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TolC-AcrA complex formation monitored by time dependent single-channel electrophysiology. Biochimie 2023; 205:102-109. [PMID: 36646205 DOI: 10.1016/j.biochi.2023.01.004] [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: 06/13/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Characterizing protein-protein interaction on a single molecular level is a challenge, experimentally as well as interpretation of the data. For example, Gram-negative bacteria contain protein complexes spanning the outer and inner cell wall devoted to efflux effectively cell toxic substances. Recent seminal work revealed the high-resolution structure of such a tripartic composition TolC-AcrA-AcrB suggesting to design inhibitors preventing efflux of antibiotics. To show that electrophysiology can provide supporting information here, we reconstitute single TolC homotrimer into a planar lipid membrane, apply a transmembrane voltage and follow the assembly of AcrA to TolC using the modulation of the ion current through TolC channel during binding. In particular, the presence of AcrA in solution increases the average ionic current through TolC and, moreover, reduces the ion-current fluctuations caused by flickering of TolC. Here, we show that statistical properties of ion-current fluctuations (the power spectral density) provide a complementary measure of the interaction of the TolC-AcrA complex in presence of putative efflux pump inhibitors. Both characteristics, the average ion current across TolC and the current noise, taken into consideration together, point to a stiffening of the tip of TolC which might reduce the formation of the complex.
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2
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Newman KE, Khalid S. Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS Comput Biol 2023; 19:e1010841. [PMID: 36638139 PMCID: PMC9879487 DOI: 10.1371/journal.pcbi.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/26/2023] [Accepted: 12/26/2022] [Indexed: 01/14/2023] Open
Abstract
The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the protein is N-glycosylated, with the glycans playing a key role in the effective function of this system. In this work we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid and a macrolide antibiotic. These, and additional equilibrium simulations suggest that the anionic bile acid utilises multivalent cations to climb the ladder of acidic residues that line the interior surface of the protein.
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Affiliation(s)
- Kahlan E. Newman
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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3
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Clinical Status of Efflux Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10091117. [PMID: 34572699 PMCID: PMC8467137 DOI: 10.3390/antibiotics10091117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/05/2021] [Accepted: 09/15/2021] [Indexed: 01/25/2023] Open
Abstract
Antibiotic efflux is a mechanism that is well-documented in the phenotype of multidrug resistance in bacteria. Efflux is considered as an early facilitating mechanism in the bacterial adaptation face to the concentration of antibiotics at the infectious site, which is involved in the acquirement of complementary efficient mechanisms, such as enzymatic resistance or target mutation. Various efflux pumps have been described in the Gram-negative bacteria most often encountered in infectious diseases and, in healthcare-associated infections. Some are more often involved than others and expel virtually all families of antibiotics and antibacterials. Numerous studies report the contribution of these pumps in resistant strains previously identified from their phenotypes. The authors characterize the pumps involved, the facilitating antibiotics and those mainly concerned by the efflux. However, today no study describes a process for the real-time quantification of efflux in resistant clinical strains. It is currently necessary to have at hospital level a reliable and easy method to quantify the efflux in routine and contribute to a rational choice of antibiotics. This review provides a recent overview of the prevalence of the main efflux pumps observed in clinical practice and provides an idea of the prevalence of this mechanism in the multidrug resistant Gram-negative bacteria. The development of a routine diagnostic tool is now an emergency need for the proper application of current recommendations regarding a rational use of antibiotics.
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4
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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5
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Queralt-Martín M, Perini DA, Alcaraz A. Specific adsorption of trivalent cations in biological nanopores determines conductance dynamics and reverses ionic selectivity. Phys Chem Chem Phys 2021; 23:1352-1362. [PMID: 33367433 DOI: 10.1039/d0cp04486e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.
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Affiliation(s)
- María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - D Aurora Perini
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
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6
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Rauly D, Vindret M, Chamberod E, Martins JMF, Xavier P. Distribution of AC Electric Field-Induced Transmembrane Voltage in Escherichia coli Cell Wall Layers. Bioelectromagnetics 2020; 41:279-288. [PMID: 32207548 DOI: 10.1002/bem.22261] [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: 07/31/2019] [Accepted: 03/14/2020] [Indexed: 11/11/2022]
Abstract
On the basis of Gram-negative bacterium Escherichia coli models previously published in the literature, the transmembrane voltage induced by the application of an alternating current (AC) electric field on a bacterial suspension is calculated using COMSOL Multiphysics software, in the range 1-20 MHz, for longitudinal and transverse field orientations. The voltages developed on each of the three layers of the cell wall are then calculated using an electrical equivalent circuit. This study shows that the overall voltage on the cell wall, whose order of magnitude is a few tens of µV, is mainly distributed on inner and outer layers, while a near-zero voltage is found on the periplasm, due to its much higher electrical conductivity compared with the other layers. Although the outer membrane electrical conductivity taken in the model is a thousand times higher than that of the inner membrane, the voltage there is about half of that on the inner membrane, due to capacitive effects. It follows that the expression of protein complexes anchored in the inner membrane could potentially be disrupted, inducing in particular a possible perturbation of biological processes related to cellular respiration and proton cycle, and leading to growth inhibition as a consequence. Protein complexes anchored in the outer membrane or constituting a bridge between the three layers of the cell wall, such as some porins, may also undergo the same action, which would add another growth inhibition factor, as a result of deficiency in porin filtration function when the external environment contains biocides. Bioelectromagnetics. 2020;41:279-288 © 2020 Bioelectromagnetics Society.
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Affiliation(s)
- Dominique Rauly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
| | - Médéric Vindret
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
| | | | - Jean M F Martins
- Univ. Grenoble Alpes, Inst. Geosci Environ. IGE HyDRIMZ, CNRS, Grenoble INP, IRD, UGA CS 40700, Grenoble, France
| | - Pascal Xavier
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
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Yang M, Qin H, Wang W, Zhang H, Long Y, Ye J. Global proteomic responses of Escherichia coli and evolution of biomarkers under tetracycline stress at acid and alkaline conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1315-1326. [PMID: 30857095 DOI: 10.1016/j.scitotenv.2018.01.342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
The global proteomic regulation and the mechanism of biomolecule evolution in acid and alkaline ecosystems triggered by tetracycline, a representative of antibiotics, are not clear. To reveal the related mechanisms, the global responses of Escherichia (E.) coli to tetracycline in acid and alkaline conditions were analyzed using a proteomic approach. The specific phospholipid C16:1ω9c showed a significant decrease between the treatment and control groups. The 77 and 111 upregulated proteins in E. coli in acid and alkaline groups were mainly involved in carbohydrate transport and metabolism and energy metabolism, whereas, the 78 downregulated proteins were related to ribosome and bacterial chemotaxis in the acid group. The 110 downregulated proteins involved in carbon, glycine, serine, threonine, glyoxylate, and dicarboxylate metabolism, biosynthesis of antibiotics, fatty acids, and secondary metabolites in the alkaline group. Protein sequence analysis showed that the respective distribution of phosphorylation, glycosylation, and methylation sites among stable-expressed, upregulated, and downregulated proteins all showed a significant difference. TolC and phosphoenolpyruvate carboxykinase (Pck) in E. coli could be biomarkers to reflect tetracycline stress under extreme conditions with high sequence homology in Homo sapiens, implying the potential impact of tetracycline on humans at the network level. Generally, E. coli in the acid group accelerated the highly efficient protection mechanism to defend against tetracycline stress, while E. coli in the alkaline group strongly impaired the protection mechanism. These findings provide important clues to reveal the microbial antibiotic resistance mechanism in E. coli under extreme conditions and perfect the antibiotic usage.
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Affiliation(s)
- Meng Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huaming Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wenhui Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hongling Zhang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan Long
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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8
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Lôme V, Brunel JM, Pagès JM, Bolla JM. Multiparametric Profiling for Identification of Chemosensitizers against Gram-Negative Bacteria. Front Microbiol 2018; 9:204. [PMID: 29556218 PMCID: PMC5845390 DOI: 10.3389/fmicb.2018.00204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/29/2018] [Indexed: 01/22/2023] Open
Abstract
Antibiotic resistance is now a worldwide therapeutic problem. Since the beginning of anti-infectious treatment bacteria have rapidly shown an incredible ability to develop and transfer resistance mechanisms. In the last decades, the design variation of pioneer bioactive molecules has strongly improved their activity and the pharmaceutical companies partly won the race against the clock. Since the 1980s, the new classes of antibiotics that emerged were mainly directed to Gram-positive bacteria. Thus, we are now facing to multidrug-resistant Gram-negative bacteria, with no therapeutic options to deal with them. These bacteria are mainly resistant because of their double membrane that conjointly impairs antibiotic accumulation and extrudes these molecules when entered. The main challenge is to allow antibiotics to cross the impermeable envelope and reach their targets. One promising solution would be to associate, in a combination therapy, a usual antibiotic with a non-antibiotic chemosensitizer. Nevertheless, for effective drug discovery, there is a prominent lack of tools required to understand the rules of permeation and accumulation into Gram-negative bacteria. By the use of a multidrug-resistant enterobacteria, we introduce a high-content screening procedure for chemosensitizers discovery by quantitative assessment of drug accumulation, alteration of barriers, and deduction of their activity profile. We assembled and analyzed a control chemicals library to perform the proof of concept. The analysis was based on real-time monitoring of the efflux alteration and measure of the influx increase in the presence of studied compounds in an automatized bio-assay. Then, synergistic activity of compounds with an antibiotic was studied and kinetic data reduction was performed which led to the calculation of a score for each barrier to be altered.
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Affiliation(s)
- Vincent Lôme
- UMR MD1, Aix-Marseille University, IRBA, TMCD2, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Jean-Michel Brunel
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, UMR7258, Institut Paoli Calmettes, Aix-Marseille Université, UM 105, Inserm, U1068, Faculté de Pharmacie, Marseille, France
| | - Jean-Marie Pagès
- UMR MD1, Aix-Marseille University, IRBA, TMCD2, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Jean-Michel Bolla
- UMR MD1, Aix-Marseille University, IRBA, TMCD2, Facultés de Médecine et de Pharmacie, Marseille, France
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