201
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Opperman TJ, Nguyen ST. Recent advances toward a molecular mechanism of efflux pump inhibition. Front Microbiol 2015; 6:421. [PMID: 25999939 PMCID: PMC4419859 DOI: 10.3389/fmicb.2015.00421] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/21/2015] [Indexed: 12/25/2022] Open
Abstract
Multidrug resistance (MDR) in Gram-negative pathogens, such as the Enterobacteriaceae and Pseudomonas aeruginosa, poses a significant threat to our ability to effectively treat infections caused by these organisms. A major component in the development of the MDR phenotype in Gram-negative bacteria is overexpression of Resistance-Nodulation-Division (RND)-type efflux pumps, which actively pump antibacterial agents and biocides from the periplasm to the outside of the cell. Consequently, bacterial efflux pumps are an important target for developing novel antibacterial treatments. Potent efflux pump inhibitors (EPIs) could be used as adjunctive therapies that would increase the potency of existing antibiotics and decrease the emergence of MDR bacteria. Several potent inhibitors of RND-type efflux pump have been reported in the literature, and at least three of these EPI series were optimized in a pre-clinical development program. However, none of these compounds have been tested in the clinic. One of the major hurdles to the development of EPIs has been the lack of biochemical, computational, and structural methods that could be used to guide rational drug design. Here, we review recent reports that have advanced our understanding of the mechanism of action of several potent EPIs against RND-type pumps.
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202
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Jardón-Valadez E, Bondar AN, Tobias DJ. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1964-1972. [PMID: 25256652 DOI: 10.1016/j.bbabio.2014.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Translocation of negatively charged ions across cell membranes by ion pumps raises the question as to how protein interactions control the location and dynamics of the ion. Here we address this question by performing extensive molecular dynamics simulations of wild type and mutant halorhodopsin, a seven-helical transmembrane protein that translocates chloride ions upon light absorption. We find that inter-helical hydrogen bonds mediated by a key arginine group largely govern the dynamics of the protein and water groups coordinating the chloride ion.
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Affiliation(s)
- Eduardo Jardón-Valadez
- Departamento de Recursos de la Tierra, Universidad Autónoma Metropolitana-Lerma, Lerma de Villada, Estado de México 52005, México
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Department of Physics, Freie University Arnimallee 14, Berlin 14195, Germany.
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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203
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Venter H, Mowla R, Ohene-Agyei T, Ma S. RND-type drug efflux pumps from Gram-negative bacteria: molecular mechanism and inhibition. Front Microbiol 2015; 6:377. [PMID: 25972857 PMCID: PMC4412071 DOI: 10.3389/fmicb.2015.00377] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/12/2015] [Indexed: 11/13/2022] Open
Abstract
Drug efflux protein complexes confer multidrug resistance on bacteria by transporting a wide spectrum of structurally diverse antibiotics. Moreover, organisms can only acquire resistance in the presence of an active efflux pump. The substrate range of drug efflux pumps is not limited to antibiotics, but it also includes toxins, dyes, detergents, lipids, and molecules involved in quorum sensing; hence efflux pumps are also associated with virulence and biofilm formation. Inhibitors of efflux pumps are therefore attractive compounds to reverse multidrug resistance and to prevent the development of resistance in clinically relevant bacterial pathogens. Recent successes on the structure determination and functional analysis of the AcrB and MexB components of the AcrAB-TolC and MexAB-OprM drug efflux systems as well as the structure of the fully assembled, functional triparted AcrAB-TolC complex significantly contributed to our understanding of the mechanism of substrate transport and the options for inhibition of efflux. These data, combined with the well-developed methodologies for measuring efflux pump inhibition, could allow the rational design, and subsequent experimental verification of potential efflux pump inhibitors (EPIs). In this review we will explore how the available biochemical and structural information can be translated into the discovery and development of new compounds that could reverse drug resistance in Gram-negative pathogens. The current literature on EPIs will also be analyzed and the reasons why no compounds have yet progressed into clinical use will be explored.
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Affiliation(s)
- Henrietta Venter
- School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia Adelaide, SA, Australia
| | - Rumana Mowla
- School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia Adelaide, SA, Australia
| | | | - Shutao Ma
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University Jinan, China
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204
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Yamaguchi A, Nakashima R, Sakurai K. Structural basis of RND-type multidrug exporters. Front Microbiol 2015; 6:327. [PMID: 25941524 PMCID: PMC4403515 DOI: 10.3389/fmicb.2015.00327] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/01/2015] [Indexed: 12/29/2022] Open
Abstract
Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.
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Affiliation(s)
- Akihito Yamaguchi
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
| | - Ryosuke Nakashima
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
| | - Keisuke Sakurai
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan
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205
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Wang B, Weng J, Wang W. Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB. Front Microbiol 2015; 6:302. [PMID: 25918513 PMCID: PMC4394701 DOI: 10.3389/fmicb.2015.00302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/27/2015] [Indexed: 11/25/2022] Open
Abstract
The tripartite efflux pump assembly AcrAB-TolC is the major multidrug resistance transporter in E. coli. The inner membrane transporter AcrB is a homotrimer, energized by the proton movement down the transmembrane electrochemical gradient. The asymmetric crystal structures of AcrB with three monomers in distinct conformational states [access (A), binding (B) and extrusion (E)] support a functional rotating mechanism, in which each monomer of AcrB cycles among the three states in a concerted way. However, the relationship between the conformational changes during functional rotation and drug translocation has not been totally understood. Here, we explored the conformational changes of the AcrB homotrimer during the ABE to BEA transition in different substrate-binding states using targeted MD simulations. It was found that the dissociation of substrate from the distal binding pocket of B monomer is closely related to the concerted conformational changes in the translocation pathway, especially the side chain reorientation of Phe628 and Tyr327. A second substrate binding at the proximal binding pocket of A monomer evidently accelerates the conformational transitions as well as substrate dissociation in B monomer. The acceleration effect of the multi-substrate binding mode provides a molecular explanation for the positive cooperativity observed in the kinetic studies of substrate efflux and deepens our understanding of the functional rotating mechanism of AcrB.
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Affiliation(s)
- Beibei Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University Shanghai, China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University Shanghai, China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China
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206
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Mornon JP, Hoffmann B, Jonic S, Lehn P, Callebaut I. Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics. Cell Mol Life Sci 2015; 72:1377-403. [PMID: 25287046 PMCID: PMC11113974 DOI: 10.1007/s00018-014-1749-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022]
Abstract
In absence of experimental 3D structures, several homology models, based on ABC exporter 3D structures, have provided significant insights into the molecular mechanisms underlying the function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a chloride channel whose defects are associated with cystic fibrosis (CF). Until now, these models, however, did not furnished much insights into the continuous way that ions could follow from the cytosol to the extracellular milieu in the open form of the channel. Here, we have built a refined model of CFTR, based on the outward-facing Sav1866 experimental 3D structure and integrating the evolutionary and structural information available today. Molecular dynamics simulations revealed significant conformational changes, resulting in a full-open channel, accessible from the cytosol through lateral tunnels displayed in the long intracellular loops (ICLs). At the same time, the region of nucleotide-binding domain 1 in contact with one of the ICLs and carrying amino acid F508, the deletion of which is the most common CF-causing mutation, was found to adopt an alternative but stable position. Then, in a second step, this first stable full-open conformation evolved toward another stable state, in which only a limited displacement of the upper part of the transmembrane helices leads to a closure of the channel, in a conformation very close to that adopted by the Atm1 ABC exporter, in an inward-facing conformation. These models, supported by experimental data, provide significant new insights into the CFTR structure-function relationships and into the possible impact of CF-causing mutations.
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Affiliation(s)
- Jean-Paul Mornon
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Brice Hoffmann
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Slavica Jonic
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
| | - Pierre Lehn
- INSERM U1078, SFR ScInBioS, Université de Bretagne Occidentale, Brest, France
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 7590, Museum National d’Histoire Naturelle, IRD UMR 206, IUC, Case 115, 4 Place Jussieu, 75005 Paris Cedex 05, France
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207
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 899] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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208
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AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity. Proc Natl Acad Sci U S A 2015; 112:3511-6. [PMID: 25737552 DOI: 10.1073/pnas.1419939112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The incidence of multidrug-resistant bacterial infections is increasing globally and the need to understand the underlying mechanisms is paramount to discover new therapeutics. The efflux pumps of Gram-negative bacteria have a broad substrate range and transport antibiotics out of the bacterium, conferring intrinsic multidrug resistance (MDR). The genomes of pre- and posttherapy MDR clinical isolates of Salmonella Typhimurium from a patient that failed antibacterial therapy and died were sequenced. In the posttherapy isolate we identified a novel G288D substitution in AcrB, the resistance-nodulation division transporter in the AcrAB-TolC tripartite MDR efflux pump system. Computational structural analysis suggested that G288D in AcrB heavily affects the structure, dynamics, and hydration properties of the distal binding pocket altering specificity for antibacterial drugs. Consistent with this hypothesis, recreation of the mutation in standard Escherichia coli and Salmonella strains showed that G288D AcrB altered substrate specificity, conferring decreased susceptibility to the fluoroquinolone antibiotic ciprofloxacin by increased efflux. At the same time, the substitution increased susceptibility to other drugs by decreased efflux. Information about drug transport is vital for the discovery of new antibacterials; the finding that one amino acid change can cause resistance to some drugs, while conferring increased susceptibility to others, could provide a basis for new drug development and treatment strategies.
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209
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Du D, van Veen HW, Luisi BF. Assembly and operation of bacterial tripartite multidrug efflux pumps. Trends Microbiol 2015; 23:311-9. [PMID: 25728476 DOI: 10.1016/j.tim.2015.01.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/13/2015] [Accepted: 01/22/2015] [Indexed: 01/21/2023]
Abstract
Microorganisms encode several classes of transmembrane pumps that can expel an enormous range of toxic substances, thereby improving their fitness in harsh environments and contributing to resistance against antimicrobial agents. In Gram-negative bacteria these pumps can take the form of tripartite assemblies that actively efflux drugs and other harmful compounds across the cell envelope. We describe recent structural and functional data that have provided insights into the transport mechanisms of these intricate molecular machines.
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Affiliation(s)
- Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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210
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Mishima H, Oshima H, Yasuda S, Kinoshita M. Statistical thermodynamics for functionally rotating mechanism of the multidrug efflux transporter AcrB. J Phys Chem B 2015; 119:3423-33. [PMID: 25633129 DOI: 10.1021/jp5120724] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AcrB, a homotrimer, is the pivotal part of a multidrug efflux pump. A "functionally rotating" picture has been proposed for the drug transport by AcrB, but its mechanism remains unresolved. Here, we investigate the energetics of the whole functional rotation cycle using our theoretical methods. We find that the packing efficiency of AcrB is ununiform, and this ununiformity plays imperative roles primarily through the solvent-entropy effect. When a proton binds to or dissociates from a protomer, the packing properties of this protomer and its two interfaces are perturbed overall in the direction that the solvent translational entropy is lowered. The packing properties of the other two protomers are then reorganized with the recovery or maintenance of closely packed interfaces, so that the solvent-entropy loss can be compensated. The functional structural change by an isolated protomer would cause a seriously large free-energy increase. By forming a trimer, any free-energy increase caused by a protomer is always canceled out by the free-energy decrease brought by the other two protomers via the mechanism mentioned above. The functional structural rotation is thus accomplished using the free-energy decrease arising from the transfer of only a single proton per cycle. The similarities to F1-ATPase are also discussed.
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Affiliation(s)
- Hirokazu Mishima
- Graduate School of Energy Science and ‡Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
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211
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A fluorescent microplate assay quantifies bacterial efflux and demonstrates two distinct compound binding sites in AcrB. Antimicrob Agents Chemother 2015; 59:2388-97. [PMID: 25645845 DOI: 10.1128/aac.05112-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A direct assay of efflux by Escherichia coli AcrAB-TolC and related multidrug pumps would have great value in discovery of new Gram-negative antibiotics. The current understanding of how efflux is affected by the chemical structure and physical properties of molecules is extremely limited, derived from antibacterial data for compounds that inhibit growth of wild-type E. coli. We adapted a previously described fluorescent efflux assay to a 96-well microplate format that measured the ability of test compounds to compete for efflux with Nile Red (an environment-sensitive fluor), independent of antibacterial activity. We show that Nile Red and the lipid-sensitive probe DiBAC4-(3) [bis-(1,3-dibutylbarbituric acid)-trimethine oxonol] can quantify efflux competition in E. coli. We extend the previous findings that the tetracyclines compete with Nile Red and show that DiBAC4-(3) competes with macrolides. The extent of the competition shows a modest correlation with the effect of the acrB deletion on MICs within the compound sets for both dyes. Crystallographic studies identified at least two substrate binding sites in AcrB, the proximal and distal pockets. High-molecular-mass substrates bound the proximal pocket, while low-mass substrates occupied the distal pocket. As DiBAC4-(3) competes with macrolides but not with Nile Red, we propose that DiBAC4-(3) binds the proximal pocket and Nile Red likely binds the distal site. In conclusion, competition with fluorescent probes can be used to study the efflux process for diverse chemical structures and may provide information as to the site of binding and, in some cases, enable rank-ordering a series of related compounds by efflux.
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212
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Wang Z, Zhong M, Lu W, Chai Q, Wei Y. Repressive mutations restore function-loss caused by the disruption of trimerization in Escherichia coli multidrug transporter AcrB. Front Microbiol 2015; 6:4. [PMID: 25657644 PMCID: PMC4303003 DOI: 10.3389/fmicb.2015.00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/03/2015] [Indexed: 11/13/2022] Open
Abstract
AcrAB-TolC and their homologs are major multidrug efflux systems in Gram-negative bacteria. The inner membrane component AcrB functions as a trimer. Replacement of Pro223 by Gly in AcrB decreases the trimer stability and drastically reduces the drug efflux activity. The goal of this study is to identify suppressor mutations that restore function to mutant AcrBP223G and explore the mechanism of function recovery. Two methods were used to introduce random mutations into the plasmid of AcrBP223G. Mutants with elevated drug efflux activity were identified, purified, and characterized to examine their expression level, trimer stability, interaction with AcrA, and substrate binding. Nine single-site repressor mutations were identified, including T199M, D256N, A209V, G257V, M662I, Q737L, D788K, P800S, and E810K. Except for M662I, all other mutations located in the docking region of the periplasmic domain. While three mutations, T199M, A209V, and D256N, significantly increased the trimer stability, none of them restored the trimer affinity to the wild type level. M662, the only site of mutation that located in the porter domain, was involved in substrate binding. Our results suggest that the function loss resulted from compromised AcrB trimerization could be restored through various mechanisms involving the compensation of trimer stability and substrate binding.
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Affiliation(s)
- Zhaoshuai Wang
- Department of Chemistry, University of Kentucky Lexington, KY, USA
| | - Meng Zhong
- Department of Chemistry, University of Kentucky Lexington, KY, USA
| | - Wei Lu
- Department of Chemistry, University of Kentucky Lexington, KY, USA
| | - Qian Chai
- Department of Chemistry, University of Kentucky Lexington, KY, USA
| | - Yinan Wei
- Department of Chemistry, University of Kentucky Lexington, KY, USA
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213
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Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A. Improving olefin tolerance and production in E. coli using native and evolved AcrB. Biotechnol Bioeng 2015; 112:879-88. [PMID: 25450012 PMCID: PMC4406151 DOI: 10.1002/bit.25511] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/16/2014] [Accepted: 11/25/2014] [Indexed: 01/10/2023]
Abstract
Microorganisms can be engineered for the production of chemicals utilized in the polymer industry. However many such target compounds inhibit microbial growth and might correspondingly limit production levels. Here, we focus on compounds that are precursors to bioplastics, specifically styrene and representative alpha-olefins; 1-hexene, 1-octene, and 1-nonene. We evaluated the role of the Escherichia coli efflux pump, AcrAB-TolC, in enhancing tolerance towards these olefin compounds. AcrAB-TolC is involved in the tolerance towards all four compounds in E. coli. Both styrene and 1-hexene are highly toxic to E. coli. Styrene is a model plastics precursor with an established route for production in E. coli (McKenna and Nielsen, 2011). Though our data indicates that AcrAB-TolC is important for its optimal production, we observed a strong negative selection against the production of styrene in E. coli. Thus we used 1-hexene as a model compound to implement a directed evolution strategy to further improve the tolerance phenotype towards this alpha-olefin. We focused on optimization of AcrB, the inner membrane domain known to be responsible for substrate binding, and found several mutations (A279T, Q584R, F617L, L822P, F927S, and F1033Y) that resulted in improved tolerance. Several of these mutations could also be combined in a synergistic manner. Our study shows efflux pumps to be an important mechanism in host engineering for olefins, and one that can be further improved using strategies such as directed evolution, to increase tolerance and potentially production. Biotechnol. Bioeng. 2015;112: 879–888. © 2015 The Authors. Biotechnology and Bioengineering Published by John Wiley & Periodicals, Inc.
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214
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Kim JS, Jeong H, Song S, Kim HY, Lee K, Hyun J, Ha NC. Structure of the tripartite multidrug efflux pump AcrAB-TolC suggests an alternative assembly mode. Mol Cells 2015; 38:180-6. [PMID: 26013259 PMCID: PMC4332038 DOI: 10.14348/molcells.2015.2277] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 11/27/2022] Open
Abstract
Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the α-barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.
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Affiliation(s)
- Jin-Sik Kim
- Department of Manufacturing Pharmacy, Pusan National University, Busan 609-735, Korea
| | - Hyeongseop Jeong
- Division of Electron Microscopic Research, Korea Basic Science Institute, Dajeon 169-148, Korea
| | - Saemee Song
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-742, Korea
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Hye-Yeon Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Chungbuk 363-883, Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Jaekyung Hyun
- Division of Electron Microscopic Research, Korea Basic Science Institute, Dajeon 169-148, Korea
| | - Nam-Chul Ha
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-742, Korea
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215
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Computational study of correlated domain motions in the AcrB efflux transporter. BIOMED RESEARCH INTERNATIONAL 2015; 2015:487298. [PMID: 25685792 PMCID: PMC4313061 DOI: 10.1155/2015/487298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/09/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
As active part of the major efflux system in E. coli bacteria, AcrB is responsible for the uptake and pumping of toxic substrates from the periplasm toward the extracellular space. In combination with the channel protein TolC and membrane fusion protein AcrA, this efflux pump is able to help the bacterium to survive different kinds of noxious compounds. With the present study we intend to enhance the understanding of the interactions between the domains and monomers, for example, the transduction of mechanical energy from the transmembrane domain into the porter domain, correlated motions of different subdomains within monomers, and cooperative effects between monomers. To this end, targeted molecular dynamics simulations have been employed either steering the whole protein complex or specific parts thereof. By forcing only parts of the complex towards specific conformational states, the risk for transient artificial conformations during the simulations is reduced. Distinct cooperative effects between the monomers in AcrB have been observed. Possible allosteric couplings have been identified providing microscopic insights that might be exploited to design more efficient inhibitors of efflux systems.
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216
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Thai KM, Do TN, Nguyen TVP, Nguyen DKT, Tran TD. QSAR Studies on Bacterial Efflux Pump Inhibitors. ACTA ACUST UNITED AC 2015. [DOI: 10.4018/978-1-4666-8136-1.ch007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Antimicrobial drug resistance occurs when bacteria undergo certain modifications to eliminate the effectiveness of drugs, chemicals, or other agents designed to cure infections. To date, the burden of resistance has remained one of the major clinical concerns as it renders prolonged and complicated treatments, thereby increasing the medical costs with lengthier hospital stays. Of complex causes for bacterial resistance, there has been increasing evidence that proved the significant role of efflux pumps in antibiotic resistance. Coadministration of Efflux Pump Inhibitors (EPIs) with antibiotics has been considered one of the promising ways not only to improve the efficacy but also to extend the clinical utility of existing antibiotics. This chapter begins with outlining current knowledge about bacterial efflux pumps and drug designs applied in identification of their modulating compounds. Following, the chapter addresses and provides a discussion on Quantitative Structure-Activity Relationship (QSAR) analyses in search of novel and potent efflux pump inhibitors.
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Affiliation(s)
| | - Trong-Nhat Do
- University of Medicine and Pharmacy at HCMC, Vietnam
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217
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Ly K, Bartho JD, Eicher T, Pos KM, Mitra AK. A novel packing arrangement of AcrB in the lipid bilayer membrane. FEBS Lett 2014; 588:4776-83. [PMID: 25451234 DOI: 10.1016/j.febslet.2014.11.010] [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: 08/24/2014] [Revised: 10/20/2014] [Accepted: 11/05/2014] [Indexed: 12/01/2022]
Abstract
The central component AcrB of the Escherichia coli drug efflux complex AcrA-AcrB-TolC has been extensively investigated by X-ray crystallography of detergent-protein 3-D crystals. In these crystals, AcrB packs as trimers - the functional unit. We visualized the AcrB-AcrB interaction in its native environment by examining E. coli lipid reconstituted 2-D crystals, which were overwhelmingly formed by asymmetric trimers stabilized by strongly-interacting monomers from adjacent trimers. Most interestingly, we observed lattices formed by an arrangement of AcrB monomers distinct from that in traditional trimers. This hitherto unobserved packing, might play a role in the biogenesis of trimeric AcrB.
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Affiliation(s)
- K Ly
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
| | - J D Bartho
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
| | - T Eicher
- Institute of Biochemistry, Max-von-Laue-Str. 9, Goethe-University Frankfurt am Main, Germany(1)
| | - K M Pos
- Institute of Biochemistry, Max-von-Laue-Str. 9, Goethe-University Frankfurt am Main, Germany(1)
| | - A K Mitra
- School of Biological Sciences, Private Bag 92019, University of Auckland, Auckland, New Zealand
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218
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Stubborn contaminants: influence of detergents on the purity of the multidrug ABC transporter BmrA. PLoS One 2014; 9:e114864. [PMID: 25517996 PMCID: PMC4269414 DOI: 10.1371/journal.pone.0114864] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022] Open
Abstract
Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six selected detergents revealed unexpected protein contamination visible for the most part on overloaded SDS-PAGE. A major contamination from the outer membrane protein OmpF was detected in purifications with Foscholine 12 (FC12) but not with Lauryldimethylamine-N-oxide (LDAO) or any of the maltose-based detergents. Consequently, in the FC12 purified BmrA, OmpF easily crystallized over BmrA in a new space group, and whose structure is reported here. We therefore devised an optimized protocol to eliminate OmpF during the FC12 purification of BmrA. On the other hand, an additional band visible at ∼110 kDa was detected in all samples purified with the maltose-based detergents. It contained AcrB that crystallized over BmrA despite its trace amounts. Highly pure BmrA preparations could be obtained using either a ΔacrAB E. coli strain and n-dodecyl-β-D-maltopyranoside, or a classical E. coli strain and lauryl maltose neopentyl glycol for the overexpression and purification, respectively. Overall our results urge to incorporate a proteomics-based purity analysis into quality control checks prior to commencing crystallization assays of membrane proteins that are notoriously arduous to crystallize. Moreover, the strategies developed here to selectively eliminate obstinate contaminants should be applicable to the purification of other membrane proteins overexpressed in E. coli.
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219
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Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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220
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Phillips JL, Gnanakaran S. A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps. Proteins 2014; 83:46-65. [PMID: 24957790 DOI: 10.1002/prot.24632] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 06/06/2014] [Accepted: 06/08/2014] [Indexed: 01/26/2023]
Abstract
Many bacterial pathogens are becoming increasingly resistant to antibiotic treatments, and a detailed understanding of the molecular basis of antibiotic resistance is critical for the development of next-generation approaches for combating bacterial infections. Studies focusing on pathogens have revealed the profile of resistance in these organisms to be due primarily to the presence of multidrug resistance efflux pumps: tripartite protein complexes which span the periplasm bridging the inner and outer membranes of Gram-negative bacteria. An atomic-level resolution tripartite structure remains imperative to advancing our understanding of the molecular mechanisms of pump function using both theoretical and experimental approaches. We develop a fast and consistent method for constructing tripartite structures which leverages existing data-driven models and provide molecular modeling approaches for constructing tripartite structures of multidrug resistance efflux pumps. Our modeling studies reveal that conformational changes in the inner membrane component responsible for drug translocation have limited impact on the conformations of the other pump components, and that two distinct models derived from conflicting experimental data are both consistent with all currently available measurements. Additionally, we investigate putative drug translocation pathways via geometric simulations based on the available crystal structures of the inner membrane pump component, AcrB, bound to two drugs which occupy distinct binding sites: doxorubicin and linezolid. These simulations suggest that smaller drugs may enter the pump through a channel from the cytoplasmic leaflet of the inner membrane, while both smaller and larger drug molecules may enter through a vestibule accessible from the periplasm.
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Affiliation(s)
- Joshua L Phillips
- Theoretical Biology and Biophysics Group (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, 87545; Department of Computer Science, Middle Tennessee State University, Murfreesboro, Tennessee, 37132
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221
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Eicher T, Seeger MA, Anselmi C, Zhou W, Brandstätter L, Verrey F, Diederichs K, Faraldo-Gómez JD, Pos KM. Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB. eLife 2014; 3. [PMID: 25248080 PMCID: PMC4359379 DOI: 10.7554/elife.03145] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 08/25/2014] [Indexed: 12/18/2022] Open
Abstract
Membrane transporters of the RND superfamily confer multidrug resistance to pathogenic bacteria, and are essential for cholesterol metabolism and embryonic development in humans. We use high-resolution X-ray crystallography and computational methods to delineate the mechanism of the homotrimeric RND-type proton/drug antiporter AcrB, the active component of the major efflux system AcrAB-TolC in Escherichia coli, and one most complex and intriguing membrane transporters known to date. Analysis of wildtype AcrB and four functionally-inactive variants reveals an unprecedented mechanism that involves two remote alternating-access conformational cycles within each protomer, namely one for protons in the transmembrane region and another for drugs in the periplasmic domain, 50 Å apart. Each of these cycles entails two distinct types of collective motions of two structural repeats, coupled by flanking α-helices that project from the membrane. Moreover, we rationalize how the cross-talk among protomers across the trimerization interface might lead to a more kinetically efficient efflux system. DOI:http://dx.doi.org/10.7554/eLife.03145.001 The interior of living cells is separated from their external environment by an enveloping membrane that serves as a protective barrier. To regulate the chemical composition of their interior, cells are equipped with specialized proteins in their membranes that move substances in and out of cells. Membrane proteins that expel molecules from the inside to the outside of the cell are called efflux pumps. In Escherichia coli bacteria, an efflux pump known as AcrB is part of a system that removes toxic substances from the bacterial cell—such as the antibiotics used to treat bacterial infections. AcrB and other closely related efflux pumps in pathogenic bacteria are often polyspecific transporters—they can transport a large number of different toxic molecules. These efflux pump systems are also more active in bacteria that have been targeted by antibiotics, and therefore they help bacteria to evolve resistance to multiple drugs. The emergence of bacterial multi-drug resistance is a global threat to human health; to combat this phenomenon, it is essential to understand its molecular basis. Each AcrB protein has three main parts or domains. The periplasmic domain, which is located between the two membranes that surround E. coli, works via an ‘alternating-access cycle’; that is, the shape of the periplasmic domain changes between three different forms in such a way that antibiotic molecules are first captured and subsequently squeezed through the protein towards the outside of the cell. However, the mechanism of the transmembrane domain—which is embedded in the innermost membrane of the bacterium and is the source of energy for the transport process—was not understood. Here, Eicher et al. use X-ray crystallography to examine the three-dimensional structures of the AcrB efflux pump—and several inactive variants—in high detail. Combining these results with computer simulations reveals the mechanism used by the transmembrane domain to take up protons from the exterior and transport them into the cell. Proton transport also proceeds according to an alternating-access mechanism—and, although the transmembrane and periplasmic domains are far apart, their movements are tightly linked. Thus, because proton uptake releases energy, the transmembrane domain effectively powers the periplasmic domain to expel drugs and other molecules. Eicher et al. note that a similar mechanism has not been seen before in other efflux pumps or transporter proteins. Understanding how AcrB works opens up new avenues that could be exploited to develop new drugs against multidrug resistant bacteria. Furthermore, Eicher et al. suggest that efflux pumps in humans closely related to AcrB might function in a similar way—including those required for regulation of cellular cholesterol, and for the correct development of embryos. DOI:http://dx.doi.org/10.7554/eLife.03145.002
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Affiliation(s)
- Thomas Eicher
- Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany
| | - Markus A Seeger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Claudio Anselmi
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | | | - François Verrey
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany
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222
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Ohene-Agyei T, Mowla R, Rahman T, Venter H. Phytochemicals increase the antibacterial activity of antibiotics by acting on a drug efflux pump. Microbiologyopen 2014; 3:885-96. [PMID: 25224951 PMCID: PMC4263512 DOI: 10.1002/mbo3.212] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/01/2014] [Accepted: 08/01/2014] [Indexed: 12/18/2022] Open
Abstract
Drug efflux pumps confer resistance upon bacteria to a wide range of antibiotics from various classes. The expression of efflux pumps are also implicated in virulence and biofilm formation. Moreover, organisms can only acquire resistance in the presence of active drug efflux pumps. Therefore, efflux pump inhibitors (EPIs) are attractive compounds to reverse multidrug resistance and to prevent the development of resistance in clinically relevant bacterial pathogens. We investigated the potential of pure compounds isolated from plants to act as EPIs. In silico screening was used to predict the bioactivity of plant compounds and to compare that with the known EPI, phe-arg-β-naphthylamide (PAβN). Subsequently, promising products have been tested for their ability to inhibit efflux. Plumbagin nordihydroguaretic acid (NDGA) and to a lesser degree shikonin, acted as sensitizers of drug-resistant bacteria to currently used antibiotics and were able to inhibit the efflux pump-mediated removal of substrate from cells. We demonstrated the feasibility of in silico screening to identify compounds that potentiate the action of antibiotics against drug-resistant strains and which might be potentially useful lead compounds for an EPI discovery program.
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Affiliation(s)
- Thelma Ohene-Agyei
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, United Kingdom
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223
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Random mutagenesis of the multidrug transporter AcrB from Escherichia coli for identification of putative target residues of efflux pump inhibitors. Antimicrob Agents Chemother 2014; 58:6870-8. [PMID: 25182653 DOI: 10.1128/aac.03775-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efflux is an important mechanism of bacterial multidrug resistance (MDR), and the inhibition of MDR pumps by efflux pump inhibitors (EPIs) could be a promising strategy to overcome MDR. 1-(1-Naphthylmethyl)-piperazine (NMP) and phenylalanine-arginine-β-naphthylamide (PAβN) are model EPIs with activity in various Gram-negative bacteria expressing AcrB, the major efflux pump of Escherichia coli, or similar homologous pumps of the resistance-nodulation-cell division class. The aim of the present study was to generate E. coli AcrB mutants resistant to the inhibitory action of the two model EPIs and to identify putative EPI target residues in order to better understand mechanisms of pump inhibition. Using an in vitro random mutagenesis approach focusing on the periplasmic domain of AcrB, we identified the double mutation G141D N282Y, which substantially compromised the synergistic activity of NMP with linezolid, was associated with similar intracellular linezolid concentrations in the presence and absence of NMP, and did not impair the intrinsic MICs of various pump substrates and dye accumulation. We propose that these mutations near the outer face of the distal substrate binding pocket reduce NMP trapping. Other residues found to be relevant for efflux inhibition by NMP were G288 and A279, but mutations at these sites also changed the susceptibility to several pump substrates. Unlike with NMP, we were unable to generate AcrB periplasmic domain mutants with resistance or partial resistance to the EPI activity of PAβN, which is consistent with the modes of action of PAβN differing from those of NMP.
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224
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Abstract
Infections caused by bacteria are a leading cause of death worldwide. Although antibiotics remain a key clinical therapy, their effectiveness has been severely compromised by the development of drug resistance in bacterial pathogens. Multidrug efflux transporters--a common and powerful resistance mechanism--are capable of extruding a number of structurally unrelated antimicrobials from the bacterial cell, including antibiotics and toxic heavy metal ions, facilitating their survival in noxious environments. Transporters of the resistance-nodulation-cell division (RND) superfamily typically assemble as tripartite efflux complexes spanning the inner and outer membranes of the cell envelope. In Escherichia coli, the CusCFBA complex, which mediates resistance to copper(I) and silver(I) ions, is the only known RND transporter specific to heavy metals. Here, we describe the current knowledge of individual pump components of the Cus system, a paradigm for efflux machinery, and speculate on how RND pumps assemble to fight diverse antimicrobials.
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225
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Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors. Antimicrob Agents Chemother 2014; 58:6224-34. [PMID: 25114133 DOI: 10.1128/aac.03283-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-generation antibiotics. To date, however, only one inhibitor has been cocrystallized with AcrB. Thus, in silico structure-based analysis is essential for elucidating the interaction between other inhibitors and the efflux pumps. In this work, we used computer docking and molecular dynamics simulations to study the interaction between AcrB and the compound MBX2319, a novel pyranopyridine efflux pump inhibitor with potent activity against RND efflux pumps of Enterobacteriaceae species, as well as other known inhibitors (D13-9001, 1-[1-naphthylmethyl]-piperazine, and phenylalanylarginine-β-naphthylamide) and the binding of doxorubicin to the efflux-defective F610A variant of AcrB. We also analyzed the binding of a substrate, minocycline, for comparison. Our results show that MBX2319 binds very tightly to the lower part of the distal pocket in the B protomer of AcrB, strongly interacting with the phenylalanines lining the hydrophobic trap, where the hydrophobic portion of D13-9001 was found to bind by X-ray crystallography. Additionally, MBX2319 binds to AcrB in a manner that is similar to the way in which doxorubicin binds to the F610A variant of AcrB. In contrast, 1-(1-naphthylmethyl)-piperazine and phenylalanylarginine-β-naphthylamide appear to bind to somewhat different areas of the distal pocket in the B protomer of AcrB than does MBX2319. However, all inhibitors (except D13-9001) appear to distort the structure of the distal pocket, impairing the proper binding of substrates.
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226
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Switch-loop flexibility affects transport of large drugs by the promiscuous AcrB multidrug efflux transporter. Antimicrob Agents Chemother 2014; 58:4767-72. [PMID: 24914123 DOI: 10.1128/aac.02733-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug efflux transporters recognize a variety of structurally unrelated compounds for which the molecular basis is poorly understood. For the resistance nodulation and cell division (RND) inner membrane component AcrB of the AcrAB-TolC multidrug efflux system from Escherichia coli, drug binding occurs at the access and deep binding pockets. These two binding areas are separated by an 11-amino-acid-residue-containing switch loop whose conformational flexibility is speculated to be essential for drug binding and transport. A G616N substitution in the switch loop has a distinct and local effect on the orientation of the loop and on the ability to transport larger drugs. Here, we report a distinct phenotypical pattern of drug recognition and transport for the G616N variant, indicating that drug substrates with minimal projection areas of >70 Å(2) are less well transported than other substrates.
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227
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Bolla JR, Su CC, Do SV, Radhakrishnan A, Kumar N, Long F, Chou TH, Delmar JA, Lei HT, Rajashankar KR, Shafer WM, Yu EW. Crystal structure of the Neisseria gonorrhoeae MtrD inner membrane multidrug efflux pump. PLoS One 2014; 9:e97903. [PMID: 24901477 PMCID: PMC4046932 DOI: 10.1371/journal.pone.0097903] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/24/2014] [Indexed: 01/07/2023] Open
Abstract
Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually-transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. The MtrCDE tripartite multidrug efflux pump, belonging to the hydrophobic and amphiphilic efflux resistance-nodulation-cell division (HAE-RND) family, spans both the inner and outer membranes of N. gonorrhoeae and confers resistance to a variety of antibiotics and toxic compounds. We here report the crystal structure of the inner membrane MtrD multidrug efflux pump, which reveals a novel structural feature that is not found in other RND efflux pumps.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Sylvia V. Do
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | | | - Nitin Kumar
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Feng Long
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Tsung-Han Chou
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Jared A. Delmar
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Hsiang-Ting Lei
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - William M. Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, VA Medical Center, Decatur, Georgia, United States of America
| | - Edward W. Yu
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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228
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Lei HT, Chou TH, Su CC, Bolla JR, Kumar N, Radhakrishnan A, Long F, Delmar JA, Do SV, Rajashankar KR, Shafer WM, Yu EW. Crystal structure of the open state of the Neisseria gonorrhoeae MtrE outer membrane channel. PLoS One 2014; 9:e97475. [PMID: 24901251 PMCID: PMC4046963 DOI: 10.1371/journal.pone.0097475] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 04/20/2014] [Indexed: 01/08/2023] Open
Abstract
Active efflux of antimicrobial agents is one of the most important strategies used by bacteria to defend against antimicrobial factors present in their environment. Mediating many cases of antibiotic resistance are transmembrane efflux pumps, composed of one or more proteins. The Neisseria gonorrhoeae MtrCDE tripartite multidrug efflux pump, belonging to the hydrophobic and amphiphilic efflux resistance-nodulation-cell division (HAE-RND) family, spans both the inner and outer membranes of N. gonorrhoeae and confers resistance to a variety of antibiotics and toxic compounds. We here describe the crystal structure of N. gonorrhoeae MtrE, the outer membrane component of the MtrCDE tripartite multidrug efflux system. This trimeric MtrE channel forms a vertical tunnel extending down contiguously from the outer membrane surface to the periplasmic end, indicating that our structure of MtrE depicts an open conformational state of this channel.
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Affiliation(s)
- Hsiang-Ting Lei
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Tsung-Han Chou
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Jani Reddy Bolla
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Nitin Kumar
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | | | - Feng Long
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
| | - Jared A. Delmar
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
| | - Sylvia V. Do
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - William M. Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, VA Medical Center, Decatur, Georgia, United States of America
| | - Edward W. Yu
- Department of Chemistry, Iowa State University, Ames, Iowa, United States of America
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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229
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Ye C, Wang Z, Lu W, Zhong M, Chai Q, Wei Y. Correlation between AcrB trimer association affinity and efflux activity. Biochemistry 2014; 53:3738-46. [PMID: 24854514 PMCID: PMC4067148 DOI: 10.1021/bi5000838] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The majority of membrane proteins
function as oligomers. However,
it remains largely unclear how the oligomer stability of protein complexes
correlates with their function. Understanding the relationship between
oligomer stability and activity is essential to protein research and
to virtually all cellular processes that depend on the function of
protein complexes. Proteins make lasting or transient interactions
as they perform their functions. Obligate oligomeric proteins exist
and function exclusively at a specific oligomeric state. Although
oligomerization is clearly critical for such proteins to function,
a direct correlation between oligomer affinity and biological activity
has not yet been reported. Here, we used an obligate trimeric membrane
transporter protein, AcrB, as a model to investigate the correlation
between its relative trimer affinity and efflux activity. AcrB is
a component of the major multidrug efflux system in Escherichia coli. We created six AcrB constructs
with mutations at the transmembrane intersubunit interface, and we
determined their activities using both a drug susceptibility assay
and an ethidium bromide accumulation assay. The relative trimer affinities
of these mutants in detergent micelles were obtained using blue native
polyacrylamide gel electrophoresis. A correlation between the relative
trimer affinity and substrate efflux activity was observed, in which
a threshold trimer stability was required to maintain efflux activity.
The trimer affinity of the wild-type protein was approximately 3 kcal/mol
more stable than the threshold value. Once the threshold was reached,
an additional increase of stability in the range observed had no observable
effect on protein activity.
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Affiliation(s)
- Cui Ye
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 2014; 453:254-67. [PMID: 24878531 DOI: 10.1016/j.bbrc.2014.05.090] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
Abstract
Multidrug resistance (MDR) refers to the capability of bacterial pathogens to withstand lethal doses of structurally diverse drugs which are capable of eradicating non-resistant strains. MDR has been identified as a major threat to the public health of human being by the World Health Organization (WHO). Among the four general mechanisms that cause antibiotic resistance including target alteration, drug inactivation, decreased permeability and increased efflux, drug extrusion by the multidrug efflux pumps serves as an important mechanism of MDR. Efflux pumps not only can expel a broad range of antibiotics owing to their poly-substrate specificity, but also drive the acquisition of additional resistance mechanisms by lowering intracellular antibiotic concentration and promoting mutation accumulation. Over-expression of multidrug efflux pumps have been increasingly found to be associated with clinically relevant drug resistance. On the other hand, accumulating evidence has suggested that efflux pumps also have physiological functions in bacteria and their expression is subject tight regulation in response to various of environmental and physiological signals. A comprehensive understanding of the mechanisms of drug extrusion, and regulation and physiological functions of efflux pumps is essential for the development of anti-resistance interventions. In this review, we summarize the development of these research areas in the recent decades and present the pharmacological exploitation of efflux pump inhibitors as a promising anti-drug resistance intervention.
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Affiliation(s)
- Jingjing Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Ziqing Deng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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231
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Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF. Structure of the AcrAB-TolC multidrug efflux pump. Nature 2014; 509:512-5. [PMID: 24747401 PMCID: PMC4361902 DOI: 10.1038/nature13205] [Citation(s) in RCA: 441] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/05/2014] [Indexed: 12/12/2022]
Abstract
The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component. A model system for such a pump is the acridine resistance complex of Escherichia coli. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB-TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species.
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Affiliation(s)
- Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nathan R James
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Jarrod E Voss
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ewa Klimont
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Henrietta Venter
- School of Pharmacy & Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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232
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Su CC, Radhakrishnan A, Kumar N, Long F, Bolla JR, Lei HT, Delmar JA, Do SV, Chou TH, Rajashankar KR, Zhang Q, Yu EW. Crystal structure of the Campylobacter jejuni CmeC outer membrane channel. Protein Sci 2014; 23:954-61. [PMID: 24753291 DOI: 10.1002/pro.2478] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 11/07/2022]
Abstract
As one of the world's most prevalent enteric pathogens, Campylobacter jejuni is a major causative agent of human enterocolitis and is responsible for more than 400 million cases of diarrhea each year. The impact of this pathogen on children is of particular significance. Campylobacter has developed resistance to many antimicrobial agents via multidrug efflux machinery. The CmeABC tripartite multidrug efflux pump, belonging to the resistance-nodulation-cell division (RND) superfamily, plays a major role in drug resistant phenotypes of C. jejuni. This efflux complex spans the entire cell envelop of C. jejuni and mediates resistance to various antibiotics and toxic compounds. We here report the crystal structure of C. jejuni CmeC, the outer membrane component of the CmeABC tripartite multidrug efflux system. The structure reveals a possible mechanism for substrate export.
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Affiliation(s)
- Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
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233
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MexY-promoted aminoglycoside resistance in Pseudomonas aeruginosa: involvement of a putative proximal binding pocket in aminoglycoside recognition. mBio 2014; 5:e01068. [PMID: 24757215 PMCID: PMC3994515 DOI: 10.1128/mbio.01068-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The resistance-nodulation-division (RND) family multidrug efflux system MexXY-OprM is a major determinant of aminoglycoside resistance in Pseudomonas aeruginosa, although the details of aminoglycoside recognition and export by MexY, the substrate-binding RND component of this efflux system, have not been elucidated. To identify regions/residues of MexY important for aminoglycoside resistance, plasmid-borne mexY was mutagenized and mutations that impaired MexY-promoted aminoglycoside (streptomycin) resistance were identified in a ΔmexY strain of P. aeruginosa. Sixty-one streptomycin-sensitive mexY mutants were recovered; among these, 7 unique mutations that yielded wild-type levels of MexY expression were identified. These mutations compromised resistance to additional aminoglycosides and to other antimicrobials and occurred in both the transmembrane and periplasmic regions of the protein. Mapping of the mutated residues onto a 3-dimensional structure of MexY modeled on Escherichia coli AcrB revealed that these tended to occur in regions implicated in general pump operation (transmembrane domain) and MexY trimer assembly (docking domain) and, thus, did not provide insights into aminoglycoside recognition. A region corresponding to a proximal binding pocket connected to a periplasm-linked cleft, part of a drug export pathway of AcrB, was identified in MexY and proposed to play a role in aminoglycoside recognition. To test this, selected residues (K79, D133, and Y613) within this pocket were mutagenized and the impact on aminoglycoside resistance was assessed. Mutations of D133 and Y613 compromised aminoglycoside resistance, while, surprisingly, the K79 mutation enhanced aminoglycoside resistance, confirming a role for this putative proximal binding pocket in aminoglycoside recognition and export. IMPORTANCE Bacterial RND pumps do not typically accommodate highly hydrophilic agents such as aminoglycosides, and it is unclear how those, such as MexY, which accommodate these unique substrates, do so. The results presented here indicate that aminoglycosides are likely not captured and exported by this RND pump component in a unique manner but rather utilize a previously defined export pathway that involves a proximal drug-binding pocket that is also implicated in the export of nonaminoglycosides. The observation, too, that a mutation in this pocket enhances MexY-mediated aminoglycoside resistance (K79A), an indication that it is not optimally designed to accommodate these agents, lends further support to earlier proposals that antimicrobials are not the intended pump substrates.
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234
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Ye C, Wang Z, Lu W, Wei Y. Unfolding study of a trimeric membrane protein AcrB. Protein Sci 2014; 23:897-905. [PMID: 24715637 DOI: 10.1002/pro.2471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 01/18/2023]
Abstract
The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB.
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Affiliation(s)
- Cui Ye
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, 40506
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235
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Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter. J Struct Biol 2014; 186:95-111. [DOI: 10.1016/j.jsb.2014.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 02/13/2014] [Accepted: 02/15/2014] [Indexed: 12/20/2022]
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236
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Kobayashi N, Tamura N, van Veen HW, Yamaguchi A, Murakami S. β-Lactam selectivity of multidrug transporters AcrB and AcrD resides in the proximal binding pocket. J Biol Chem 2014; 289:10680-10690. [PMID: 24558035 DOI: 10.1074/jbc.m114.547794] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
β-Lactams are mainstream antibiotics that are indicated for the prophylaxis and treatment of bacterial infections. The AcrA-AcrD-TolC multidrug efflux system confers much stronger resistance on Escherichia coli to clinically relevant anionic β-lactam antibiotics than the homologous AcrA-AcrB-TolC system. Using an extensive combination of chimeric analysis and site-directed mutagenesis, we searched for residues that determine the difference in β-lactam specificity between AcrB and AcrD. We identified three crucial residues at the "proximal" (or access) substrate binding pocket. The simultaneous replacement of these residues in AcrB by those in AcrD (Q569R, I626R, and E673G) transferred the β-lactam specificity of AcrD to AcrB. Our findings indicate for the first time that the difference in β-lactam specificity between AcrB and AcrD relates to interactions of the antibiotic with residues in the proximal binding pocket.
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Affiliation(s)
- Naoki Kobayashi
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan; Faculty of Pharmaceutical Science, Teikyo Heisei University, Nakano, Nakano-ku, Tokyo 164-8530, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Norihisa Tamura
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Akihito Yamaguchi
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Satoshi Murakami
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan; Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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237
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Verchère A, Dezi M, Broutin I, Picard M. In vitro investigation of the MexAB efflux pump from Pseudomonas aeruginosa. J Vis Exp 2014:e50894. [PMID: 24638061 PMCID: PMC4124871 DOI: 10.3791/50894] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
There is an emerging scientific need for reliable tools for monitoring membrane protein transport. We present a methodology leading to the reconstitution of efflux pumps from the Gram-negative bacteria Pseudomonas aeruginosa in a biomimetic environment that allows for an accurate investigation of their activity of transport. Three prerequisites are fulfilled: compartmentation in a lipidic environment, use of a relevant index for transport, and generation of a proton gradient. The membrane protein transporter is reconstituted into liposomes together with bacteriorhodopsin, a light-activated proton pump that generates a proton gradient that is robust as well as reversible and tunable. The activity of the protein is deduced from the pH variations occurring within the liposome, using pyranin, a pH-dependent fluorescent probe. We describe a step-by-step procedure where membrane protein purification, liposome formation, protein reconstitution, and transport analysis are addressed. Although they were specifically designed for an RND transporter, the described methods could potentially be adapted for use with any other membrane protein transporter energized by a proton gradient.
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Affiliation(s)
- Alice Verchère
- Laboratoire de Cristallographie & RMN Biologiques, CNRS & Université Paris Descartes
| | - Manuela Dezi
- Laboratoire de Cristallographie & RMN Biologiques, CNRS & Université Paris Descartes
| | - Isabelle Broutin
- Laboratoire de Cristallographie & RMN Biologiques, CNRS & Université Paris Descartes
| | - Martin Picard
- Laboratoire de Cristallographie & RMN Biologiques, CNRS & Université Paris Descartes;
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238
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Lu W, Zhong M, Chai Q, Wang Z, Yu L, Wei Y. Functional relevance of AcrB Trimerization in pump assembly and substrate binding. PLoS One 2014; 9:e89143. [PMID: 24551234 PMCID: PMC3925222 DOI: 10.1371/journal.pone.0089143] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/15/2014] [Indexed: 12/26/2022] Open
Abstract
AcrB is a multidrug transporter in the inner membrane of Escherichia coli. It is an obligate homotrimer and forms a tripartite efflux complex with AcrA and TolC. AcrB is the engine of the efflux machinery and determines substrate specificity. Active efflux depends on several functional features including proton translocation across the inner membrane through a proton relay pathway in the transmembrane domain of AcrB; substrate binding and migration through the substrate translocation pathway; the interaction of AcrB with AcrA and TolC; and the formation of AcrB homotrimer. Here we investigated two aspects of the inter-correlation between these functional features, the dependence of AcrA-AcrB interaction on AcrB trimerization, and the reliance of substrate binding and penetration on protein-protein interaction. Interaction between AcrA and AcrB was investigated through chemical crosslinking, and a previously established in vivo fluorescent labeling method was used to probe substrate binding. Our data suggested that dissociation of the AcrB trimer drastically decreased its interaction with AcrA. In addition, while substrate binding with AcrB seemed to be irrelevant to the presence or absence of AcrA and TolC, the capability of trimerization and conduction of proton influx did affect substrate binding at selected sites along the substrate translocation pathway in AcrB.
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Affiliation(s)
- Wei Lu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Meng Zhong
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Qian Chai
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaoshuai Wang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Linliang Yu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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239
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Weiß K, Neef A, Van Q, Kramer S, Gregor I, Enderlein J. Quantifying the diffusion of membrane proteins and peptides in black lipid membranes with 2-focus fluorescence correlation spectroscopy. Biophys J 2014; 105:455-62. [PMID: 23870266 DOI: 10.1016/j.bpj.2013.06.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022] Open
Abstract
Protein diffusion in lipid membranes is a key aspect of many cellular signaling processes. To quantitatively describe protein diffusion in membranes, several competing theoretical models have been proposed. Among these, the Saffman-Delbrück model is the most famous. This model predicts a logarithmic dependence of a protein's diffusion coefficient on its inverse hydrodynamic radius (D ∝ ln 1/R) for small radius values. For large radius values, it converges toward a D ∝ 1/R scaling. Recently, however, experimental data indicate a Stokes-Einstein-like behavior (D ∝ 1/R) of membrane protein diffusion at small protein radii. In this study, we investigate protein diffusion in black lipid membranes using dual-focus fluorescence correlation spectroscopy. This technique yields highly accurate diffusion coefficients for lipid and protein diffusion in membranes. We find that despite its simplicity, the Saffman-Delbrück model is able to describe protein diffusion extremely well and a Stokes-Einstein-like behavior can be ruled out.
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Affiliation(s)
- Kerstin Weiß
- III. Institute of Physics, Georg-August-University Göttingen, Göttingen, Germany
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240
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Lee S, Song S, Lee M, Hwang S, Kim JS, Ha NC, Lee K. Interaction between the α-barrel tip of Vibrio vulnificus TolC homologs and AcrA implies the adapter bridging model. J Microbiol 2014; 52:148-53. [PMID: 24500479 DOI: 10.1007/s12275-014-3578-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/05/2013] [Accepted: 12/06/2013] [Indexed: 10/25/2022]
Abstract
The AcrAB-TolC multidrug efflux pump confers resistance to Escherichia coli against many antibiotics and toxic compounds. The TolC protein is an outer membrane factor that participates in the formation of type I secretion systems. The genome of Vibrio vulnificus encodes two proteins homologous to the E. coli TolC, designated TolCV1 and TolCV2. Here, we show that both TolCV1 and TolCV2 partially complement the E. coli TolC function and physically interact with the membrane fusion protein AcrA, a component of the E. coli AcrAB-TolC efflux pump. Using site-directed mutational analyses and an in vivo cross-linking assay, we demonstrated that the α-barrel tip region of TolC homologs plays a critical role in the formation of functional AcrAB-TolC efflux pumps. Our findings suggest the adapter bridging model as a general assembly mechanism for tripartite drug efflux pumps in Gram-negative bacteria.
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Affiliation(s)
- Seunghwa Lee
- Department of Life Science, Chung-Ang University, Seoul, 156-756, Republic of Korea
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241
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Fischer N, Raunest M, Schmidt TH, Koch DC, Kandt C. Efflux pump-mediated antibiotics resistance: Insights from computational structural biology. Interdiscip Sci 2014; 6:1-12. [DOI: 10.1007/s12539-014-0191-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 09/03/2013] [Accepted: 11/18/2013] [Indexed: 01/08/2023]
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242
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Lei HT, Bolla JR, Bishop NR, Su CC, Yu EW. Crystal structures of CusC review conformational changes accompanying folding and transmembrane channel formation. J Mol Biol 2014; 426:403-11. [PMID: 24099674 PMCID: PMC4800009 DOI: 10.1016/j.jmb.2013.09.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/25/2013] [Accepted: 09/29/2013] [Indexed: 10/26/2022]
Abstract
Gram-negative bacteria, such as Escherichia coli, frequently utilize tripartite efflux complexes in the RND (resistance-nodulation-cell division) family to expel diverse toxic compounds from the cell. These complexes span both the inner and outer membranes of the bacterium via an α-helical, inner membrane transporter; a periplasmic membrane fusion protein; and a β-barrel, outer membrane channel. One such efflux system, CusCBA, is responsible for extruding biocidal Cu(I) and Ag(I) ions. To remove these toxic ions, the CusC outer membrane channel must form a β-barrel structural domain, which creates a pore and spans the entire outer membrane. We here report the crystal structures of wild-type CusC, as well as two CusC mutants, suggesting that the first N-terminal cysteine residue plays an important role in protein-membrane interactions and is critical for the insertion of this channel protein into the outer membrane. These structures provide insight into the mechanisms on CusC folding and transmembrane channel formation. It is found that the interactions between CusC and membrane may be crucial for controlling the opening and closing of this β-barrel, outer membrane channel.
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Affiliation(s)
- Hsiang-Ting Lei
- Department of Chemistry, Department of Physics & Astronomy, Iowa State University, Ames, IA 50011, USA
| | - Jani Reddy Bolla
- Department of Chemistry, Department of Physics & Astronomy, Iowa State University, Ames, IA 50011, USA
| | - Nicholas R Bishop
- Department of Chemistry, Department of Physics & Astronomy, Iowa State University, Ames, IA 50011, USA
| | - Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA
| | - Edward W Yu
- Department of Chemistry, Department of Physics & Astronomy, Iowa State University, Ames, IA 50011, USA; Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA.
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243
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Weeks JW, Bavro VN, Misra R. Genetic assessment of the role of AcrB β-hairpins in the assembly of the TolC-AcrAB multidrug efflux pump of Escherichia coli. Mol Microbiol 2014; 91:965-75. [PMID: 24386963 DOI: 10.1111/mmi.12508] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2014] [Indexed: 01/08/2023]
Abstract
The tripartite AcrAB-TolC multidrug efflux pump of Escherichia coli is the central conduit for cell-toxic compounds and contributes to antibiotic resistance. While high-resolution structures of all three proteins have been solved, much remains to be learned as to how the individual components come together to form a functional complex. In this study, we investigated the importance of the AcrB β-hairpins belonging to the DN and DC subdomains, which are presumed to dock with TolC, in complex stability and activity of the complete pump. Our data show that the DN subdomain β-hairpin residues play a more critical role in complex stability and activity than the DC subdomain hairpin residues. The failure of the AcrB DN β-hairpin deletion mutant to engage with TolC leads to the drug hypersensitivity phenotype, which is reversed by compensatory alterations in the lipoyl and β-barrel domains of AcrA. Moreover, AcrA and TolC mutants that induce TolC opening also reverse the drug hypersensitivity phenotype of the AcrB β-hairpin mutants, indicating a failure by the AcrB mutant to interact and thus induce TolC opening on its own. Together, these data suggest that both AcrB β-hairpins and AcrA act to stabilize the tripartite complex and induce TolC opening for drug expulsion.
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Affiliation(s)
- Jon W Weeks
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, OK, 73019, USA
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244
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Fisher MA, Boyarskiy S, Yamada MR, Kong N, Bauer S, Tullman-Ercek D. Enhancing tolerance to short-chain alcohols by engineering the Escherichia coli AcrB efflux pump to secrete the non-native substrate n-butanol. ACS Synth Biol 2014; 3:30-40. [PMID: 23991711 DOI: 10.1021/sb400065q] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microbial conversion of sugars to fuels is a promising technology, but the byproducts of biomass pretreatment processes and the fuels themselves are often toxic at industrially relevant levels. One promising solution to these problems is to engineer efflux pumps to secrete fuels and inhibitory chemicals from the cell, increasing microbial tolerance and enabling higher fuel titer. Toward that end, we used a directed evolution strategy to generate variants of the Escherichia coli AcrB efflux pump that act on the non-native substrate n-butanol, enhancing growth rates of E. coli in the presence of this biofuel by up to 25%. Furthermore, these variants confer improved tolerance to isobutanol and straight-chain alcohols up to n-heptanol. Single amino acid changes in AcrB responsible for this phenotype were identified. We have also shown that both the chemical and genetic inactivation of pump activity eliminate the tolerance conferred by AcrB pump variants, supporting our assertion that the variants secrete the non-native substrates. This strategy can be applied to create an array of efflux pumps that modulate the intracellular concentrations of small molecules of interest to microbial fuel and chemical production.
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Affiliation(s)
- Michael A. Fisher
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
| | - Sergey Boyarskiy
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
- Department
of Bioengineering, University of California Berkeley, 306 Stanley
Hall MC #1762, Berkeley, California 94720, United States
| | - Masaki R. Yamada
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
| | - Niwen Kong
- Department
of Molecular and Cell Biology, University of California Berkeley, 142 LSA #3200, Berkeley, California 94720, United States
| | - Stefan Bauer
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
| | - Danielle Tullman-Ercek
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
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Wong K, Ma J, Rothnie A, Biggin PC, Kerr ID. Towards understanding promiscuity in multidrug efflux pumps. Trends Biochem Sci 2013; 39:8-16. [PMID: 24316304 DOI: 10.1016/j.tibs.2013.11.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/31/2013] [Accepted: 11/05/2013] [Indexed: 10/25/2022]
Abstract
Drug export from cells is a major factor in the acquisition of cellular resistance to antimicrobial and cancer chemotherapy, and poses a significant threat to future clinical management of disease. Many of the proteins that catalyse drug efflux do so with remarkably low substrate specificity, a phenomenon known as multidrug transport. For these reasons we need a greater understanding of drug recognition and transport in multidrug pumps to inform research that attempts to circumvent their action. Structural and computational studies have been heralded as being great strides towards a full elucidation of multidrug recognition and transport. In this review we summarise these advances and ask how close we are to a molecular understanding of this remarkable phenomenon.
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Affiliation(s)
- Kelvin Wong
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Jerome Ma
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alice Rothnie
- Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ian D Kerr
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
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246
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Kinana AD, Vargiu AV, Nikaido H. Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB. Biochemistry 2013; 52:8342-51. [PMID: 24205856 DOI: 10.1021/bi401303v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By measuring quantitatively the active efflux of cephalosporins by the RND (resistance-nodulation-division) family efflux pump AcrB in intact cells of Escherichia coli, we found that the simultaneous presence of another substrate, such as chloramphenicol, benzene, cyclohexane, or Arg β-naphthilamide, significantly enhanced the extrusion of cephalosporins. The stimulation occurred also in a strain expressing the covalently linked trimer of AcrB, and thus cannot be ascribed to the enhanced assembly of the trimer from AcrB monomers. When Val139 of AcrB was changed into Phe, the stimulation by benzene was found to occur at much lower concentration of the solvent. A plausible explanation of these observations is that the AcrB pump is constructed to pump out very rapidly the solvent or chloramphenicol molecules, and thus the efflux of cephalosporins, which presumably bind to a different subsite within the large binding pocket of AcrB, can become facilitated. Computer simulations of ligand binding to AcrB, both by docking and by molecular dynamics simulations, produced results supporting and extending this hypothesis. Benzene and the cephalosporin nitrocefin can bind simultaneously to the distal binding pocket of AcrB, both in the wild type and in the V139F variant. Interestingly, while the binding position and strength of benzene are almost unaffected by the presence of nitrocefin, this latter substrate is significantly displaced toward the exit gate in both wild type and mutant transporter in the presence of benzene. Additionally, the cephalosporin efflux may be enhanced by the binding of solvents (sometimes to the cephalosporin-free protomer), which could accelerate AcrB conformational changes necessary for substrate extrusion.
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Affiliation(s)
- Alfred D Kinana
- Department of Molecular and Cell Biology, University of California , Berkeley California 94720, United States
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247
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Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter. Proc Natl Acad Sci U S A 2013; 110:18484-9. [PMID: 24173033 DOI: 10.1073/pnas.1318705110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Efflux pumps belonging to the ubiquitous resistance-nodulation-cell division (RND) superfamily transport substrates out of cells by coupling proton conduction across the membrane to a conformationally driven pumping cycle. The heavy metal-resistant bacteria Cupriavidus metallidurans CH34 relies notably on as many as 12 heavy metal efflux pumps of the RND superfamily. Here we show that C. metallidurans CH34 ZneA is a proton driven efflux pump specific for Zn(II), and that transport of substrates through the transmembrane domain may be electrogenic. We report two X-ray crystal structures of ZneA in intermediate transport conformations, at 3.0 and 3.7 Å resolution. The trimeric ZneA structures capture protomer conformations that differ in the spatial arrangement and Zn(II) occupancies at a proximal and a distal substrate binding site. Structural comparison shows that transport of substrates through a tunnel that links the two binding sites, toward an exit portal, is mediated by the conformation of a short 14-aa loop. Taken together, the ZneA structures presented here provide mechanistic insights into the conformational changes required for substrate efflux by RND superfamily transporters.
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248
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Yamane T, Murakami S, Ikeguchi M. Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations. Biochemistry 2013; 52:7648-58. [PMID: 24083838 DOI: 10.1021/bi400119v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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249
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Thomas S, Holland IB, Schmitt L. The Type 1 secretion pathway - the hemolysin system and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1629-41. [PMID: 24129268 DOI: 10.1016/j.bbamcr.2013.09.017] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/21/2013] [Accepted: 09/23/2013] [Indexed: 12/27/2022]
Abstract
Type 1 secretion systems (T1SS) are wide-spread among Gram-negative bacteria. An important example is the secretion of the hemolytic toxin HlyA from uropathogenic strains. Secretion is achieved in a single step directly from the cytosol to the extracellular space. The translocation machinery is composed of three indispensable membrane proteins, two in the inner membrane, and the third in the outer membrane. The inner membrane proteins belong to the ABC transporter and membrane fusion protein families (MFPs), respectively, while the outer membrane component is a porin-like protein. Assembly of the three proteins is triggered by accumulation of the transport substrate (HlyA) in the cytoplasm, to form a continuous channel from the inner membrane, bridging the periplasm and finally to the exterior. Interestingly, the majority of substrates of T1SS contain all the information necessary for targeting the polypeptide to the translocation channel - a specific sequence at the extreme C-terminus. Here, we summarize our current knowledge of regulation, channel assembly, translocation of substrates, and in the case of the HlyA toxin, its interaction with host membranes. We try to provide a complete picture of structure function of the components of the translocation channel and their interaction with the substrate. Although we will place the emphasis on the paradigm of Type 1 secretion systems, the hemolysin A secretion machinery from E. coli, we also cover as completely as possible current knowledge of other examples of these fascinating translocation systems. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Sabrina Thomas
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr, 1, 40225 Düsseldorf, Germany
| | - I Barry Holland
- Institute of Genetics and Microbiology, CNRS UMR 8621, University Paris-Sud XI, Building 409, 91405 Orsay Cedex, France
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr, 1, 40225 Düsseldorf, Germany.
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250
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Yu L, Lu W, Ye C, Wang Z, Zhong M, Chai Q, Sheetz M, Wei Y. Role of a conserved residue R780 in Escherichia coli multidrug transporter AcrB. Biochemistry 2013; 52:6790-6. [PMID: 24007302 DOI: 10.1021/bi400452v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multidrug efflux pumps play important roles in bacteria drug resistance. A major multidrug efflux system in Gram-negative bacteria is composed of the inner membrane transporter AcrB, outer membrane protein channel TolC, and membrane fusion protein AcrA. These three proteins form a large complex that spans both layers of cell membranes and the periplasmic space. AcrB exists and functions as a homotrimer. To identify residues at the trimer interface that play important roles in AcrB function, we conducted site directed mutagenesis and discovered a key residue, R780. Although R780K was partially functional, all other R780 mutants tested were completely nonfunctional. Replacement of R780 by other residues disrupted trimer association. However, a decrease of trimer stability was not the lone cause for the observed loss of activity, because the activity loss could not be restored by strengthening trimer interaction. Using both heat and chemical denaturation methods, we found that the mutation decreased protein stability. Finally, we identified a repressor mutation, M774K, through random mutagenesis. It restored the activity of AcrBR780A to a level close to that of the wild-type protein. To examine the mechanism of activity restoration, we monitored denaturation of AcrBR780A/M774K and found that the repressor mutation improved protein stability. These results suggest that R780 is critical for AcrB stability. When R780 was replaced by Ala, the protein retained the overall structure, still trimerized in the cell membrane, and interacted with AcrA. However, local structural rearrangement might have occurred and lead to the decrease of protein stability and loss of substrate efflux activity.
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Affiliation(s)
- Linliang Yu
- Department of Chemistry, University of Kentucky ,Lexington, Kentucky 40506, United States
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