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Lewis BR, Uddin MR, Kuo KM, Shah LMN, Harris NJ, Booth PJ, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Mg 2+-dependent mechanism of environmental versatility in a multidrug efflux pump. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597921. [PMID: 38915626 PMCID: PMC11195059 DOI: 10.1101/2024.06.10.597921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug efflux pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting in domain specific organisation in neutral to weakly acidic regimes. We establish a unique histidine residue directs these structural dynamics and is essential for sustaining pump efflux activity across acidic, neutral, and alkaline conditions. Overall, we propose Mg2+ conserves the structural mobility of AcrA to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced by the periplasm during bacterial infection and colonization. This work highlights that Mg2+ is an important mechanistic component in this pump class and possibly across other periplasmic lipoproteins.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Katie M. Kuo
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Laila M. N. Shah
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Nicola J. Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Paula J. Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Dietmar Hammerschmid
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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2
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Rong C, Chen H, Wang Z, Zhao S, Dong D, Qu J, Zheng N, Liu H, Hua X. Inactivation of antibiotic resistant bacteria by Fe 3O 4 @MoS 2 activated persulfate and control of antibiotic resistance dissemination risk. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133533. [PMID: 38286046 DOI: 10.1016/j.jhazmat.2024.133533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/31/2024]
Abstract
Antibiotic resistance poses a global environmental challenge that jeopardizes human health and ecosystem stability. Antibiotic resistant bacteria (ARB) significantly promote the spreading and diffusion of antibiotic resistance. This study investigated the efficiency and mechanism of inactivating tetracycline-resistant Escherichia coli (TR E. coli) using Fe3O4 @MoS2 activated persulfate (Fe3O4 @MoS2/PS). Under optimized conditions (200 mg/L Fe3O4 @MoS2, 4 mM PS, 35 °C), TR E. coli (∼7.5 log CFU/mL) could be fully inactivated within 20 min. The primary reactive oxygen species (ROS) responsible for TR E. coli inactivation in the Fe3O4 @MoS2/PS system were hydroxyl radicals (•OH) and superoxide radicals (•O2-). Remarkably, the efflux pump protein was targeted and damaged by the generated ROS during the inactivation process, resulting in cell membrane rupture and efflux of cell content. Additionally, the horizontal transmission ability of residual antibiotic resistance genes (ARGs) harboring in the TR E. coli was also reduced after the inactivation treatment. This study offers an efficient approach for TR E. coli inactivation and substantial mitigation of antibiotic resistance dissemination risk.
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Affiliation(s)
- Chang Rong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Haijun Chen
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Zhuowen Wang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Shiyi Zhao
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Deming Dong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Jiao Qu
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Na Zheng
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Haiyang Liu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China; School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Xiuyi Hua
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China.
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3
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Russell Lewis B, Uddin MR, Moniruzzaman M, Kuo KM, Higgins AJ, Shah LMN, Sobott F, Parks JM, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein. Nat Commun 2023; 14:3900. [PMID: 37463890 PMCID: PMC10354078 DOI: 10.1038/s41467-023-39615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA
| | - Anna J Higgins
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Laila M N Shah
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jerry M Parks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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4
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Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Comput Struct Biotechnol J 2022; 20:252-260. [PMID: 35024097 PMCID: PMC8717590 DOI: 10.1016/j.csbj.2021.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.
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Affiliation(s)
- Pierpaolo Cacciotto
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Andrea Basciu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesco Oliva
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Martin Zacharias
- Physics Department, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
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5
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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6
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Fabre L, Ntreh AT, Yazidi A, Leus IV, Weeks JW, Bhattacharyya S, Ruickoldt J, Rouiller I, Zgurskaya HI, Sygusch J. A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa. Structure 2020; 29:261-274.e6. [PMID: 32966762 DOI: 10.1016/j.str.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/30/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The complete structure of the inner membrane transporter TriC of the resistance-nodulation-division (RND) superfamily was solved, including a partial structure of the fused periplasmic membrane fusion subunits, TriA and TriB. The substrate-free conformation of TriABC represents an intermediate step in efflux complex assembly before the engagement of the outer membrane channel. Structural analysis identified a tunnel network whose constriction impedes substrate efflux, indicating inhibition of TriABC in the unengaged state. Blind docking studies revealed binding to TriC at the same loci by substrates and bulkier non-substrates. Together with functional analyses, we propose that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux.
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Affiliation(s)
- Lucien Fabre
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada
| | - Abigail T Ntreh
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Amira Yazidi
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Inga V Leus
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Jon W Weeks
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Jakob Ruickoldt
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Isabelle Rouiller
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada; Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA.
| | - Jurgen Sygusch
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada.
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7
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Zhang HY, Xu Q, Li F, Tian PC, Wang YH, Xiong Y, Zhang YH, Wei DQ. Recent progresses of simulations on passive membrane permeations in China. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1135333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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8
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Symmons MF, Marshall RL, Bavro VN. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies. Front Microbiol 2015; 6:513. [PMID: 26074901 PMCID: PMC4446572 DOI: 10.3389/fmicb.2015.00513] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Recent years have seen major advances in the structural understanding of the different components of tripartite efflux assemblies, which encompass the multidrug efflux (MDR) pumps and type I secretion systems. The majority of these investigations have focused on the role played by the inner membrane transporters and the outer membrane factor (OMF), leaving the third component of the system – the Periplasmic Adaptor Proteins (PAPs) – relatively understudied. Here we review the current state of knowledge of these versatile proteins which, far from being passive linkers between the OMF and the transporter, emerge as active architects of tripartite assemblies, and play diverse roles in the transport process. Recognition between the PAPs and OMFs is essential for pump assembly and function, and targeting this interaction may provide a novel avenue for combating multidrug resistance. With the recent advances elucidating the drug efflux and energetics of the tripartite assemblies, the understanding of the interaction between the OMFs and PAPs is the last piece remaining in the complete structure of the tripartite pump assembly puzzle.
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Affiliation(s)
- Martyn F Symmons
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Robert L Marshall
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
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9
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Zgurskaya HI, Weeks JW, Ntreh AT, Nickels LM, Wolloscheck D. Mechanism of coupling drug transport reactions located in two different membranes. Front Microbiol 2015; 6:100. [PMID: 25759685 PMCID: PMC4338810 DOI: 10.3389/fmicb.2015.00100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Abstract
Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of the cell. Some transporters, together with periplasmic membrane fusion proteins (MFPs) and outer membrane channels, assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protects bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates) to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Abigail T Ntreh
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Logan M Nickels
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
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10
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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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11
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Ruggerone P, Vargiu AV, Collu F, Fischer N, Kandt C. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps. Comput Struct Biotechnol J 2013; 5:e201302008. [PMID: 24688701 PMCID: PMC3962194 DOI: 10.5936/csbj.201302008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 01/13/2023] Open
Abstract
Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
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Affiliation(s)
- Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesca Collu
- Departement fu r Chemie und Biochemie, Universita t Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Nadine Fischer
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| | - Christian Kandt
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
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12
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Wang B, Weng J, Fan K, Wang W. Interdomain flexibility and pH-induced conformational changes of AcrA revealed by molecular dynamics simulations. J Phys Chem B 2012; 116:3411-20. [PMID: 22339851 DOI: 10.1021/jp212221v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The membrane fusion protein (MFP) AcrA is proposed to link the inner membrane transporter AcrB and outer membrane protein TolC, forming the tripartite AcrAB-TolC efflux pump, and was shown to be functionally indispensible. Structural and EPR studies showed that AcrA has high conformational flexibility and exhibited pH-induced conformational change. In this study, we built the complete structure of AcrA through homology modeling and performed atomistic simulations of AcrA at different pH values. It was shown that the conformational flexibility of AcrA originates from the motions of α-hairpin and MP domains. The conformational dynamics of AcrA is sensitive to specific point mutations and pH values. In agreement with the EPR experiments, the interdomain motions were restrained upon lowering pH from 7.0 to 5.0 in the simulations. It was found that the protonation/deprotonation of His285 underlies the pH-regulated conformational dynamics of AcrA by disturbing the local hydrogen bond interactions, suggesting that the changes of pH in the periplasm accompanying the drug efflux could act as a signal to trigger the action of AcrA, which undergoes reversible conformational rearrangement.
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Affiliation(s)
- Beibei Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, PR China
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13
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Sequential mechanism of assembly of multidrug efflux pump AcrAB-TolC. ACTA ACUST UNITED AC 2011; 18:454-63. [PMID: 21513882 DOI: 10.1016/j.chembiol.2011.02.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/16/2011] [Accepted: 02/28/2011] [Indexed: 01/29/2023]
Abstract
Multidrug efflux pumps adversely affect both the clinical effectiveness of existing antibiotics and the discovery process to find new ones. In this study, we reconstituted and characterized by surface plasmon resonance the assembly of AcrAB-TolC, the archetypal multidrug efflux pump from Escherichia coli. We report that the periplasmic AcrA and the outer membrane channel TolC assemble high-affinity complexes with AcrB transporter independently from each other. Antibiotic novobiocin and MC-207,110 inhibitor bind to the immobilized AcrB but do not affect interactions between components of the complex. In contrast, DARPin inhibits interactions between AcrA and AcrB. Mutational opening of TolC channel decreases stability of interactions and promotes disassembly of the complex. The conformation of the membrane proximal domain of AcrA is critical for the formation of AcrAB-TolC and could be targeted for the development of new inhibitors.
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Nikaido H. Structure and mechanism of RND-type multidrug efflux pumps. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 77:1-60. [PMID: 21692366 DOI: 10.1002/9780470920541.ch1] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- Hiroshi Nikaido
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, California, USA
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15
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Lu JJ, Zhu Z, Wang W, Liu S. Coupling sodium dodecyl sulfate-capillary polyacrylamide gel electrophoresis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry via a poly(tetrafluoroethylene) membrane. Anal Chem 2011; 83:1784-90. [PMID: 21309548 DOI: 10.1021/ac103148k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) is a fundamental analytical technique for proteomic research, and SDS-capillary gel electrophoresis (CGE) is its miniaturized version. Compared to conventional slab-gel electrophoresis, SDS-CGE has many advantages such as increased separation efficiency, reduced separation time, and automated operation. SDS-CGE is not widely accepted in proteomic research primarily due to the difficulties in identifying the well-resolved proteins. MALDI-TOF-MS is an outstanding platform for protein identifications. Coupling the two would solve the problem but is extremely challenging because the MS detector has no access to the SDS-CGE-resolved proteins and the SDS interferes with MS detection. In this work we introduce an approach to address these issues. We discover that poly(tetrafluoroethylene) (PTFE) membranes are excellent materials for collecting SDS-CGE-separated proteins. We demonstrate that we can wash off the SDS bound to the collected proteins and identify these proteins on-membrane with MALDI-TOF-MS. We also show that we can immunoblot and Coomassie-stain the proteins collected on these membranes.
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Affiliation(s)
- Joann J Lu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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16
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Zgurskaya HI. Multicomponent drug efflux complexes: architecture and mechanism of assembly. Future Microbiol 2009; 4:919-32. [PMID: 19722844 DOI: 10.2217/fmb.09.62] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multidrug efflux pumps are major contributors to intrinsic antibiotic resistance in Gram-negative pathogens. The basic structure of these pumps comprises an inner membrane transporter, a periplasmic membrane fusion protein and an outer membrane channel. However, the architecture and composition of multidrug efflux complexes vary significantly because of the topological and functional diversity of the inner membrane transporters. This article presents the current views on architecture and assembly of multicomponent drug efflux transporters from Gram-negative bacteria.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry & Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019, USA.
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17
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Blair JMA, Piddock LJV. Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update. Curr Opin Microbiol 2009; 12:512-9. [DOI: 10.1016/j.mib.2009.07.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/02/2009] [Accepted: 07/08/2009] [Indexed: 01/07/2023]
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18
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Kinetic control of TolC recruitment by multidrug efflux complexes. Proc Natl Acad Sci U S A 2009; 106:16416-21. [PMID: 19805313 DOI: 10.1073/pnas.0906601106] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Gram-negative pathogens, multidrug efflux pumps that provide clinically significant levels of antibiotic resistance function as three-component complexes. They are composed of the inner membrane transporters belonging to one of three superfamilies of proteins, RND, ABC, or MF; periplasmic proteins belonging to the membrane fusion protein (MFP) family; and outer membrane channels exemplified by the Escherichia coli TolC. The three-component complexes span the entire two-membrane envelope of Gram-negative bacteria and expel toxic molecules from the cytoplasmic membrane to the medium. The architecture of these complexes is expected to vary significantly because of the structural diversity of the inner membrane transporters. How the three-component pumps are assembled, their architecture, and their dynamics remain unclear. In this study, we reconstituted interactions and compared binding kinetics of the E. coli TolC with AcrA, MacA, and EmrA, the periplasmic MFPs that function in multidrug efflux with transporters from the RND, ABC, and MF superfamilies, respectively. By using surface plasmon resonance, we demonstrate that TolC interactions with MFPs are highly dynamic and sensitive to pH. The affinity of TolC to MFPs decreases in the order MacA > EmrA > AcrA. We further show that MFPs are prone to oligomerization, but differ dramatically from each other in oligomerization kinetics and stability of oligomers. The propensity of MFPs to oligomerize correlates with the stability of MFP-TolC complexes and structural features of inner membrane transporters. We propose that recruitment of TolC by various MFPs is determined not only by kinetics of MFP-TolC interactions but also by oligomerization kinetics of MFPs and pH.
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Abstract
Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A OK9, Canada
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA
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20
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The assembled structure of a complete tripartite bacterial multidrug efflux pump. Proc Natl Acad Sci U S A 2009; 106:7173-8. [PMID: 19342493 DOI: 10.1073/pnas.0900693106] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria like Escherichia coli and Pseudomonas aeruginosa expel drugs via tripartite multidrug efflux pumps spanning both inner and outer membranes and the intervening periplasm. In these pumps a periplasmic adaptor protein connects a substrate-binding inner membrane transporter to an outer membrane-anchored TolC-type exit duct. High-resolution structures of all 3 components are available, but a pump model has been precluded by the incomplete adaptor structure, because of the apparent disorder of its N and C termini. We reveal that the adaptor termini assemble a beta-roll structure forming the final domain adjacent to the inner membrane. The completed structure enabled in vivo cross-linking to map intermolecular contacts between the adaptor AcrA and the transporter AcrB, defining a periplasmic interface between several transporter subdomains and the contiguous beta-roll, beta-barrel, and lipoyl domains of the adaptor. With short and long cross-links expressed as distance restraints, the flexible linear topology of the adaptor allowed a multidomain docking approach to model the transporter-adaptor complex, revealing that the adaptor docks to a transporter region of comparative stability distinct from those key to the proposed rotatory pump mechanism, putative drug-binding pockets, and the binding site of inhibitory DARPins. Finally, we combined this docking with our previous resolution of the AcrA hairpin-TolC interaction to develop a model of the assembled tripartite complex, satisfying all of the experimentally-derived distance constraints. This AcrA(3)-AcrB(3)-TolC(3) model presents a 610,000-Da, 270-A-long efflux pump crossing the entire bacterial cell envelope.
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21
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Reffay M, Gambin Y, Benabdelhak H, Phan G, Taulier N, Ducruix A, Hodges RS, Urbach W. Tracking membrane protein association in model membranes. PLoS One 2009; 4:e5035. [PMID: 19337368 PMCID: PMC2659767 DOI: 10.1371/journal.pone.0005035] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/26/2009] [Indexed: 11/18/2022] Open
Abstract
Membrane proteins are essential in the exchange processes of cells. In spite of great breakthrough in soluble proteins studies, membrane proteins structures, functions and interactions are still a challenge because of the difficulties related to their hydrophobic properties. Most of the experiments are performed with detergent-solubilized membrane proteins. However widely used micellar systems are far from the biological two-dimensions membrane. The development of new biomimetic membrane systems is fundamental to tackle this issue.We present an original approach that combines the Fluorescence Recovery After fringe Pattern Photobleaching technique and the use of a versatile sponge phase that makes it possible to extract crucial informations about interactions between membrane proteins embedded in the bilayers of a sponge phase. The clear advantage lies in the ability to adjust at will the spacing between two adjacent bilayers. When the membranes are far apart, the only possible interactions occur laterally between proteins embedded within the same bilayer, whereas when membranes get closer to each other, interactions between proteins embedded in facing membranes may occur as well.After validating our approach on the streptavidin-biotinylated peptide complex, we study the interactions between two membrane proteins, MexA and OprM, from a Pseudomonas aeruginosa efflux pump. The mode of interaction, the size of the protein complex and its potential stoichiometry are determined. In particular, we demonstrate that: MexA is effectively embedded in the bilayer; MexA and OprM do not interact laterally but can form a complex if they are embedded in opposite bilayers; the population of bound proteins is at its maximum for bilayers separated by a distance of about 200 A, which is the periplasmic thickness of Pseudomonas aeruginosa. We also show that the MexA-OprM association is enhanced when the position and orientation of the protein is restricted by the bilayers. We extract a stoichiometry for the complex that exhibits a strong pH dependance: from 2 to 6 MexA per OprM trimer when the pH decreases from 7.5 to 5.5.Our technique allows to study membrane protein associations in a membrane environment. It provides some challenging information about complexes such as geometry and stoichiometry.
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Affiliation(s)
- Myriam Reffay
- Laboratoire de Physique Statistique, École Normale Supérieure, UMR 8550 CNRS-UPMC, Université Paris 06, Paris, France
| | - Yann Gambin
- Laboratoire de Physique Statistique, École Normale Supérieure, UMR 8550 CNRS-UPMC, Université Paris 06, Paris, France
| | - Houssain Benabdelhak
- UPMC Université Paris 06, UMR 7623, Laboratoire d'Imagerie Paramétrique, Paris, France
- CNRS, UMR 7623, LIP, Paris, France
| | - Gilles Phan
- Laboratoire de Cristallographie et R.M.N. Biologiques, Université Paris Descartes, UMR8015 CNRS, Paris, France
| | - Nicolas Taulier
- UPMC Université Paris 06, UMR 7623, Laboratoire d'Imagerie Paramétrique, Paris, France
- CNRS, UMR 7623, LIP, Paris, France
| | - Arnaud Ducruix
- Laboratoire de Cristallographie et R.M.N. Biologiques, Université Paris Descartes, UMR8015 CNRS, Paris, France
| | - Robert S. Hodges
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Denver, Colorado, United States of America
| | - Wladimir Urbach
- Laboratoire de Physique Statistique, École Normale Supérieure, UMR 8550 CNRS-UPMC, Université Paris 06, Paris, France
- UPMC Université Paris 06, UMR 7623, Laboratoire d'Imagerie Paramétrique, Paris, France
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22
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Zgurskaya HI, Yamada Y, Tikhonova EB, Ge Q, Krishnamoorthy G. Structural and functional diversity of bacterial membrane fusion proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:794-807. [PMID: 19041958 DOI: 10.1016/j.bbapap.2008.10.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/21/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
Membrane Fusion Proteins (MFPs) are functional subunits of multi-component transporters that perform diverse physiological functions in both Gram-positive and Gram-negative bacteria. MFPs associate with transporters belonging to Resistance-Nodulation-cell Division (RND), ATP-Binding Cassette (ABC) and Major Facilitator (MF) superfamilies of proteins. Recent studies suggested that MFPs interact with substrates and play an active role in transport reactions. In addition, the MFP-dependent transporters from Gram-negative bacteria recruit the outer membrane channels to expel various substrates across the outer membrane into external medium. This review is focused on the diversity, structure and molecular mechanism of MFPs that function in multidrug efflux. Using phylogenetic approaches we analyzed diversity and representation of multidrug MFPs in sequenced bacterial genomes. In addition to previously characterized MFPs from Gram-negative bacteria, we identified MFPs that associate with RND-, MF- and ABC-type transporters in Gram-positive bacteria. Sequence analyses showed that MFPs vary significantly in size (200-650 amino acid residues) with some of them lacking the signature alpha-helical domain of multidrug MFPs. Furthermore, many transport operons contain two- or three genes encoding distinct MFPs. We further discuss the diversity of MFPs in the context of current views on the mechanism and structure of MFP-dependent transporters.
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Affiliation(s)
- Helen I Zgurskaya
- University of Oklahoma Department of Chemistry and Biochemistry 620 Parrington Oval, Room 208 Norman, OK 73019, USA.
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23
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Bagai I, Liu W, Rensing C, Blackburn NJ, McEvoy MM. Substrate-linked conformational change in the periplasmic component of a Cu(I)/Ag(I) efflux system. J Biol Chem 2007; 282:35695-702. [PMID: 17893146 DOI: 10.1074/jbc.m703937200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gram-negative bacteria utilize dual membrane resistance nodulation division-type efflux systems to export a variety of substrates. These systems contain an essential periplasmic component that is important for assembly of the protein complex. We show here that the periplasmic protein CusB from the Cus copper/silver efflux system has a critical role in Cu(I) and Ag(I) binding. Isothermal titration calorimetry experiments demonstrate that one Ag(I) ion is bound per CusB molecule with high affinity. X-ray absorption spectroscopy data indicate that the metal environment is an all-sulfur 3-coordinate environment. Candidates for the metal-coordinating residues were identified from sequence analysis, which showed four conserved methionine residues. Mutations of three of these methionine residues to isoleucine resulted in significant effects on CusB metal binding in vitro. Cells containing these CusB variants also show a decrease in their ability to grow on copper-containing plates, indicating an important functional role for metal binding by CusB. Gel filtration chromatography demonstrates that upon binding metal, CusB undergoes a conformational change to a more compact structure. Based on these structural and functional effects of metal binding, we propose that the periplasmic component of resistance nodulation division-type efflux systems plays an active role in export through substrate-linked conformational changes.
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Affiliation(s)
- Ireena Bagai
- Department of Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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24
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Lomovskaya O, Zgurskaya HI, Totrov M, Watkins WJ. Waltzing transporters and 'the dance macabre' between humans and bacteria. Nat Rev Drug Discov 2006; 6:56-65. [PMID: 17159924 DOI: 10.1038/nrd2200] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Multidrug-resistance efflux pumps - in particular those belonging to the resistance-nodulation-cell-division (RND) family of transporters, with their unusually high degree of substrate promiscuity - significantly restrict the effectiveness of antibacterial therapy. Recent years have heralded remarkable insights into the structure and mechanisms of these fascinating molecular machines. Here, we review recent advances in the field and describe various approaches used in combating efflux-mediated resistance.
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Affiliation(s)
- Olga Lomovskaya
- Mpex Pharmaceuticals, Inc. 3030 Bunker Hill Street, Suite 200 San Diego, California 92109, USA.
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25
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Kiralj R, Ferreira MMC. Molecular graphics approach to bacterial AcrB protein–β-lactam antibiotic molecular recognition in drug efflux mechanism. J Mol Graph Model 2006; 25:126-45. [PMID: 16406715 DOI: 10.1016/j.jmgm.2005.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 08/30/2005] [Accepted: 10/25/2005] [Indexed: 11/16/2022]
Abstract
AcrAB-TolC is the most important multidrug efflux pump system of Gram-negative bacteria, responsible for their resistance to lipophilic and amphiphilic drugs. In this work, a molecular graphics study of the pump components AcrB and TolC, 16 beta-lactam antibiotics and 7 other substrates, as well as of AcrB-substrate complexes, was performed in order to give a mechanistic proposal for the efflux process at molecular level. AcrAB-TolC is a proton-dependent electromechanical device which opens to extrude drugs from the bacterial periplasm and perhaps cytoplasm, by means of a series of structural changes within the complex and its components AcrA, AcrB and TolC. These changes are initiated by protonation and disruption of salt bridges and certain hydrogen bonds, and are followed by conformational changes in which a number of intra- and interchain interactions are rearranged. Molecular properties of beta-lactams accounting for their lipophilicity, shape/conformation and other sterical features, polar/charge group distribution and other electronic properties, and hydrogen bonding potency determine their interaction with polar headpieces of the inner membrane, recognition and binding to receptors of AcrB and TolC. The orientation of the beta-lactam molecular dipoles with respect the efflux system is maintained during the drug efflux. Elongated cylinder-like beta-lactam antibiotics with lipophylic side chains, a significantly negative component of the dipole moment and low hydrogen bonding capacity seem to be good substrates of AcrAB-TolC.
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Affiliation(s)
- Rudolf Kiralj
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP 13084-971, Brazil
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26
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Mikolosko J, Bobyk K, Zgurskaya HI, Ghosh P. Conformational flexibility in the multidrug efflux system protein AcrA. Structure 2006; 14:577-87. [PMID: 16531241 PMCID: PMC1997295 DOI: 10.1016/j.str.2005.11.015] [Citation(s) in RCA: 226] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2005] [Revised: 11/15/2005] [Accepted: 11/15/2005] [Indexed: 11/30/2022]
Abstract
Intrinsic resistance to multiple drugs in many gram-negative bacterial pathogens is conferred by resistance nodulation cell division efflux pumps, which are composed of three essential components as typified by the extensively characterized Escherichia coli AcrA-AcrB-TolC system. The inner membrane drug:proton antiporter AcrB and the outer membrane channel TolC export chemically diverse compounds out of the bacterial cell, and require the activity of the third component, the periplasmic protein AcrA. The crystal structures of AcrB and TolC have previously been determined, and we complete the molecular picture of the efflux system by presenting the structure of a stable fragment of AcrA. The AcrA fragment resembles the elongated sickle shape of its homolog Pseudomonas aeruginosa MexA, being composed of three domains: beta-barrel, lipoyl, and alpha-helical hairpin. Notably, unsuspected conformational flexibility in the alpha-helical hairpin domain of AcrA is observed, which has potential mechanistic significance in coupling between AcrA conformations and TolC channel opening.
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Affiliation(s)
- Jonathan Mikolosko
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, USA
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27
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Vaccaro L, Koronakis V, Sansom MSP. Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA. Biophys J 2006; 91:558-64. [PMID: 16648168 PMCID: PMC1483075 DOI: 10.1529/biophysj.105.080010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drug resistance in gram-negative bacteria may be conferred via efflux through a tripartite complex of an inner membrane pump, an outer membrane pore, and a periplasmic adaptor protein. These are AcrB, TolC, and AcrA, respectively, in Escherichia coli. In Pseudomonas aerugonisa, their homologs are MexB, OprM, and MexA. Defining the interdomain dynamics of the adaptor protein is essential to understanding the mechanism of complex formation. Extended (25 ns) molecular dynamics simulations of MexA have been performed to determine such interdomain dynamics. Analysis of conformational drift demonstrates substantial motions of the three domains of MexA relative to one another. Principal components analysis reveals a hinge-bending motion and rotation of the alpha-helical hairpin relative to the other domains to be the two dominant motions. These two motions provide an element of considerable flexibility which is likely to be exploited in the adaptor function of MexA.
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Affiliation(s)
- Loredana Vaccaro
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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28
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Lomovskaya O, Bostian KA. Practical applications and feasibility of efflux pump inhibitors in the clinic--a vision for applied use. Biochem Pharmacol 2006; 71:910-8. [PMID: 16427026 DOI: 10.1016/j.bcp.2005.12.008] [Citation(s) in RCA: 293] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 12/05/2005] [Accepted: 12/08/2005] [Indexed: 11/25/2022]
Abstract
The world of antibiotic drug discovery and development is driven by the necessity to overcome antibiotic resistance in common Gram-positive and Gram-negative pathogens. However, the lack of Gram-negative activity among both recently approved antibiotics and compounds in the developmental pipeline is a general trend despite the fact that the plethora of covered drug targets are well-conserved across the bacterial kingdom. Such intrinsic resistance in Gram-negative bacteria is largely attributed to the activity of multidrug resistance (MDR) efflux pumps. Moreover, these pumps also play a significant role in acquired clinical resistance. Together, these considerations make efflux pumps attractive targets for inhibition in that the resultant efflux pump inhibitor (EPI)/antibiotic combination drug should exhibit increased potency, enhanced spectrum of activity and reduced propensity for acquired resistance. To date, at least one class of broad-spectrum EPI has been extensively characterized. While these efforts indicated a significant potential for developing small molecule inhibitors against efflux pumps, they did not result in a clinically useful compound. Stemming from the continued clinical pressure for novel approaches to combat drug resistant bacterial infections, second-generation programs have been initiated and show early promise to significantly improve the clinical usefulness of currently available and future antibiotics against otherwise recalcitrant Gram-negative infections. It is also apparent that some changes in regulatory decision-making regarding resistance would be very helpful in order to facilitate approval of agents aiming to reverse resistance and prevent its further development.
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Affiliation(s)
- Olga Lomovskaya
- Mpex Pharmaceuticals Inc., 3030 Bunker Hill Street, San Diego, CA 92109, USA
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29
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Rose A, Schraegle SJ, Stahlberg EA, Meier I. Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control. BMC Evol Biol 2005; 5:66. [PMID: 16288662 PMCID: PMC1322226 DOI: 10.1186/1471-2148-5-66] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 11/16/2005] [Indexed: 11/16/2022] Open
Abstract
Background Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. Mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. Using the coiled-coil prediction program MultiCoil, we have previously identified all long coiled-coil proteins from the model plant Arabidopsis thaliana and have established a searchable Arabidopsis coiled-coil protein database. Results Here, we have identified all proteins with long coiled-coil domains from 21 additional fully sequenced genomes. Because regions predicted to form coiled-coils interfere with sequence homology determination, we have developed a sequence comparison and clustering strategy based on masking predicted coiled-coil domains. Comparing and grouping all long coiled-coil proteins from 22 genomes, the kingdom-specificity of coiled-coil protein families was determined. At the same time, a number of proteins with unknown function could be grouped with already characterized proteins from other organisms. Conclusion MultiCoil predicts proteins with extended coiled-coil domains (more than 250 amino acids) to be largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell.
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Affiliation(s)
- Annkatrin Rose
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
| | | | - Eric A Stahlberg
- Ohio Super Computer Center, 1224 Kinnear Road, Columbus, OH 43212, USA
| | - Iris Meier
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
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30
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Aires JR, Nikaido H. Aminoglycosides are captured from both periplasm and cytoplasm by the AcrD multidrug efflux transporter of Escherichia coli. J Bacteriol 2005; 187:1923-9. [PMID: 15743938 PMCID: PMC1064028 DOI: 10.1128/jb.187.6.1923-1929.2005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To understand better the mechanisms of resistance-nodulation-division (RND)-type multidrug efflux pumps, we examined the Escherichia coli AcrD pump, whose typical substrates, aminoglycosides, are not expected to diffuse spontaneously across the lipid bilayer. The hexahistidine-tagged AcrD protein was purified and reconstituted into unilamellar proteoliposomes. Its activity was measured by the proton flux accompanying substrate transport. When the interior of the proteoliposomes was acidified, the addition of aminoglycosides to the external medium stimulated proton efflux and the intravesicular accumulation of radiolabeled gentamicin, suggesting that aminoglycosides can be captured and transported from the external medium in this system (corresponding to cytosol). This activity required the presence of AcrA within the proteoliposomes. Interestingly, the increase in proton efflux also occurred when aminoglycosides were present only in the intravesicular space. This result suggested that AcrD can also capture aminoglycosides from the periplasm to extrude them into the medium in intact cells, acting as a "periplasmic vacuum cleaner."
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Affiliation(s)
- Julio Ramos Aires
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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31
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Tikhonova EB, Zgurskaya HI. AcrA, AcrB, and TolC of Escherichia coli Form a Stable Intermembrane Multidrug Efflux Complex. J Biol Chem 2004; 279:32116-24. [PMID: 15155734 DOI: 10.1074/jbc.m402230200] [Citation(s) in RCA: 209] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many transporters of Gram-negative bacteria involved in the extracellular secretion of proteins and the efflux of toxic molecules operate by forming intermembrane complexes. These complexes are proposed to span both inner and outer membranes and create a bridge across the periplasm. In this study, we analyzed interactions between the inner and outer membrane components of the tri-partite multidrug efflux pump AcrAB-TolC from Escherichia coli. We found that, once assembled, the intermembrane AcrAB-TolC complex is stable during the separation of the inner and outer membranes and subsequent purification. All three components of the complex co-purify when the affinity tag is attached to either of the proteins suggesting bi-partite interactions between AcrA, AcrB, and TolC. We show that antibiotics, the substrates of AcrAB-TolC, stabilize interactions within the complex. However, the formation of the AcrAB-TolC complex does not require an input of energy.
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Affiliation(s)
- Elena B Tikhonova
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, USA
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