1
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Yu Z, Shi X, Wang Z. Structures and Efflux Mechanisms of the AcrAB-TolC Pump. Subcell Biochem 2024; 104:1-16. [PMID: 38963480 DOI: 10.1007/978-3-031-58843-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The global emergence of multidrug resistance (MDR) in gram-negative bacteria has become a matter of worldwide concern. MDR in these pathogens is closely linked to the overexpression of certain efflux pumps, particularly the resistance-nodulation-cell division (RND) efflux pumps. Inhibition of these pumps presents an attractive and promising strategy to combat antibiotic resistance, as the efflux pump inhibitors can effectively restore the potency of existing antibiotics. AcrAB-TolC is one well-studied RND efflux pump, which transports a variety of substrates, therefore providing resistance to a broad spectrum of antibiotics. To develop effective pump inhibitors, a comprehensive understanding of the structural aspect of the AcrAB-TolC efflux pump is imperative. Previous studies on this pump's structure have been limited to individual components or in vitro determination of fully assembled pumps. Recent advancements in cellular cryo-electron tomography (cryo-ET) have provided novel insights into this pump's assembly and functional mechanism within its native cell membrane environment. Here, we present a summary of the structural data regarding the AcrAB-TolC efflux pump, shedding light on its assembly pathway and operational mechanism.
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Affiliation(s)
- Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Xiaodong Shi
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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2
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Rajapaksha P, Ojo I, Yang L, Pandeya A, Abeywansha T, Wei Y. Insight into the AcrAB-TolC Complex Assembly Process Learned from Competition Studies. Antibiotics (Basel) 2021; 10:antibiotics10070830. [PMID: 34356751 PMCID: PMC8300762 DOI: 10.3390/antibiotics10070830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
The RND family efflux pump AcrAB-TolC in E. coli and its homologs in other Gram-negative bacteria are major players in conferring multidrug resistance to the cells. While the structure of the pump complex has been elucidated with ever-increasing resolution through crystallography and Cryo-EM efforts, the dynamic assembly process remains poorly understood. Here, we tested the effect of overexpressing functionally defective pump components in wild type E. coli cells to probe the pump assembly process. Incorporation of a defective component is expected to reduce the efflux efficiency of the complex, leading to the so called "dominant negative" effect. Being one of the most intensively studied bacterial multidrug efflux pumps, many AcrA and AcrB mutations have been reported that disrupt efflux through different mechanisms. We examined five groups of AcrB and AcrA mutants, defective in different aspects of assembly and substrate efflux. We found that none of them demonstrated the expected dominant negative effect, even when expressed at concentrations many folds higher than their genomic counterpart. The assembly of the AcrAB-TolC complex appears to have a proof-read mechanism that effectively eliminated the formation of futile pump complex.
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3
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Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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4
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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5
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Zgurskaya HI, Walker JK, Parks JM, Rybenkov VV. Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors. Acc Chem Res 2021; 54:930-939. [PMID: 33539084 PMCID: PMC8208102 DOI: 10.1021/acs.accounts.0c00843] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antibiotics are miracle drugs that can cure infectious bacterial diseases. However, their utility is challenged by antibiotic-resistant bacteria emerging in clinics and straining modern medicine and our ways of life. Certain bacteria such as Gram-negative (Gram(-)) and Mycobacteriales species are intrinsically resistant to most clinical antibiotics and can further gain multidrug resistance through mutations and plasmid acquisition. These species stand out by the presence of an additional external lipidic membrane, the outer membrane (OM), that is composed of unique glycolipids. Although formidable, the OM is a passive permeability barrier that can reduce penetration of antibiotics but cannot affect intracellular steady-state concentrations of drugs. The two-membrane envelopes are further reinforced by active efflux transporters that expel antibiotics from cells against their concentration gradients. The major mechanism of antibiotic resistance in Gram(-) pathogens is the active efflux of drugs, which acts synergistically with the low permeability barrier of the OM and other mutational and plasmid-borne mechanisms of antibiotic resistance.The synergy between active efflux and slow uptake offers Gram(-) bacteria an impressive degree of protection from potentially harmful chemicals, but it is also their Achilles heel. Kinetic studies have revealed that even small changes in the efficiency of either of the two factors can have dramatic effects on drug penetration into the cell. In line with these expectations, two major approaches to overcome this antibiotic resistance mechanism are currently being explored: (1) facilitation of antibiotic penetration across the outer membranes and (2) avoidance and inhibition of clinically relevant multidrug efflux pumps. Herein we summarize the progress in the latter approach with a focus on efflux pumps from the resistance-nodulation-division (RND) superfamily. The ability to export various substrates across the OM at the expense of the proton-motive force acting on the inner membrane and the engagement of accessory proteins for their functions are the major mechanistic advantages of these pumps. Both the RND transporters and their accessory proteins are being targeted in the discovery of efflux pump inhibitors, which in combination with antibiotics can potentiate antibacterial activities. We discuss intriguing relationships between substrates and inhibitors of efflux pumps, as these two types of ligands face similar barriers and binding sites in the transporters and accessory proteins and both types of activities often occur with the same chemical scaffold. Several distinct chemical classes of efflux inhibitors have been discovered that are as structurally diverse as the substrates of efflux pumps. Recent mechanistic insights, both empirical and computational, have led to the identification of features that distinguish OM permeators and efflux pump avoiders as well as efflux inhibitors from substrates. These findings suggest a path forward for optimizing the OM permeation and efflux-inhibitory activities in antibiotics and other chemically diverse compounds.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - John K Walker
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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6
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Hazel AJ, Abdali N, Leus IV, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly. ACS Infect Dis 2019; 5:1926-1935. [PMID: 31517484 DOI: 10.1021/acsinfecdis.9b00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.
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Affiliation(s)
- Anthony J. Hazel
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
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7
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Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC. Nat Commun 2019; 10:2635. [PMID: 31201302 PMCID: PMC6570770 DOI: 10.1038/s41467-019-10512-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.
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Affiliation(s)
- Xiaodong Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James M Bell
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hans Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joanita Jakana
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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8
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Remenár M, Kamlárová A, Harichová J, Zámocký M, Ferianc P. The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia. Pol J Microbiol 2019; 67:191-201. [PMID: 30015457 PMCID: PMC7256691 DOI: 10.21307/pjm-2018-022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/18/2022] Open
Abstract
A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp) sequences tentatively assigned to CzcA family heavy metal efflux pump [YP_001899332] from Ralstonia picketii 12J with 99% similarity. In this study the bacterium MR-CH-I2 and its heavy-metal resistance determinant were more precisely identified. This bacterial isolate was on the base of phylogenetic analysis of almost the whole (1,500 bp) 16S rDNA (16S rRNA) sequence, MR-CH-I2 [MF102046], and sequence for gyrB gene and its product respectively, MR-CH-I2-gyrB [MF134666], assigned to R. picketii 12J [CP001068] with 99 and 100% similarities, respectively. In addition, the whole nccA-like heavy-metal resistance gene sequence (3,192 bp), marked as MR-CH-I2-nccA [KR476581], was obtained and on the base of phylogenetic analysis its assignment was confirmed to MULTISPECIES: cation efflux system protein CzcA [WP_004635342] from Burkholderiaceae with 98% similarity. Furthermore, although the bacterium carried one high molecular plasmid of about 50 kb in size, nccA-like gene was not located on this plasmid. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.
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Affiliation(s)
- Matej Remenár
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Anna Kamlárová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Jana Harichová
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
| | - Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia.,Metalloprotein Research Group, Division of Biochemistry, Department of Chemistry, University of Natural Resources and Applied Life Sciences,Vienna,Austria
| | - Peter Ferianc
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology of the Slovak Academy of Sciences,Bratislava,Slovakia
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9
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In silico epitope identification of unique multidrug resistance proteins from Salmonella Typhi for vaccine development. Comput Biol Chem 2019; 78:74-80. [DOI: 10.1016/j.compbiolchem.2018.11.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/14/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
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10
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Baarda BI, Zielke RA, Jerse AE, Sikora AE. Lipid-Modified Azurin of Neisseria gonorrhoeae Is Not Surface Exposed and Does Not Interact With the Nitrite Reductase AniA. Front Microbiol 2018; 9:2915. [PMID: 30538694 PMCID: PMC6277709 DOI: 10.3389/fmicb.2018.02915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Lipid-modified cupredoxin azurin (Laz) is involved in electron transport in Neisseria and proposed to act as an electron donor to the surface-displayed nitrite reductase AniA. We identified Laz in Neisseria gonorrhoeae cell envelopes and naturally elaborated membrane vesicles in proteomic investigations focused on discovering new vaccine and therapeutic targets for this increasingly difficult to treat pathogen. Its surface exposure in N. meningitidis suggested Laz could be a vaccine candidate for N. gonorrhoeae. Here we characterized the localization, expression, and role of Laz within the gonococcal cell envelope and challenged the hypothesis that Laz and AniA interact. While we demonstrate that Laz indeed shows some good features of a vaccine antigen, such as stable expression, high conservation, and ability to elicit antibodies that cross-react with a diverse panel of Neisseria, it is not a surface-displayed lipoprotein in the gonococcus. This discovery eliminates Laz as a gonorrhea vaccine candidate, further highlighting the necessity of examining homologous protein localization between closely related species. Absence of Laz slightly altered cell envelope integrity but was not associated with growth defects in vitro, including during anoxia, implicating the presence of other electron pathways to AniA. To further dissect the implied AniA-Laz interaction, we utilized biolayer interferometry and optimized and executed chemical cross-linking coupled with immunoblotting to covalently link interacting protein partners in living gonococci. This method, applied for the first time in N. gonorrhoeae research to interrogate protein complexes, was validated by the appearance of the trimer form of AniA, as well as by increased formation of the β-barrel assembly machinery complex, in the presence of cross-linker. We conclude that Laz is not an electron donor to AniA based on their distinct subcellular localization, discordant expression during infection of the female mouse lower genital tract, and lack of interaction in vivo and in vitro.
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Affiliation(s)
- Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Ann E Jerse
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States.,Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
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11
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Horikawa T, Hung LW, Kim HB, Shaya D, Kim CY, Terwilliger TC, Yamashita E, Aoki M, Okada U, Murakami S. BpeB, a major resistance-nodulation-cell division transporter from Burkholderia cenocepacia: construct design, crystallization and preliminary structural analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:710-716. [PMID: 30387776 PMCID: PMC6213979 DOI: 10.1107/s2053230x18013547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that infects cystic fibrosis patients, causing pneumonia and septicemia. B. cenocepacia has intrinsic antibiotic resistance against monobactams, aminoglycosides, chloramphenicol and fluoroquinolones that is contributed by a homologue of BpeB, which is a member of the resistance-nodulation-cell division (RND)-type multidrug-efflux transporters. Here, the cloning, overexpression, purification, construct design for crystallization and preliminary X-ray diffraction analysis of this BpeB homologue from B. cenocepacia are reported. Two truncation variants were designed to remove possible disordered regions based on comparative sequence and structural analysis to salvage the wild-type protein, which failed to crystallize. The 17-residue carboxyl-terminal truncation yielded crystals that diffracted to 3.6 Å resolution. The efflux function measured using minimal inhibitory concentration assays indicated that the truncation decreased, but did not eliminate, the efflux activity of the transporter.
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Affiliation(s)
- Tomonari Horikawa
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Li-Wei Hung
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Heung-Bok Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Shaya
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chang-Yub Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas C. Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Maho Aoki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Ui Okada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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12
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Miladi H, Zmantar T, Kouidhi B, Al Qurashi YMA, Bakhrouf A, Chaabouni Y, Mahdouani K, Chaieb K. Synergistic effect of eugenol, carvacrol, thymol, p-cymene and γ-terpinene on inhibition of drug resistance and biofilm formation of oral bacteria. Microb Pathog 2017; 112:156-163. [DOI: 10.1016/j.micpath.2017.09.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 02/07/2023]
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13
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Miladi H, Zmantar T, Kouidhi B, Chaabouni Y, Mahdouani K, Bakhrouf A, Chaieb K. Use of carvacrol, thymol, and eugenol for biofilm eradication and resistance modifying susceptibility of Salmonella enterica serovar Typhimurium strains to nalidixic acid. Microb Pathog 2017; 104:56-63. [PMID: 28062292 DOI: 10.1016/j.micpath.2017.01.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
The Aims of the study was to evaluate the antibacterial susceptibility and the biofilm eradication of three natural compounds carvacrol (CAR), thymol (TH) and eugenol (EUG), alone or in combination with nalidixic acid (NA) against twelve Salmonella Typhimurium strains. The minimum inhibitory concentration (MIC) and the minimum biofilm eradication concentration (BEC50) of the tested compounds (CAR, TH and EUG) and their combinations with NA were evaluated. In order to assess whether these bacteria had active efflux pumps, ethidium bromide (EtBr) accumulation assays was achieved using spectrophotometric accumulation assays. Moreover, scanning electron microscopy was used to visualize the bacterial biofilm formation on stainless steel surfaces after exposed to NA, CAR, TH and EUG alone and in combination. TH was the most effective essential oil, with the lowest MICs values ranging from 32 to 128 μg/mL followed by EUG and CAR. In addition, the combination of NA with the different compounds enhances antibiotic susceptibility of the tested bacterial strains. These results were confirmed by EtBr accumulation assays. A pronounced effect in decreasing biofilm mass was also noticed. Moreover, SEM revealed that bacterial membrane was disrupted and a complete loss of membrane integrity was also evident. The combination of natural compounds with antibiotic enhances bacterial susceptibility to NA. This combination ameliorates eradication of biofilm formed by S. Typhimurium on polystyrene microtitre plates. Additionally, this synergy induces an alteration of the bacterial cell surface visualized by SEM.
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Affiliation(s)
- Hanene Miladi
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir University, Tunisia
| | - Tarek Zmantar
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir University, Tunisia
| | - Bochra Kouidhi
- College of Applied Medical Sciences, Medical Laboratory Department, Yanbu el Bahr, Taibah University, Al Madinah Al Monawarah, Saudi Arabia.
| | - Yassine Chaabouni
- Laboratory of Bacteriology and Molecular Biology, Hôspital of Ibn El Jazzar, Kairouan, Tunisia
| | - Kacem Mahdouani
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir University, Tunisia; Laboratory of Bacteriology and Molecular Biology, Hôspital of Ibn El Jazzar, Kairouan, Tunisia
| | - Amina Bakhrouf
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir University, Tunisia
| | - Kamel Chaieb
- College of Sciences, Biology Department, Yanbu el Bahr, Taibah University, Al Madinah Al Monawarah, Kingdom Saudi Arabia
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Puzari M, Chetia P. RND efflux pump mediated antibiotic resistance in Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa: a major issue worldwide. World J Microbiol Biotechnol 2017; 33:24. [PMID: 28044273 DOI: 10.1007/s11274-016-2190-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Abstract
Therapeutic failures against diseases due to resistant Gram-negative bacteria have become a major threat nowadays as confirmed by surveillance reports across the world. One of the methods of development of multidrug resistance in Escherichia coli and Pseudomonas aeruginosa is by means of RND efflux pumps. Inhibition of these pumps might help to combat the antibiotic resistance problem, for which the structure and regulation of the pumps have to be known. Moreover, judicious antibiotic use is needed to control the situation. This paper focuses on the issue of antibiotic resistance as well as the structure, regulation and inhibition of the efflux pumps present in Escherichia coli and Pseudomonas aeruginosa.
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Affiliation(s)
- Minakshi Puzari
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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15
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Zmantar T, Miladi H, Kouidhi B, Chaabouni Y, Ben Slama R, Bakhrouf A, Mahdouani K, Chaieb K. Use of juglone as antibacterial and potential efflux pump inhibitors in Staphylococcus aureus isolated from the oral cavity. Microb Pathog 2016; 101:44-49. [PMID: 27816681 DOI: 10.1016/j.micpath.2016.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
Abstract
In this study the minimal inhibitory concentration (MICs) of tetracycline (Tet), erythromycin (Ery) and benzalkonium chloride (BC) in absence and in presence of a sub-MIC of juglone (Jug) were determined. In addition, the Ethidium bromide (EtBr) efflux assay was performed to assess the effect of Jug on EtBr cells accumulation. Our results showed a selective antimicrobial activity of Jug against the tested strains. A synergistic effect of Jug, drugs (Tet and Ery) and disinfectant (BC) was noticed with a reduction rate varied from 2 to 16-fold. In addition, the efflux of EtBr was inhibited depending on the Jug concentration. In the presence of Jug, a decrease in loss of EtBr from bacteria was observed. The concentration inducing 50 % of EtBr efflux inhibition after 15 min was about 182 μg ml-1 for S. aureus ATCC 25923, 236 μg ml-1 for S. aureus B193 and 195 μg ml-1 for S. aureus B456. It appears from this study that Jug may be used as a natural source for resistance-modifying activity in same bacteria.
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Affiliation(s)
- Tarek Zmantar
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir 5000, Tunisia
| | - Hanene Miladi
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir 5000, Tunisia
| | - Bochra Kouidhi
- College of Applied Medical Sciences, Medical Laboratory Department, Yanbu el Bahr, Taibah University, Al Madinah Al Monawarah, Saudi Arabia.
| | - Yassine Chaabouni
- Laboratory of Bacteriology and Molecular Biology, Hôspital of Ibn El Jazzar, Kairouan, Tunisia
| | - Rihab Ben Slama
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir 5000, Tunisia
| | - Amina Bakhrouf
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir 5000, Tunisia
| | - Kacem Mahdouani
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, Rue Avicenne, Monastir 5000, Tunisia; Laboratory of Bacteriology and Molecular Biology, Hôspital of Ibn El Jazzar, Kairouan, Tunisia
| | - Kamel Chaieb
- College of Sciences, Biology Department, Yanbu el Bahr, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
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16
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Sandoval R, Oliver C, Valdivia S, Valenzuela K, Haro RE, Sánchez P, Olavarría VH, Valenzuela P, Avendaño-Herrera R, Romero A, Cárcamo JG, Figueroa JE, Yáñez AJ. Resistance-nodulation-division efflux pump acrAB is modulated by florfenicol and contributes to drug resistance in the fish pathogenPiscirickettsia salmonis. FEMS Microbiol Lett 2016; 363:fnw102. [DOI: 10.1093/femsle/fnw102] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 12/20/2022] Open
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17
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In vitro characterization and inhibition of the interaction between ciprofloxacin and berberine against multidrug-resistant Klebsiella pneumoniae. J Antibiot (Tokyo) 2016; 69:741-746. [PMID: 26932407 PMCID: PMC5399161 DOI: 10.1038/ja.2016.15] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 01/07/2016] [Accepted: 01/24/2016] [Indexed: 11/26/2022]
Abstract
Ciprofloxacin is a quinolone antibiotic used to treat Klebsiella pneumoniae infections in the clinic. Previous studies have demonstrated that berberine exhibits antibacterial activity and less acquired resistance related to efflux pumps. The multidrug efflux pump acrAB-tolC can be stimulated to expel as much toxic material as possible from the cells, but a detrimental effect can be produced owing to an overcrowded periplasm with excess expression products, which inhibits bacterial growth. In this study, the in vitro antibacterial activities of ciprofloxacin in combination with berberine were evaluated and compared with those of ciprofloxacin and berberine alone by evaluating the MIC, MBC and summation fractional IC against 20 clinical multidrug-resistant K. pneumoniae isolates, 1 quality control bacterium and 1 induced-resistance bacterium. Susceptibility tests showed that the MIC for the combination of berberine and ciprofloxacin was 1/2 that of the individual agents or less. Antimicrobial activities of 18.18% synergy and 77.27% additivity were found. Furthermore, synergism was verified through a time-kill assay, which suggested that the synergistic antibacterial effect of the two-drug combination may, to some extent, be related to the high expression of the acrAB-tolC and acrR multidrug efflux pumps. Indeed, the expression of these genes was increased >14-fold in the isolates affected by ciprofloxacin–berberine combination synergism.
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18
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An overview of bacterial efflux pumps and computational approaches to study efflux pump inhibitors. Future Med Chem 2016; 8:195-210. [DOI: 10.4155/fmc.15.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Micro-organisms express a wide range of transmembrane pumps known as multidrug efflux pumps that improve the micro-organism's ability to survive in severe environments and contribute to resistance against antibiotic and antimicrobial agents. There is significant interest in developing efflux inhibitors as an adjunct to treatment with current and next generation of antibiotics. A greater understanding of drug recognition and transport by multidrug efflux pumps is needed to develop clinically useful inhibitors, given the breadth of molecules that can be effluxed by these systems. We summarize some structural and functional data that could provide insights into the inhibition of transport mechanisms of these intricate molecular nanomachines with a focus on the advances in computational approaches.
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19
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Abstract
Two membranes enclose Gram-negative bacteria-an inner membrane consisting of phospholipid and an outer membrane having an asymmetric structure in which the inner leaflet contains phospholipid and the outer leaflet consists primarily of lipopolysaccharide. The impermeable nature of the outer membrane imposes a need for numerous outer membrane pores and transporters to ferry substances in and out of the cell. These outer membrane proteins have structures distinct from their inner membrane counterparts and most often function without any discernable energy source. In this chapter, we review the structures and functions of four classes of outer membrane protein: general and specific porins, specific transporters, TonB-dependent transporters, and export channels. While not an exhaustive list, these classes exemplify small-molecule transport across the outer membrane and illustrate the diversity of structures and functions found in Gram-negative bacteria.
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20
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Anes J, McCusker MP, Fanning S, Martins M. The ins and outs of RND efflux pumps in Escherichia coli. Front Microbiol 2015; 6:587. [PMID: 26113845 PMCID: PMC4462101 DOI: 10.3389/fmicb.2015.00587] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/28/2015] [Indexed: 11/13/2022] Open
Abstract
Infectious diseases remain one of the principal causes of morbidity and mortality in the world. Relevant authorities including the WHO and CDC have expressed serious concern regarding the continued increase in the development of multidrug resistance among bacteria. They have also reaffirmed the urgent need for investment in the discovery and development of new antibiotics and therapeutic approaches to treat multidrug resistant (MDR) bacteria. The extensive use of antimicrobial compounds in diverse environments, including farming and healthcare, has been identified as one of the main causes for the emergence of MDR bacteria. Induced selective pressure has led bacteria to develop new strategies of defense against these chemicals. Bacteria can accomplish this by several mechanisms, including enzymatic inactivation of the target compound; decreased cell permeability; target protection and/or overproduction; altered target site/enzyme and increased efflux due to over-expression of efflux pumps. Efflux pumps can be specific for a single substrate or can confer resistance to multiple antimicrobials by facilitating the extrusion of a broad range of compounds including antibiotics, heavy metals, biocides and others, from the bacterial cell. To overcome antimicrobial resistance caused by active efflux, efforts are required to better understand the fundamentals of drug efflux mechanisms. There is also a need to elucidate how these mechanisms are regulated and how they respond upon exposure to antimicrobials. Understanding these will allow the development of combined therapies using efflux inhibitors together with antibiotics to act on Gram-negative bacteria, such as the emerging globally disseminated MDR pathogen Escherichia coli ST131 (O25:H4). This review will summarize the current knowledge on resistance-nodulation-cell division efflux mechanisms in E. coli, a bacteria responsible for community and hospital-acquired infections, as well as foodborne outbreaks worldwide.
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Affiliation(s)
- João Anes
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Matthew P McCusker
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Marta Martins
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
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21
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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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22
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Ramos JL, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E, Gómez-García MR, Udaondo Z, Roca A. Mechanisms of solvent resistance mediated by interplay of cellular factors inPseudomonas putida. FEMS Microbiol Rev 2015; 39:555-66. [DOI: 10.1093/femsre/fuv006] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2015] [Indexed: 11/14/2022] Open
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23
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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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24
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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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25
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The in vitro interaction of CmeA with CmeC. CHINESE SCIENCE BULLETIN-CHINESE 2014. [DOI: 10.1007/s11434-014-0325-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Bianco MI, Jacobs M, Salinas SR, Salvay AG, Ielmini MV, Ielpi L. Biophysical characterization of the outer membrane polysaccharide export protein and the polysaccharide co-polymerase protein from Xanthomonas campestris. Protein Expr Purif 2014; 101:42-53. [PMID: 24927643 DOI: 10.1016/j.pep.2014.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/26/2014] [Accepted: 06/01/2014] [Indexed: 11/18/2022]
Abstract
This study investigated the structural and biophysical characteristics of GumB and GumC, two Xanthomonas campestris membrane proteins that are involved in xanthan biosynthesis. Xanthan is an exopolysaccharide that is thought to be a virulence factor that contributes to bacterial in planta growth. It also is one of the most important industrial biopolymers. The first steps of xanthan biosynthesis are well understood, but the polymerization and export mechanisms remain unclear. For this reason, the key proteins must be characterized to better understand these processes. Here we characterized, by biochemical and biophysical techniques, GumB, the outer membrane polysaccharide export protein, and GumC, the polysaccharide co-polymerase protein of the xanthan biosynthesis system. Our results suggested that recombinant GumB is a tetrameric protein in solution. On the other hand, we observed that both native and recombinant GumC present oligomeric conformation consistent with dimers and higher-order oligomers. The transmembrane segments of GumC are required for GumC expression and/or stability. These initial results provide a starting point for additional studies that will clarify the roles of GumB and GumC in the xanthan polymerization and export processes and further elucidate their functions and mechanisms of action.
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Affiliation(s)
- M I Bianco
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET (C1405BWE) Ciudad de Buenos Aires, Argentina
| | - M Jacobs
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET (C1405BWE) Ciudad de Buenos Aires, Argentina
| | - S R Salinas
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET (C1405BWE) Ciudad de Buenos Aires, Argentina
| | - A G Salvay
- Institute of Physics of Liquids and Biological Systems, Universidad Nacional de La Plata, La Plata (B1900BTE) Buenos Aires, Argentina; Department of Science and Technology, Universidad Nacional de Quilmes, Bernal (B1876BXD) Buenos Aires, Argentina
| | - M V Ielmini
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET (C1405BWE) Ciudad de Buenos Aires, Argentina
| | - L Ielpi
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET (C1405BWE) Ciudad de Buenos Aires, Argentina.
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27
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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: 443] [Impact Index Per Article: 44.3] [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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28
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Laehnemann D, Peña-Miller R, Rosenstiel P, Beardmore R, Jansen G, Schulenburg H. Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification. Genome Biol Evol 2014; 6:1287-301. [PMID: 24850796 PMCID: PMC4079197 DOI: 10.1093/gbe/evu106] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination. In particular, higher dosage of such antibiotic combinations coincided with higher copy number of the sequence region. The amplification appears to be evolutionarily costly, because amplification levels rapidly dropped after removal of the drugs. Our results suggest that amplification is a scalable process, as copy number rapidly changes in response to the selective pressure encountered. Moreover, repeated patterns of convergent evolution were found across the experimentally evolved bacterial populations, including those with lower antibiotic selection intensities. Intriguingly, convergent evolution was identified on different organizational levels, ranging from the above sequence amplification, high variant frequencies in specific genes, prevalence of individual nonsynonymous mutations to the unusual repeated occurrence of a particular synonymous mutation in Glycine codons. We conclude that constrained evolutionary trajectories underlie rapid adaptation to antibiotics. Of the identified genomic changes, sequence amplification seems to represent the most potent, albeit costly genomic response mechanism to high antibiotic stress.
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Affiliation(s)
- David Laehnemann
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Rafael Peña-Miller
- Biosciences, Geoffrey Pope Building, University of Exeter, United KingdomDepartment of Zoology, University of Oxford, United Kingdom
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, Germany
| | - Robert Beardmore
- Biosciences, Geoffrey Pope Building, University of Exeter, United Kingdom
| | - Gunther Jansen
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
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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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Bai J, Bhagavathi R, Tran P, Muzzarelli K, Wang D, Fralick JA. Evidence that the C-terminal region is involved in the stability and functionality of OprM in E. coli. Microbiol Res 2013; 169:425-31. [PMID: 24140154 DOI: 10.1016/j.micres.2013.08.006] [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: 05/22/2013] [Revised: 08/16/2013] [Accepted: 08/27/2013] [Indexed: 01/17/2023]
Abstract
In order to understand the specificity of interactions between the components of multidrug-resistant (MDR) efflux pumps and how they are recruited/assembled, we analyzed the effect of C-terminal truncation, deletion, and peptide swapping on the stability and functionality of OprM in Escherichia coli. The efflux activity of OprM was not affected by removing up to 19 amino acid residues from the C-terminus, while depletion of more than 20 residues or disruption the ₄₆₃LGGG₄₆₆ motif diminished both the stability and activity of OprM. The replacement of the OprM C-terminus 23 residues with the corresponding part of TolC or VceC did not affect the stability and the functionality of OprM. Therefore, it is confirmed that the C-terminal ₄₆₃LGGG₄₆₆ motif is one of the crucial components for the stability of OprM and for the functionality of the OprM-VceAB chimeric pump in E.coli. The results also indicate that one residue substitution on the hairpin domain of the membrane fusion protein (MFP) VceA could suppress the null like mutations on the C-terminal modified OprM. This finding will be the direct genetic evidence that the C-terminal domain of outer efflux protein (OEP) is involved in the functional assembly of OEP-MFP.
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Affiliation(s)
- Jiangping Bai
- Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China; Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79410, USA.
| | - Ramasubramanian Bhagavathi
- Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79410, USA
| | - Phat Tran
- Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79410, USA
| | | | - Di Wang
- Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Key Lab of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China; Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79410, USA
| | - Joe A Fralick
- Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79410, USA
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31
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Ucisik MN, Chakravorty DK, Merz KM. Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry 2013; 52:6911-23. [PMID: 23988152 DOI: 10.1021/bi400606b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CusCFBA is one of the metal efflux systems in Escherichia coli that is highly specific for its substrates, Cu(I) and Ag(I). It serves to protect the bacteria in environments that have lethal concentrations of these metals. The membrane fusion protein CusB is the periplasmic piece of CusCFBA, which has not been fully characterized by crystallography because of its extremely disordered N-terminal region. This region has both structural and functional importance because it has been experimentally proven to transfer the metal by itself from the metallochaperone CusF and to induce a structural change in the rest of CusB to increase Cu(I)/Ag(I) resistance. Understanding metal uptake from the periplasm is critical to gain insight into the mechanism of the whole CusCFBA pump, which makes resolving a structure for the N-terminal region necessary because it contains the metal binding site. We ran extensive molecular dynamics simulations to reveal the structural and dynamic properties of both the apo and Cu(I)-bound versions of the CusB N-terminal region. In contrast to its functional companion CusF, Cu(I) binding to the N-terminus of CusB causes only a slight, local stabilization around the metal site. The trajectories were analyzed in detail, revealing extensive structural disorder in both the apo and holo forms of the protein. CusB was further analyzed by breaking the protein up into three subdomains according to the extent of the observed disorder: the N- and C-terminal tails, the central beta strand motif, and the M21-M36 loop connecting the two metal-coordinating methionine residues. Most of the observed disorder was traced back to the tail regions, leading us to hypothesize that the latter two subdomains (residues 13-45) may form a functionally competent metal-binding domain because the tail regions appear to play no role in metal binding.
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Affiliation(s)
- Melek N Ucisik
- Department of Chemistry and Quantum Theory Project, University of Florida , 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, United States
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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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33
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Elkins CA, Beenken KE. Modeling the Tripartite Drug Efflux Pump Archetype: Structural and Functional Studies of the Macromolecular Constituents Reveal More Than Their Names Imply. J Chemother 2013; 17:581-92. [PMID: 16433187 DOI: 10.1179/joc.2005.17.6.581] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
It is a remarkable age in molecular biology when one can argue that our current understanding of a process is influenced as much by structural studies as it is by genetic and physiological manipulations. This statement is particularly poignant with membrane proteins for which structural knowledge has been long impeded by the inability to easily obtain crystal structures in a lipid matrix. Thus, several high-resolution structures of the components comprising tripartite multidrug efflux pumps from Escherichia coli and Pseudomonas aeruginosa are now available and were received with much acclaim over ever-evolving crystal structures of soluble, aqueous proteins. These structures, in conjunction with functional mutagenesis studies, have provided insight into substrate capture and binding domains and redefined the potential interactions between individual pump constituents. However, correct assembly of the components is still a matter of debate as is the functional contribution of each to the translocation of drug substrates over long distances spanning the Gram-negative cell envelope.
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Affiliation(s)
- C A Elkins
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079-9502, USA.
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Yao XQ, Kimura N, Murakami S, Takada S. Drug uptake pathways of multidrug transporter AcrB studied by molecular simulations and site-directed mutagenesis experiments. J Am Chem Soc 2013; 135:7474-85. [PMID: 23627437 DOI: 10.1021/ja310548h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Multidrug resistance has been a critical issue in current chemotherapy. In Escherichia coli , a major efflux pump responsible for the multidrug resistance contains a transporter AcrB. Crystallographic studies and mutational assays of AcrB provided much of structural and overall functional insights, which led to the functionally rotating mechanism. However, the drug uptake pathways are somewhat controversial because at least two possible pathways, the vestibule and the cleft paths, were suggested. Here, combining molecular simulations and site-directed mutagenesis experiments, we addressed the uptake mechanism finding that the drug uptake pathways can be significantly different depending on the properties of drugs. First, in the computational free energy analysis of drug movements along AcrB tunnels, we found a ligand-dependent drug uptake mechanism. With the same molecular sizes, drugs that are both strongly hydrophobic and lipophilic were preferentially taken in via the vestibule path, while other drugs favored the cleft path. Second, direct simulations realized totally about 3500 events of drug uptake by AcrB for a broad range of drug property. These simulations confirmed the ligand-dependent drug uptake and further suggested that a smaller drug favors the vestibule path, while a larger one is taken in via the cleft path. Moreover, the direct simulations identified an alternative uptake path which is not visible in the crystal structure. Third, site-directed mutagenesis of AcrB in E. coli verified that mutations of residues located along the newly identified path significantly reduced the efflux efficiency, supporting its relevance in in vivo function.
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Affiliation(s)
- Xin-Qiu Yao
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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35
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Deng W, Li C, Xie J. The underling mechanism of bacterial TetR/AcrR family transcriptional repressors. Cell Signal 2013; 25:1608-13. [PMID: 23602932 DOI: 10.1016/j.cellsig.2013.04.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 03/31/2013] [Accepted: 04/02/2013] [Indexed: 11/27/2022]
Abstract
Bacteria transcriptional regulators are classified by their functional and sequence similarities. Member of the TetR/AcrR family is two-domain proteins including an N-terminal HTH DNA-binding motif and a C-terminal ligand recognition domain. The C-terminal ligand recognition domain can recognize the very same compounds as their target transporters transferred. TetRs act as chemical sensors to monitor both the cellular environmental dynamics and their regulated genes underlying many events, such as antibiotics production, osmotic stress, efflux pumps, multidrug resistance, metabolic modulation, and pathogenesis. Compounds targeting Mycobacterium tuberculosis ethR represent promising novel antibiotic potentiater. TetR-mediated multidrug efflux pumps regulation might be good target candidate for the discovery of better new antibiotics against drug resistance.
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Affiliation(s)
- Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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36
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Mealman TD, Zhou M, Affandi T, Chacón KN, Aranguren ME, Blackburn NJ, Wysocki VH, McEvoy MM. N-terminal region of CusB is sufficient for metal binding and metal transfer with the metallochaperone CusF. Biochemistry 2012; 51:6767-75. [PMID: 22812620 DOI: 10.1021/bi300596a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Gram-negative bacteria, such as Escherichia coli, utilize efflux resistance systems in order to expel toxins from their cells. Heavy-metal resistance is mediated by resistance nodulation cell division (RND)-based efflux pumps composed of a tripartite complex that includes an RND-transporter, an outer-membrane factor (OMF), and a membrane fusion protein (MFP) that spans the periplasmic space. MFPs are necessary for complex assembly and have been hypothesized to play an active role in substrate efflux. Crystal structures of MFPs are available, however incomplete, as large portions of the apparently disordered N- and C-termini are unresolved. Such is the case for CusB, the MFP of the E. coli Cu(I)/Ag(I) efflux pump CusCFBA. In this work, we have investigated the structure and function of the N-terminal region of CusB, which includes the metal-binding site and is missing from previously determined crystal structures. Results from mass spectrometry and X-ray absorption spectroscopy show that the isolated N-terminal 61 residues (CusB-NT) bind metal in a 1:1 stoichiometry with a coordination site composed of M21, M36, and M38, consistent with full-length CusB. NMR spectra show that CusB-NT is mostly disordered in the apo state; however, some slight structure is adopted upon metal binding. Much of the intact protein's function is maintained in this fragment as CusB-NT binds metal in vivo and in vitro, and metal is transferred between the metallochaperone CusF and CusB-NT in vitro. Functional analysis in vivo shows that full-length CusB is necessary in an intact polypeptide for full metal resistance, though CusB-NT alone can contribute partial metal resistance. These findings reinforce the theory that the role of CusB is not only to bind metal but also to play an active role in efflux.
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Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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37
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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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38
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Fischer N, Kandt C. Three ways in, one way out: water dynamics in the trans-membrane domains of the inner membrane translocase AcrB. Proteins 2011; 79:2871-85. [PMID: 21905112 DOI: 10.1002/prot.23122] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 06/03/2011] [Accepted: 07/10/2011] [Indexed: 01/21/2023]
Abstract
Powered by proton-motive force, the inner membrane translocase AcrB is the engine of the AcrAB-TolC efflux pump in Escherichia coli. As proton conduction in proteins occurs along hydrogen-bonded networks of polar residues and water molecules, knowledge of the protein-internal water distribution and water-interacting residues allows drawing conclusions to possible pathways of proton conduction. Here, we report a series of 6× 50 ns independent molecular dynamics simulations of asymmetric AcrB embedded in a phospholipid/water environment. Simulating each monomer in its proposed protonation state, we calculated for each trans-membrane domain the average water distribution, identified residues interacting with these waters and quantified each residue's frequency of water hydrogen bond contact. Combining this information we find three possible routes of proton transfer connecting a continuously hydrated region of known key residues in the TMD interior to bulk water by one cytoplasmic and up to three periplasm water channels in monomer B and A. We find that water access of the trans-membrane domains is regulated by four groups of residues in a combination of side chain re-orientations and shifts of trans-membrane helices. Our findings support a proton release event via Arg971 during the C intermediate or in the transition to A, and proton uptake occurring in the A or B state or during a so far unknown intermediate in between B and C where cytoplasmic water access is still possible. Our simulations suggest experimentally testable hypotheses, which have not been investigated so far.
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Affiliation(s)
- Nadine Fischer
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Center, University of Bonn, Bonn, Germany
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39
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Routh MD, Zalucki Y, Su CC, Zhang Q, Shafer WM, Yu EW. Efflux pumps of the resistance-nodulation-division family: a perspective of their structure, function, and regulation in gram-negative bacteria. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 77:109-46. [PMID: 21692368 DOI: 10.1002/9780470920541.ch3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Mathew D Routh
- Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Ames, Iowa, USA
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40
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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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41
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New insights into the Lpt machinery for lipopolysaccharide transport to the cell surface: LptA-LptC interaction and LptA stability as sensors of a properly assembled transenvelope complex. J Bacteriol 2010; 193:1042-53. [PMID: 21169485 DOI: 10.1128/jb.01037-10] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lipopolysaccharide (LPS) is a major glycolipid present in the outer membrane (OM) of Gram-negative bacteria. The peculiar permeability barrier of the OM is due to the presence of LPS at the outer leaflet of this membrane that prevents many toxic compounds from entering the cell. In Escherichia coli LPS synthesized inside the cell is first translocated over the inner membrane (IM) by the essential MsbA flippase; then, seven essential Lpt proteins located in the IM (LptBCDF), in the periplasm (LptA), and in the OM (LptDE) are responsible for LPS transport across the periplasmic space and its assembly at the cell surface. The Lpt proteins constitute a transenvelope complex spanning IM and OM that appears to operate as a single device. We show here that in vivo LptA and LptC physically interact, forming a stable complex and, based on the analysis of loss-of-function mutations in LptC, we suggest that the C-terminal region of LptC is implicated in LptA binding. Moreover, we show that defects in Lpt components of either IM or OM result in LptA degradation; thus, LptA abundance in the cell appears to be a marker of properly bridged IM and OM. Collectively, our data support the recently proposed transenvelope model for LPS transport.
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42
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Bai J, Mosley L, Fralick JA. Evidence that the C-terminus of OprM is involved in the assembly of the VceAB-OprM efflux pump. FEBS Lett 2010; 584:1493-7. [PMID: 20206171 DOI: 10.1016/j.febslet.2010.02.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/23/2010] [Accepted: 02/25/2010] [Indexed: 10/19/2022]
Abstract
Although the architecture of tripartite multiple drug resistance (MDR) efflux pumps of Gram-negative bacteria has been well characterized, the means by which the components recognize each other and assemble into a functional pump remains obscure. In this study we present evidence that the C-terminal domain of the Pseudomonas aeruginosa OprM and the alpha-helical hairpin domain of Vibrio cholerae VceA play an important role in the recognition/specificity/recruitment step in the assembly of a functional, VceAB-OprM chimeric efflux pump. To our knowledge, this is the first evidence directly linking the C-terminal domain of an outer membrane efflux protein to its recruitment during the assembly of a tripartite efflux pump.
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Affiliation(s)
- Jiangping Bai
- Department of Microbiology and Immunology, Texas Tech University Health Science Center, Lubbock, TX 79430, USA
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43
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Blair JMA, La Ragione RM, Woodward MJ, Piddock LJV. Periplasmic adaptor protein AcrA has a distinct role in the antibiotic resistance and virulence of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2009; 64:965-72. [PMID: 19744979 DOI: 10.1093/jac/dkp311] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES AcrA can function as the periplasmic adaptor protein (PAP) in several RND tripartite efflux pumps, of which AcrAB-TolC is considered the most important. This system confers innate multiple antibiotic resistance. Disruption of acrB or tolC impairs the ability of Salmonella Typhimurium to colonize and persist in the host. The aim of this study was to investigate the role of AcrA alone in multidrug resistance and pathogenicity. METHODS The acrA gene was inactivated in Salmonella Typhimurium SL1344 by insertion of the aph gene and this mutant complemented with pWKS30acrA. The antimicrobial susceptibility of the mutant to six antibiotics as well as various dyes and detergents was determined. In addition, efflux activity was quantified. The ability of the mutant to adhere to, and invade, tissue culture cells in vitro was measured. RESULTS Following disruption of acrA, RT-PCR and western blotting confirmed that acrB/AcrB was still expressed when acrA was disrupted. The acrA mutant was hypersusceptible to antibiotics, dyes and detergents. In some cases, lower MICs were seen than for the acrB or tolC mutants. Efflux of the fluorescent dye Hoechst H33342 was less than in wild-type following disruption of acrA. acrA was also required for adherence to, and invasion of, tissue culture cells. CONCLUSIONS Inactivation of acrA conferred a phenotype distinct to that of acrB::aph and tolC::aph. These data indicate a role for AcrA distinct to that of other protein partners in both efflux of substrates and virulence.
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Affiliation(s)
- Jessica M A Blair
- School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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44
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Yoshihara E, Eda S, Kaitou S. Functional interaction sites of OprM with MexAB in the Pseudomonas aeruginosa multidrug efflux pump. FEMS Microbiol Lett 2009; 299:200-4. [PMID: 19709308 DOI: 10.1111/j.1574-6968.2009.01752.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Subunit-swapping between Pseudomonas aeruginosa MexAB-OprM and MexEF-OprN efflux pumps has shown that OprM can interact with MexEF to produce a functional efflux pump, but that OprN cannot functionally interact with MexAB. Taking advantage of this subunit selectivity, we carried out experiments using chimeric proteins composed of OprM and OprN to determine which regions of OprM are necessary for functional interaction with MexAB. We constructed two types of chimeric proteins: one with the N-terminal half of OprM and the C-terminal half of OprN (OprMN), and the second with these halves reversed (OprNM). Introduction of either of the chimeric protein genes into a mutant expressing MexEF alone restored the functionality of the efflux pump. However, expression of OprMN or OprNM in the presence of MexAB did not restore the pump functionality, indicating that the both the N- and C-terminal halves of OprM are necessary for a functional interaction with MexAB.
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Affiliation(s)
- Eisaku Yoshihara
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan.
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45
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Abstract
Large amounts of antibiotics used for human therapy, as well as for farm animals and even for fish in aquaculture, resulted in the selection of pathogenic bacteria resistant to multiple drugs. Multidrug resistance in bacteria may be generated by one of two mechanisms. First, these bacteria may accumulate multiple genes, each coding for resistance to a single drug, within a single cell. This accumulation occurs typically on resistance (R) plasmids. Second, multidrug resistance may also occur by the increased expression of genes that code for multidrug efflux pumps, extruding a wide range of drugs. This review discusses our current knowledge on the molecular mechanisms involved in both types of resistance.
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Affiliation(s)
- Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
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46
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Lim S, Roongsawang N, Washio K, Morikawa M. Flexible exportation mechanisms of arthrofactin inPseudomonassp. MIS38. J Appl Microbiol 2009; 107:157-66. [DOI: 10.1111/j.1365-2672.2009.04189.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Schulz R, Kleinekathöfer U. Transitions between closed and open conformations of TolC: the effects of ions in simulations. Biophys J 2009; 96:3116-25. [PMID: 19383457 DOI: 10.1016/j.bpj.2009.01.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 01/06/2009] [Accepted: 01/14/2009] [Indexed: 11/19/2022] Open
Abstract
Bacteria, such as Escherichia coli, use multidrug efflux pumps to export toxic substrates through their cell membranes. Upon formation of an efflux pump, the aperture of its outer membrane protein TolC opens and thereby enables the extrusion of substrate molecules. The specialty of TolC is its ability to dock to different transporters, making it a highly versatile export protein. Within this study, the transition between two conformations of TolC that are both available as crystal structures was investigated using all-atom molecular dynamics simulations. To create a partially open conformation from a closed one, the stability of the periplasmic aperture was weakened by a double point mutation at the constricting ring, which removes some salt bridges and hydrogen bonds. These mutants, which showed partial opening in previous experiments, did not spontaneously open during a 20-ns equilibration at physiological values of the KCl solution. Detailed analysis of the constricting ring revealed that the cations of the solvent were able to constitute ionic bonds in place of the removed salt bridges, which inhibited the opening of the aperture in simulations. To remove the ions from these binding positions within the available simulation time, an extra force was applied onto the ions. To keep the effect of this additional force rather flexible, it was applied in form of an artificial external electric field perpendicular to the membrane. Depending on the field direction and the ion concentration, these simulations led to a partial opening. In experiments, this energy barrier for the ions can be overcome by thermal fluctuations on a longer timescale.
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Routh MD, Su CC, Zhang Q, Yu EW. Structures of AcrR and CmeR: insight into the mechanisms of transcriptional repression and multi-drug recognition in the TetR family of regulators. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1794:844-51. [PMID: 19130905 PMCID: PMC2729549 DOI: 10.1016/j.bbapap.2008.12.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 11/26/2008] [Accepted: 12/01/2008] [Indexed: 11/27/2022]
Abstract
The transcriptional regulators of the TetR family act as chemical sensors to monitor the cellular environment in many bacterial species. To perform this function, members of the TetR family harbor a diverse ligand-binding domain capable of recognizing the same series of compounds as the transporters they regulate. Many of the regulators can be induced by a wide array of structurally unrelated compounds. Binding of these structurally unrelated ligands to the regulator results in a conformational change that is transmitted to the DNA-binding region, causing the repressor to lose its DNA-binding capacity and allowing for the initiation of transcription. The multi-drug binding proteins AcrR of Escherichia coli and CmeR from Campylobacter jejuni are members of the TetR family of transcriptional repressors that regulate the expression of the multidrug resistant efflux pumps AcrAB and CmeABC, respectively. To gain insights into the mechanisms of transcriptional regulation and how multiple ligands induce the same physiological response, we determined the crystal structures of the AcrR and CmeR regulatory proteins. In this review, we will summarize the new findings with AcrR and CmeR, and discuss the novel features of these two proteins in comparison with other regulators in the TetR family.
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Affiliation(s)
- Mathew D. Routh
- Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, IA 50011, USA
| | - Chih-Chia Su
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Edward W. Yu
- Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, IA 50011, USA
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA
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49
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Misra R, Bavro VN. Assembly and transport mechanism of tripartite drug efflux systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:817-25. [PMID: 19289182 DOI: 10.1016/j.bbapap.2009.02.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Revised: 02/21/2009] [Accepted: 02/26/2009] [Indexed: 12/30/2022]
Abstract
Multidrug efflux (MDR) pumps remove a variety of compounds from the cell into the external environment. There are five different classes of MDR pumps in bacteria, and quite often a single bacterial species expresses multiple classes of pumps. Although under normal circumstances MDR pumps confer low-level intrinsic resistance to drugs, the presence of drugs and mutations in regulatory genes lead to high level expression of MDR pumps that can pose problems with therapeutic treatments. This review focuses on the resistance nodulation cell division (RND)-class of MDR pumps that assemble from three proteins. Significant recent advancement in structural aspects of the three pump components has shed new light on the mechanism by which the tripartite efflux pumps extrude drugs. This new information will be critical in developing inhibitors against MDR pumps to improve the potency of prescribed drugs.
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Affiliation(s)
- Rajeev Misra
- Faculty of Cellular and Molecular Biosciences, School of Life Sciences, Arizona State University, Tempe, AZ 85285-4501, USA.
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50
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Yum S, Xu Y, Piao S, Sim SH, Kim HM, Jo WS, Kim KJ, Kweon HS, Jeong MH, Jeon H, Lee K, Ha NC. Crystal structure of the periplasmic component of a tripartite macrolide-specific efflux pump. J Mol Biol 2009; 387:1286-97. [PMID: 19254725 DOI: 10.1016/j.jmb.2009.02.048] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 02/17/2009] [Accepted: 02/18/2009] [Indexed: 11/24/2022]
Abstract
In Gram-negative bacteria, type I protein secretion systems and tripartite drug efflux pumps have a periplasmic membrane fusion protein (MFP) as an essential component. MFPs bridge the outer membrane factor and an inner membrane transporter, although the oligomeric state of MFPs remains unclear. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance-nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli. MacA is the periplasmic MFP in the MacAB-TolC pump, where MacB was characterized as a macrolide-specific ATP-binding-cassette-type efflux transporter. Here, we report the crystal structure of E. coli MacA and the experimentally phased map of Actinobacillus actinomycetemcomitans MacA, which reveal a domain orientation of MacA different from that of AcrA. Notably, a hexameric assembly of MacA was found in both crystals, exhibiting a funnel-like structure with a central channel and a conical mouth. The hexameric MacA assembly was further confirmed by electron microscopy and functional studies in vitro and in vivo. The hexameric structure of MacA provides insight into the oligomeric state in the functional complex of the drug efflux pump and type I secretion system.
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Affiliation(s)
- Soohwan Yum
- College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 609-735, Korea
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