1
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Haeberle AL, Greenwood-Quaintance KE, Zar S, Johnson S, Patel R, Willett JLE. Genotypic and phenotypic characterization of Enterococcus faecalis isolates from periprosthetic joint infections. Microbiol Spectr 2024; 12:e0056524. [PMID: 38912797 PMCID: PMC11302728 DOI: 10.1128/spectrum.00565-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/25/2024] Open
Abstract
Over 2.5 million prosthetic joint implantation surgeries occur annually in the United States. Periprosthetic joint infections (PJIs), though occurring in only 1-2% of patients receiving replacement joints, are challenging to diagnose and treat and are associated with significant morbidity. The Gram-positive bacterium Enterococcus faecalis, which can be highly antibiotic-resistant and is a robust biofilm producer on indwelling medical devices, accounts for 2-11% of PJIs. E. faecalis PJIs are understudied compared to those caused by other pathogens, such as Staphylococcus aureus. This motivates the need to generate a comprehensive understanding of E. faecalis PJIs to guide future treatments for these infections. To address this, we describe a panel of E. faecalis strains isolated from the surface of prosthetic joints in a cohort of individuals treated at the Mayo Clinic in Rochester, MN. Here, we present the first complete genome assemblage of E. faecalis PJI isolates. Comparative genomics shows differences in genome size, virulence factors, antimicrobial resistance genes, plasmids, and prophages, underscoring the genetic diversity of these strains. These isolates have strain-specific differences in in vitro biofilm biomass, biofilm burden, and biofilm morphology. We measured robust changes in biofilm architecture and aggregation for all isolates when grown in simulated synovial fluid (SSF). Finally, we evaluated the antibiotic efficacy of these isolates and found strain-specific changes across all strains when grown in SSF. Results of this study highlight the existence of genetic and phenotypic heterogeneity among E. faecalis PJI isolates which will provide valuable insight and resources for future E. faecalis PJI research. IMPORTANCE Periprosthetic joint infections (PJIs) affect ~1-2% of those who undergo joint replacement surgery. Enterococcus faecalis is a Gram-positive opportunistic pathogen that causes ~10% of PJIs in the United States each year, but our understanding of how and why E. faecalis causes PJIs is limited. E. faecalis infections are typically biofilm-associated and can be difficult to clear with antibiotic therapy. Here, we provide complete genomes for four E. faecalis PJI isolates from the Mayo Clinic. These isolates have strain-specific differences in biofilm formation, aggregation, and antibiotic susceptibility in simulated synovial fluid. These results provide important insight into the genomic and phenotypic features of E. faecalis isolates from PJI.
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Affiliation(s)
- Amanda L. Haeberle
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah Zar
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia L. E. Willett
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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2
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Pereira AP, Antunes P, Peixe L, Freitas AR, Novais C. Current insights into the effects of cationic biocides exposure on Enterococcus spp. Front Microbiol 2024; 15:1392018. [PMID: 39006755 PMCID: PMC11242571 DOI: 10.3389/fmicb.2024.1392018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Cationic biocides (CBs), such as quaternary ammonium compounds and biguanides, are critical for controlling the spread of bacterial pathogens like Enterococcus spp., a leading cause of multidrug-resistant healthcare-associated infections. The widespread use of CBs in recent decades has prompted concerns about the potential emergence of Enterococcus spp. populations exhibiting resistance to both biocides and antibiotics. Such concerns arise from their frequent exposure to subinhibitory concentrations of CBs in clinical, food chain and diverse environmental settings. This comprehensive narrative review aimed to explore the complexity of the Enterococcus' response to CBs and of their possible evolution toward resistance. To that end, CBs' activity against diverse Enterococcus spp. collections, the prevalence and roles of genes associated with decreased susceptibility to CBs, and the potential for co- and cross-resistance between CBs and antibiotics are reviewed. Significant methodological and knowledge gaps are identified, highlighting areas that future studies should address to enhance our comprehension of the impact of exposure to CBs on Enterococcus spp. populations' epidemiology. This knowledge is essential for developing effective One Health strategies that ensure the continued efficacy of these critical agents in safeguarding Public Health.
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Affiliation(s)
- Ana P Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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3
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Haeberle A, Greenwood-Quaintance K, Zar S, Johnson S, Patel R, Willett JLE. Genotypic and phenotypic characterization of Enterococcus faecalis isolates from periprosthetic joint infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579140. [PMID: 38370742 PMCID: PMC10871183 DOI: 10.1101/2024.02.06.579140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Over 2.5 million prosthetic joint implantation surgeries occur annually in the United States. Periprosthetic joint infections (PJIs), though occurring in only 1-2% of patients receiving replacement joints, are challenging to diagnose and treat and are associated with significant morbidity. The Gram-positive bacterium Enterococcus faecalis, which can be highly antibiotic resistant and is a robust biofilm producer on indwelling medical devices, accounts for 2-11% of PJIs. E. faecalis PJIs are understudied compared to those caused by other pathogens, such as Staphylococcus aureus. This motivates the need to generate a comprehensive understanding of E. faecalis PJIs to guide future treatments for these infections. To address this, we describe a panel of E. faecalis strains isolated from the surface of prosthetic joints in a cohort of individuals treated at Mayo Clinic in Rochester, MN. Here, we present the first complete genome assemblage of E. faecalis PJI isolates. Comparative genomics shows differences in genome size, virulence factors, antimicrobial resistance genes, plasmids, and prophages, underscoring the genetic diversity of these strains. These isolates have strain-specific differences in in vitro biofilm biomass, biofilm burden, and biofilm morphology. We measured robust changes in biofilm architecture and aggregation for all isolates when grown in simulated synovial fluid (SSF). Lastly, we evaluated antibiotic efficacy of these isolates and found strain specific changes across all strains when grown in SSF. Results of this study highlight the existence of genetic and phenotypic heterogeneity among E. faecalis PJI isolates which will provide valuable insight and resources for future E. faecalis PJI research.
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Affiliation(s)
- Amanda Haeberle
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota USA
| | - Kerryl Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah Zar
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota USA
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia L. E. Willett
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota USA
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4
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Meier G, Thavarasah S, Ehrenbolger K, Hutter CAJ, Hürlimann LM, Barandun J, Seeger MA. Deep mutational scan of a drug efflux pump reveals its structure-function landscape. Nat Chem Biol 2023; 19:440-450. [PMID: 36443574 PMCID: PMC7615509 DOI: 10.1038/s41589-022-01205-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Drug efflux is a common resistance mechanism found in bacteria and cancer cells, but studies providing comprehensive functional insights are scarce. In this study, we performed deep mutational scanning (DMS) on the bacterial ABC transporter EfrCD to determine the drug efflux activity profile of more than 1,430 single variants. These systematic measurements revealed that the introduction of negative charges at different locations within the large substrate binding pocket results in strongly increased efflux activity toward positively charged ethidium, whereas additional aromatic residues did not display the same effect. Data analysis in the context of an inward-facing cryogenic electron microscopy structure of EfrCD uncovered a high-affinity binding site, which releases bound drugs through a peristaltic transport mechanism as the transporter transits to its outward-facing conformation. Finally, we identified substitutions resulting in rapid Hoechst influx without affecting the efflux activity for ethidium and daunorubicin. Hence, single mutations can convert EfrCD into a drug-specific ABC importer.
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Affiliation(s)
- Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Kai Ehrenbolger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Jonas Barandun
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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5
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Orelle C, Schmitt L, Jault JM. Waste or die: The price to pay to stay alive. Trends Microbiol 2023; 31:233-241. [PMID: 36192292 DOI: 10.1016/j.tim.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022]
Abstract
Microorganisms need to constantly exchange with their habitat to capture nutrients and expel toxic compounds. The ATP-binding cassette (ABC) transporters, a family of membrane proteins especially abundant in microorganisms, are at the core of these processes. Due to their extraordinary ability to expel structurally unrelated compounds, some transporters play a protective role in different organisms. Yet, the downside of these multidrug transporters is their entanglement in the resistance to therapeutic treatments. Intriguingly, some multidrug ABC transporters show a high level of ATPase activity, even in the absence of transported substrates. Although this basal ATPase activity might seem a waste, we surmise that this inherent capacity allows multidrug transporters to promptly translocate any bound drug before it penetrates into the cell.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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6
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Pereira AP, Antunes P, Willems R, Corander J, Coque TM, Peixe L, Freitas AR, Novais C. Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiol Spectr 2022; 10:e0117622. [PMID: 35862993 PMCID: PMC9430118 DOI: 10.1128/spectrum.01176-22] [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: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization's list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.
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Affiliation(s)
- Ana P. Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Rob Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teresa M. Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBER-EII), Madrid, Spain
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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7
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Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
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Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
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8
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Frelet-Barrand A. Lactococcus lactis, an Attractive Cell Factory for the Expression of Functional Membrane Proteins. Biomolecules 2022; 12:180. [PMID: 35204681 PMCID: PMC8961550 DOI: 10.3390/biom12020180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
Membrane proteins play key roles in most crucial cellular processes, ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded membrane proteins in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult to predict whether a protein can be overproduced in a functional state in some expression system(s), though studies of high-throughput screens have been published in recent years. Prokaryotic expression systems present several advantages over eukaryotic ones. Among them, Lactococcus lactis (L. lactis) has emerged in the last two decades as a good alternative expression system to E. coli. The purpose of this chapter is to describe L. lactis and its tightly inducible system, NICE, for the effective expression of membrane proteins from both prokaryotic and eukaryotic origins.
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Affiliation(s)
- Annie Frelet-Barrand
- FEMTO-ST Institute, UMR 6174, CNRS, Université Bourgogne Franche-Comté, 15B Avenue des Montboucons, CEDEX, 25030 Besançon, France
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9
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Roche B, Garcia-Rivera MA, Normant V, Kuhn L, Hammann P, Brönstrup M, Mislin GLA, Schalk IJ. A role for PchHI as the ABC transporter in iron acquisition by the siderophore pyochelin in Pseudomonas aeruginosa. Environ Microbiol 2021; 24:866-877. [PMID: 34664350 DOI: 10.1111/1462-2920.15811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022]
Abstract
Iron is an essential nutrient for bacterial growth but poorly bioavailable. Bacteria scavenge ferric iron by synthesizing and secreting siderophores, small compounds with a high affinity for iron. Pyochelin (PCH) is one of the two siderophores produced by the opportunistic pathogen Pseudomonas aeruginosa. After capturing a ferric iron molecule, PCH-Fe is imported back into bacteria first by the outer membrane transporter FptA and then by the inner membrane permease FptX. Here, using molecular biology, 55 Fe uptake assays, and LC-MS/MS quantification, we first find a role for PchHI as the heterodimeric ABC transporter involved in the siderophore-free iron uptake into the bacterial cytoplasm. We also provide the first evidence that PCH is able to reach the bacterial periplasm and cytoplasm when both FptA and FptX are expressed. Finally, we detected an interaction between PchH and FptX, linking the ABC transporter PchHI with the inner permease FptX in the PCH-Fe uptake pathway. These results pave the way for a better understanding of the PCH siderophore pathway, giving future directions to tackle P. aeruginosa infections.
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Affiliation(s)
- Béatrice Roche
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Mariel A Garcia-Rivera
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, 38124, Germany
| | - Vincent Normant
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 2 allée Konrad Roentgen, Strasbourg Cedex, F-67084, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 2 allée Konrad Roentgen, Strasbourg Cedex, F-67084, France
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, 38124, Germany
| | - Gaëtan L A Mislin
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Isabelle J Schalk
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
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10
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Remm S, Earp JC, Dick T, Dartois V, Seeger MA. Critical discussion on drug efflux in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 46:6391500. [PMID: 34637511 PMCID: PMC8829022 DOI: 10.1093/femsre/fuab050] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can withstand months of antibiotic treatment. An important goal of tuberculosis research is to shorten the treatment to reduce the burden on patients, increase adherence to the drug regimen and thereby slow down the spread of drug resistance. Inhibition of drug efflux pumps by small molecules has been advocated as a promising strategy to attack persistent Mtb and shorten therapy. Although mycobacterial drug efflux pumps have been broadly investigated, mechanistic studies are scarce. In this critical review, we shed light on drug efflux in its larger mechanistic context by considering the intricate interplay between membrane transporters annotated as drug efflux pumps, membrane energetics, efflux inhibitors and cell wall biosynthesis processes. We conclude that a great wealth of data on mycobacterial transporters is insufficient to distinguish by what mechanism they contribute to drug resistance. Recent studies suggest that some drug efflux pumps transport structural lipids of the mycobacterial cell wall and that the action of certain drug efflux inhibitors involves dissipation of the proton motive force, thereby draining the energy source of all active membrane transporters. We propose recommendations on the generation and interpretation of drug efflux data to reduce ambiguities and promote assigning novel roles to mycobacterial membrane transporters.
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Affiliation(s)
- Sille Remm
- Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Jennifer C Earp
- Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA.,Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA.,Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zürich, Switzerland
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11
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Pipatthana M, Harnvoravongchai P, Pongchaikul P, Likhitrattanapisal S, Phanchana M, Chankhamhaengdecha S, Janvilisri T. The repertoire of ABC proteins in Clostridioides difficile. Comput Struct Biotechnol J 2021; 19:2905-2920. [PMID: 34094001 PMCID: PMC8144104 DOI: 10.1016/j.csbj.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 11/07/2022] Open
Abstract
ABC transporters transport substrates across membranes driven by ATP hydrolysis. ABC proteins of C. difficile 630 can be classified into 12 sub-families. Most NPs are found within sub-families involving in drug export. Most core NPs in C. difficile are associated with drug efflux system. ABC proteins in sub-families 3, 6, 7, and 9 may participate in drug resistance.
ATP-binding cassette (ABC) transporters belong to one of the largest membrane protein superfamilies, which function in translocating substrates across biological membranes using energy from ATP hydrolysis. Currently, the classification of ABC transporters in Clostridioides difficile is not complete. Therefore, the sequence-function relationship of all ABC proteins encoded within the C. difficile genome was analyzed. Identification of protein domains associated with the ABC system in the C. difficile 630 reference genome revealed 226 domains: 97 nucleotide-binding domains (NBDs), 98 transmembrane domains (TMDs), 30 substrate-binding domains (SBDs), and one domain with features of an adaptor protein. Gene organization and transcriptional unit analyses indicated the presence of 78 ABC systems comprising 28 importers and 50 exporters. Based on NBD sequence similarity, ABC transporters were classified into 12 sub-families according to their substrates. Interestingly, all ABC exporters, accounting for 64% of the total ABC systems, are involved in antibiotic resistance. Based on analysis of ABC proteins from 49 C. difficile strains, the majority of core NBDs are predicted to be involved in multidrug resistance systems, consistent with the ability of this organism to survive exposure to an array of antibiotics. Our findings herein provide another step toward a better understanding of the function and evolutionary relationships of ABC proteins in this pathogen.
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Affiliation(s)
- Methinee Pipatthana
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakarn, Thailand
| | - Somsak Likhitrattanapisal
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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12
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High-Level Antibiotic Tolerance of a Clinically Isolated Enterococcus faecalis Strain. Appl Environ Microbiol 2020; 87:AEM.02083-20. [PMID: 33097497 DOI: 10.1128/aem.02083-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/14/2020] [Indexed: 01/11/2023] Open
Abstract
Bacteria can survive antibiotic treatment both by acquiring antibiotic resistance genes and through mechanisms of tolerance that are based on phenotypic changes and the formation of metabolically inactive cells. Here, we report an Enterococcus faecalis strain (E. faecalis UM001B) that was isolated from a cystic fibrosis patient and had no increase in resistance but extremely high-level tolerance to ampicillin, vancomycin, and tetracycline. Specifically, the percentages of cells that survived 3.5-h antibiotic treatment (at 100 μg · ml-1) were 25.4% ± 4.3% and 51.9% ± 4.0% for ampicillin and tetracycline, respectively; vancomycin did not exhibit any significant killing. Consistent with the changes in antibiotic susceptibility, UM001B was found to have reduced penetration of ampicillin and vancomycin and accumulation of tetracycline compared to the reference strain ATCC 29212. Based on whole-genome sequencing, four amino acid substitutions were identified in one of the tetracycline efflux pump repressors (TetRs), compared to ATCC 29212. Results of molecular simulations and experimental assays revealed that these mutations could lead to higher levels of tetracycline efflux activity. Consistently, replicating these mutations in Escherichia coli MG1655 increased its tolerance to tetracycline. Overall, these findings provide new insights into the development of multidrug tolerance in E. faecalis, which can facilitate future studies to better control enterococcal infections.IMPORTANCE Enterococcus faecalis represents a major group of pathogens causing nosocomial infections that are resistant to multiple classes of antibiotics. An important challenge associated with E. faecalis infection is the emergence of multidrug-tolerant strains, which have normal MICs but do not respond to antibiotic treatment. Here, we report a strain of E. faecalis that was isolated from a cystic fibrosis patient and demonstrated high-level tolerance to ampicillin, vancomycin, and tetracycline. Whole-genome sequencing revealed critical substitutions in one of the tetracycline efflux pump repressors that are consistent with the increased tolerance of E. faecalis UM001B to tetracycline. These findings provide new information about bacterial antibiotic tolerance and may help develop more effective therapeutics.
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13
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Alayande KA, Aiyegoro OA, Ateba CN. Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3. Foods 2020; 9:E1840. [PMID: 33321968 PMCID: PMC7762991 DOI: 10.3390/foods9121840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 01/21/2023] Open
Abstract
The genome of Lactobacillus acidophilus PNW3 was assessed for probiotic and safety potentials. The genome was completely sequenced, assembled using SPAdes, and thereafter annotated with NCBI prokaryotic genome annotation pipeline (PGAP) and rapid annotation using subsystem technology (RAST). Further downstream assessment was determined using appropriate bioinformatics tools. The production of biogenic amines was confirmed through HPLC analysis and the evolutionary trend of the strain was determined through the Codon Tree pipeline. The strain was predicted as a non-human pathogen. A plethora of encoding genes for lactic acids and bioactive peptides production, adhesion molecules, resistance to the harsh gut environmental conditions, and improvement of the host metabolism, which are putative for important probiotic functionalities, were located at different loci within the genome. A bacteriocin predicted to be helveticin J was identified as one of the secondary metabolites. The maximum zone of inhibition exhibited by the crude bacteriocin against STEC E. coli O177 was 21.7 ± 0.58 mm and 24.3 ± 1.15 mm after partial purification (250 µg/mL). Three coding sequences were identified for insertion sequences and one for the CRISPR-Cas fragment. The protein-encoding sequence for Ornithine decarboxylase was found within the genome. L. acidophilus PNW3 presents important features categorizing it as a viable and safe probiotic candidate, though further safety investigations are necessary. The application of probiotics in livestock-keeping would ensure improved public health and food security.
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Affiliation(s)
- Kazeem Adekunle Alayande
- Antibiotic Resistance and Phage Biocontrol Research Group, Department of Microbiology, North-West University, Mmabatho 2745, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2745, South Africa
| | - Olayinka Ayobami Aiyegoro
- Gastrointestinal Microbiology and Biotechnology Division, Agricultural Research Council, Animal Production Institute, Irene 0062, South Africa;
- Unit for Environmental Sciences and Management, North West University, Potchefstroom 2520, South Africa
| | - Collins Njie Ateba
- Antibiotic Resistance and Phage Biocontrol Research Group, Department of Microbiology, North-West University, Mmabatho 2745, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2745, South Africa
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14
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Lewinson O, Orelle C, Seeger MA. Structures of ABC transporters: handle with care. FEBS Lett 2020; 594:3799-3814. [PMID: 33098660 PMCID: PMC7756565 DOI: 10.1002/1873-3468.13966] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
In the past two decades, the ATP‐binding cassette (ABC) transporters' field has undergone a structural revolution. The importance of structural biology to the development of the field of ABC transporters cannot be overstated, as the ensemble of structures not only revealed the architecture of ABC transporters but also shaped our mechanistic view of these remarkable molecular machines. Nevertheless, we advocate that the mechanistic interpretation of the structures is not trivial and should be carried out with prudence. Herein, we bring several examples of structures of ABC transporters that merit re‐interpretation via careful comparison to experimental data. We propose that it is of the upmost importance to place new structures within the context of the available experimental data.
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Affiliation(s)
- Oded Lewinson
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Cédric Orelle
- CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), University of Lyon, Lyon, France
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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15
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Popović N, Brdarić E, Đokić J, Dinić M, Veljović K, Golić N, Terzić-Vidojević A. Yogurt Produced by Novel Natural Starter Cultures Improves Gut Epithelial Barrier In Vitro. Microorganisms 2020; 8:E1586. [PMID: 33076224 PMCID: PMC7602395 DOI: 10.3390/microorganisms8101586] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Yogurt is a traditional fermented dairy product, prepared with starter cultures containing Streptococcus thermophilus and Lactobacillus bulgaricus that has gained widespread consumer acceptance as a healthy food. It is widely accepted that yogurt cultures have been recognized as probiotics, due to their beneficial effects on human health. In this study, we have characterized technological and health-promoting properties of autochthonous strains S. thermophilus BGKMJ1-36 and L. bulgaricus BGVLJ1-21 isolated from artisanal sour milk and yogurt, respectively, in order to be used as functional yogurt starter cultures. Both BGKMJ1-36 and BGVLJ1-21 strains have the ability to form curd after five hours at 42 °C, hydrolyze αs1-, β-, and κ- casein, and to show antimicrobial activity toward Listeria monocytogenes. The strain BGKMJ1-36 produces exopolysaccharides important for rheological properties of the yogurt. The colonies of BGKMJ1-36 and BGVLJ1-21 strains that successfully survived transit of the yogurt through simulated gastrointestinal tract conditions have been tested for adhesion to intestinal epithelial Caco-2 cells. The results reveal that both strains adhere to Caco-2 cells and significantly upregulate the expression of autophagy-, tight junction proteins-, and anti-microbial peptides-related genes. Hence, both strains may be interesting for use as a novel functional starter culture for production of added-value yogurt with health-promoting properties.
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Affiliation(s)
| | | | | | | | | | | | - Amarela Terzić-Vidojević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.P.); (E.B.); (J.Đ.); (M.D.); (K.V.); (N.G.)
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16
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Shiadeh SMJ, Azimi L, Azimi T, Pourmohammad A, Goudarzi M, Chaboki BG, Hashemi A. Upregulation of efrAB efflux pump among Enterococcus faecalis ST480, ST847 in Iran. Acta Microbiol Immunol Hung 2020; 67:187-192. [PMID: 32986605 DOI: 10.1556/030.2020.01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022]
Abstract
Antibiotic resistance and especially multiresistance in Enterococci, is a serious public health issue especially in infections of immunocompromised patients. EfrAB is a heterodimeric multidrug ATP-binding cassette (ABC) transporter that causes endogenous resistance to antimicrobials including fluoroquinolones in Enterococcus spp. The aim of this study was to seek the gene expression rate and role of efrAB efflux pump in ciprofloxacin resistant Enterococcus faecalis and Multilocus Sequence Typing (MLST) of multiresistant isolates. Phenotypic and genotyping identification of 80 E. faecalis isolates were performed. Minimum inhibitory concentrations (MICs) to ciprofloxacin (CIP) were measured with and without carbonylcyanide 3-chlorophenylhydrazone (CCCP) by broth microdilution. After DNA extraction and sequencing for detection of efrA and efrB genes, the efrAB efflux positive isolates that were resistant to ciprofloxacin and showed decrease of ciprofloxacin MIC range were identified. Isolates that exhibited decrease in ciprofloxacin MIC range from two to ten folds were assessed for biofilm formation and finally, the expression levels of efrB, efrA genes were measured by quantitative Real-Time PCR (qRT-PCR). High rates of resistance to tetracycline and minocycline and low rates of resistance to the most antibiotics used in this study were detected. The results in this study indicated that the incidence of Multiple drug resistance (MDR) was 23.7% and all isolates that were resistant to ciprofloxacin revealed several degrees of overexpression in efrA and efrB genes. Our study found two ST480 and one ST847 in E. faecalis isolates. In conclusion, despite of low frequency of resistance to the most antibiotics and MDRs in our region, we found one ST480 isolate with resistance to eight antibiotics that also exists in other parts of the world.
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Affiliation(s)
| | - Leila Azimi
- 2Pediatric Infections Research Center, Mofid Children's Hospital, Shahid Beheshti, University of Medical Sciences, Tehran, Iran
| | - Taher Azimi
- 3Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Pourmohammad
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahare Gholami Chaboki
- 4Department of Biostatistics, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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17
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Feng Z, Liu D, Liu Z, Liang Y, Wang Y, Liu Q, Liu Z, Zang Z, Cui Y. Cloning and Functional Characterization of Putative Escherichia coli ABC Multidrug Efflux Transporter YddA. J Microbiol Biotechnol 2020; 30:982-995. [PMID: 32347079 PMCID: PMC9728188 DOI: 10.4014/jmb.2003.03003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
A putative multidrug efflux gene, yddA, was cloned from the Escherichia coli K-12 strain. A drugsensitive strain of E. coli missing the main multidrug efflux pump AcrB was constructed as a host and the yddA gene was knocked out in wild-type (WT) and drug-sensitive E. coliΔacrB to study the yddA function. Sensitivity to different substrates of WT E.coli, E. coliΔyddA, E. coliΔacrB and E. coliΔacrBΔyddA strains was compared with minimal inhibitory concentration (MIC) assays and fluorescence tests. MIC assay and fluorescence test results showed that YddA protein was a multidrug efflux pump that exported multiple substrates. Three inhibitors, ortho-vanadate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and reserpine, were used in fluorescence tests. Ortho-vanadate and reserpine significantly inhibited the efflux and increased accumulation of ethidium bromide and norfloxacin, while CCCP had no significant effect on YddA-regulated efflux. The results indicated that YddA relies on energy released from ATP hydrolysis to transfer the substrates and YddA is an ABC-type multidrug exporter. Functional study of unknown ATP-binding cassette (ABC) superfamily transporters in the model organism E. coli is conducive to discovering new multidrug resistance-reversal targets and providing references for studying other ABC proteins of unknown function.
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Affiliation(s)
- Zhenyue Feng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ziwen Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Qingpeng Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yudong Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,Corresponding author Phone/Fax: +459-6031177 E-mail:
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18
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Arnold FM, Weber MS, Gonda I, Gallenito MJ, Adenau S, Egloff P, Zimmermann I, Hutter CAJ, Hürlimann LM, Peters EE, Piel J, Meloni G, Medalia O, Seeger MA. The ABC exporter IrtAB imports and reduces mycobacterial siderophores. Nature 2020; 580:413-417. [PMID: 32296173 PMCID: PMC7170716 DOI: 10.1038/s41586-020-2136-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Intracellular replication of the deadly pathogen Mycobacterium tuberculosis relies on the production of small organic molecules called siderophores to scavenge iron from host proteins1. M. tuberculosis produces two classes of siderophores, lipid-bound mycobactin and soluble carboxymycobactin2, 3. Functional studies revealed that iron-loaded carboxymycobactin is imported into the cytoplasm by the ABC transporter IrtAB4, which features an additional cytoplasmic siderophore interaction domain (SID)5. However, IrtAB’s predicted ABC exporter fold seemingly contradicts its import function. Here, we show that membrane-reconstituted IrtAB is sufficient to import mycobactins, which are then reduced by the SID to facilitate iron release. Structure determination by X-ray crystallography and cryo-EM confirms IrtAB’s ABC exporter fold, but also reveals structural peculiarities at the transmembrane region of IrtAB resulting in a partially collapsed inward-facing substrate binding cavity. The SID is positioned in close proximity to the inner membrane leaflet, which allows the reduction of membrane-inserted mycobactin. Enzymatic ATPase activity and in vivo growth assays show that IrtAB prefers mycobactin over carboxymycobactin as its substrate. Our study provides insights into an unusual ABC exporter that evolved as highly specialized siderophore import machinery in mycobacteria.
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Affiliation(s)
- Fabian M Arnold
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Marc J Gallenito
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Sophia Adenau
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Eike E Peters
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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19
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Chilambi GS, Hinks J, Matysik A, Zhu X, Choo PY, Liu X, Chan-Park MB, Bazan GC, Kline KA, Rice SA. Enterococcus faecalis Adapts to Antimicrobial Conjugated Oligoelectrolytes by Lipid Rearrangement and Differential Expression of Membrane Stress Response Genes. Front Microbiol 2020; 11:155. [PMID: 32117172 PMCID: PMC7033496 DOI: 10.3389/fmicb.2020.00155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 11/17/2022] Open
Abstract
Conjugated oligoelectrolytes (COEs) are emerging antimicrobials with broad spectrum activity against Gram positive and Gram negative bacteria as well as fungi. Our previous in vitro evolution studies using Enterococcus faecalis grown in the presence of two related COEs (COE1-3C and COE1-3Py) led to the emergence of mutants (changes in liaF and liaR) with a moderate 4- to16-fold increased resistance to COEs. The contribution of liaF and liaR mutations to COE resistance was confirmed by complementation of the mutants, which restored sensitivity to COEs. To better understand the cellular target of COEs, and the mechanism of resistance to COEs, transcriptional changes associated with resistance in the evolved mutants were investigated in this study. The differentially transcribed genes encoded membrane transporters, in addition to proteins associated with cell envelope synthesis and stress responses. Genes encoding membrane transport proteins from the ATP binding cassette superfamily were the most significantly induced or repressed in COE tolerant mutants compared to the wild type when exposed to COEs. Additionally, differences in the membrane localization of a lipophilic dye in E. faecalis exposed to COEs suggested that resistance was associated with lipid rearrangement in the cell membrane. The membrane adaptation to COEs in EFC3C and EFC3Py resulted in an improved tolerance to bile salt and sodium chloride stress. Overall, this study showed that bacterial cell membranes are the primary target of COEs and that E. faecalis adapts to membrane interacting COE molecules by both lipid rearrangement and changes in membrane transporter activity. The level of resistance to COEs suggests that E. faecalis does not have a specific response pathway to elicit resistance against these molecules and this is supported by the rather broad and diverse suite of genes that are induced upon COE exposure as well as cross-resistance to membrane perturbing stressors.
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Affiliation(s)
- Gayatri Shankar Chilambi
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Artur Matysik
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xinyi Zhu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mary B. Chan-Park
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guillermo C. Bazan
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry and Materials, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
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20
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Genome mining and homologous comparison strategy for digging exporters contributing self-resistance in natamycin-producing Streptomyces strains. Appl Microbiol Biotechnol 2019; 104:817-831. [DOI: 10.1007/s00253-019-10131-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/30/2019] [Accepted: 09/08/2019] [Indexed: 02/04/2023]
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21
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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22
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Bock C, Zollmann T, Lindt KA, Tampé R, Abele R. Peptide translocation by the lysosomal ABC transporter TAPL is regulated by coupling efficiency and activation energy. Sci Rep 2019; 9:11884. [PMID: 31417173 PMCID: PMC6695453 DOI: 10.1038/s41598-019-48343-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/25/2019] [Indexed: 11/15/2022] Open
Abstract
The lysosomal polypeptide transporter TAPL belongs to the superfamily of ATP-binding cassette transporters. TAPL forms a homodimeric transport complex, which translocates oligo- and polypeptides into the lumen of lysosomes driven by ATP hydrolysis. Although the structure and the function of ABC transporters were intensively studied in the past, details about the single steps of the transport cycle are still elusive. Therefore, we analyzed the coupling of peptide binding, transport and ATP hydrolysis for different substrate sizes. Although longer and shorter peptides bind with the same affinity and are transported with identical Km values, they differ significantly in their transport rates. This difference can be attributed to a higher activation energy for the longer peptide. TAPL shows a basal ATPase activity, which is inhibited in the presence of longer peptides. Uncoupling between ATP hydrolysis and peptide transport increases with peptide length. Remarkably, also the type of nucleotide determines the uncoupling. While GTP is hydrolyzed as good as ATP, peptide transport is significantly reduced. In conclusion, TAPL does not differentiate between transport substrates in the binding process but during the following steps in the transport cycle, whereas, on the other hand, not only the coupling efficiency but also the activation energy varies depending on the size of peptide substrate.
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Affiliation(s)
- Christoph Bock
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Tina Zollmann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Katharina-Astrid Lindt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Rupert Abele
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.
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23
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Fitness Restoration of a Genetically Tractable Enterococcus faecalis V583 Derivative To Study Decoration-Related Phenotypes of the Enterococcal Polysaccharide Antigen. mSphere 2019; 4:4/4/e00310-19. [PMID: 31292230 PMCID: PMC6620374 DOI: 10.1128/msphere.00310-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
E. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle. Commensal and generally harmless in healthy individuals, Enterococcus faecalis causes opportunistic infections in immunocompromised patients. Plasmid-cured E. faecalis strain VE14089, derived from sequenced reference strain V583, is widely used for functional studies due to its improved genetic amenability. Although strain VE14089 has no major DNA rearrangements, with the exception of an ∼20-kb integrated region of pTEF1 plasmid, the strain presented significant growth differences from the V583 reference strain of our collection (renamed VE14002). In the present study, genome sequencing of strain VE14089 identified additional point mutations. Excision of the integrated pTEF1 plasmid region and sequential restoration of wild-type alleles showing nonsilent mutations were performed to obtain the VE18379 reference-derivative strain. Recovery of the growth ability of the restored VE18379 strain at a level similar to that seen with the reference strain points to GreA and Spx as bacterial fitness determinants. Virulence potential in Galleria mellonella and intestinal colonization in mouse demonstrated host adaptation of the VE18379 strain equivalent to VE14002 host adaptation. We further demonstrated that deletion of the 16.8-kb variable region of the epa locus recapitulates the key role of Epa decoration in host adaptation, providing a genetic system to study the role of specific epa-variable regions in host adaptation independently of other genetic variations. IMPORTANCEE. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle.
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24
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The extracellular gate shapes the energy profile of an ABC exporter. Nat Commun 2019; 10:2260. [PMID: 31113958 PMCID: PMC6529423 DOI: 10.1038/s41467-019-09892-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/04/2019] [Indexed: 11/08/2022] Open
Abstract
ABC exporters harness the energy of ATP to pump substrates across membranes. Extracellular gate opening and closure are key steps of the transport cycle, but the underlying mechanism is poorly understood. Here, we generated a synthetic single domain antibody (sybody) that recognizes the heterodimeric ABC exporter TM287/288 exclusively in the presence of ATP, which was essential to solve a 3.2 Å crystal structure of the outward-facing transporter. The sybody binds to an extracellular wing and strongly inhibits ATPase activity by shifting the transporter's conformational equilibrium towards the outward-facing state, as shown by double electron-electron resonance (DEER). Mutations that facilitate extracellular gate opening result in a comparable equilibrium shift and strongly reduce ATPase activity and drug transport. Using the sybody as conformational probe, we demonstrate that efficient extracellular gate closure is required to dissociate the NBD dimer after ATP hydrolysis to reset the transporter back to its inward-facing state.
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25
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Gao L, Ma Y, Li X, Zhang L, Zhang C, Chen Q, Zhao C. Research on the roles of genes coding ATP‐binding cassette transporters in
Porphyromonas gingivalis
pathogenicity. J Cell Biochem 2019; 121:93-102. [PMID: 31081181 DOI: 10.1002/jcb.28887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Li Gao
- Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology Sun Yat‐Sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
| | - Yuanyuan Ma
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology Sun Yat‐Sen University Guangzhou China
| | - Xiting Li
- Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology Sun Yat‐Sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
| | - Liping Zhang
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
| | - Chi Zhang
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
| | - Qianying Chen
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
| | - Chuanjiang Zhao
- Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology Sun Yat‐Sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Stomatology Guangzhou China
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26
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Hohl M, Remm S, Eskandarian HA, Dal Molin M, Arnold FM, Hürlimann LM, Krügel A, Fantner GE, Sander P, Seeger MA. Increased drug permeability of a stiffened mycobacterial outer membrane in cells lacking MFS transporter Rv1410 and lipoprotein LprG. Mol Microbiol 2019; 111:1263-1282. [PMID: 30742339 PMCID: PMC6519032 DOI: 10.1111/mmi.14220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2019] [Indexed: 12/18/2022]
Abstract
The major facilitator superfamily transporter Rv1410 and the lipoprotein LprG (Rv1411) are encoded by a conserved two-gene operon and contribute to virulence in Mycobacterium tuberculosis. Rv1410 was originally postulated to function as a drug efflux pump, but recent studies suggested that Rv1410 and LprG work in concert to insert triacylglycerides and lipoarabinomannans into the outer membrane. Here, we conducted microscopic analyses of Mycobacterium smegmatis lacking the operon and observed a cell separation defect, while surface rigidity measured by atomic force microscopy was found to be increased. Whereas Rv1410 expressed in Lactococcus lactis did not confer drug resistance, deletion of the operon in Mycobacterium abscessus and M. smegmatis resulted in increased susceptibility toward vancomycin, novobiocin and rifampicin. A homology model of Rv1410 revealed a periplasmic loop as well as a highly conserved aspartate, which were found to be essential for the operon's function. Interestingly, influx of the fluorescent dyes BCECF-AM and calcein-AM in de-energized M. smegmatis cells was faster in the deletion mutant. Our results unambiguously show that elevated drug susceptibility in the deletion mutant is caused by increased drug influx through a defective mycobacterial cell envelope and not by drug efflux mediated by Rv1410.
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Affiliation(s)
- Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Haig A Eskandarian
- Global Health Institute, École polytechnique fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Michael Dal Molin
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Fabian M Arnold
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Andri Krügel
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Georg E Fantner
- Interfaculty Institute for Bioengineering, École polytechnique fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland.,National Center for Mycobacteria, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
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27
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Shiadeh SMJ, Hashemi A, Fallah F, Lak P, Azimi L, Rashidan M. First detection of efrAB, an ABC multidrug efflux pump in Enterococcus faecalis in Tehran, Iran. Acta Microbiol Immunol Hung 2019; 66:57-68. [PMID: 30246548 DOI: 10.1556/030.65.2018.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Enterococcus faecalis is one of the most significant pathogen in both nosocomial and community-acquired infections. Reduced susceptibility to antibiotics is in part due to efflux pumps. This study was conducted on 80 isolates of E. faecalis isolated from outpatients with urinary tract infection during a period of 1 year from April 2014 to April 2015. The antibiotic susceptibility patterns of isolates were determined by the disk diffusion method and presence of efrA and efrB genes was detected by PCR and sequencing. Minimum inhibitory concentrations (MICs) to ciprofloxacin (CIP) were measured with and without carbonyl cyanide 3-chlorophenylhydrazone (CCCP) by broth microdilution. The highest resistance rate was observed to erythromycin (83.3%) and the prevalence of efrA and efrB genes in all E. faecalis isolates was 100%. This study showed that 9 out of 13 (69.2%) ciprofloxacin-resistant isolates became less resistant at least fourfolds to CIP in the presence of efflux pump inhibitor. Our result showed that CCCP as an efflux inhibitor can increase effect of CIP as an efficient antibiotic and it is suggested that efrAB efflux pumps are involved in resistance to fluoroquinolone.
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Affiliation(s)
| | - Ali Hashemi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- 2 Pediatric Infections Research Center, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parnian Lak
- 3 Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Leila Azimi
- 2 Pediatric Infections Research Center, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Rashidan
- 4 School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
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28
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Methods of reconstitution to investigate membrane protein function. Methods 2018; 147:126-141. [DOI: 10.1016/j.ymeth.2018.02.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
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29
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A uniform cloning platform for mycobacterial genetics and protein production. Sci Rep 2018; 8:9539. [PMID: 29934571 PMCID: PMC6015033 DOI: 10.1038/s41598-018-27687-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
Molecular research on mycobacteria relies on a multitude of tools for the genetic manipulation of these clinically important bacteria. However, a uniform set of vectors allowing for standardized cloning procedures is not available. Here, we developed a versatile series of mycobacterial vectors for gene deletion, complementation and protein production and purification. The vectors are compatible with fragment exchange (FX) cloning, a recently developed high-throughput cloning principle taking advantage of the type IIS restriction enzyme SapI and its capacity to generate sticky trinucleotide ends outside of its recognition sequence. FX cloning allows for the efficient cloning into an entry vector and the facile transfer of the sequenced insert into a variety of destination vectors. We generated a set of mycobacterial expression vectors spanning a wide range of expression strengths, tagging variants and selection markers to rapidly screen for the optimal expression construct in order to purify membrane proteins from the model organism Mycobacterium smegmatis. Further, we generated a series of suicide vectors containing two counterselection markers and used them to delete twenty genes encoding for potential drug efflux pumps in M. smegmatis. The vectors will further facilitate genetic and biochemical research on various mycobacterial species.
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30
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EfrEF and the Transcription Regulator ChlR Are Required for Chlorhexidine Stress Response in Enterococcus faecalis V583. Antimicrob Agents Chemother 2018; 62:AAC.00267-18. [PMID: 29610200 PMCID: PMC5971576 DOI: 10.1128/aac.00267-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/16/2018] [Indexed: 12/28/2022] Open
Abstract
Enterococcus faecalis is an opportunistic pathogen and leading cause of health care-associated infections. Daily chlorhexidine gluconate (CHG) bathing of patients is generally regarded as an effective strategy to reduce the occurrence of health care-associated infections. It is likely that E. faecalis is frequently exposed to inhibitory and subinhibitory concentrations of CHG in clinical settings. The goal of this study was to investigate how the vancomycin-resistant strain E. faecalis V583 transcriptionally responds to and tolerates stress from CHG. We used transcriptome (microarray) analysis to identify genes upregulated by E. faecalis V583 in response to CHG. The genes efrE (EF2226) and efrF (EF2227), encoding a heterodimeric ABC transport system, were the most highly upregulated genes. efrEF expression was induced by CHG at concentrations several 2-fold dilutions below the MIC. Deletion of efrEF increased E. faecalis V583 susceptibility to CHG. We found that ChlR, a MerR-like regulator encoded by a sequence upstream of efrEF, mediated the CHG-dependent upregulation of efrEF, and deletion of chlR also increased chlorhexidine susceptibility. Overall, our study gives insight into E. faecalis stress responses to a commonly used antiseptic.
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31
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Reduced Chlorhexidine and Daptomycin Susceptibility in Vancomycin-Resistant Enterococcus faecium after Serial Chlorhexidine Exposure. Antimicrob Agents Chemother 2017; 62:AAC.01235-17. [PMID: 29038276 PMCID: PMC5740357 DOI: 10.1128/aac.01235-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium strains (VREfm) are critical public health concerns because they are among the leading causes of hospital-acquired bloodstream infections. Chlorhexidine (CHX) is a bisbiguanide cationic antiseptic that is routinely used for patient bathing and other infection control practices. VREfm are likely frequently exposed to CHX; however, the long-term effects of CHX exposure have not been studied in enterococci. In this study, we serially exposed VREfm to increasing concentrations of CHX for a period of 21 days in two independent experimental evolution trials. Reduced CHX susceptibility emerged (4-fold shift in CHX MIC). Subpopulations with reduced daptomycin (DAP) susceptibility were detected, which were further analyzed by genome sequencing and lipidomic analysis. Across the trials, we identified adaptive changes in genes with predicted or experimentally confirmed roles in chlorhexidine susceptibility (efrE), global nutritional stress response (relA), nucleotide metabolism (cmk), phosphate acquisition (phoU), and glycolipid biosynthesis (bgsB), among others. Moreover, significant alterations in membrane phospholipids were identified for some populations with reduced DAP susceptibility. Our results are clinically significant because they identify a link between serial subinhibitory CHX exposure and reduced DAP susceptibility. In addition, the CHX-induced genetic and lipidomic changes described in this study offer new insights into the mechanisms underlying the emergence of antibiotic resistance in VREfm.
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32
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Seeger MA. Membrane transporter research in times of countless structures. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:804-808. [PMID: 28867210 DOI: 10.1016/j.bbamem.2017.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 01/16/2023]
Abstract
Structural biology has advanced our understanding of membrane proteins like no other scientific discipline in the past two decades and the number of high resolution membrane transporter structures solved by X-ray crystallography has increased exponentially over this time period. Currently, single particle cryo-EM is in full swing due to a recent resolution revolution and permits for structural insights of proteins that were refractory to crystallization. It is foreseeable that multiple structures of many human transporters will be solved in the coming five years. Nevertheless, many scientifically important questions remain unanswered despite of available structures, as is illustrated in this article at the example of multidrug efflux pumps and ABC transporters. Structure-function studies likely continue to be a supporting pillar of membrane transporter research. However, there is a trend towards the "integrated structural biologist", whose research focusses on a biological question and who closely collaborates with other research groups specialized in spectroscopy techniques or molecular dynamics simulation. Future membrane protein research requires joint efforts from specialists of various disciplines to finally work towards a molecular understanding of membrane transport in the context of the living cell. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland.
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33
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Hürlimann LM, Hohl M, Seeger MA. Split tasks of asymmetric nucleotide-binding sites in the heterodimeric ABC exporter EfrCD. FEBS J 2017; 284:1672-1687. [PMID: 28417533 DOI: 10.1111/febs.14065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/30/2022]
Abstract
Many heterodimeric ATP-binding cassette (ABC) exporters evolved asymmetric ATP-binding sites containing a degenerate site incapable of ATP hydrolysis due to noncanonical substitutions in conserved sequence motifs. Recent studies revealed that nucleotide binding to the degenerate site stabilizes contacts between the nucleotide-binding domains (NBDs) of the inward-facing transporter and regulates ATP hydrolysis at the consensus site via allosteric coupling mediated by the D-loops. However, it is unclear whether nucleotide binding to the degenerate site is strictly required for substrate transport. In this study, we examined the functional consequences of a systematic set of mutations introduced at the degenerate and consensus site of the multidrug efflux pump EfrCD of Enterococcus faecalis. Mutating motifs which differ among the two ATP-binding sites (Walker B, switch loop, and ABC signature) or which are involved in interdomain communication (D-loop and Q-loop) led to asymmetric results in the functional assays and were better tolerated at the degenerate site. This highlights the importance of the degenerate site to allosterically regulate the events at the consensus site. Mutating invariant motifs involved in ATP binding and NBD closure (A-loop and Walker A) resulted in equally reduced transport activities, regardless at which ATP-binding site they were introduced. In contrast to previously investigated heterodimeric ABC exporters, mutation of the degenerate site Walker A lysine completely inactivated ATPase activity and substrate transport, indicating that ATP binding to the degenerate site is essential for EfrCD. This study provides novel insights into the split tasks of asymmetric ATP-binding sites of heterodimeric ABC exporters.
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Affiliation(s)
- Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland
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34
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El-Awady R, Saleh E, Hashim A, Soliman N, Dallah A, Elrasheed A, Elakraa G. The Role of Eukaryotic and Prokaryotic ABC Transporter Family in Failure of Chemotherapy. Front Pharmacol 2017; 7:535. [PMID: 28119610 PMCID: PMC5223437 DOI: 10.3389/fphar.2016.00535] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/23/2016] [Indexed: 12/13/2022] Open
Abstract
Over the years chemotherapy failure has been a vital research topic as researchers have been striving to discover reasons behind it. The extensive studies carried out on chemotherapeutic agents confirm that resistance to chemotherapy is a major reason for treatment failure. “Resistance to chemotherapy,” however, is a comprehensive phrase that refers to a variety of different mechanisms in which ATP-binding cassette (ABC) mediated efflux dominates. The ABC is one of the largest gene superfamily of transporters among both eukaryotes and prokaryotes; it represents a variety of genes that code for proteins, which perform countless functions, including drug efflux – a natural process that protects cells from foreign chemicals. Up to date, chemotherapy failure due to ABC drug efflux is an active research topic that continuously provides further evidence on multiple drug resistance (MDR), aiding scientists in tackling and overcoming this issue. This review focuses on drug resistance by ABC efflux transporters in human, viral, parasitic, fungal and bacterial cells and highlights the importance of the MDR permeability glycoprotein being the mutual ABC transporter among all studied organisms. Current developments and future directions to overcome this problem are also discussed.
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Affiliation(s)
- Raafat El-Awady
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
| | - Ekram Saleh
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of SharjahSharjah, United Arab Emirates; National Cancer Institute - Cancer Biology Department, Cairo UniversityCairo, Egypt
| | - Amna Hashim
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
| | - Nehal Soliman
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
| | - Alaa Dallah
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
| | - Azza Elrasheed
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
| | - Ghada Elakraa
- Department of Pharmacy Practice and Pharmacotherapeutics, Sharjah Institute for Medical Research and College of Pharmacy, University of Sharjah Sharjah, United Arab Emirates
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35
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Timachi MH, Hutter CA, Hohl M, Assafa T, Böhm S, Mittal A, Seeger MA, Bordignon E. Exploring conformational equilibria of a heterodimeric ABC transporter. eLife 2017; 6. [PMID: 28051765 PMCID: PMC5216877 DOI: 10.7554/elife.20236] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/01/2016] [Indexed: 01/04/2023] Open
Abstract
ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift. At physiologically high temperatures and in the absence of nucleotides, the NBDs disengage asymmetrically while the conformation of the TMDs remains unchanged. Nucleotide binding at the degenerate ATP site prevents complete NBD separation, a molecular feature differentiating heterodimeric from homodimeric ABC exporters. Our data suggest hydrolysis-independent closure of the NBD dimer, which is further stabilized as the consensus site nucleotide is committed to hydrolysis. DOI:http://dx.doi.org/10.7554/eLife.20236.001
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Affiliation(s)
- M Hadi Timachi
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Cedric Aj Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Tufa Assafa
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Simon Böhm
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Anshumali Mittal
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
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36
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Reynolds LJ, Roberts AP, Anjum MF. Efflux in the Oral Metagenome: The Discovery of a Novel Tetracycline and Tigecycline ABC Transporter. Front Microbiol 2016; 7:1923. [PMID: 27999567 PMCID: PMC5138185 DOI: 10.3389/fmicb.2016.01923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance in human bacterial pathogens and commensals is threatening our ability to treat infections and conduct common medical procedures. As novel antibiotics are discovered and marketed it is important that we understand how resistance to them may arise and know what environments may act as reservoirs for such resistance genes. In this study a tetracycline and tigecycline resistant clone was identified by screening a human saliva metagenomic library in Escherichia coli EPI300 on agar containing 5 μg/ml tetracycline. Sequencing of the DNA insert present within the tetracycline resistant clone revealed it to contain a 7,765 bp fragment harboring novel ABC half transporter genes, tetAB(60). Mutagenesis studies performed on these genes confirmed that they were responsible for the tetracycline and tigecycline resistance phenotypes. Growth studies performed using E. coli EPI300 clones that harbored either the wild type, the mutated, or none of these genes indicated that there was a fitness cost associated with presence of these genes, with the isolate harboring both genes exhibiting a significantly slower growth than control strains. Given the emergence of E. coli strains that are sensitive only to tigecycline and doxycycline it is concerning that such a resistance mechanism has been identified in the human oral cavity.
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Affiliation(s)
- Liam J Reynolds
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College LondonLondon, UK; Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
| | - Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College London London, UK
| | - Muna F Anjum
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College LondonLondon, UK; Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
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