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Caradec T, Plé C, Sicoli G, Petrov R, Pradel E, Sobieski C, Antoine R, Orio M, Herledan A, Willand N, Hartkoorn RC. Small molecule MarR modulators potentiate metronidazole antibiotic activity in aerobic E. coli by inducing activation by the nitroreductase NfsA. J Biol Chem 2024; 300:107431. [PMID: 38825006 PMCID: PMC11259696 DOI: 10.1016/j.jbc.2024.107431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
Antibiotic-resistant Enterobacterales pose a major threat to healthcare systems worldwide, necessitating the development of novel strategies to fight such hard-to-kill bacteria. One potential approach is to develop molecules that force bacteria to hyper-activate prodrug antibiotics, thus rendering them more effective. In the present work, we aimed to obtain proof-of-concept data to support that small molecules targeting transcriptional regulators can potentiate the antibiotic activity of the prodrug metronidazole (MTZ) against Escherichia coli under aerobic conditions. By screening a chemical library of small molecules, a series of structurally related molecules were identified that had little inherent antibiotic activity but showed substantial activity in combination with ineffective concentrations of MTZ. Transcriptome analyses, functional genetics, thermal shift assays, and electrophoretic mobility shift assays were then used to demonstrate that these MTZ boosters target the transcriptional repressor MarR, resulting in the upregulation of the marRAB operon and its downstream MarA regulon. The associated upregulation of the flavin-containing nitroreductase, NfsA, was then shown to be critical for the booster-mediated potentiation of MTZ antibiotic activity. Transcriptomic studies, biochemical assays, and electron paramagnetic resonance measurements were then used to show that under aerobic conditions, NfsA catalyzed 1-electron reduction of MTZ to the MTZ radical anion which in turn induced lethal DNA damage in E. coli. This work reports the first example of prodrug boosting in Enterobacterales by transcriptional modulators and highlights that MTZ antibiotic activity can be chemically induced under anaerobic growth conditions.
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Affiliation(s)
- Thibault Caradec
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Coline Plé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Giuseppe Sicoli
- CNRS UMR 8516, Univ. Lille, LASIRE - Laboratory of Advanced Spectroscopy on Interactions, Reactivity and Environment, Villeneuve d'Ascq, France
| | - Ravil Petrov
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Elizabeth Pradel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Cécilia Sobieski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Maylis Orio
- Aix Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | - Ruben Christiaan Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.
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2
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Verma T, Nandini SS, Singh V, Raghavan A, Annappa H, Bhaskarla C, Dubey AK, Nandi D. Divergent Roles of Escherichia Coli Encoded Lon Protease in Imparting Resistance to Uncouplers of Oxidative Phosphorylation: Roles of marA, rob, soxS and acrB. Curr Microbiol 2024; 81:98. [PMID: 38372817 DOI: 10.1007/s00284-024-03632-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024]
Abstract
Uncouplers of oxidative phosphorylation dissipate the proton gradient, causing lower ATP production. Bacteria encounter several non-classical uncouplers in the environment, leading to stress-induced adaptations. Here, we addressed the molecular mechanisms responsible for the effects of uncouplers in Escherichia coli. The expression and functions of genes involved in phenotypic antibiotic resistance were studied using three compounds: two strong uncouplers, i.e., Carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and 2,4-Dinitrophenol (DNP), and one moderate uncoupler, i.e., Sodium salicylate (NaSal). Quantitative expression studies demonstrated induction of transcripts encoding marA, soxS and acrB with NaSal and DNP, but not CCCP. Since MarA and SoxS are degraded by the Lon protease, we investigated the roles of Lon using a lon-deficient strain (Δlon). Compared to the wild-type strain, Δlon shows compromised growth upon exposure to NaSal or 2, 4-DNP. This sensitivity is dependent on marA but not rob and soxS. On the other hand, the Δlon strain shows enhanced growth in the presence of CCCP, which is dependent on acrB. Interestingly, NaSal and 2,4-DNP, but not CCCP, induce resistance to antibiotics, such as ciprofloxacin and tetracycline. This study addresses the effects of uncouplers and the roles of genes involved during bacterial growth and phenotypic antibiotic resistance. Strong uncouplers are often used to treat wastewater, and these results shed light on the possible mechanisms by which bacteria respond to uncouplers. Also, the rampant usage of some uncouplers to treat wastewater may lead to the development of antibiotic resistance.
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Affiliation(s)
- Taru Verma
- Department of Bioengineering, Indian Institute of Science, Bengaluru, 560012, India
| | - Santhi Sanil Nandini
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Varsha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Abinaya Raghavan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Harshita Annappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Chetana Bhaskarla
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Ashim Kumar Dubey
- Undergraduate program, Indian Institute of Science, Bengaluru, 560012, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India.
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3
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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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4
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Freyre-González JA, Escorcia-Rodríguez JM, Gutiérrez-Mondragón LF, Martí-Vértiz J, Torres-Franco CN, Zorro-Aranda A. System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks. Front Bioeng Biotechnol 2022; 10:888732. [PMID: 35646858 PMCID: PMC9135355 DOI: 10.3389/fbioe.2022.888732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Synthetic biology aims to apply engineering principles for the rational, systematical design and construction of biological systems displaying functions that do not exist in nature or even building a cell from scratch. Understanding how molecular entities interconnect, work, and evolve in an organism is pivotal to this aim. Here, we summarize and discuss some historical organizing principles identified in bacterial gene regulatory networks. We propose a new layer, the concilion, which is the group of structural genes and their local regulators responsible for a single function that, organized hierarchically, coordinate a response in a way reminiscent of the deliberation and negotiation that take place in a council. We then highlight the importance that the network structure has, and discuss that the natural decomposition approach has unveiled the system-level elements shaping a common functional architecture governing bacterial regulatory networks. We discuss the incompleteness of gene regulatory networks and the need for network inference and benchmarking standardization. We point out the importance that using the network structural properties showed to improve network inference. We discuss the advances and controversies regarding the consistency between reconstructions of regulatory networks and expression data. We then discuss some perspectives on the necessity of studying regulatory networks, considering the interactions’ strength distribution, the challenges to studying these interactions’ strength, and the corresponding effects on network structure and dynamics. Finally, we explore the ability of evolutionary systems biology studies to provide insights into how evolution shapes functional architecture despite the high evolutionary plasticity of regulatory networks.
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Affiliation(s)
- Julio A Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Juan M Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Luis F Gutiérrez-Mondragón
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jerónimo Martí-Vértiz
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Camila N Torres-Franco
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Andrea Zorro-Aranda
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Chemical Engineering, Universidad de Antioquia, Medellín, Colombia
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Control of Escherichia coli O157:H7 Motility and Biofilm Formation by Salicylate and Decanoate: MarA/SoxS/Rob and pchE Interactions. Appl Environ Microbiol 2021; 88:e0189121. [PMID: 34788062 DOI: 10.1128/aem.01891-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prophage-encoded Escherichia coli O157:H7 transcription factor (TF), PchE, inhibits biofilm formation and attachment to cultured epithelial cells by reducing curli fimbriae expression and increasing flagella expression. To identify pchE regulators that might be used in intervention strategies to reduce environmental persistence or host infections, we performed a computational search of O157:H7 strain PA20 pchE promoter sequences for binding sites used by known TFs. A common site shared by MarA/SoxS/Rob TFs was identified and the typical MarA/Rob inducers, salicylate and decanoate, were tested for biofilm and motility effects. Sodium salicylate, a proven biofilm inhibitor, but not sodium decanoate, strongly reduced O157:H7 biofilms by a pchE-independent mechanism. Both salicylate and decanoate enhanced O157:H7 motility dependent on pchE using media and incubation temperatures optimum for culturing human epithelial cells. However, induction of pchE by salicylate did not activate the SOS response. MarA/SoxS/Rob inducers provide new potential agents for controlling O157:H7 interactions with the host and its persistence in the environment. IMPORTANCE There is a need to develop E. coli serotype O157:H7 non-antibiotic interventions that do not precipitate the release and activation of virulence factor-encoded prophage and transferrable genetic elements. One method is to stimulate existing regulatory pathways that repress bacterial persistence and virulence genes. Here we show that certain inducers of MarA and Rob have that ability, working through both pchE-dependent and -independent pathways.
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Optimised Heterologous Expression and Functional Analysis of the Yersinia pestis F1-Capsular Antigen Regulator Caf1R. Int J Mol Sci 2021; 22:ijms22189805. [PMID: 34575967 PMCID: PMC8470410 DOI: 10.3390/ijms22189805] [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: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The bacterial pathogen, Yersinia pestis, has caused three historic pandemics and continues to cause small outbreaks worldwide. During infection, Y. pestis assembles a capsule-like protective coat of thin fibres of Caf1 subunits. This F1 capsular antigen has attracted much attention due to its clinical value in plague diagnostics and anti-plague vaccine development. Expression of F1 is tightly regulated by a transcriptional activator, Caf1R, of the AraC/XylS family, proteins notoriously prone to aggregation. Here, we have optimised the recombinant expression of soluble Caf1R. Expression from the native and synthetic codon-optimised caf1R cloned in three different expression plasmids was examined in a library of E. coli host strains. The functionality of His-tagged Caf1R was demonstrated in vivo, but insolubility was a problem with overproduction. High levels of soluble MBP-Caf1R were produced from codon optimised caf1R. Transcriptional-lacZ reporter fusions defined the PM promoter and Caf1R binding site responsible for transcription of the cafMA1 operon. Use of the identified Caf1R binding caf DNA sequence in an electrophoretic mobility shift assay (EMSA) confirmed correct folding and functionality of the Caf1R DNA-binding domain in recombinant MBP-Caf1R. Availability of functional recombinant Caf1R will be a valuable tool to elucidate control of expression of F1 and Caf1R-regulated pathophysiology of Y. pestis.
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Wójcicki M, Świder O, Daniluk KJ, Średnicka P, Akimowicz M, Roszko MŁ, Sokołowska B, Juszczuk-Kubiak E. Transcriptional Regulation of the Multiple Resistance Mechanisms in Salmonella-A Review. Pathogens 2021; 10:pathogens10070801. [PMID: 34202800 PMCID: PMC8308502 DOI: 10.3390/pathogens10070801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
The widespread use of antibiotics, especially those with a broad spectrum of activity, has resulted in the development of multidrug resistance in many strains of bacteria, including Salmonella. Salmonella is among the most prevalent causes of intoxication due to the consumption of contaminated food and water. Salmonellosis caused by this pathogen is pharmacologically treated using antibiotics such as fluoroquinolones, ceftriaxone, and azithromycin. This foodborne pathogen developed several molecular mechanisms of resistance both on the level of global and local transcription modulators. The increasing rate of antibiotic resistance in Salmonella poses a significant global concern, and an improved understanding of the multidrug resistance mechanisms in Salmonella is essential for choosing the suitable antibiotic for the treatment of infections. In this review, we summarized the current knowledge of molecular mechanisms that control gene expression related to antibiotic resistance of Salmonella strains. We characterized regulators acting as transcription activators and repressors, as well as two-component signal transduction systems. We also discuss the background of the molecular mechanisms of the resistance to metals, regulators of multidrug resistance to antibiotics, global regulators of the LysR family, as well as regulators of histone-like proteins.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (O.Ś.); (M.Ł.R.)
| | - Kamila J. Daniluk
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (K.J.D.); (B.S.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Monika Akimowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
| | - Marek Ł. Roszko
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (O.Ś.); (M.Ł.R.)
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (K.J.D.); (B.S.)
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.A.)
- Correspondence: ; Tel.: +48-22-6063605
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Gregorchuk BSJ, Reimer SL, Green KAC, Cartwright NH, Beniac DR, Hiebert SL, Booth TF, Chong PM, Westmacott GR, Zhanel GG, Bay DC. Phenotypic and Multi-Omics Characterization of Escherichia coli K-12 Adapted to Chlorhexidine Identifies the Role of MlaA and Other Cell Envelope Alterations Regulated by Stress Inducible Pathways in CHX Resistance. Front Mol Biosci 2021; 8:659058. [PMID: 34095221 PMCID: PMC8170033 DOI: 10.3389/fmolb.2021.659058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/09/2021] [Indexed: 11/27/2022] Open
Abstract
Chlorhexidine (CHX) is an essential medicine used as a topical antiseptic in skin and oral healthcare treatments. The widespread use of CHX has increased concerns regarding the development of antiseptic resistance in Enterobacteria and its potential impact on cross-resistance to other antimicrobials. Similar to other cationic antiseptics, resistance to CHX is believed to be driven by three membrane-based mechanisms: lipid synthesis/transport, altered porin expression, and increased efflux pump activity; however, specific gene and protein alterations associated with CHX resistance remain unclear. Here, we adapted Escherichia coli K-12 BW25113 to increasing concentrations of CHX to determine what phenotypic, morphological, genomic, transcriptomic, and proteomic changes occurred. We found that CHX-adapted E. coli isolates possessed no cross-resistance to any other antimicrobials we tested. Scanning electron microscopy imaging revealed that CHX adaptation significantly altered mean cell widths and lengths. Proteomic analyses identified changes in the abundance of porin OmpF, lipid synthesis/transporter MlaA, and efflux pump MdfA. Proteomic and transcriptomic analyses identified that CHX adaptation altered E. coli transcripts and proteins controlling acid resistance (gadE, cdaR) and antimicrobial stress-inducible pathways Mar-Sox-Rob, stringent response systems. Whole genome sequencing analyses revealed that all CHX-resistant isolates had single nucleotide variants in the retrograde lipid transporter gene mlaA as well as the yghQ gene associated with lipid A transport and synthesis. CHX resistant phenotypes were reversible only when complemented with a functional copy of the mlaA gene. Our results highlight the importance of retrograde phospholipid transport and stress response systems in CHX resistance and the consequences of prolonged CHX exposure.
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Affiliation(s)
- Branden S J Gregorchuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Shelby L Reimer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Kari A C Green
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Nicola H Cartwright
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel R Beniac
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Shannon L Hiebert
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Timothy F Booth
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Patrick M Chong
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Garrett R Westmacott
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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9
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Verma T, Annappa H, Singh S, Umapathy S, Nandi D. Profiling antibiotic resistance in Escherichia coli strains displaying differential antibiotic susceptibilities using Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000231. [PMID: 32981183 DOI: 10.1002/jbio.202000231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/22/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The rapid identification of antibiotic resistant bacteria is important for public health. In the environment, bacteria are exposed to sub-inhibitory antibiotic concentrations which has implications in the generation of multi-drug resistant strains. To better understand these issues, Raman spectroscopy was employed coupled with partial least squares-discriminant analysis to profile Escherichia coli strains treated with sub-inhibitory concentrations of antibiotics. Clear differences were observed between cells treated with bacteriostatic (tetracycline and rifampicin) and bactericidal (ampicillin, ciprofloxacin, and ceftriaxone) antibiotics for 6 hr: First, atomic force microscopy revealed that bactericidal antibiotics cause extensive cell elongation whereas short filaments are observed with bacteriostatic antibiotics. Second, Raman spectral analysis revealed that bactericidal antibiotics lower nucleic acid to protein (I812 /I830 ) and nucleic acid to lipid ratios (I1483 /I1452 ) whereas the opposite is seen with bacteriostatic antibiotics. Third, the protein to lipid ratio (I2936 /I2885 and I2936 /I2850 ) is a Raman stress signature common to both the classes. These signatures were validated using two mutants, Δlon and ΔacrB, that exhibit relatively high and low resistance towards antibiotics, respectively. In addition, these spectral markers correlated with the emergence of phenotypic antibiotic resistance. Overall, this study demonstrates the efficacy of Raman spectroscopy to identify resistance in bacteria to sub-lethal concentrations of antibiotics.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Harshitha Annappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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10
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Gu Y, Wang S, Huang L, Sa W, Li J, Huang J, Dai M, Cheng G. Development of Resistance in Escherichia coli ATCC25922 under Exposure of Sub-Inhibitory Concentration of Olaquindox. Antibiotics (Basel) 2020; 9:E791. [PMID: 33182563 PMCID: PMC7696260 DOI: 10.3390/antibiotics9110791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/31/2023] Open
Abstract
Quinoxaline1,4-di-N-oxides (QdNOs) are a class of important antibacterial drugs of veterinary use, of which the drug resistance mechanism has not yet been clearly explained. This study investigated the molecular mechanism of development of resistance in Escherichia coli (E. coli) under the pressure of sub-inhibitory concentration (sub-MIC) of olaquindox (OLA), a representative QdNOs drug. In vitro challenge of E. coli with 1/100× MIC to 1/2× MIC of OLA showed that the bacteria needed a longer time to develop resistance and could only achieve low to moderate levels of resistance as well as form weak biofilms. The transcriptomic and genomic profiles of the resistant E. coli induced by sub-MIC of OLA demonstrated that genes involved in tricarboxylic acid cycle, oxidation-reduction process, biofilm formation, and efflux pumps were up-regulated, while genes involved in DNA repair and outer membrane porin were down-regulated. Mutation rates were significantly increased in the sub-MIC OLA-treated bacteria and the mutated genes were mainly involved in the oxidation-reduction process, DNA repair, and replication. The SNPs were found in degQ, ks71A, vgrG, bigA, cusA, and DR76-4702 genes, which were covered in both transcriptomic and genomic profiles. This study provides new insights into the resistance mechanism of QdNOs and increases the current data pertaining to the development of bacterial resistance under the stress of antibacterials at sub-MIC concentrations.
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Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuge Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Sa
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Jun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Menghong Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
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11
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Chetri S, Das BJ, Bhowmik D, Chanda DD, Chakravarty A, Bhattacharjee A. Transcriptional response of mar, sox and rob regulon against concentration gradient carbapenem stress within Escherichia coli isolated from hospital acquired infection. BMC Res Notes 2020; 13:168. [PMID: 32192538 PMCID: PMC7083032 DOI: 10.1186/s13104-020-04999-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/10/2020] [Indexed: 12/01/2022] Open
Abstract
Objective The present study was carried out to investigate the transcriptional response of marA (Multiple antibiotic resistance A gene), soxS (Superoxide S gene) and rob (Right-origin-binding gene) under carbapenem stress. Results 12 isolates were found over-expressing AcrAB-TolC efflux pump system and showed reduced expression of OmpF (Outer membrane porin) gene were selected for further study. Among them, over expression of marA and rob was observed in 7 isolates. Increasing pattern of expression of marA and rob against meropenem was observed. The clones of marA and rob showed reduced susceptibility towards carbapenems.
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12
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Zhang C, Chen S, Bai X, Dedkova LM, Hecht SM. Alteration of Transcriptional Regulator Rob In Vivo: Enhancement of Promoter DNA Binding and Antibiotic Resistance in the Presence of Nucleobase Amino Acids. Biochemistry 2020; 59:1217-1220. [PMID: 32157864 DOI: 10.1021/acs.biochem.0c00103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of proteins that bind selectively to nucleic acid sequences is an ongoing challenge. We previously synthesized nucleobase amino acids designed to replace proteinogenic amino acids; these were incorporated into proteins to bind specific nucleic acids predictably. An early example involved selective cell free binding of the hnRNP LL RRM1 domain to its i-motif DNA target via Watson-Crick-like H-bonding interactions. In this study, we employ the X-ray crystal structure of transcriptional regulator Rob bound to its micF promoter, which occurred without DNA distortion. Rob proteins modified in vivo with nucleobase amino acids at position 40 exhibited altered DNA promoter binding, as predicted on the basis of their Watson-Crick-like H-bonding interactions with promoter DNA A-box residue Gua-6. Rob protein expression ultimately controls phenotypic changes, including resistance to antibiotics. Although Rob proteins with nucleobase amino acids were expressed in Escherichia coli at levels estimated to be only a fraction of that of the wild-type Rob protein, those modified proteins that bound to the micF promoter more avidly than the wild type in vitro also produced greater resistance to macrolide antibiotics roxithromycin and clarithromycin in vivo, as well as the β-lactam antibiotic ampicillin. Also demonstrated is the statistical significance of altered DNA binding and antibiotic resistance for key Rob analogues. These preliminary findings suggest the ultimate utility of nucleobase amino acids in altering and controlling preferred nucleic acid target sequences by proteins, for probing molecular interactions critical to protein function, and for enhancing phenotypic changes in vivo by regulatory protein analogues.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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13
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Colclough AL, Alav I, Whittle EE, Pugh HL, Darby EM, Legood SW, McNeil HE, Blair JM. RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance. Future Microbiol 2020; 15:143-157. [PMID: 32073314 DOI: 10.2217/fmb-2019-0235] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Rresistance-nodulation-division (RND) efflux pumps in Gram-negative bacteria remove multiple, structurally distinct classes of antimicrobials from inside bacterial cells therefore directly contributing to multidrug resistance. There is also emerging evidence that many other mechanisms of antibiotic resistance rely on the intrinsic resistance conferred by RND efflux. In addition to their role in antibiotic resistance, new information has become available about the natural role of RND pumps including their established role in virulence of many Gram-negative organisms. This review also discusses the recent advances in understanding the regulation and structure of RND efflux pumps.
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Affiliation(s)
- Abigail L Colclough
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Emily E Whittle
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Hannah L Pugh
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Elizabeth M Darby
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Simon W Legood
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen E McNeil
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jessica Ma Blair
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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14
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Multidrug Resistance Regulators MarA, SoxS, Rob, and RamA Repress Flagellar Gene Expression and Motility in Salmonella enterica Serovar Typhimurium. J Bacteriol 2019; 201:JB.00385-19. [PMID: 31501286 DOI: 10.1128/jb.00385-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
Production of flagella is costly and subject to global multilayered regulation, which is reflected in the hierarchical control of flagellar production in many bacterial species. For Salmonella enterica serovar Typhimurium and its relatives, global regulation of flagellar production primarily occurs through the control of flhDC transcription and mRNA translation. In this study, the roles of the homologous multidrug resistance regulators MarA, SoxS, Rob, and RamA (constituting the mar-sox-rob regulon in S Typhimurium) in regulating flagellar gene expression were explored. Each of these regulators was found to inhibit flagellar gene expression, production of flagella, and motility. To different degrees, repression via these transcription factors occurred through direct interactions with the flhDC promoter, particularly for MarA and Rob. Additionally, SoxS repressed flagellar gene expression via a posttranscriptional pathway, reducing flhDC translation. The roles of these transcription factors in reducing motility in the presence of salicylic acid were also elucidated, adding a genetic regulatory element to the response of S Typhimurium to this well-characterized chemorepellent. Integration of flagellar gene expression into the mar-sox-rob regulon in S Typhimurium contrasts with findings for closely related species such as Escherichia coli, providing an example of plasticity in the mar-sox-rob regulon throughout the Enterobacteriaceae family.IMPORTANCE The mar-sox-rob regulon is a large and highly conserved stress response network in the Enterobacteriaceae family. Although it is well characterized in E. coli, the extent of this regulon in related species is unclear. Here, the control of costly flagellar gene expression is connected to the mar-sox-rob regulon of S Typhimurium, contrasting with the E. coli regulon model. These findings demonstrate the flexibility of the mar-sox-rob regulon to accommodate novel regulatory targets, and they provide evidence for its broader regulatory role within this family of diverse bacteria.
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15
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Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun 2019; 10:4828. [PMID: 31645551 PMCID: PMC6811581 DOI: 10.1038/s41467-019-12823-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023] Open
Abstract
Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance. Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christine Boinett
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Phat Voong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phu Huong Lan Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, The Department of Medicine, University of Cambridge, Cambridge, UK
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16
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Wang T, Kunze C, Dunlop MJ. Salicylate Increases Fitness Cost Associated with MarA-Mediated Antibiotic Resistance. Biophys J 2019; 117:563-571. [PMID: 31349991 DOI: 10.1016/j.bpj.2019.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 01/12/2023] Open
Abstract
Antibiotic resistance is generally associated with a fitness deficit resulting from the burden of producing and maintaining resistance machinery. This additional cost suggests that resistant bacteria will be outcompeted by susceptible bacteria in conditions without antibiotics. However, in practice, this process is slow in part because of regulation that minimizes expression of these genes in the absence of antibiotics. This suggests that if it were possible to turn on their expression, the cost would increase, thereby accelerating removal of resistant strains. Experimental and theoretical studies have shown that environmental chemicals can change the fitness cost associated with resistance and therefore have a significant impact on population dynamics. The multiple antibiotic resistance activator (MarA) is a clinically important regulator in Escherichia coli that activates downstream genes to increase resistance against multiple classes of antibiotics. Salicylate is an inducer of MarA that can be found in the environment and derepresses marA's expression. In this study, we sought to unravel the interplay between salicylate and the fitness cost of MarA-mediated antibiotic resistance. Using salicylate as an inducer of MarA, we found that a wide spectrum of concentrations can increase burden in resistant strains compared to susceptible strains. Induction resulted in rapid exclusion of resistant bacteria from mixed populations of antibiotic-resistant and susceptible cells. A mathematical model captures the process and predicts its effect in various environmental conditions. Our work provides a quantitative understanding of salicylate exposure on the fitness of different MarA variants and suggests that salicylate can lead to selection against MarA-mediated resistant strains. More generally, our findings show that natural inducers may serve to bias population membership and could impact antibiotic resistance and other important phenotypes.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts; Biological Design Center, Boston University, Boston, Massachusetts
| | - Colin Kunze
- Biological Design Center, Boston University, Boston, Massachusetts; Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Mary J Dunlop
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts; Biological Design Center, Boston University, Boston, Massachusetts; Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
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17
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Pattrick CA, Webb JP, Green J, Chaudhuri RR, Collins MO, Kelly DJ. Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli. mSystems 2019; 4:e00163-19. [PMID: 31186336 PMCID: PMC6561319 DOI: 10.1128/msystems.00163-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/27/2019] [Indexed: 01/19/2023] Open
Abstract
Vanillin (4-hydroxy-3-methoxybenzaldehyde) is an economically important flavor compound that can be made in bacterial cell factories, but toxicity is a major problem for cells producing this aromatic aldehyde. Using (i) a global proteomic analysis supported by multiple physiological experiments, mutant analyses, and inferred transcription factor modeling and (ii) adaptive laboratory evolution (ALE) of vanillin tolerance combined with genome-wide analysis of the underlying mutations, mechanisms of vanillin toxicity in Escherichia coli have been elucidated. We identified 147 proteins that exhibited a significant change in abundance in response to vanillin, giving the first detailed insight into the cellular response to this aldehyde. Vanillin caused accumulation of reactive oxygen species invoking adaptations coordinated by a MarA, OxyR, and SoxS regulatory network and increased RpoS/DksA-dependent gene expression. Differential fumarase C upregulation was found to prevent oxidative damage to FumA and FumB during growth with vanillin. Surprisingly, vanillin-dependent reduction pf copper (II) to copper (I) led to upregulation of the copA gene and growth in the presence of vanillin was shown to be hypersensitive to inhibition by copper ions. AcrD and AaeAB were identified as potential vanillin efflux systems. Vanillin-tolerant strains isolated by ALE had distinct nonsynonymous single nucleotide polymorphisms (SNPs) in gltA that led to increased citrate synthase activity. Strain-specific mutations in cpdA, rob, and marC were also present. One strain had a large (∼10-kb) deletion that included the marRAB region. Our data provide new understanding of bacterial vanillin toxicity and identify novel gene targets for future engineering of vanillin-tolerant strains of E. coli IMPORTANCE A particular problem for the biotechnological production of many of the valuable chemicals that we are now able to manufacture in bacterial cells is that these products often poison the cells producing them. Solutions to improve product yields or alleviate such toxicity using the techniques of modern molecular biology first require a detailed understanding of the mechanisms of product toxicity. Here we have studied the economically important flavor compound vanillin, an aromatic aldehyde that exerts significant toxic effects on bacterial cells. We used high-resolution protein abundance analysis as a starting point to determine which proteins are upregulated and which are downregulated by growth with vanillin, followed by gene expression and mutant studies to understand the mechanism of the response. In a second approach, we evolved bacterial strains with higher vanillin tolerance. Their genome sequences have yielded novel insights into vanillin tolerance that are complementary to the proteomics data set.
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Affiliation(s)
- Calum A Pattrick
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Joseph P Webb
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Mark O Collins
- Department of Biomedical Science, The University of Sheffield, Sheffield, United Kingdom
- biOMICS Biological Mass Spectrometry Facility, The University of Sheffield, Sheffield, United Kingdom
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
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18
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Rossi NA, Mora T, Walczak AM, Dunlop MJ. Active degradation of MarA controls coordination of its downstream targets. PLoS Comput Biol 2018; 14:e1006634. [PMID: 30589845 PMCID: PMC6307708 DOI: 10.1371/journal.pcbi.1006634] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 01/01/2023] Open
Abstract
Several key transcription factors have unusually short half-lives compared to other cellular proteins. Here, we explore the utility of active degradation in shaping how the multiple antibiotic resistance activator MarA coordinates its downstream targets. MarA controls a variety of stress response genes in Escherichia coli. We modify its half-life either by knocking down the protease that targets it via CRISPRi or by engineering MarA to protect it from degradation. Our experimental and analytical results indicate that active degradation can impact both the rate of coordination and the maximum coordination that downstream genes can achieve. In the context of multi-gene regulation, trade-offs between these properties show that perfect information fidelity and instantaneous coordination cannot coexist.
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Affiliation(s)
- Nicholas A. Rossi
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, Sorbonne Université, Université Paris-Diderot, and École Normale Supérieure (PSL), Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, and École Normale Supérieure (PSL), Paris, France
| | - Mary J. Dunlop
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
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19
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Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Savitski MM, Bork P, Göttig S, Typas A. Species-specific activity of antibacterial drug combinations. Nature 2018; 559:259-263. [PMID: 29973719 DOI: 10.1038/s41586-018-0278-9] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements of modern medicine1,2. Drug combinations can help to fight multi-drug-resistant bacterial infections, yet they are largely unexplored and rarely used in clinics. Here we profile almost 3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in six strains from three Gram-negative pathogens-Escherichia coli, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa-to identify general principles for antibacterial drug combinations and understand their potential. Despite the phylogenetic relatedness of the three species, more than 70% of the drug-drug interactions that we detected are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs that target different cellular processes, whereas synergies are more conserved and are enriched in drugs that target the same process. We provide mechanistic insights into this dichotomy and further dissect the interactions of the food additive vanillin. Finally, we demonstrate that several synergies are effective against multi-drug-resistant clinical isolates in vitro and during infections of the larvae of the greater wax moth Galleria mellonella, with one reverting resistance to the last-resort antibiotic colistin.
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Affiliation(s)
- Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anja Telzerow
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jacob Bobonis
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emily Huth
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Stefan Bassler
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jordi Zamarreño Beas
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Matylda Zietek
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Natalie Ng
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sunniva Foerster
- Institute of Social & Preventive Medicine, Institute of Infectious Diseases, University of Bern, Bern, Switzerland
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Frédéric Barras
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France.,Institut Pasteur, Paris, France
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Stephan Göttig
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.
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20
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Gingras H, Dridi B, Leprohon P, Ouellette M. Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli. Microb Genom 2018; 4. [PMID: 29319470 PMCID: PMC5857375 DOI: 10.1099/mgen.0.000148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In order to expedite the discovery of genes coding for either drug targets or antibiotic resistance, we have developed a functional genomic strategy termed Plas-Seq. This technique involves coupling a multicopy suppressor library to next-generation sequencing. We generated an Escherichia coli plasmid genomic library that was transformed into E. coli. These transformants were selected step by step using 0.25× to 2× minimum inhibitory concentrations for ceftriaxone, gentamicin, levofloxacin, tetracycline or trimethoprim. Plasmids were isolated at each selection step and subjected to Illumina sequencing. By searching for genomic loci whose sequencing coverage increased with antibiotic pressure we were able to detect 48 different genomic loci that were enriched by at least one antibiotic. Fifteen of these loci were studied functionally, and we showed that 13 can decrease the susceptibility of E. coli to antibiotics when overexpressed. These genes coded for drug targets, transcription factors, membrane proteins and resistance factors. The technique of Plas-Seq is expediting the discovery of genes associated with the mode of action or resistance to antibiotics and led to the isolation of a novel gene influencing drug susceptibility. It has the potential for being applied to novel molecules and to other microbial species.
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Affiliation(s)
- Hélène Gingras
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Bédis Dridi
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
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Weston N, Sharma P, Ricci V, Piddock LJV. Regulation of the AcrAB-TolC efflux pump in Enterobacteriaceae. Res Microbiol 2017; 169:425-431. [PMID: 29128373 DOI: 10.1016/j.resmic.2017.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/16/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022]
Abstract
Bacterial multidrug efflux systems are a major mechanism of antimicrobial resistance and are fundamental to the physiology of Gram-negative bacteria. The resistance-nodulation-division (RND) family of efflux pumps is the most clinically significant, as it is associated with multidrug resistance. Expression of efflux systems is subject to multiple levels of regulation, involving local and global transcriptional regulation as well as post-transcriptional and post-translational regulation. The best-characterised RND system is AcrAB-TolC, which is present in Enterobacteriaceae. This review describes the current knowledge and new data about the regulation of the acrAB and tolC genes in Escherichia coli and Salmonella enterica.
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Affiliation(s)
- Natasha Weston
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Prateek Sharma
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Vito Ricci
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Laura J V Piddock
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom.
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Rodrigo G, Bajić D, Elola I, Poyatos JF. Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. NPJ Syst Biol Appl 2017; 3:30. [PMID: 29018569 PMCID: PMC5630622 DOI: 10.1038/s41540-017-0031-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 09/01/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022] Open
Abstract
Many essential bacterial responses present complex transcriptional regulation of gene expression. To what extent can the study of these responses substantiate the logic of their regulation? Here, we show how the input function of the genes constituting the response, i.e., the information of how their transcription rates change as function of the signals acting on the regulators, can serve as a quantitative tool to deconstruct the corresponding regulatory logic. To demonstrate this approach, we consider the multiple antibiotic resistance (mar) response in Escherichia coli. By characterizing the input function of its representative genes in wild-type and mutant bacteria, we recognize a dual autoregulation motif as main determinant of the response, which is further adjusted by the interplay with other regulators. We show that basic attributes, like its reaction to a wide range of stress or its moderate expression change, are associated with a strong negative autoregulation, while others, like the buffering of metabolic signals or the lack of memory to previous stress, are related to a weak positive autoregulation. With a mathematical model of the input functions, we identify some constraints fixing the molecular attributes of the regulators, and also notice the relevance of the bicystronic architecture harboring the dual autoregulation that is unique in E. coli. The input function emerges then as a tool to disentangle the rationale behind most of the attributes defining the mar phenotype. Overall, the present study supports the value of characterizing input functions to deconstruct the complexity of regulatory architectures in prokaryotic and eukaryotic systems. Many cellular responses result from the integration of numerous regulatory signals. To deconstruct the regulation of one of these responses, which enables resistance to multiple antibiotics in Escherichia coli, a team led by Juan F. Poyatos at the National Center for Biotechnology in Madrid studied the response input function by combining theoretical models and experiments. This function quantifies the rate of transcription of the genes constituting the response with respect to the signals acting on its cognate regulators. By examining how the shape of the function changes in different situations, e.g., when a given regulator is mutated, the team identified the implications for the specificity and dynamics of the response of a dual autoregulation at the core of the control architecture. The use of input functions as quantitative tools allows us to reverse engineer the complex regulations that dictate essential physiological functions in both prokaryotic and eukaryotic cells.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 Valencia, Spain
| | - Djordje Bajić
- Logic of Genomic Systems Laboratory, CNB-CSIC, 28049 Madrid, Spain.,Present Address: Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
| | - Ignacio Elola
- Logic of Genomic Systems Laboratory, CNB-CSIC, 28049 Madrid, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB-CSIC, 28049 Madrid, Spain
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Jain K, Saini S. MarRA, SoxSR, and Rob encode a signal dependent regulatory network in Escherichia coli. MOLECULAR BIOSYSTEMS 2017; 12:1901-12. [PMID: 27098660 DOI: 10.1039/c6mb00263c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When exposed to low concentrations of toxic chemicals, bacteria modulate the expression of a number of cellular processes. Typically, these processes include those related to porin production, dismutases, and metabolic fluxes. In Escherichia coli (E. coli), the expression of these systems is largely controlled by three homologous transcriptional regulators: MarA, SoxS, and Rob. Each of the three regulators responds to distinct chemical signals (salicylate for MarA; paraquat for SoxS; and bipyridyl for Rob) and controls the expression of an overlapping set of downstream targets. In addition, the three systems autoregulate their own expression, and cross-regulate each other's expression. Specifically, MarA is known to activate SoxS expression, and Rob is known to activate MarA expression. In addition, a number of conflicting regulatory interactions are known to exist between the three loci. Thus, the three systems encode a complex regulatory topology with multiple feedback loops, the precise nature of whose interactions or their significance in cellular physiology is not well understood currently. In this work, we focus on understanding the details of this crosstalk between the Mar-Sox-Rob systems in E. coli, and the resulting control and dynamics of the expression of cellular processes by studying gene expression at the population level and at single-cell resolution in wild type and mutants. Our results indicate that the regulatory architecture between MarA, SoxS, and Rob is dependent on the signal (inducer) present in the environment. The regulators, in response to an inducer, form a Feed Forward Loop (FFL), which leads to faster and stronger induction of target genes in the cell, consequently resulting in better cellular growth. Through the FFL, the cell is able to integrate qualitatively different signals in the network, and consequently, control cellular physiology. In addition, we present two intriguing dynamic features of the Mar-Sox-Rob regulon. First, in the presence of salicylate, the activation of target genes via MarA and Rob, at single-cell resolution, is qualitatively different. Second, we report the synergistic activation of target and Mar/Sox systems in the presence of both salicylate and paraquat. These results strongly indicate that there exists a complex control of gene regulation in the Mar-Sox-Rob regulon. Mechanistic details of this control are likely quite complex, and may involve additional regulators.
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Affiliation(s)
- Kirti Jain
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai - 400 076, India.
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai - 400 076, India.
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Hickman RA, Munck C, Sommer MOA. Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs. Front Microbiol 2017; 8:893. [PMID: 28596757 PMCID: PMC5442168 DOI: 10.3389/fmicb.2017.00893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/03/2017] [Indexed: 12/18/2022] Open
Abstract
Understanding the evolutionary processes that lead to antibiotic resistance can help to achieve better treatment strategies. Yet, little is known about the dynamics of the resistance alleles during adaptation. Here, we use population sequencing to monitor genetic changes in putative resistance loci at several time-points during adaptive evolution experiments involving five different antibiotic conditions. We monitor the mutational spectra in lineages evolved to be resistant to single antibiotics [amikacin (AMK), chloramphenicol (CHL), and ciprofloxacin (CIP)], as well as antibiotic combinations (AMK + CHL and CHL + CIP). We find that lineages evolved to antibiotic combinations exhibit different resistance allele dynamics compared with those of single-drug evolved lineages, especially for a drug pair with reciprocal collateral sensitivity. During adaptation, we observed interfering, superimposing and fixation allele dynamics. To further understand the selective forces driving specific allele dynamics, a subset of mutations were introduced into the ancestral wild type enabling differentiation between clonal interference and negative epistasis.
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Affiliation(s)
- Rachel A Hickman
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Christian Munck
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Morten O A Sommer
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
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Mukherjee A, Chettri B, Langpoklakpam JS, Basak P, Prasad A, Mukherjee AK, Bhattacharyya M, Singh AK, Chattopadhyay D. Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments. Sci Rep 2017; 7:1108. [PMID: 28439121 PMCID: PMC5430712 DOI: 10.1038/s41598-017-01126-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/22/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.
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Affiliation(s)
- Arghya Mukherjee
- Department of Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Bobby Chettri
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | | | - Pijush Basak
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Aravind Prasad
- Dr. D.Y.Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | | | - Arvind K Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
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26
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Rossi NA, Dunlop MJ. Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA. PLoS Comput Biol 2017; 13:e1005310. [PMID: 28060821 PMCID: PMC5257004 DOI: 10.1371/journal.pcbi.1005310] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 01/23/2017] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Stress response networks frequently have a single upstream regulator that controls many downstream genes. However, the downstream targets are often diverse, therefore it remains unclear how their expression is specialized when under the command of a common regulator. To address this, we focused on a stress response network where the multiple antibiotic resistance activator MarA from Escherichia coli regulates diverse targets ranging from small RNAs to efflux pumps. Using single-cell experiments and computational modeling, we showed that each downstream gene studied has distinct activation, noise, and information transmission properties. Critically, our results demonstrate that understanding biological context is essential; we found examples where strong activation only occurs outside physiologically relevant ranges of MarA and others where noise is high at wild type MarA levels and decreases as MarA reaches its physiological limit. These results demonstrate how a single regulatory protein can maintain specificity while orchestrating the response of many downstream genes. Bacteria can sense and respond to stress in their environment. This process is often coordinated by a master regulator that turns on or off many downstream genes, allowing the cell to survive the stress. However, individual genes encode products that are diverse and optimal expression for each gene may differ. Here, we focus on how expression of diverse downstream genes is optimized by targets of the multiple antibiotic resistance activator MarA. Using single-cell experiments and computational modeling we show that downstream genes process MarA signals differently, with unique activation, noise, and information transmission properties. We find that each downstream gene’s response depends critically on the level of the input MarA. Furthermore, by swapping parts of the regulatory elements of genes we were able to create novel responses. This suggests that these properties can be readily tuned by evolution. Our findings show how a network with diverse downstream genes can be used to process the same command to achieve many distinct outputs, which work together to coordinate the response to stress.
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Affiliation(s)
- Nicholas A. Rossi
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA United States of America
| | - Mary J. Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA United States of America
- * E-mail:
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27
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Rodrigo G, Bajic D, Elola I, Poyatos JF. Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. Sci Rep 2016; 6:36196. [PMID: 27796341 PMCID: PMC5086920 DOI: 10.1038/srep36196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 01/15/2023] Open
Abstract
By integrating positive and negative feedback loops, biological systems establish intricate gene expression patterns linked to multistability, pulsing, and oscillations. This depends on the specific characteristics of each interlinked feedback, and thus one would expect additional expression programs to be found. Here, we investigate one such program associated with an antagonistic positive and negative transcriptional autoregulatory motif derived from the multiple antibiotic resistance (mar) system of Escherichia coli. We studied the dynamics of the system by combining a predictive mathematical model with high-resolution experimental measures of the response both at the population and single-cell level. We show that in this motif the weak positive autoregulation does not slow down but rather enhances response speedup in combination with a strong negative feedback loop. This balance of feedback strengths anticipates a homogeneous population phenotype, which we corroborate experimentally. Theoretical analysis also emphasized the specific molecular properties that determine the dynamics of the mar phenotype. More broadly, response acceleration could provide a rationale for the presence of weak positive feedbacks in other biological scenarios exhibiting these interlinked regulatory architectures.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Cellular de Plantas, CSIC–UPV, 46022 Valencia, Spain
| | - Djordje Bajic
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
| | - Ignacio Elola
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
| | - Juan F. Poyatos
- Logic of Genomic Systems Laboratory, CNB–CSIC, 28049 Madrid, Spain
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28
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Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression. Biophys J 2016; 109:1497-508. [PMID: 26445450 DOI: 10.1016/j.bpj.2015.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/15/2015] [Accepted: 08/12/2015] [Indexed: 12/21/2022] Open
Abstract
Choice of network topology for gene regulation has been a question of interest for a long time. How do simple and more complex topologies arise? In this work, we analyze the topology of the marRAB operon in Escherichia coli, which is associated with control of expression of genes associated with conferring resistance to low-level antibiotics to the bacterium. Among the 2102 promoters in E. coli, the marRAB promoter is the only one that encodes for an autoactivator and an autorepressor. What advantages does this topology confer to the bacterium? In this work, we demonstrate that, compared to control by a single regulator, the marRAB regulatory arrangement has the least control cost associated with modulating gene expression in response to environmental stimuli. In addition, the presence of dual regulators allows the regulon to exhibit a diverse range of dynamics, a feature that is not observed in genes controlled by a single regulator.
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29
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Lee HJ, Gottesman S. sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 2016; 44:6907-23. [PMID: 27137887 PMCID: PMC5001588 DOI: 10.1093/nar/gkw358] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional regulation of transcription factors contributes to regulatory circuits. We created translational reporter fusions for multiple central regulators in Escherichia coli and examined the effect of Hfq-dependent non-coding RNAs on these fusions. This approach yields an 'RNA landscape,' identifying Hfq-dependent sRNAs that regulate a given fusion. No significant sRNA regulation of crp or fnr was detected. hns was regulated only by DsrA, as previously reported. Lrp and SoxS were both found to be regulated post-transcriptionally. Lrp, ' L: eucine-responsive R: egulatory P: rotein,' regulates genes involved in amino acid biosynthesis and catabolism and other cellular functions. sRNAs DsrA, MicF and GcvB each independently downregulate the lrp translational fusion, confirming previous reports for MicF and GcvB. MicF and DsrA interact with an overlapping site early in the lrp ORF, while GcvB acts upstream at two independent sites in the long lrp leader. Surprisingly, GcvB was found to be responsible for significant downregulation of lrp after oxidative stress; MicF also contributed. SoxS, an activator of genes used to combat oxidative stress, is negatively regulated by sRNA MgrR. This study demonstrates that while not all global regulators are subject to sRNA regulation, post-transcriptional control by sRNAs allows multiple environmental signals to affect synthesis of the transcriptional regulator.
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Affiliation(s)
- Hyun-Jung Lee
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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30
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Roles of Lon protease and its substrate MarA during sodium salicylate-mediated growth reduction and antibiotic resistance in Escherichia coli. Microbiology (Reading) 2016; 162:764-776. [DOI: 10.1099/mic.0.000271] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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El Meouche I, Siu Y, Dunlop MJ. Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells. Sci Rep 2016; 6:19538. [PMID: 26758525 PMCID: PMC4725842 DOI: 10.1038/srep19538] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/07/2015] [Indexed: 12/30/2022] Open
Abstract
Transient resistance can allow microorganisms to temporarily survive lethal concentrations of antibiotics. This can be accomplished through stochastic mechanisms, where individual cells within a population display diverse phenotypes to hedge against the appearance of an antibiotic. To date, research on transient stochastic resistance has focused primarily on mechanisms where a subpopulation of cells enters a dormant, drug-tolerant state. However, a fundamental question is whether stochastic gene expression can also generate variable resistance levels among growing cells in a population. We hypothesized that stochastic expression of antibiotic-inducible resistance mechanisms might play such a role. To investigate this, we focused on a prototypical example of such a system: the multiple antibiotic resistance activator MarA. Previous studies have shown that induction of MarA can lead to a multidrug resistant phenotype at the population level. We asked whether MarA expression also has a stochastic component, even when uninduced. Time lapse microscopy showed that isogenic cells express heterogeneous, dynamic levels of MarA, which were correlated with transient antibiotic survival. This finding has important clinical implications, as stochastic expression of resistance genes may be widespread, allowing populations to hedge against the sudden appearance of an antibiotic.
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Affiliation(s)
- Imane El Meouche
- School of Engineering, University of Vermont, Burlington, VT USA 05405
| | - Yik Siu
- School of Engineering, University of Vermont, Burlington, VT USA 05405
| | - Mary J Dunlop
- School of Engineering, University of Vermont, Burlington, VT USA 05405
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32
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Overproduction of AcrR increases organic solvent tolerance mediated by modulation of SoxS regulon in Escherichia coli. Appl Microbiol Biotechnol 2014; 98:8763-73. [DOI: 10.1007/s00253-014-6024-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022]
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33
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Keating DH, Zhang Y, Ong IM, McIlwain S, Morales EH, Grass JA, Tremaine M, Bothfeld W, Higbee A, Ulbrich A, Balloon AJ, Westphall MS, Aldrich J, Lipton MS, Kim J, Moskvin OV, Bukhman YV, Coon JJ, Kiley PJ, Bates DM, Landick R. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification. Front Microbiol 2014; 5:402. [PMID: 25177315 PMCID: PMC4132294 DOI: 10.3389/fmicb.2014.00402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/17/2014] [Indexed: 11/13/2022] Open
Abstract
Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.
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Affiliation(s)
- David H Keating
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Irene M Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Eduardo H Morales
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Jeffrey A Grass
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Biochemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Mary Tremaine
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - William Bothfeld
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Alan Higbee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Allison J Balloon
- Department of Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI, USA ; Department of Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Josh Aldrich
- Pacific Northwest National Laboratory Richland, WA, USA
| | - Mary S Lipton
- Pacific Northwest National Laboratory Richland, WA, USA
| | - Joonhoon Kim
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Chemical and Biological Engineering, University of Wisconsin-Madison Madison, WI, USA
| | - Oleg V Moskvin
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Yury V Bukhman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI, USA ; Department of Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Patricia J Kiley
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI, USA
| | - Donna M Bates
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison Madison, WI, USA ; Department of Biochemistry, University of Wisconsin-Madison Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
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Robijns SCA, Roberfroid S, Van Puyvelde S, De Pauw B, Uceda Santamaría E, De Weerdt A, De Coster D, Hermans K, De Keersmaecker SCJ, Vanderleyden J, Steenackers HPL. A GFP promoter fusion library for the study of Salmonella biofilm formation and the mode of action of biofilm inhibitors. BIOFOULING 2014; 30:605-625. [PMID: 24735176 DOI: 10.1080/08927014.2014.907401] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Salmonella, an important foodborne pathogen, forms biofilms in many different environments. The composition of these biofilms differs depending on the growth conditions, and their development is highly coordinated in time. To develop efficient treatments, it is therefore essential that biofilm formation and its inhibition be understood in different environments and in a time-dependent manner. Many currently used techniques, such as transcriptomics or proteomics, are still expensive and thus limited in their application. Therefore, a GFP-promoter fusion library with 79 important Salmonella biofilm genes was developed (covering among other things matrix production, fimbriae and flagella synthesis, and c-di-GMP regulation). This library is a fast, inexpensive, and easy-to-use tool, and can therefore be conducted in different experimental setups in a time-dependent manner. In this paper, four possible applications are highlighted to illustrate and validate the use of this reporter fusion library.
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Affiliation(s)
- S C A Robijns
- a Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics , KU Leuven , Leuven , Belgium
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Nicoloff H, Andersson DI. Lon protease inactivation, or translocation of thelongene, potentiate bacterial evolution to antibiotic resistance. Mol Microbiol 2013; 90:1233-48. [DOI: 10.1111/mmi.12429] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Hervé Nicoloff
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-751 23 Uppsala Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-751 23 Uppsala Sweden
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Garcia-Bernardo J, Dunlop MJ. Tunable stochastic pulsing in the Escherichia coli multiple antibiotic resistance network from interlinked positive and negative feedback loops. PLoS Comput Biol 2013; 9:e1003229. [PMID: 24086119 PMCID: PMC3784492 DOI: 10.1371/journal.pcbi.1003229] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/03/2013] [Indexed: 11/19/2022] Open
Abstract
Cells live in uncertain, dynamic environments and have many mechanisms for sensing and responding to changes in their surroundings. However, sudden fluctuations in the environment can be catastrophic to a population if it relies solely on sensory responses, which have a delay associated with them. Cells can reconcile these effects by using a tunable stochastic response, where in the absence of a stressor they create phenotypic diversity within an isogenic population, but use a deterministic response when stressors are sensed. Here, we develop a stochastic model of the multiple antibiotic resistance network of Escherichia coli and show that it can produce tunable stochastic pulses in the activator MarA. In particular, we show that a combination of interlinked positive and negative feedback loops plays an important role in setting the dynamics of the stochastic pulses. Negative feedback produces a pulsatile response that is tunable, while positive feedback serves to amplify the effect. Our simulations show that the uninduced native network is in a parameter regime that is of low cost to the cell (taxing resistance mechanisms are expressed infrequently) and also elevated noise strength (phenotypic variability is high). The stochastic pulsing can be tuned by MarA induction such that variability is decreased once stresses are sensed, avoiding the detrimental effects of noise when an optimal MarA concentration is needed. We further show that variability in the expression of MarA can act as a bet hedging mechanism, allowing for survival in time-varying stress environments, however this effect is tunable to allow for a fully induced, deterministic response in the presence of a stressor.
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Affiliation(s)
- Javier Garcia-Bernardo
- School of Engineering, University of Vermont, Burlington, Vermont, United States of America
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
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Duval V, Lister IM. MarA, SoxS and Rob of Escherichia coli - Global regulators of multidrug resistance, virulence and stress response. ACTA ACUST UNITED AC 2013; 2:101-124. [PMID: 24860636 DOI: 10.6000/1927-3037.2013.02.03.2] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Bacteria have a great capacity for adjusting their metabolism in response to environmental changes by linking extracellular stimuli to the regulation of genes by transcription factors. By working in a co-operative manner, transcription factors provide a rapid response to external threats, allowing the bacteria to survive. This review will focus on transcription factors MarA, SoxS and Rob in Escherichia coli, three members of the AraC family of proteins. These homologous proteins exemplify the ability to respond to multiple threats such as oxidative stress, drugs and toxic compounds, acidic pH, and host antimicrobial peptides. MarA, SoxS and Rob recognize similar DNA sequences in the promoter region of more than 40 regulatory target genes. As their regulons overlap, a finely tuned adaptive response allows E. coli to survive in the presence of different assaults in a co-ordinated manner. These regulators are well conserved amongst Enterobacteriaceae and due to their broad involvement in bacterial adaptation in the host, have recently been explored as targets to develop new anti-virulence agents. The regulators are also being examined for their roles in novel technologies such as biofuel production.
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Affiliation(s)
- Valérie Duval
- Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111
| | - Ida M Lister
- Arietis Corporation, 650 Albany Street, Room 130, Boston, MA 02118
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