA, Franco OL. Comparative transcriptome analyses of magainin I-susceptible and -resistant Escherichia coli strains. Microbiology (Reading) 2018; 164:1383-1393. [DOI: 10.1099/mic.0.000725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marlon H. Cardoso
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
| | - Keyla C. de Almeida
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
| | - Elizabete S. Cândido
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
| | - Gabriel da R. Fernandes
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 4Oswaldo Cruz Foundation, René Rachou Research Center, Belo Horizonte, MG, Brazil
| | - Simoni C. Dias
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 5Programa de Pós Graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil
| | - Sérgio A. de Alencar
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
| | - Octávio L. Franco
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
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Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC. Sci Rep 2018; 8:15607. [PMID: 30353119 PMCID: PMC6199258 DOI: 10.1038/s41598-018-33963-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/08/2018] [Indexed: 12/02/2022] Open
Abstract
The arginine-agmatine antiporter (AdiC) is a component of an acid resistance system developed by enteric bacteria to resist gastric acidity. In order to avoid neutral proton antiport, the monovalent form of arginine, about as abundant as its divalent form under acidic conditions, should be selectively bound by AdiC for transport into the cytosol. In this study, we shed light on the mechanism through which AdiC distinguishes Arg+ from Arg2+ of arginine by investigating the binding of both forms in addition to that of divalent agmatine, using a combination of molecular dynamics simulations with molecular and quantum mechanics calculations. We show that AdiC indeed preferentially binds Arg+. The weaker binding of divalent compounds results mostly from their greater tendency to remain hydrated than Arg+. Our data suggests that the binding of Arg+ promotes the deprotonation of Glu208, a gating residue, which in turn reinforces its interactions with AdiC, leading to longer residence times of Arg+ in the binding site. Although the total electric charge of the ligand appears to be the determinant factor in the discrimination process, two local interactions formed with Trp293, another gating residue of the binding site, also contribute to the selection mechanism: a cation-π interaction with the guanidinium group of Arg+ and an anion-π interaction involving Glu208.
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45
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Chaurasiya SK. Tuberculosis: Smart manipulation of a lethal host. Microbiol Immunol 2018; 62:361-379. [PMID: 29687912 DOI: 10.1111/1348-0421.12593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/21/2018] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a global threat to human health. Development of drug resistance and co-infection with HIV has increased the morbidity and mortality caused by TB. Macrophages serve as primary defense against microbial infections, including TB. Upon recognition and uptake of mycobacteria, macrophages initiate a series of events designed to lead to generation of effective immune responses and clearance of infection. However, pathogenic mycobacteria utilize multiple mechanisms for manipulating macrophage responses to protect itself from being killed and to survive within these cells that are designed to kill them. The outcomes of mycobacterial infection are determined by several host- and pathogen-related factors. Significant advancements in understanding mycobacterial pathogenesis have been made in recent years. In this review, some of the important factors/mechanisms regulating mycobacterial survival inside macrophages are discussed.
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Affiliation(s)
- Shivendra K Chaurasiya
- Host-pathogen Interaction and Signal Transduction Laboratory, Department of Microbiology, School of Biological Sciences, Dr. Hari Singh Gour University, Sagar, MP-470003, India
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46
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Chen S, Li X, Wang Y, Zeng J, Ye C, Li X, Guo L, Zhang S, Yu X. Induction of Escherichia coli into a VBNC state through chlorination/chloramination and differences in characteristics of the bacterium between states. WATER RESEARCH 2018; 142:279-288. [PMID: 29890476 DOI: 10.1016/j.watres.2018.05.055] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 05/22/2023]
Abstract
Many pathogens can enter into a viable but nonculturable (VBNC) state in response to harsh environmental stresses. Bacteria in this state can retain certain features of viable cells, such as cellular integrity, metabolic activity, or virulence and may present health risks associated with drinking water. In this study, we investigated the ability of chlorination and chloramination, which are widely used methods to disinfect drinking water, to induce Escherichia coli into a VBNC state. After treatment with chlorine and chloramine at concentrations of 1, 2, 3, and 4 mg/L, the counts of culturable E. coli cells decreased from 106 CFU/mL to 0 CFU/mL at 5-60 min post treatment. Meanwhile, viable cell counts were still approximately 103-105 cells/mL. These viable E. coli cells may be induced into a VBNC state by chlorination and chloramination. Scanning electron microscopy and laser confocal microscopy showed that some bacteria maintained cellular integrity, but the average length of VBNC cells was less than that of culturable cells. Respiratory activity of VBNC cells decreased approximately 50% relative to that of culturable cells. We also used heavy water (D2O) combined with Raman microspectroscopy to show that E. coli in a VBNC state retained metabolic activity involving water (e.g. condensation reactions) at the single-cell level. Furthermore, soxR, gadA, and katG genes remained highly expressed, suggesting that VBNC cells were physiologically active. Finally, resuscitation of VBNC cells induced by chlorine in Luria-Bertani (LB) broth was identified by calculating the generation time. Results of this study will facilitate a better understanding of the health risks associated with VBNC bacteria and the development of more effective strategies for drinking water disinfection.
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Affiliation(s)
- Sheng Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xi Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yahong Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jie Zeng
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xianping Li
- College of Environment & Ecology, Xiamen University, Xiamen 361021, PR China
| | - Lizheng Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shenghua Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China.
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China.
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Zhang B, Ran L, Wu M, Li Z, Jiang J, Wang Z, Cheng S, Fu J, Liu X. Shigellaflexneri Regulator SlyA Controls Bacterial Acid Resistance by Directly Activating the Glutamate Decarboxylation System. Front Microbiol 2018; 9:2071. [PMID: 30233544 PMCID: PMC6128205 DOI: 10.3389/fmicb.2018.02071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 01/02/2023] Open
Abstract
Shigella flexneri is an important foodborne bacterial pathogen with infectious dose as low as 10–100 cells. SlyA, a transcriptional regulator of the MarR family, has been shown to regulate virulence in a closely related bacterial pathogen, Salmonella Typhimurium. However, the regulatory role of SlyA in S. flexneri is less understood. Here we applied unbiased proteomic profiling to define the SlyA regulon in S. flexneri. We found that the genetic ablation of slyA led to the alteration of 18 bacterial proteins among over 1400 identifications. Intriguingly, most down-regulated proteins (whose expression is SlyA-dependent) were associated with bacterial acid resistance such as the glutamate decarboxylation system. We further demonstrated that SlyA directly regulates the expression of GadA, a glutamate decarboxylase, by binding to the promotor region of its coding gene. Importantly, overexpression of GadA was able to rescue the survival defect of the ΔslyA mutant under acid stress. Therefore, our study highlights a major role of SlyA in controlling S. flexneri acid resistance and provides a molecular mechanism underlying such regulation as well.
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Affiliation(s)
- Buyu Zhang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Longhao Ran
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Mei Wu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Zezhou Li
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jiezhang Jiang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Zhen Wang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Sen Cheng
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jiaqi Fu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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48
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Smith A, Kaczmar A, Bamford RA, Smith C, Frustaci S, Kovacs-Simon A, O'Neill P, Moore K, Paszkiewicz K, Titball RW, Pagliara S. The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli. Front Microbiol 2018; 9:1739. [PMID: 30158905 PMCID: PMC6104134 DOI: 10.3389/fmicb.2018.01739] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.
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Affiliation(s)
- Ashley Smith
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kaczmar
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Simona Frustaci
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
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Biofuel production with a stress-resistant and growth phase-independent promoter: mechanism revealed by in vitro transcription assays. Appl Microbiol Biotechnol 2018; 102:2929-2940. [DOI: 10.1007/s00253-018-8809-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
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50
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PknG supports mycobacterial adaptation in acidic environment. Mol Cell Biochem 2017; 443:69-80. [PMID: 29124568 DOI: 10.1007/s11010-017-3211-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/14/2017] [Indexed: 01/20/2023]
Abstract
Mycobacterium tuberculosis (Mtb), causative agent of human tuberculosis (TB), has the remarkable ability to adapt to the hostile environment inside host cells. Eleven eukaryotic like serine-threonine protein kinases (STPKs) are present in Mtb. Protein kinase G (PknG) has been shown to promote mycobacterial survival inside host cells. A homolog of PknG is also present in Mycobacterium smegmatis (MS), a fast grower, non-pathogenic mycobacterium. In the present study, we have analyzed the role of PknG in mycobacteria during exposure to acidic environment. Expression of pknG in MS was decreased in acidic medium. Recombinant MS ectopically expressing pknG (MS-G) showed higher growth in acidic medium compared to wild type counterpart. MS-G also showed higher resistance upon exposure to 3.0 pH and better adaptability to acidic pH. Western blot analysis showed differential threonine but not serine phosphorylation of cellular proteins in MS at acidic pH which was restored by ectopic expression of pknG in MS. In Mtb H37Ra (Mtb-Ra), expression of pknG was increased at acidic pH. We also observed decreased expression of pknG in MS during infection in macrophages while the expression of pknG in Mtb-Ra was increased in similar conditions. Taken together, our data strongly suggests that pknG regulates growth of mycobacteria in acidic environment and is differentially transcribed in MS and Mtb under these conditions.
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