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Unni R, Andreani NA, Vallier M, Heinzmann SS, Taubenheim J, Guggeis MA, Tran F, Vogler O, Künzel S, Hövener JB, Rosenstiel P, Kaleta C, Dempfle A, Unterweger D, Baines JF. Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance. Gut Microbes 2023; 15:2286675. [PMID: 38059748 PMCID: PMC10730162 DOI: 10.1080/19490976.2023.2286675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a persistent inflammatory condition that affects the gastrointestinal tract and presents significant challenges in its management and treatment. Despite the knowledge that within-host bacterial evolution occurs in the intestine, the disease has rarely been studied from an evolutionary perspective. In this study, we aimed to investigate the evolution of resident bacteria during intestinal inflammation and whether- and how disease-related bacterial genetic changes may present trade-offs with potential therapeutic importance. Here, we perform an in vivo evolution experiment of E. coli in a gnotobiotic mouse model of IBD, followed by multiomic analyses to identify disease-specific genetic and phenotypic changes in bacteria that evolved in an inflamed versus a non-inflamed control environment. Our results demonstrate distinct evolutionary changes in E. coli specific to inflammation, including a single nucleotide variant that independently reached high frequency in all inflamed mice. Using ex vivo fitness assays, we find that these changes are associated with a higher fitness in an inflamed environment compared to isolates derived from non-inflamed mice. Further, using large-scale phenotypic assays, we show that bacterial adaptation to inflammation results in clinically relevant phenotypes, which intriguingly include collateral sensitivity to antibiotics. Bacterial evolution in an inflamed gut yields specific genetic and phenotypic signatures. These results may serve as a basis for developing novel evolution-informed treatment approaches for patients with intestinal inflammation.
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Affiliation(s)
- Rahul Unni
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Nadia Andrea Andreani
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Marie Vallier
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Silke S. Heinzmann
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Neuherberg, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Martina A. Guggeis
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Olga Vogler
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Daniel Unterweger
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - John F. Baines
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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3
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Gandarilla-Pérez CA, Pinilla S, Bitbol AF, Weigt M. Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. PLoS Comput Biol 2023; 19:e1011010. [PMID: 36996234 PMCID: PMC10089317 DOI: 10.1371/journal.pcbi.1011010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/11/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023] Open
Abstract
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use phylogeny or residue coevolution to infer which paralogs are specific interaction partners within each species. We show that these two signals can be combined to improve the performance of the inference of interaction partners among paralogs. For this, we first align the sequence-similarity graphs of the two families through simulated annealing, yielding a robust partial pairing. We next use this partial pairing to seed a coevolution-based iterative pairing algorithm. This combined method improves performance over either separate method. The improvement obtained is striking in the difficult cases where the average number of paralogs per species is large or where the total number of sequences is modest.
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Affiliation(s)
- Carlos A Gandarilla-Pérez
- Facultad de Física, Universidad de la Habana, San Lázaro y L, Vedado, Habana, Cuba
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative (LCQB, UMR 7238), Paris, France
| | - Sergio Pinilla
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative (LCQB, UMR 7238), Paris, France
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), Paris, France
| | - Anne-Florence Bitbol
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative (LCQB, UMR 7238), Paris, France
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4
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Rothman JA, Saghir A, Chung SA, Boyajian N, Dinh T, Kim J, Oval J, Sharavanan V, York C, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. WATER RESEARCH 2023; 229:119421. [PMID: 36455460 DOI: 10.1016/j.watres.2022.119421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.
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Affiliation(s)
- Jason A Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America.
| | - Andrew Saghir
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Seung-Ah Chung
- Genomics High-Throughput Facility, Department of Biological Chemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Nicholas Boyajian
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Thao Dinh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Jinwoo Kim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Jordan Oval
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Vivek Sharavanan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Courtney York
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America.
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5
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Blair JMA, Siasat P, McNeil HE, Colclough A, Ricci V, Lawler AJ, Abdalaal H, Buckner MMC, Baylay A, Busby SJ, Piddock LJV. EnvR is a potent repressor of acrAB transcription in Salmonella. J Antimicrob Chemother 2022; 78:133-140. [PMID: 36308324 PMCID: PMC9780535 DOI: 10.1093/jac/dkac364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/06/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Resistance nodulation division (RND) family efflux pumps, including the major pump AcrAB-TolC, are important mediators of intrinsic and evolved antibiotic resistance. Expression of these pumps is carefully controlled by a network of regulators that respond to different environmental cues. EnvR is a TetR family transcriptional regulator encoded upstream of the RND efflux pump acrEF. METHODS Binding of EnvR protein upstream of acrAB was determined by electrophoretic mobility shift assays and the phenotypic consequence of envR overexpression on antimicrobial susceptibility, biofilm motility and invasion of eukaryotic cells in vitro was measured. Additionally, the global transcriptome of clinical Salmonella isolates overexpressing envR was determined by RNA-Seq. RESULTS EnvR bound to the promoter region upstream of the genes coding for the major efflux pump AcrAB in Salmonella, inhibiting transcription and preventing production of AcrAB protein. The phenotype conferred by overexpression of envR mimicked deletion of acrB as it conferred multidrug susceptibility, decreased motility and decreased invasion into intestinal cells in vitro. Importantly, we demonstrate the clinical relevance of this regulatory mechanism because RNA-Seq revealed that a drug-susceptible clinical isolate of Salmonella had low acrB expression even though expression of its major regulator RamA was very high; this was caused by very high EnvR expression. CONCLUSIONS In summary, we show that EnvR is a potent repressor of acrAB transcription in Salmonella, and can override binding by RamA so preventing MDR to clinically useful drugs. Finding novel tools to increase EnvR expression may form the basis of a new way to prevent or treat MDR infections.
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Affiliation(s)
| | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Helen E McNeil
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Abigail Colclough
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Vito Ricci
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Amelia J Lawler
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Hind Abdalaal
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Michelle M C Buckner
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Alison Baylay
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Stephen J Busby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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6
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Rothman JA, Saghir A, Chung SA, Boyajian N, Dinh T, Kim J, Oval J, Sharavanan V, York C, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.02.502560. [PMID: 35982656 PMCID: PMC9387120 DOI: 10.1101/2022.08.02.502560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Andrew Saghir
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Seung-Ah Chung
- Genomics High-Throughput Facility, Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Nicholas Boyajian
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Thao Dinh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Jinwoo Kim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Jordan Oval
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Vivek Sharavanan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Courtney York
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
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7
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Su T, Che C, Han J, Zhao Y, Zhang Z, An G, Si M, Chen C. The TetR-type regulator AtsR is involved in multidrug response in Corynebacterium glutamicum. Microb Cell Fact 2022; 21:123. [PMID: 35729563 PMCID: PMC9210681 DOI: 10.1186/s12934-022-01850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background The TetR (tetracycline repressor) family is one of the major transcription factor families that regulate expression of genes involved in bacterial antimicrobial resistance systems. NCgl0886 protein, designated as AtsR, is a member of the TetR family identified in Corynebacterium glutamicum, which is conserved in several species of the genera Corynebacterium, also including the well-known pathogen C. diphtheriae. AtsR is located at no far upstream of the identically oriented ncgl0884 gene, encoding a putative multidrug efflux pump protein, and in the same operon with ncgl0887, encoding a resistance, nodulation and cell division (RND) superfamily drug exporter. However, the role of AtsR is not clearly understood. Results Here we showed that dimeric AtsR directly repressed the expression of the ncgl0887-atsR operon, as well as indirectly controlled the ncgl0884 transcription. Antibiotics and toxic compounds induced the expression of ncgl0887-atsR operon. A perfect palindromic motif (5΄-TGCAA-N2-TTGCA-3΄; 12 bp) was identified in the upstream region of ncgl0887-atsR operon. Electrophoretic mobility shift assays (EMSAs) demonstrated specific binding of AtsR to this motif, and hydrogen peroxide (H2O2) blocked binding. H2O2 oxidized cysteine residues to form Cys123-Cys187 intermolecular disulfide bonds between two subunits in AtsR dimer, which altered its DNA-binding characteristics and caused its dissociation, thereby leading to derepression of the drug efflux protein. Deletion of ncgl0884 and ncgl0887 increased the susceptibilities of C. glutamicum for several toxic compounds, but overexpression of atsR decreased the drug tolerance of C. glutamicum. Conclusions Our study revealed that AtsR was a redox regulator that sensed oxidative stress via thiol modification. The results obtained here will contribute to our understanding of the drug response mechanism not only in C. glutamicum but also in the related bacteria C. diphtheriae. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01850-0.
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Affiliation(s)
- Tao Su
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China.
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Jiyu Han
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Yuying Zhao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Zihan Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Guangdi An
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, 273165, China
| | - Can Chen
- Key Laboratory of Plant Genetics and Molecular Breeding, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, 466001, China.
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8
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Youlden G, McNeil HE, Blair JMA, Jabbari S, King JR. Mathematical Modelling Highlights the Potential for Genetic Manipulation as an Adjuvant to Counter Efflux-Mediated MDR in Salmonella. Bull Math Biol 2022; 84:56. [PMID: 35380320 PMCID: PMC8983579 DOI: 10.1007/s11538-022-01011-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/02/2022] [Indexed: 11/18/2022]
Abstract
Bacteria have developed resistance to antibiotics by various mechanisms, notable amongst these is the use of permeation barriers and the expulsion of antibiotics via efflux pumps. The resistance-nodulation-division (RND) family of efflux pumps is found in Gram-negative bacteria and a major contributor to multidrug resistance (MDR). In particular, Salmonella encodes five RND efflux pump systems: AcrAB, AcrAD, AcrEF, MdsAB and MdtAB which have different substrate ranges including many antibiotics. We produce a spatial partial differential equation (PDE) model governing the diffusion and efflux of antibiotic in Salmonella, via these RND efflux pumps. Using parameter fitting techniques on experimental data, we are able to establish the behaviour of multiple wild-type and efflux mutant Salmonella strains, which enables us to produce efflux profiles for each individual efflux pump system. By combining the model with a gene regulatory network (GRN) model of efflux regulation, we simulate how the bacteria respond to their environment. Finally, performing a parameter sensitivity analysis, we look into various different targets to inhibit the efflux pumps. The model provides an in silico framework with which to test these potential adjuvants to counter MDR.
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Affiliation(s)
- George Youlden
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Helen E McNeil
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jessica M A Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sara Jabbari
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - John R King
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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9
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Nishino K, Yamasaki S, Nakashima R, Zwama M, Hayashi-Nishino M. Function and Inhibitory Mechanisms of Multidrug Efflux Pumps. Front Microbiol 2021; 12:737288. [PMID: 34925258 PMCID: PMC8678522 DOI: 10.3389/fmicb.2021.737288] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
Multidrug efflux pumps are inner membrane transporters that export multiple antibiotics from the inside to the outside of bacterial cells, contributing to bacterial multidrug resistance (MDR). Postgenomic analysis has demonstrated that numerous multidrug efflux pumps exist in bacteria. Also, the co-crystal structural analysis of multidrug efflux pumps revealed the drug recognition and export mechanisms, and the inhibitory mechanisms of the pumps. A single multidrug efflux pump can export multiple antibiotics; hence, developing efflux pump inhibitors is crucial in overcoming infectious diseases caused by multidrug-resistant bacteria. This review article describes the role of multidrug efflux pumps in MDR, and their physiological functions and inhibitory mechanisms.
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Affiliation(s)
- Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Seiji Yamasaki
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Ryosuke Nakashima
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Mitsuko Hayashi-Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
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10
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Baron SA, Cassir N, Hamel M, Hadjadj L, Saidani N, Dubourg G, Rolain JM. Risk factors for acquisition of colistin-resistant Klebsiella pneumoniae and expansion of a colistin-resistant ST307 epidemic clone in hospitals in Marseille, France, 2014 to 2017. ACTA ACUST UNITED AC 2021; 26. [PMID: 34047270 PMCID: PMC8161728 DOI: 10.2807/1560-7917.es.2021.26.21.2000022] [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] [Indexed: 11/20/2022]
Abstract
BackgroundFrance is a low prevalence country for colistin resistance. Molecular and epidemiological events contributing to the emergence of resistance to colistin, one of the 'last-resort' antibiotics to treat multidrug-resistant Gram-negative infections, are important to investigate.AimThis retrospective (2014 to 2017) observational study aimed to identify risk factors associated with acquisition of colistin-resistant Klebsiella pneumoniae (CRKP) in hospitals in Marseille, France, and to molecularly characterise clinical isolates.MethodsTo identify risk factors for CRKP, a matched-case-control (1:2) study was performed in two groups of patients with CRKP or colistin-susceptible K. pneumoniae respectively. Whole-genome-sequences (WGS) of CRKP were compared with 6,412 K. pneumoniae genomes available at the National Center for Biotechnology Information (NCBI).ResultsMultivariate analysis identified male sex and contact with a patient carrying a CRKP as significant independent factors (p < 0.05) for CRKP acquisition, but not colistin administration. WGS of nine of 14 CRKP clinical isolates belonged to the same sequence type (ST)307. These isolates were from patients who had been hospitalised in the same wards, suggesting an outbreak. Comparison of the corresponding strains' WGS to K. pneumoniae genomes in NCBI revealed that in chromosomal genes likely playing a role in colistin resistance, a subset of five specific mutations were significantly associated with ST307 (p < 0.001).ConclusionA ST307 CRKP clone was identified in this study, with specific chromosomal mutations in genes potentially implicated in colistin resistance. ST307 might have a propensity to be or become resistant to colistin, however confirming this requires further investigations.
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Affiliation(s)
- Sophie Alexandra Baron
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Nadim Cassir
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Mouna Hamel
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Linda Hadjadj
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Nadia Saidani
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Jean-Marc Rolain
- IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
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11
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Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli. J Bacteriol 2021; 203:e0010921. [PMID: 33972351 DOI: 10.1128/jb.00109-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a "stringent" RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli's ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.
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12
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Limited Multidrug Resistance Efflux Pump Overexpression among Multidrug-Resistant Escherichia coli Strains of ST131. Antimicrob Agents Chemother 2021; 65:AAC.01735-20. [PMID: 33468485 DOI: 10.1128/aac.01735-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/28/2020] [Indexed: 12/30/2022] Open
Abstract
Gram-negative bacteria partly rely on efflux pumps to facilitate growth under stressful conditions and to increase resistance to a wide variety of commonly used drugs. In recent years, Escherichia coli sequence type 131 (ST131) has emerged as a major cause of extraintestinal infection frequently exhibiting a multidrug resistance (MDR) phenotype. The contribution of efflux to MDR in emerging E. coli MDR clones, however, is not well studied. We characterized strains from an international collection of clinical MDR E. coli isolates by MIC testing with and without the addition of the AcrAB-TolC efflux inhibitor 1-(1-naphthylmethyl)-piperazine (NMP). MIC data for 6 antimicrobial agents and their reversion by NMP were analyzed by principal-component analysis (PCA). PCA revealed a group of 17 MDR E. coli isolates (n = 34) exhibiting increased susceptibility to treatment with NMP, suggesting an enhanced contribution of efflux pumps to antimicrobial resistance in these strains (termed enhanced efflux phenotype [EEP] strains). Only 1/17 EEP strains versus 12/17 non-EEP MDR strains belonged to the ST131 clonal group. Whole-genome sequencing revealed marked differences in efflux-related genes between EEP and control strains, with the majority of notable amino acid substitutions occurring in AcrR, MarR, and SoxR. Quantitative reverse transcription-PCR (qRT-PCR) of multiple efflux-related genes showed significant overexpression of the AcrAB-TolC system in EEP strains, whereas in the remaining strains, we found enhanced expression of alternative efflux proteins. We conclude that a proportion of MDR E. coli strains exhibit an EEP, which is linked to an overexpression of the AcrAB-TolC efflux pump and a distinct array of genomic variations. Members of ST131, although highly successful, are less likely to exhibit the EEP.
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13
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A Major Facilitator Superfamily (MFS) Efflux Pump, SCO4121, from Streptomyces coelicolor with Roles in Multidrug Resistance and Oxidative Stress Tolerance and Its Regulation by a MarR Regulator. Appl Environ Microbiol 2021; 87:AEM.02238-20. [PMID: 33483304 DOI: 10.1128/aem.02238-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Overexpression of efflux pumps is one of the major determinants of resistance in bacteria. Streptomyces species harbor a large array of efflux pumps that are transcriptionally silenced under laboratory conditions. However, their dissemination results in multidrug resistance in different clinical pathogens. In this study, we have identified an efflux pump from Streptomyces coelicolor, SCO4121, belonging to the major facilitator superfamily (MFS) family of transporters and characterized its role in antibiotic resistance. SCO4121 provided resistance to multiple dissimilar drugs upon overexpression in both native and heterologous hosts. Further, deletion of SCO4121 resulted in increased sensitivity toward ciprofloxacin and chloramphenicol, suggesting the pump to be a major transporter of these substrates. Apart from providing multidrug resistance, SCO4121 imparted increased tolerance against the strong oxidant HOCl. In wild-type Streptomyces coelicolor cells, these drugs were found to transcriptionally regulate the pump in a concentration-dependent manner. Additionally, we identified SCO4122, a MarR regulator that positively regulates SCO4121 in response to various drugs and the oxidant HOCl. Thus, through these studies we present the multiple roles of SCO4121 in S. coelicolor and highlight the intricate mechanisms via which it is regulated in response to antibiotics and oxidative stress.IMPORTANCE One of the key mechanisms of drug resistance in bacteria is overexpression of efflux pumps. Streptomyces species are a reservoir of a large number of efflux pumps, potentially to provide resistance to both endogenous and nonendogenous antibiotics. While many of these pumps are not expressed under standard laboratory conditions, they result in resistance to multiple drugs when spread to other bacterial pathogens through horizontal gene transfer. In this study, we have identified a widely conserved efflux pump SCO4121 from Streptomyces coelicolor with roles in both multidrug resistance and oxidative stress tolerance. We also report the presence of an adjacent MarR regulator, SCO4122, which positively regulates SCO4121 in the presence of diverse substrates in a redox-responsive manner. This study highlights that soil bacteria such as Streptomyces can reveal novel mechanisms of antibiotic resistance that may potentially emerge in clinically important bacteria.
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14
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Youlden GH, Ricci V, Wang-Kan X, Piddock LJV, Jabbari S, King JR. Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria. J Math Biol 2021; 82:31. [PMID: 33694073 PMCID: PMC7946726 DOI: 10.1007/s00285-021-01576-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/27/2020] [Accepted: 02/14/2021] [Indexed: 12/12/2022]
Abstract
Efflux pumps are a mechanism of intrinsic and evolved resistance in bacteria. If an efflux pump can expel an antibiotic so that its concentration within the cell is below a killing threshold the bacteria are resistant to the antibiotic. Efflux pumps may be specific or they may pump various different substances. This is why many efflux pumps confer multi drug resistance (MDR). In particular over expression of the AcrAB−TolC efflux pump system confers MDR in both Salmonella and Escherichia coli. We consider the complex gene regulation network that controls expression of genes central to controlling the efflux associated genes acrAB and acrEF in Salmonella. We present the first mathematical model of this gene regulatory network in the form of a system of ordinary differential equations. Using a time dependent asymptotic analysis, we examine in detail the behaviour of the efflux system on various different timescales. Asymptotic approximations of the steady states provide an analytical comparison of targets for efflux inhibition.
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Affiliation(s)
- George H Youlden
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK. .,School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK. .,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Vito Ricci
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Xuan Wang-Kan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.,Gyrd-Hansen Group, Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Laura J V Piddock
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sara Jabbari
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - John R King
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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15
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Reding C, Catalán P, Jansen G, Bergmiller T, Wood E, Rosenstiel P, Schulenburg H, Gudelj I, Beardmore R. The Antibiotic Dosage of Fastest Resistance Evolution: gene amplifications underpinning the inverted-U. Mol Biol Evol 2021; 38:3847-3863. [PMID: 33693929 PMCID: PMC8382913 DOI: 10.1093/molbev/msab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an “inverted-U” pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.
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Affiliation(s)
- Carlos Reding
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Pablo Catalán
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Departamento de Matemáticas, Universidad Carlos III, Madrid, Spain
| | | | | | - Emily Wood
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Phillip Rosenstiel
- Institute of Clinical Molecular Biology (IKMB), CAU Kiel, Kiel 24105, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Kiel 24118, Germany
| | - Ivana Gudelj
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Robert Beardmore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
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16
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Biofilms as Promoters of Bacterial Antibiotic Resistance and Tolerance. Antibiotics (Basel) 2020; 10:antibiotics10010003. [PMID: 33374551 PMCID: PMC7822488 DOI: 10.3390/antibiotics10010003] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistant bacteria are a global threat for human and animal health. However, they are only part of the problem of antibiotic failure. Another bacterial strategy that contributes to their capacity to withstand antimicrobials is the formation of biofilms. Biofilms are associations of microorganisms embedded a self-produced extracellular matrix. They create particular environments that confer bacterial tolerance and resistance to antibiotics by different mechanisms that depend upon factors such as biofilm composition, architecture, the stage of biofilm development, and growth conditions. The biofilm structure hinders the penetration of antibiotics and may prevent the accumulation of bactericidal concentrations throughout the entire biofilm. In addition, gradients of dispersion of nutrients and oxygen within the biofilm generate different metabolic states of individual cells and favor the development of antibiotic tolerance and bacterial persistence. Furthermore, antimicrobial resistance may develop within biofilms through a variety of mechanisms. The expression of efflux pumps may be induced in various parts of the biofilm and the mutation frequency is induced, while the presence of extracellular DNA and the close contact between cells favor horizontal gene transfer. A deep understanding of the mechanisms by which biofilms cause tolerance/resistance to antibiotics helps to develop novel strategies to fight these infections.
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17
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Langevin AM, El Meouche I, Dunlop MJ. Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition. mSphere 2020; 5:e01056-20. [PMID: 33328350 PMCID: PMC7771234 DOI: 10.1128/msphere.01056-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has become a major public health concern as bacteria evolve to evade drugs, leading to recurring infections and a decrease in antibiotic efficacy. Systematic efforts have revealed mechanisms involved in resistance. Yet, in many cases, how these specific mechanisms accelerate or slow the evolution of resistance remains unclear. Here, we conducted a systematic study of the impact of the AcrAB-TolC efflux pump on the evolution of antibiotic resistance. We mapped how population growth rate and resistance change over time as a function of both the antibiotic concentration and the parent strain's genetic background. We compared the wild-type strain to a strain overexpressing AcrAB-TolC pumps and a strain lacking functional pumps. In all cases, resistance emerged when cultures were treated with chloramphenicol concentrations near the MIC of their respective parent strain. The genetic background of the parent strain also influenced resistance acquisition. The wild-type strain evolved resistance within 24 h through mutations in the acrAB operon and its associated regulators. Meanwhile, the strain overexpressing AcrAB-TolC evolved resistance more slowly than the wild-type strain; this strain achieved resistance in part through point mutations in acrB and the acrAB promoter. Surprisingly, the strain without functional AcrAB-TolC efflux pumps still gained resistance, which it achieved through upregulation of redundant efflux pumps. Overall, our results suggest that treatment conditions just above the MIC pose the largest risk for the evolution of resistance and that AcrAB-TolC efflux pumps impact the pathway by which chloramphenicol resistance is achieved.IMPORTANCE Combatting the rise of antibiotic resistance is a significant challenge. Efflux pumps are an important contributor to drug resistance; they exist across many cell types and can export numerous classes of antibiotics. Cells can regulate pump expression to maintain low intracellular drug concentrations. Here, we explored how resistance emerged depending on the antibiotic concentration, as well as the presence of efflux pumps and their regulators. We found that treatments near antibiotic concentrations that inhibit the parent strain's growth were most likely to promote resistance. While wild-type, pump overexpression, and pump knockout strains were all able to evolve resistance, they differed in the absolute level of resistance evolved, the speed at which they achieved resistance, and the genetic pathways involved. These results indicate that specific treatment regimens may be especially problematic for the evolution of resistance and that the strain background can influence how resistance is achieved.
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Affiliation(s)
- Ariel M Langevin
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston, Massachusetts, USA
| | - Imane El Meouche
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston, Massachusetts, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston, Massachusetts, USA
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18
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Casalone E, Vignolini T, Braconi L, Gardini L, Capitanio M, Pavone FS, Dei S, Teodori E. 1-benzyl-1,4-diazepane reduces the efflux of resistance-nodulation-cell division pumps in Escherichia coli. Future Microbiol 2020; 15:987-999. [PMID: 32840130 DOI: 10.2217/fmb-2019-0296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate the action mechanism of 1-benzyl-1,4-diazepane (1-BD) as efflux pump inhibitor (EPI) in Escherichia coli mutants: ΔacrAB or overexpressing AcrAB and AcrEF efflux pumps. Materials & methods: Effect of 1-BD on: antibiotic potentiation, by microdilution method; membrane functionality, by fluorimetric assays; ethidium bromide accumulation, by fluorometric real-time efflux assay; AcrB expression, by quantitative photoactivated localization microscopy. Results: 1-BD decreases the minimal inhibitory concentration of levofloxacin and other antibiotics and increase ethidium bromide accumulation in E. coli overexpressing efflux pumps but not in the ΔacrAB strain. 1-BD increases membranes permeability, without sensibly affecting inner membrane polarity and decreases acrAB transcription. Conclusion: 1-BD acts as an EPI in E. coli with a mixed mechanism, different from that of major reference EPIs.
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Affiliation(s)
- Enrico Casalone
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tiziano Vignolini
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Laura Braconi
- Department of Neuroscience, Psychology, Drug Research & Child Health (NEUROFARBA), Via U. Schiff, 6 - 50019 Sesto Fiorentino, Italy
| | - Lucia Gardini
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics & Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Francesco S Pavone
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy.,Department of Physics & Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Silvia Dei
- Department of Neuroscience, Psychology, Drug Research & Child Health (NEUROFARBA), Via U. Schiff, 6 - 50019 Sesto Fiorentino, Italy
| | - Elisabetta Teodori
- Department of Neuroscience, Psychology, Drug Research & Child Health (NEUROFARBA), Via U. Schiff, 6 - 50019 Sesto Fiorentino, Italy
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19
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Srinivasan VB, Rajamohan G. Protein phosphorylation mechanisms: a novel paradigm of antimicrobial resistance in 'critical threat' pathogens. Future Microbiol 2020; 15:837-840. [PMID: 32657616 DOI: 10.2217/fmb-2020-0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Vijaya Bharathi Srinivasan
- Council of Scientific & Industrial Research- Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Govindan Rajamohan
- Council of Scientific & Industrial Research- Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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20
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The role of RND-type efflux pumps in multidrug-resistant mutants of Klebsiella pneumoniae. Sci Rep 2020; 10:10876. [PMID: 32616840 PMCID: PMC7331594 DOI: 10.1038/s41598-020-67820-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/10/2020] [Indexed: 11/23/2022] Open
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae is a worldwide problem. K. pneumoniae possesses numerous resistant genes in its genome. We isolated mutants resistant to various antimicrobials in vitro and investigated the importance of intrinsic genes in acquired resistance. The isolation frequency of the mutants was 10−7–10−9. Of the multidrug-resistant mutants, hyper-multidrug-resistant mutants (EB256-1, EB256-2, Nov1-8, Nov2-2, and OX128) were identified, and accelerated efflux activity of ethidium from the inside to the outside of the cells was observed in these mutants. Therefore, we hypothesized that the multidrug efflux pump, especially RND-type efflux pump, would be related to changes of the phenotype. We cloned all RND-type multidrug efflux pumps from the K. pneumoniae genome and characterized them. KexEF and KexC were powerful multidrug efflux pumps, in addition to AcrAB, KexD, OqxAB, and EefABC, which were reported previously. It was revealed that the expression of eefA was increased in EB256-1 and EB256-2: the expression of oqxA was increased in OX128; the expression of kexF was increased in Nov2-2. It was found that a region of 1,485 bp upstream of kexF, was deleted in the genome of Nov2-2. K. pneumoniae possesses more potent RND-multidrug efflux systems than E. coli. However, we revealed that most of them did not contribute to the drug resistance of our strain at basic levels of expression. On the other hand, it was also noted that the overexpression of these pumps could lead to multidrug resistance based on exposure to antimicrobial chemicals. We conclude that these pumps may have a role to maintain the intrinsic resistance of K. pneumoniae when they are overexpressed. The antimicrobial chemicals selected many resistant mutants at the same minimum inhibitory concentration (MIC) or a concentration slightly higher than the MIC. These results support the importance of using antibiotics at appropriate concentrations at clinical sites.
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21
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Construction of a "nutrition supply-detoxification" coculture consortium for medium-chain-length polyhydroxyalkanoate production with a glucose-xylose mixture. J Ind Microbiol Biotechnol 2020; 47:343-354. [PMID: 32140930 DOI: 10.1007/s10295-020-02267-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
In this study, we constructed a coculture consortium comprising engineered Pseudomonas putida KT2440 and Escherichia coli MG1655. Provision of "related" carbon sources and synthesis of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) were separately assigned to these strains via a modular construction strategy. To avoid growth competition, a preference for the use of a carbon source was constructed. Further, the main intermediate metabolite acetate played an important role in constructing the expected "nutrition supply-detoxification" relationship between these strains. The coculture consortium showed a remarkable increase in the mcl-PHA titer (0.541 g/L) with a glucose-xylose mixture (1:1). Subsequently, the titer of mcl-PHA produced by the coculture consortium when tested with actual lignocellulosic hydrolysate (0.434 g/L) was similar to that achieved with laboratory sugars' mixture (0.469 g/L). These results indicate a competitive potential of the engineered E. coli-P. putida coculture consortium for mcl-PHA production with lignocellulosic hydrolysate.
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22
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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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Genome engineering of E. coli for improved styrene production. Metab Eng 2020; 57:74-84. [DOI: 10.1016/j.ymben.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/18/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
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Phylogenetic correlations can suffice to infer protein partners from sequences. PLoS Comput Biol 2019; 15:e1007179. [PMID: 31609984 PMCID: PMC6812855 DOI: 10.1371/journal.pcbi.1007179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/24/2019] [Accepted: 09/25/2019] [Indexed: 12/30/2022] Open
Abstract
Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners among paralogous proteins from sequence data. This success of DCA at predicting protein-protein interactions could be mainly based on its known ability to identify pairs of residues that are in contact in the three-dimensional structure of protein complexes and that coevolve to remain physicochemically complementary. However, interacting proteins possess similar evolutionary histories. What is the role of purely phylogenetic correlations in the performance of DCA-based methods to infer interaction partners? To address this question, we employ controlled synthetic data that only involve phylogeny and no interactions or contacts. We find that DCA accurately identifies the pairs of synthetic sequences that share evolutionary history. While phylogenetic correlations confound the identification of contacting residues by DCA, they are thus useful to predict interacting partners among paralogs. We find that DCA performs as well as phylogenetic methods to this end, and slightly better than them with large and accurate training sets. Employing DCA or phylogenetic methods within an Iterative Pairing Algorithm (IPA) allows to predict pairs of evolutionary partners without a training set. We further demonstrate the ability of these various methods to correctly predict pairings among real paralogous proteins with genome proximity but no known direct physical interaction, illustrating the importance of phylogenetic correlations in natural data. However, for physically interacting and strongly coevolving proteins, DCA and mutual information outperform phylogenetic methods. We finally discuss how to distinguish physically interacting proteins from proteins that only share a common evolutionary history. Many biologically important protein-protein interactions are conserved over evolutionary time scales. This leads to two different signals that can be used to computationally predict interactions between protein families and to identify specific interaction partners. First, the shared evolutionary history leads to highly similar phylogenetic relationships between interacting proteins of the two families. Second, the need to keep the interaction surfaces of partner proteins biophysically compatible causes a correlated amino-acid usage of interface residues. Employing simulated data, we show that the shared history alone can be used to detect partner proteins. Similar accuracies are achieved by algorithms comparing phylogenetic relationships and by methods based on Direct Coupling Analysis (DCA), which are primarily known for their ability to detect the second type of signal. Using natural sequence data, we show that in cases with shared evolutionary history but without known physical interactions, both methods work with similar accuracy, while for some physically interacting systems, DCA and mutual information outperform phylogenetic methods. We propose methods allowing both to predict interactions between protein families and to find interacting partners among paralogs.
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Colclough AL, Scadden J, Blair JMA. TetR-family transcription factors in Gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance. BMC Genomics 2019; 20:731. [PMID: 31606035 PMCID: PMC6790063 DOI: 10.1186/s12864-019-6075-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Background TetR-family transcriptional regulators (TFTRs) are DNA binding factors that regulate gene expression in bacteria. Well-studied TFTRs, such as AcrR, which regulates efflux pump expression, are usually encoded alongside target operons. Recently, it has emerged that there are many TFTRs which act as global multi-target regulators. Our classical view of TFTRs as simple, single-target regulators therefore needs to be reconsidered. As some TFTRs regulate essential processes (e.g. metabolism) or processes which are important determinants of resistance and virulence (e.g. biofilm formation and efflux gene expression) and as TFTRs are present throughout pathogenic bacteria, they may be good drug discovery targets for tackling antimicrobial resistant infections. However, the prevalence and conservation of individual TFTR genes in Gram-negative species, has to our knowledge, not yet been studied. Results Here, a wide-scale search for TFTRs in available proteomes of clinically relevant pathogens Salmonella and Escherichia species was performed and these regulators further characterised. The majority of identified TFTRs are involved in efflux regulation in both Escherichia and Salmonella. The percentage variance in TFTR genes of these genera was found to be higher in those regulating genes involved in efflux, bleach survival or biofilm formation than those regulating more constrained processes. Some TFTRs were found to be present in all strains and species of these two genera, whereas others (i.e. TetR) are only present in some strains and some (i.e. RamR) are genera-specific. Two further pathogens on the WHO priority pathogen list (K. pneumoniae and P. aeruginosa) were then searched for the presence of the TFTRs conserved in Escherichia and Salmonella. Conclusions Through bioinformatics and literature analyses, we present that TFTRs are a varied and heterogeneous family of proteins required for the regulation of numerous important processes, with consequences to antimicrobial resistance and virulence, and that the roles and responses of these proteins are frequently underestimated. Electronic supplementary material The online version of this article (10.1186/s12864-019-6075-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A L Colclough
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J Scadden
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J M A Blair
- Institute of Microbiology and Infection, Biosciences Building, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Pinto L, Torres C, Gil C, Nunes-Miranda JD, Santos HM, Borges V, Gomes JP, Silva C, Vieira L, Pereira JE, Poeta P, Igrejas G. Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131 Escherichia coli. Front Microbiol 2019; 10:831. [PMID: 31130921 PMCID: PMC6509150 DOI: 10.3389/fmicb.2019.00831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strain C999 was isolated of a Spanish patient with urinary tract infection. Previous genotyping indicated that this strain presented a multidrug-resistance phenotype and carried beta-lactamase genes encoding CTX-M-15, TEM-1, and OXA-1 enzymes. The whole-cell proteome, and the membrane, cytoplasmic, periplasmic and extracellular sub-proteomes of C999 were obtained in this work by two-dimensional gel electrophoresis (2DE) followed by fingerprint sequencing through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). A total of 602 proteins were identified in the different cell fractions, several of which are related to stress response systems, cellular responses, and antibiotic and drug responses, consistent with the multidrug-resistance phenotype. In parallel, whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) was done to identify and quantify the genes present and expressing. The in silico prediction following WGS confirmed our strain as being serotype O25:H4 and sequence type ST131. The presence of proteins related to antibiotic resistance and virulence in an O25:H4-ST131 E. coli clone are serious indicators of the continued threat of antibiotic resistance spread amongst healthcare institutions. On a positive note, a multiomics approach can facilitate surveillance and more detailed characterization of virulent bacterial clones from hospital environments.
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Affiliation(s)
- Luís Pinto
- Department of Genetics and Biotechnology, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Concha Gil
- Departamento de Microbiologia II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Júlio D Nunes-Miranda
- Department of Genetics and Biotechnology, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Hugo M Santos
- LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Catarina Silva
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - José E Pereira
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,CECAV, Centro de Ciência Animal e Veterinária, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Patrícia Poeta
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unit, School of Life and Environment Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
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27
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SCO3129, a TetR family regulator, is responsible for osmotic stress in Streptomyces coelicolor. Synth Syst Biotechnol 2018; 3:261-267. [PMID: 30417142 PMCID: PMC6223229 DOI: 10.1016/j.synbio.2018.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/09/2023] Open
Abstract
Streptomyces are the soil-dwelling bacteria with a complex lifecycle and a considerable ability to produce a variety of secondary metabolites. Osmoregulation is important for their lifecycle in nature. In the genome of Streptomyces coelicolor M145, SCO3128 (encodes a putative fatty acid desaturase), SCO3129 (encodes a putative TetR family regulator) and SCO3130 (encodes a putative l-carnitine dehydratase) constitute a transcriptional unit, and its transcript was found to be in response to osmotic stress. Disruption of SCO3130 led to a bald phenotype on MMG medium and the mycelia lysis on the edge of the colony when KCl/NaCl was added to the medium. These results indicated that SCO3130 is important for the osmotic stress resistance in S. coelicolor. Transcriptional analysis and electrophoretic mobility shift assays (EMSA) demonstrated that SCO3129 repressed the transcription of SCO3128-3130 operon through directly binding to the promoter region of SCO3128, indicating that SCO3129 regulates the transcription of SCO3128-3130 in response to osmotic stress.
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Wang M, Fang K, Hong SMC, Kim I, Jang IS, Hong SH. Medium chain unsaturated fatty acid ethyl esters inhibit persister formation of Escherichia coli via antitoxin HipB. Appl Microbiol Biotechnol 2018; 102:8511-8524. [PMID: 30088019 DOI: 10.1007/s00253-018-9271-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Persisters represent a small bacterial population that is dormant and that survives under antibiotic treatment without experiencing genetic adaptation. Persisters are also considered one of the major reasons for recalcitrant chronic bacterial infections. Although several mechanisms of persister formation have been proposed, it is not clear how cells enter the dormant state in the presence of antibiotics or how persister cell formation can be effectively controlled. A fatty acid compound, cis-2-decenoic acid, was reported to decrease persister formation as well as revert the dormant cells to a metabolically active state. We reasoned that some fatty acid compounds may be effective in controlling bacterial persistence because they are known to benefit host immune systems. This study investigated persister cell formation by pathogens that were exposed to nine fatty acid compounds during antibiotic treatment. We found that three medium chain unsaturated fatty acid ethyl esters (ethyl trans-2-decenoate, ethyl trans-2-octenoate, and ethyl cis-4-decenoate) decreased the level of Escherichia coli persister formation up to 110-fold when cells were exposed to ciprofloxacin or ampicillin antibiotics. RNA sequencing analysis and gene deletion persister studies elucidated that these fatty acids inhibit bacterial persistence by regulating antitoxin HipB. A similar persister cell reduction was observed for pathogenic E. coli EDL933, Pseudomonas aeruginosa PAO1, and Serratia marcescens ICU2-4 strains. This study demonstrates that fatty acid ethyl esters can be used to disrupt bacterial dormancy to combat persistent infectious diseases.
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Affiliation(s)
- Mengya Wang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Sung Min Choi Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Inwha Kim
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, 305-333, Republic of Korea
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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29
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Shin KS, Lee SK. Increasing Extracellular Free Fatty Acid Production in Escherichia coli by Disrupting Membrane Transport Systems. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:11243-11250. [PMID: 29188707 DOI: 10.1021/acs.jafc.7b04521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Transposon mutagenesis was used to identify three mutants of E. coli that exhibited increased free fatty acid (FFA) production, which resulted from the disruption of genes related to membrane transport. Deletion of envR, gusC, and mdlA individually in a recombinant E. coli strain resulted in 1.4-, 1.8-, and 1.2-fold increases in total FFA production, respectively. In particular, deletion of envR increased the percentage of extracellular FFA to 46%, compared with 29% for the control strain. Multiple deletion of envR, gusC, mdlA, ompF, and fadL had a synergistic effect on FFA production, resulting in high extracellular FFA production, comprising up to 50% of total FFA production. This study has identified new membrane proteins involved in FFA production and showed that genetic engineering targeting these membrane transporters is important to increase both total FFA and extracellular FFA production.
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Affiliation(s)
- Kwang Soo Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919, Republic of Korea
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919, Republic of Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919, Republic of Korea
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30
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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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31
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The role played by drug efflux pumps in bacterial multidrug resistance. Essays Biochem 2017; 61:127-139. [DOI: 10.1042/ebc20160064] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
Abstract
Antimicrobial resistance is a current major challenge in chemotherapy and infection control. The ability of bacterial and eukaryotic cells to recognize and pump toxic compounds from within the cell to the environment before they reach their targets is one of the important mechanisms contributing to this phenomenon. Drug efflux pumps are membrane transport proteins that require energy to export substrates and can be selective for a specific drug or poly-specific that can export multiple structurally diverse drug compounds. These proteins can be classified into seven groups based on protein sequence homology, energy source and overall structure. Extensive studies on efflux proteins have resulted in a wealth of knowledge that has made possible in-depth understanding of the structures and mechanisms of action, substrate profiles, regulation and possible inhibition of many clinically important efflux pumps. This review focuses on describing known families of drug efflux pumps using examples that are well characterized structurally and/or biochemically.
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Tigecycline Nonsusceptibility Occurs Exclusively in Fluoroquinolone-Resistant Escherichia coli Clinical Isolates, Including the Major Multidrug-Resistant Lineages O25b:H4-ST131-H30R and O1-ST648. Antimicrob Agents Chemother 2017; 61:AAC.01654-16. [PMID: 27855067 DOI: 10.1128/aac.01654-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/08/2016] [Indexed: 11/20/2022] Open
Abstract
Tigecycline (TGC) is a last-line drug for multidrug-resistant Enterobacteriaceae We investigated the mechanism(s) underlying TGC nonsusceptibility (TGC resistant/intermediate) in Escherichia coli clinical isolates. The MIC of TGC was determined for 277 fluoroquinolone-susceptible isolates (ciprofloxacin [CIP] MIC, <0.125 mg/liter) and 194 fluoroquinolone-resistant isolates (CIP MIC, >2 mg/liter). The MIC50 and MIC90 for TGC in fluoroquinolone-resistant isolates were 2-fold higher than those in fluoroquinolone-susceptible isolates (MIC50, 0.5 mg/liter versus 0.25 mg/liter; MIC90, 1 mg/liter versus 0.5 mg/liter, respectively). Two fluoroquinolone-resistant isolates (O25b:H4-ST131-H30R and O125:H37-ST48) were TGC resistant (MICs of 4 and 16 mg/liter, respectively), and four other isolates of O25b:H4-ST131-H30R and an isolate of O1-ST648 showed an intermediate interpretation (MIC, 2 mg/liter). No TGC-resistant/intermediate strains were found among the fluoroquinolone-susceptible isolates. The TGC-resistant/intermediate isolates expressed higher levels of acrA and acrB and had lower intracellular TGC concentrations than susceptible isolates, and they possessed mutations in acrR and/or marR The MICs of acrAB-deficient mutants were markedly lower (0.25 mg/liter) than those of the parental strain. After continuous stepwise exposure to CIP in vitro, six of eight TGC-susceptible isolates had reduced TGC susceptibility. Two of them acquired TGC resistance (TGC MIC, 4 mg/liter) and exhibited expression of acrA and acrB and mutations in acrR and/or marR In conclusion, a population of fluoroquinolone-resistant E. coli isolates, including major extraintestinal pathogenic lineages O25b:H4-ST131-H30R and O1-ST648, showed reduced susceptibility to TGC due to overexpression of the efflux pump AcrAB-TolC, leading to decreased intracellular concentrations of the antibiotics that may be associated with the development of fluoroquinolone resistance.
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Yamanaka Y, Shimada T, Yamamoto K, Ishihama A. Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology (Reading) 2016; 162:1253-1264. [DOI: 10.1099/mic.0.000292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Yuki Yamanaka
- Research Center for Micro-Nano Technology, Nano Technology, Koganei, Tokyo 184-8584, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Nano Technology, Koganei, Tokyo 184-8584, Japan
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Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters. J Bacteriol 2016; 198:1101-13. [PMID: 26811318 DOI: 10.1128/jb.00971-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/19/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Bacteria use multidrug efflux pumps to export drugs and toxic compounds out of the cell. One of the most important efflux pumps in Escherichia coli is the AcrAB-TolC system. Small regulatory RNAs (sRNAs) are known to be major posttranscriptional regulators that can enhance or repress translation by binding to the 5' untranslated region (UTR) of mRNA targets with the help of a chaperone protein, Hfq. In this study, we investigated the expression of acrA, acrB, and tolC translational fusions using 27 Hfq-dependent sRNAs overexpressed from plasmids. No significant sRNA regulation of acrA or acrB was detected. SdsR (also known as RyeB), an abundant and well-conserved stationary-phase sRNA, was found to repress the expression of tolC, the gene encoding the outer membrane protein of many multidrug resistance efflux pumps. This repression was shown to be by direct base pairing occurring upstream from the ribosomal binding site. SdsR overexpression and its regulation of tolC were found to reduce resistance to novobiocin and crystal violet. Our results suggest that additional targets for SdsR exist that contribute to increased antibiotic sensitivity and reduced biofilm formation. In an effort to identify phenotypes associated with single-copy SdsR and its regulation of tolC, the effect of a deletion of sdsR or mutations in tolC that should block SdsR pairing were investigated using a Biolog phenotypic microarray. However, no significant phenotypes were identified. Therefore, SdsR appears to modulate rather than act as a major regulator of its targets. IMPORTANCE AcrAB-TolC is a major efflux pump present in E. coli and Gram-negative bacteria used to export toxic compounds; the pump confers resistance to many antibiotics of unrelated classes. In this study, we found that SdsR, a small RNA expressed in stationary phase, repressed the expression of tolC, resulting in increased sensitivity to some antibiotics. This extends the findings of previous studies showing that sRNAs contribute to the regulation of many outer membrane proteins; manipulating or enhancing their action might help in sensitizing bacteria to antibiotics.
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AcrB-AcrA Fusion Proteins That Act as Multidrug Efflux Transporters. J Bacteriol 2015; 198:332-42. [PMID: 26527645 DOI: 10.1128/jb.00587-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The AcrAB-TolC system in Escherichia coli is an intrinsic RND-type multidrug efflux transporter that functions as a tripartite complex of the inner membrane transporter AcrB, the outer membrane channel TolC, and the adaptor protein AcrA. Although the crystal structures of each component of this system have been elucidated, the crystal structure of the whole complex has not been solved. The available crystal structures have shown that AcrB and TolC function as trimers, but the number of AcrA molecules in the complex is now under debate. Disulfide chemical cross-linking experiments have indicated that the stoichiometry of AcrB-AcrA-TolC is 1:1:1; on the other hand, recent cryo-electron microscopy images of AcrAB-TolC suggested a 1:2:1 stoichiometry. In this study, we constructed 1:1-fixed AcrB-AcrA fusion proteins using various linkers. Surprisingly, all the 1:1-fixed linker proteins showed drug export activity under both acrAB-deficient conditions and acrAB acrEF double-pump-knockout conditions regardless of the lengths of the linkers. Finally, we optimized a shorter linker lacking the conformational freedom imparted by the AcrB C terminus. These results suggest that a complex with equal amounts of AcrA and AcrB is sufficient for drug export function. IMPORTANCE The structure and stoichiometry of the RND-type multidrug exporter AcrB-AcrA-TolC complex are still under debate. Recently, electron microscopic images of the AcrB-AcrA-TolC complex have been reported, suggesting a 1:2:1 stoichiometry. However, we report here that the AcrB-AcrA 1:1 fusion protein is active for drug export under acrAB-deficient conditions and also under acrAB acrEF double-deficient conditions, which eliminate the aid of free AcrA and its close homolog AcrE, indicating that the AcrB-AcrA 1:1 stoichiometry is enough for drug export function. In addition, the AcrB-AcrA fusion protein can function without the aid of free AcrA. We believe that these results are very important for considering the structure and mechanism of AcrAB-TolC-mediated multidrug export.
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36
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Hong EJ, Kim P, Kim ES, Kim Y, Lee HS. Involvement of the osrR gene in the hydrogen peroxide-mediated stress response of Corynebacterium glutamicum. Res Microbiol 2015; 167:20-8. [PMID: 26433092 DOI: 10.1016/j.resmic.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/30/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023]
Abstract
A transcriptional profile of the H2O2-adapted Corynebacterium glutamicum HA strain reveals a list of upregulated regulatory genes. Among them, we selected ORF NCgl2298, designated osrR and analyzed its role in H2O2 adaptation. The osrR-deleted (ΔosrR) mutant had defective growth in minimal medium, which was even more pronounced in an osrR deletion mutant of an HA strain. The ΔosrR strain displayed increased sensitivity to H2O2. In addition to H2O2 sensitivity, the ΔosrR strain was found to be temperature-sensitive at 37 °C. 2D-PAGE analysis of the ΔosrR mutant found that MetE and several other proteins involved in redox metabolism were affected by the mutation. Accordingly, the NADPH/NADP(+) ratio of the ΔosrR strain (0.85) was much lower than that of the wild-type strain (2.01). In contrast, the NADH/NAD(+) ratio of the mutant (0.54) was considerably higher than that of the wild-type (0.21). Based on these findings, we propose that H2O2-detoxifying metabolic systems, excluding those involving catalase, are present in C. glutamicum and are regulated, in part, by osrR.
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Affiliation(s)
- Eun-Ji Hong
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si 339-700, Republic of Korea.
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyeonggi 420-743, Republic of Korea.
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 402-751, Republic of Korea.
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, 65 Semyeong-ro, Jecheon-si, Chungbuk 390-711, Republic of Korea.
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si 339-700, Republic of Korea.
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Anes J, McCusker MP, Fanning S, Martins M. The ins and outs of RND efflux pumps in Escherichia coli. Front Microbiol 2015; 6:587. [PMID: 26113845 PMCID: PMC4462101 DOI: 10.3389/fmicb.2015.00587] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/28/2015] [Indexed: 11/13/2022] Open
Abstract
Infectious diseases remain one of the principal causes of morbidity and mortality in the world. Relevant authorities including the WHO and CDC have expressed serious concern regarding the continued increase in the development of multidrug resistance among bacteria. They have also reaffirmed the urgent need for investment in the discovery and development of new antibiotics and therapeutic approaches to treat multidrug resistant (MDR) bacteria. The extensive use of antimicrobial compounds in diverse environments, including farming and healthcare, has been identified as one of the main causes for the emergence of MDR bacteria. Induced selective pressure has led bacteria to develop new strategies of defense against these chemicals. Bacteria can accomplish this by several mechanisms, including enzymatic inactivation of the target compound; decreased cell permeability; target protection and/or overproduction; altered target site/enzyme and increased efflux due to over-expression of efflux pumps. Efflux pumps can be specific for a single substrate or can confer resistance to multiple antimicrobials by facilitating the extrusion of a broad range of compounds including antibiotics, heavy metals, biocides and others, from the bacterial cell. To overcome antimicrobial resistance caused by active efflux, efforts are required to better understand the fundamentals of drug efflux mechanisms. There is also a need to elucidate how these mechanisms are regulated and how they respond upon exposure to antimicrobials. Understanding these will allow the development of combined therapies using efflux inhibitors together with antibiotics to act on Gram-negative bacteria, such as the emerging globally disseminated MDR pathogen Escherichia coli ST131 (O25:H4). This review will summarize the current knowledge on resistance-nodulation-cell division efflux mechanisms in E. coli, a bacteria responsible for community and hospital-acquired infections, as well as foodborne outbreaks worldwide.
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Affiliation(s)
- João Anes
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Matthew P McCusker
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Marta Martins
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
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The functional landscape bound to the transcription factors of Escherichia coli K-12. Comput Biol Chem 2015; 58:93-103. [PMID: 26094112 DOI: 10.1016/j.compbiolchem.2015.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 05/31/2015] [Accepted: 06/03/2015] [Indexed: 01/05/2023]
Abstract
Motivated by the experimental evidences accumulated in the last ten years and based on information deposited in RegulonDB, literature look up, and sequence analysis, we analyze the repertoire of 304 DNA-binding Transcription factors (TFs) in Escherichia coli K-12. These regulators were grouped in 78 evolutionary families and are regulating almost half of the total genes in this bacterium. In structural terms, 60% of TFs are composed by two-domains, 30% are monodomain, and 10% three- and four-structural domains. As previously noticed, the most abundant DNA-binding domain corresponds to the winged helix-turn-helix, with few alternative DNA-binding structures, resembling the hypothesis of successful protein structures with the emergence of new ones at low scales. In summary, we identified and described the characteristics associated to the DNA-binding TF in E. coli K-12. We also identified twelve functional modules based on a co-regulated gene matrix. Finally, diverse regulons were predicted based on direct associations between the TFs and potential regulated genes. This analysis should increase our knowledge about the gene regulation in the bacterium E. coli K-12, and provide more additional clues for comprehensive modelling of transcriptional regulatory networks in other bacteria.
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Importance of Real-Time Assays To Distinguish Multidrug Efflux Pump-Inhibiting and Outer Membrane-Destabilizing Activities in Escherichia coli. J Bacteriol 2015; 197:2479-88. [PMID: 25962916 DOI: 10.1128/jb.02456-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 05/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The constitutively expressed AcrAB multidrug efflux system of Escherichia coli shows a high degree of homology with the normally silent AcrEF system. Exposure of a strain with acrAB deleted to antibiotic selection pressure frequently leads to the insertion sequence-mediated activation of the homologous AcrEF system. In this study, we used strains constitutively expressing either AcrAB or AcrEF from their normal chromosomal locations to resolve a controversy about whether phenylalanylarginine β-naphthylamide (PAβN) inhibits the activities of AcrAB and AcrEF and/or acts synergistically with antibiotics by destabilizing the outer membrane permeability barrier. Real-time efflux assays allowed a clear distinction between the efflux pump-inhibiting activity of PAβN and the outer membrane-destabilizing action of polymyxin B nonapeptide (PMXBN). When added in equal amounts, PAβN, but not PMXBN, strongly inhibited the efflux activities of both AcrAB and AcrEF pumps. In contrast, when outer membrane destabilization was assessed by the nitrocefin hydrolysis assay, PMXBN exerted a much greater damaging effect than PAβN. Strong action of PAβN in inhibiting efflux activity compared to its weak action in destabilizing the outer membrane permeability barrier suggests that PAβN acts mainly by inhibiting efflux pumps. We concluded that at low concentrations, PAβN acts specifically as an inhibitor of both AcrAB and AcrEF efflux pumps; however, at high concentrations, PAβN in the efflux-proficient background not only inhibits efflux pump activity but also destabilizes the membrane. The effects of PAβN on membrane integrity are compounded in cells unable to extrude PAβN. IMPORTANCE The increase in multidrug-resistant bacterial pathogens at an alarming rate has accelerated the need for implementation of better antimicrobial stewardship, discovery of new antibiotics, and deeper understanding of the mechanism of drug resistance. The work carried out in this study highlights the importance of employing real-time fluorescence-based assays in differentiating multidrug efflux-inhibitory and outer membrane-destabilizing activities of antibacterial compounds.
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 924] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Blair JMA, Smith HE, Ricci V, Lawler AJ, Thompson LJ, Piddock LJV. Expression of homologous RND efflux pump genes is dependent upon AcrB expression: implications for efflux and virulence inhibitor design. J Antimicrob Chemother 2014; 70:424-31. [PMID: 25288678 PMCID: PMC4291234 DOI: 10.1093/jac/dku380] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Objectives Enterobacteriaceae have multiple efflux pumps that confer intrinsic resistance to antibiotics. AcrB mediates clinically relevant multidrug resistance and is required for virulence and biofilm formation, making it an attractive target for the design of inhibitors. The aim of this study was to assess the viability of single transporters as a target for efflux inhibition using Salmonella Typhimurium as the model pathogen. Methods The expression of resistance–nodulation–division (RND) efflux pump genes in response to the inactivation of single or multiple homologues was measured using real-time RT–PCR. Phenotypes of mutants were characterized by measuring antimicrobial susceptibility, dye accumulation and the ability to cause infection in vitro. Results The expression of all RND efflux pump genes was increased when single or multiple acr genes were inactivated, suggesting a feedback mechanism that activates the transcription of homologous efflux pump genes. When two or three acr genes were inactivated, the mutants had further reduced efflux, altered susceptibility to antimicrobials (including increased susceptibility to some, but conversely and counterintuitively, decreased susceptibility to some others) and were more attenuated in the tissue culture model than mutants lacking single pumps were. Conclusions These data indicate that it is critical to understand which pumps an inhibitor is active against and the effect of this on the expression of homologous systems. For some antimicrobials, an inhibitor with activity against multiple pumps will have a greater impact on susceptibility, but an unintended consequence of this may be decreased susceptibility to other drugs, such as aminoglycosides.
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Affiliation(s)
- Jessica M A Blair
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
| | - Helen E Smith
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
| | - Vito Ricci
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
| | - Amelia J Lawler
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
| | - Louisa J Thompson
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
| | - Laura J V Piddock
- Antimicrobials Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, and Institute of Microbiology and Infection, The University of Birmingham, Birmingham B15 2TT, UK
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Blair JMA, Richmond GE, Piddock LJV. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol 2014; 9:1165-77. [DOI: 10.2217/fmb.14.66] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT Gram-negative bacteria express a plethora of efflux pumps that are capable of transporting structurally varied molecules, including antibiotics, out of the bacterial cell. This efflux lowers the intracellular antibiotic concentration, allowing bacteria to survive at higher antibiotic concentrations. Overexpression of some efflux pumps can cause clinically relevant levels of antibiotic resistance in Gram-negative pathogens. This review discusses the role of efflux in resistance of clinical isolates of Gram-negative bacteria, the regulatory mechanisms that control efflux pump expression, the recent advances in our understanding of efflux pump structure and how inhibition of efflux is a promising future strategy for tackling multidrug resistance in Gram-negative pathogens.
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Affiliation(s)
- Jessica MA Blair
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Grace E Richmond
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Laura JV Piddock
- Antimicrobials Research Group, Institute of Microbiology & Infection, School of Immunity & Infection, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Ospina Barrero M, Pietralonga P, Schwarz D, Silva Junior A, Paula S, Moreira M. Effect of the inhibitors phenylalanine arginyl ß-naphthylamide (PAßN) and 1-(1-naphthylmethyl)-piperazine (NMP) on expression of genes in multidrug efflux systems of Escherichia coli isolates from bovine mastitis. Res Vet Sci 2014; 97:176-81. [DOI: 10.1016/j.rvsc.2014.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/05/2014] [Accepted: 05/25/2014] [Indexed: 11/29/2022]
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Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 2014; 453:254-67. [PMID: 24878531 DOI: 10.1016/j.bbrc.2014.05.090] [Citation(s) in RCA: 438] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
Abstract
Multidrug resistance (MDR) refers to the capability of bacterial pathogens to withstand lethal doses of structurally diverse drugs which are capable of eradicating non-resistant strains. MDR has been identified as a major threat to the public health of human being by the World Health Organization (WHO). Among the four general mechanisms that cause antibiotic resistance including target alteration, drug inactivation, decreased permeability and increased efflux, drug extrusion by the multidrug efflux pumps serves as an important mechanism of MDR. Efflux pumps not only can expel a broad range of antibiotics owing to their poly-substrate specificity, but also drive the acquisition of additional resistance mechanisms by lowering intracellular antibiotic concentration and promoting mutation accumulation. Over-expression of multidrug efflux pumps have been increasingly found to be associated with clinically relevant drug resistance. On the other hand, accumulating evidence has suggested that efflux pumps also have physiological functions in bacteria and their expression is subject tight regulation in response to various of environmental and physiological signals. A comprehensive understanding of the mechanisms of drug extrusion, and regulation and physiological functions of efflux pumps is essential for the development of anti-resistance interventions. In this review, we summarize the development of these research areas in the recent decades and present the pharmacological exploitation of efflux pump inhibitors as a promising anti-drug resistance intervention.
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Affiliation(s)
- Jingjing Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Ziqing Deng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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Aly SA, Debavalya N, Suh SJ, Oryazabal OA, Boothe DM. Molecular mechanisms of antimicrobial resistance in fecal Escherichia coli of healthy dogs after enrofloxacin or amoxicillin administration. Can J Microbiol 2012; 58:1288-94. [PMID: 23145826 DOI: 10.1139/w2012-105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli respond to selective pressure of antimicrobial therapy by developing resistance through a variety of mechanisms. The purpose of this study was to characterize the genetic mechanisms of antimicrobial resistance in fecal E. coli after the routine use of 2 popular antimicrobials. Fourteen resistant E. coli isolates, representing predominant clones that emerged in healthy dogs' feces after treatment with either amoxicillin (11 E. coli isolates) or enrofloxacin (3 E. coli isolates), were tested for mutations in DNA gyrase (gyrA and gyrB) and in topoisomerase IV (parC) and for the presence of β-lactamases (bla(TEM), bla(SHV), bla(PSE-1) and bla(CTX-M)) and plasmid-mediated quinolone resistance (qnrA, qnrB, qnrS, aac(6')-Ib, and qepA), by polymerase chain reaction. Escherichia coli isolates cultured following amoxicillin therapy only expressed single-drug resistance to β-lactams, while the isolates cultured from dogs receiving enrofloxacin therapy expressed multidrug resistance (MDR). The use of RND efflux pump inhibitors increased the susceptibility of the 3 MDR E. coli isolates to doxycycline, chloramphenicol, enrofloxacin, and ciprofloxacin, which indicates a role of the efflux pump in the acquisition of the MDR phenotype. Amplification and sequencing of AcrAB efflux pump regulators (soxR, soxS, marR, and acrR) revealed only the presence of a single mutation in soxS in the 3 MDR isolates.
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Affiliation(s)
- Sherine A Aly
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
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Zhou X, Jia F, Liu X, Wang Y. Total alkaloids of Sophorea alopecuroides-induced down-regulation of AcrAB-TolC efflux pump reverses susceptibility to ciprofloxacin in clinical multidrug resistant Escherichia coli isolates. Phytother Res 2012; 26:1637-43. [PMID: 22371352 DOI: 10.1002/ptr.4623] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 11/10/2022]
Abstract
In this report, total alkaloids extracted from the seeds of Sophorea alopecuroides (TASA) was evaluated against clinical Escherichia coli isolates resistant to four tested antibiotics, ampicillin (AM), amikacin (AN), cefotaxime (CTX) and ciprofloxacin (CIP). The TASA showed an antibacterial activity against the multidrug resistant (MDR) isolates. In combination with TASA, synergistic effects on the tested antibiotics against the MRD isolates were observed. Similarly, the isolates pretreated with a lower dose of TASA yielded increased and stable susceptibilities to CIP by 16-32-fold determined by a microbroth dilution checkerboard method. Moreover, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed a constitutive overexpression of the AcrAB-TolC pump system in the tested MDR isolates. The pretreatment of MDR isolates with TASA resulted in a statistically down-regulated expression of acrA and acrB genes, and an up-regulated expression of acrR gene (p < 0.05). But the expression of tolC gene was not significantly altered (p > 0.05). These results suggested that the TASA-induced reversal resistance to CIP might be partially through a mechanism of inhibition of the AcrAB-TolC pump activity in these isolates, implying that the TASA can be used as a potential natural source to develop efflux pump inhibitors (EPI) against AcrAB-TolC pump mediated MDR in E. coli isolates.
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Affiliation(s)
- Xuezhang Zhou
- Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China
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Nishino K, Yamasaki S, Hayashi-Nishino M, Yamaguchi A. Effect of overexpression of small non-coding DsrA RNA on multidrug efflux in Escherichia coli. J Antimicrob Chemother 2010; 66:291-6. [PMID: 21088020 DOI: 10.1093/jac/dkq420] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Several putative and proven drug efflux pumps are present in Escherichia coli. Because many such efflux pumps have overlapping substrate spectra, it is intriguing that bacteria, with their economically organized genomes, harbour such large sets of multidrug efflux genes. To understand how bacteria utilize these multiple efflux pumps, it is important to elucidate the process of pump expression regulation. The aim of this study was to determine a regulator of the multidrug efflux pump in this organism. METHODS We screened a genomic library of E. coli for genes that decreased drug susceptibility in this organism. The library was developed from the chromosomal DNA of the MG1655 strain, and then the recombinant plasmids were transformed into an acrB-deleted strain. Transformants were screened for resistance to various antibiotics including oxacillin. RESULTS We found that the multidrug susceptibilities of the acrB-deleted strain were decreased by the overexpression of small non-coding DsrA RNA as well as by the overexpression of known regulators of multidrug efflux pumps. Plasmids carrying the dsrA gene conferred resistance to oxacillin, cloxacillin, erythromycin, rhodamine 6G and novobiocin. DsrA decreased the accumulation of ethidium bromide in E. coli cells. Furthermore, expression of mdtE was significantly increased by dsrA overexpression, and the decreased multidrug susceptibilities modulated by DsrA were dependent on the MdtEF efflux pump. CONCLUSIONS These results indicate that DsrA modulates multidrug efflux through activation of genes encoding the MdtEF pump in E. coli.
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Affiliation(s)
- Kunihiko Nishino
- Laboratory of Microbiology and Infectious Diseases, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-047, Japan
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Effect of NlpE overproduction on multidrug resistance in Escherichia coli. Antimicrob Agents Chemother 2010; 54:2239-43. [PMID: 20211889 DOI: 10.1128/aac.01677-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NlpE, an outer membrane lipoprotein, functions during envelope stress responses in Gram-negative bacteria. In this study, we report that overproduction of NlpE increases multidrug and copper resistance through activation of the genes encoding the AcrD and MdtABC multidrug efflux pumps in Escherichia coli.
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Yamada J, Yamasaki S, Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K. Impact of the RNA chaperone Hfq on multidrug resistance in Escherichia coli. J Antimicrob Chemother 2010; 65:853-8. [PMID: 20211861 DOI: 10.1093/jac/dkq067] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Hfq is a bacterial RNA chaperone involved in the post-transcriptional regulation of many stress-inducible genes via small non-coding RNAs. Although Hfq is related to important phenotypes including virulence in many bacterial pathogens, its role in drug resistance is unknown. The aim of this study was to investigate the role of Hfq in bacterial multidrug resistance. METHODS The hfq gene was inactivated in Escherichia coli by use of pKO3, which is a gene replacement vector. The drug susceptibility and drug accumulation of the hfq mutant were determined. The level of production of the AcrB multidrug efflux pump in this mutant was also measured. RESULTS The hfq mutant was susceptible to acriflavine, benzalkonium, cefamandole, chloramphenicol, Crystal Violet, nalidixic acid, novobiocin, oxacillin and rhodamine 6G. E. coli cells were strongly stained with rhodamine 6G compared with the wild-type on deletion of hfq, indicating that Hfq affects the accumulation of the drug in bacterial cells. The deletion of the drug efflux gene acrB impairs the effect of hfq deletion on E. coli susceptibility. Furthermore, the level of AcrB protein production was reduced in the hfq mutant, whereas hfq deletion did not affect the promoter activity of the acrAB operon. CONCLUSIONS These results indicate that Hfq regulates the drug efflux system at the post-transcriptional level and reveals the previously uncharacterized role of Hfq in bacterial multidrug resistance.
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Affiliation(s)
- Junko Yamada
- Laboratory of Microbiology and Infectious Diseases, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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