1
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Novischi SYP, Karoly-Lakatos A, Chok K, Bonifer C, Becker-Baldus J, Glaubitz C. Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR. Commun Biol 2024; 7:43. [PMID: 38182790 PMCID: PMC10770068 DOI: 10.1038/s42003-023-05617-0] [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: 06/11/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
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Affiliation(s)
- S Y Phoebe Novischi
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Andrea Karoly-Lakatos
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Kerby Chok
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Christian Bonifer
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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2
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Bombelli A, Araya-Cloutier C, Boeren S, Vincken JP, Abee T, den Besten HMW. Effects of the antimicrobial glabridin on membrane integrity and stress response activation in Listeria monocytogenes. Food Res Int 2024; 175:113687. [PMID: 38128979 DOI: 10.1016/j.foodres.2023.113687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
Glabridin is a prenylated isoflavan which can be extracted from liquorice roots and has shown antimicrobial activity against foodborne pathogens and spoilage microorganisms. However, its application may be hindered due to limited information about its mode of action. In this study, we aimed to investigate the mode of action of glabridin using a combined phenotypic and proteomic approach on Listeria monocytogenes. Fluorescence and transmission electron microscopy of cells exposed to glabridin showed membrane permeabilization upon treatment with lethal concentrations of glabridin. Comparative proteomics analysis of control cells and cells exposed to sub-lethal concentrations of glabridin showed upregulation of proteins related to the two-component systems LiaSR and VirRS, confirming cell envelope damage during glabridin treatment. Additional upregulation of SigmaB regulon members signified activation of the general stress response in L. monocytogenes during this treatment. In line with the observed upregulation of cell envelope and general stress response proteins, sub-lethal treatment of glabridin induced (cross)protection against lethal heat and low pH stress and against antimicrobials such as nisin and glabridin itself. Overall, this study sheds light on the mode of action of glabridin and activation of the main stress responses to this antimicrobial isoflavan and highlights possible implications of its use as a naturally derived antimicrobial compound.
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Affiliation(s)
- Alberto Bombelli
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands; Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Jean-Paul Vincken
- Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Heidy M W den Besten
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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3
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Di Cesare M, Kaplan E, Rendon J, Gerbaud G, Valimehr S, Gobet A, Ngo TAT, Chaptal V, Falson P, Martinho M, Dorlet P, Hanssen E, Jault JM, Orelle C. The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains. J Biol Chem 2024; 300:105546. [PMID: 38072053 PMCID: PMC10821409 DOI: 10.1016/j.jbc.2023.105546] [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] [Received: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
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Affiliation(s)
- Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Elise Kaplan
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Julia Rendon
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | | | - Sepideh Valimehr
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Thu-Anh Thi Ngo
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | | | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
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4
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Conformational space exploration of cryo-EM structures by variability refinement. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184133. [PMID: 36738875 DOI: 10.1016/j.bbamem.2023.184133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. In order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.
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5
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Orelle C, Schmitt L, Jault JM. Waste or die: The price to pay to stay alive. Trends Microbiol 2023; 31:233-241. [PMID: 36192292 DOI: 10.1016/j.tim.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022]
Abstract
Microorganisms need to constantly exchange with their habitat to capture nutrients and expel toxic compounds. The ATP-binding cassette (ABC) transporters, a family of membrane proteins especially abundant in microorganisms, are at the core of these processes. Due to their extraordinary ability to expel structurally unrelated compounds, some transporters play a protective role in different organisms. Yet, the downside of these multidrug transporters is their entanglement in the resistance to therapeutic treatments. Intriguingly, some multidrug ABC transporters show a high level of ATPase activity, even in the absence of transported substrates. Although this basal ATPase activity might seem a waste, we surmise that this inherent capacity allows multidrug transporters to promptly translocate any bound drug before it penetrates into the cell.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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6
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Zwitterionic fluorinated detergents: From design to membrane protein applications. Biochimie 2023; 205:40-52. [PMID: 36375632 DOI: 10.1016/j.biochi.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
We report herein the synthesis of zwitterionic sulfobetaine (SB) and dimethylamine oxide (AO) detergents whose alkyl chain is made of either a perfluorohexyl (F6H3) or a perfluoropentyl (F5H5) group linked to a hydrogenated spacer arm. In aqueous solution, the critical micellar concentrations (CMCs) measured by surface tensiometry (SFT) and isothermal titration calorimetry (ITC) were found in the millimolar range (1.3-2.4 mM). The morphologies of the aggregates were evaluated by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM), demonstrating that the two perfluoropentyl derivatives formed small micelles less than 10 nm in diameter, whereas the perfluorohexyl derivatives formed larger and more heterogeneous micelles. The two SB detergents were able to solubilize synthetic lipid vesicles in a few hours; by contrast, the perfluoropentyl AO induced much faster solubilization, whereas the perfluorohexyl AO did not show any solubilization. All detergents were tested for their abilities to stabilize three membrane proteins, namely, bacteriorhodopsin (bR), the Bacillus subtilis ABC transporter BmrA, and the Streptococcus pneumoniae enzyme SpNOX. The SB detergents outperformed the AO derivatives as well as their hydrogenated analogs in stabilizing these proteins. Among the four new compounds, F5H5SB combines many desirable properties for membrane-protein study, as it is a powerful yet gentle detergent.
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7
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Gobet A, Zampieri V, Magnard S, Pebay-Peyroula E, Falson P, Chaptal V. The non-Newtonian behavior of detergents during concentration is increased by macromolecules, in trans, and results in their over-concentration. Biochimie 2023; 205:53-60. [PMID: 36087644 DOI: 10.1016/j.biochi.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022]
Abstract
Concentration of pure membrane proteins in detergent solution results in detergent concentration, albeit in unknown amounts. This phenomenon is observed in every lab working on membrane proteins, but has seldom been investigated. In this study, we explored the behavior of detergents mixed with membrane proteins during the step of sample concentration using centrifugal devices. We show that detergent over-concentrate with the presence of polymers, typically membrane or soluble proteins but also polysaccharides. The over-concentration of detergents depends on centrifugal force applied to the device. With the use of a specific dye, we observed the formation of a mesh on the concentrator device. Importantly, reducing the centrifugal speed allows to reduce the concentration of detergents when mixed to macromolecules, as tested with 3 different membrane proteins. All together, these results highlight the non-Newtonian behavior of detergents and provides a solid framework to investigators to improve drastically biochemical and structural studies of membrane proteins.
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Affiliation(s)
- Alexia Gobet
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France
| | - Veronica Zampieri
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Sandrine Magnard
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France
| | | | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France.
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS University lyon1, 7 passage du vercors, 69007, Lyon, France.
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8
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Rothia nasimurium as a Cause of Disease: First Isolation from Farmed Chickens. Vet Sci 2022; 9:vetsci9120653. [PMID: 36548814 PMCID: PMC9783258 DOI: 10.3390/vetsci9120653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rothia nasimurium is a facultative anaerobic Gram-positive coccus belonging to the Rothia genus of the Micrococcaceae family. While Rothia nasimurium is considered an opportunistic pathogen, to date few studies have investigated its pathogenicity and drug resistance. In January 2022, chickens at a poultry farm in China's Xinjiang Uygur Autonomous Region became ill and died. Treatment with commonly used Chinese medicines and antibiotics was ineffective, causing economic losses to the poultry farm. In order to determine the cause of the disease in these poultry farm chickens, the isolation and identification of the pathogens in the livers and other internal organs of the sick and dead chickens were performed. Further, animal pathogenicity tests, antibiotic susceptibility tests, and the detection of antibiotic resistance genes were carried out to analyze the pathogenicity and drug resistance of the identified pathogens. A Gram-positive coccus was isolated from the livers of the diseased chickens. The isolate was resistant to 17 antibiotics, including ciprofloxacin, chloramphenicol, and florfenicol, and was only sensitive to penicillin, amikacin, and tigecycline, to varying degrees. The results of the drug resistance gene testing indicated that the isolated bacterium carried 13 kinds of resistance genes. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, morphological observations, biochemical tests, and 16S rRNA gene sequence analysis were performed on the isolated bacterium, and it was determined that the isolated bacterial strain was Rothia nasimurium. The animal pathogenicity tests showed that the isolate caused feather loss and death in chicks; the clinical symptoms and necropsy lesions of the test chicks were consistent with those observed in the farmed chickens. A review of the literature revealed that, to date, there are no reports of infection with Rothia nasimurium in chickens. Thus, in this study, Rothia nasimurium was isolated from chickens for the first time and an investigation of the biological characteristics of the bacterium was carried out in order to provide a reference for the clinical treatment, prevention, and control of Rothia nasimurium infection.
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9
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Li Z, Wang J, Gu C, Guo Y, Wu S. Marine bacteria-mediated abiotic-biotic coupling degradation mechanism of ibuprofen. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128960. [PMID: 35472552 DOI: 10.1016/j.jhazmat.2022.128960] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 06/14/2023]
Abstract
Knowledge on the behavior and fate of pharmaceuticals and personal care products (PPCPs) is poorly explored in marine aphotic environment. In this study, the degradation mechanism of a typical PPCPs-ibuprofen (IBP) by a ubiquitous marine Pseudoalteromonas sp. was investigated based on transcriptome and key enzymes analysis. More importantly, a novel enzymatic-nonenzymatic coupling degradation mechanism was uncovered for the first time, namely, the degradation of IBP was firstly initiated by extracellular reactive oxygen species (ROS), then the intermediate (e.g.4-ethylresorcinol) was further degraded by intracellular enzymes. It was showed that biogenic •OH, O2•-and H2O2 were responsible for extracellular nonenzymatic degradation, in which IBP was degraded to 4-ethylresorcinol through hydrogenation, isobutyl moiety cleavage, oxidation and decarboxylation. 4-Hydroxyphenylpyruvate dioxygenase, homogentisate 1,2-dioxygenase, long-chain acyl-CoA synthetase, acetyl-CoA acyltransferase and enoyl-CoA hydratase were identified to be involved in intracellular degradation, leading 4-ethylresorcinol cracked and eventually mineralized. Ultimately, this novel degradation mechanism was demonstrated to be amino acids-driven through KEGG enrichment analysis and experimental data. Overall, our work uncovered a yet undiscovered abiotic-biotic coupling degradation mechanism in PPCPs biotransformation, thereby updating the conventional concept that contaminants transformation is solely accomplished by enzymes or non-enzymes, which can also provide new insights into PPCPs environmental behavior and fate.
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Affiliation(s)
- Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Chen Gu
- Power China Huadong Engineering Corporation Limited, Hangzhou 311122, China
| | - Yali Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuo Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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10
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Lacabanne D, Wiegand T, Di Cesare M, Orelle C, Ernst M, Jault JM, Meier BH, Böckmann A. Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA. J Am Chem Soc 2022; 144:12431-12442. [PMID: 35776907 PMCID: PMC9284561 DOI: 10.1021/jacs.2c04287] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The detailed mechanism
of ATP hydrolysis in ATP-binding cassette
(ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and
dynamics during the catalytic cycle by locking the multidrug ABC transporter
BmrA in prehydrolytic, transition, and posthydrolytic states, using
a combination of mutants and ATP analogues. The 31P spectra
reveal that ATP binds strongly in the prehydrolytic state to both
ATP-binding sites as inferred from the analysis of the nonhydrolytic
E504A mutant. In the transition state of wild-type BmrA, the symmetry
of the dimer is broken and only a single site is tightly bound to
ADP:Mg2+:vanadate, while the second site is more ‘open’
allowing exchange with the nucleotides in the solvent. In the posthydrolytic
state, weak binding, as characterized by chemical exchange with free
ADP and by asymmetric 31P–31P two-dimensional
(2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational
nonequivalence of the two nucleotide-binding sites in the transition
state. Our results show that following ATP binding, the symmetry of
the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step,
but is then recovered in the posthydrolytic ADP-bound state.
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Affiliation(s)
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
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11
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Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
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Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
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12
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Atas B, Aksoy CS, Avci FG, Sayar NA, Ulgen K, Ozkirimli E, Akbulut BS. Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis. Curr Microbiol 2022; 79:135. [PMID: 35303184 DOI: 10.1007/s00284-022-02823-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/21/2022] [Indexed: 11/26/2022]
Abstract
The essential oil carvacrol from oregano displays a wide range of biological activities among which is found the inhibition of efflux pumps. Thus, using carvacrol, the current work undertook the effort to potentiate the antimicrobial activity of berberine, a natural product with limited antimicrobial efficacy due to its efflux. Following the selection of concentrations for the combinatorial treatments, guided by checkerboard microtiter plate assay and growth experiments, ethidium bromide accumulation assay was used to find that 25 μg mL-1 carvacrol displayed a weak efflux pump inhibitor character in Bacillus subtilis. Scanning electron microscopy images and cellular material leakage assays showed that carvacrol at this concentration neither altered the morphology nor the permeability of the membrane alone but when combined with 75 μg mL-1 berberine. Among the efflux pumps of different families found in B. subtilis, except for BmrA and Mdr, the increase in the expressional changes was striking, with Blt displaying ~ 4500-fold increase in expression under the combination treatment. Overall, the findings demonstrated that carvacrol potentiated the effect of berberine; however, not only multiple pumps but also different targets may be responsible for the observed activity.
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Affiliation(s)
- Basak Atas
- Bioengineering Department, Marmara University, Kadikoy, 34722, Istanbul, Turkey
| | - Cemile Selin Aksoy
- Bioengineering Department, Marmara University, Kadikoy, 34722, Istanbul, Turkey
| | - Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Istanbul, Turkey
| | - Nihat Alpagu Sayar
- Bioengineering Department, Marmara University, Kadikoy, 34722, Istanbul, Turkey
| | - Kutlu Ulgen
- Chemical Engineering Department, Bogazici University, Bebek, 34342, Istanbul, Turkey
| | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342, Istanbul, Turkey
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13
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Marín-Miret J, González-Serrano F, Rosas T, Baixeras J, Latorre A, Pérez-Cobas AE, Moya A. Temporal variations shape the gut microbiome ecology of the moth Brithys crini. Environ Microbiol 2022; 24:3939-3953. [PMID: 35243736 DOI: 10.1111/1462-2920.15952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jesús Marín-Miret
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain
| | - Francisco González-Serrano
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Tania Rosas
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Joaquín Baixeras
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain.,Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain.,Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain.,Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain.,Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), Madrid, Spain
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14
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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15
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Garcia ÍR, de Oliveira Garcia FA, Pereira PS, Coutinho HDM, Siyadatpanah A, Norouzi R, Wilairatana P, de Lourdes Pereira M, Nissapatorn V, Tintino SR, Rodrigues FFG. Microbial resistance: The role of efflux pump superfamilies and their respective substrates. Life Sci 2022; 295:120391. [PMID: 35149116 DOI: 10.1016/j.lfs.2022.120391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 12/24/2022]
Abstract
The microorganism resistance to antibiotics has become one of the most worrying issues for science due to the difficulties related to clinical treatment and the rapid spread of diseases. Efflux pumps are classified into six groups of carrier proteins that are part of the different types of mechanisms that contribute to resistance in microorganisms, allowing their survival. The present study aimed to carry out a bibliographic review on the superfamilies of carriers in order to understand their compositions, expressions, substrates, and role in intrinsic resistance. At first, a search for manuscripts was carried out in the databases Medline, Pubmed, ScienceDirect, and Scielo, using as descriptors: efflux pump, expression, pump inhibitors and efflux superfamily. For article selection, two criteria were taken into account: for inclusion, those published between 2000 and 2020, including textbooks, and for exclusion, duplicates and academic collections. In this research, 139,615 published articles were obtained, with 312 selected articles and 7 book chapters that best met the aim. From the comprehensive analysis, it was possible to consider that the chromosomes and genetic elements can contain genes encoding efflux pumps and are responsible for multidrug resistance. Even though this is a well-explored topic in the scientific community, understanding the behavior of antibiotics as substrates that increase the expression of pump-encoding genes has challenged medicine. This review study succinctly summarizes the most relevant features of these systems, as well as their contribution to multidrug resistance.
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Affiliation(s)
| | | | | | | | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials & Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences and Research Excellence Center for Innovation and Health, Walailak University, Thailand
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16
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 DOI: 10.1101/2021.03.12.435132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
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17
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 PMCID: PMC8791611 DOI: 10.1126/sciadv.abg9215] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Corresponding author.
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18
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Di Cesare M, Diagne AM, Bourgey B, Jault JM, Orelle C. Functional Overexpression of Membrane Proteins in E. coli: The Good, the Bad, and the Ugly. Methods Mol Biol 2022; 2507:41-58. [PMID: 35773576 DOI: 10.1007/978-1-0716-2368-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Overexpression of properly folded membrane proteins is a mandatory step for their functional and structural characterization. One of the most used expression systems for the production of proteins is Escherichia coli. Many advantageous strains combined with T7 expression systems have been developed over the years. Recently, we showed that the choice of the strain is critical for the functionality of membrane proteins, even when the proteins are successfully incorporated in the membrane (Mathieu et al. Sci Rep. 2019; 9(1):2654). Notably, the amount and/or activity of the T7-RNA polymerase, which drives the transcription of the genes of interest, may indirectly affect the folding and functionality of overexpressed membrane proteins. Moreover, we reported a general trend in which mild detergents mainly extract the population of active membrane proteins, whereas a harsher detergent like Fos-choline 12 could solubilize them irrespectively of their functionality. Based on these observations, we provide some guidelines to optimize the quality of membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Benjamin Bourgey
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
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19
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Gobet A, Jaxel C, Magnard S, Garrigos M, Orlowski S, Jamin N, Falson P, Chaptal V. Overexpression of the ABC Transporter BmrA Within Intracellular Caveolae in Escherichia coli. Methods Mol Biol 2022; 2507:79-89. [PMID: 35773578 DOI: 10.1007/978-1-0716-2368-8_5] [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: 06/15/2023]
Abstract
We describe here the overproduction and oriented membrane insertion of membrane protein inside intracellular vesicles named heterologous caveolae within E. coli. The method is described with BmrA, a multidrug efflux pump from Bacillus subtilis. BmrA is produced in these vesicles, thanks to the coexpression with the canine caveolin-1β, one of the two isoforms of caveolin-1. Enriched by sucrose gradient, the caveolae-containing fraction allows to probe the ATPase and Hoechst 33342 transport activities, the latter displaying a higher specific activity than the same without caveolin-1β.
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Affiliation(s)
- Alexia Gobet
- Drug Resistance and Membrane Proteins Team, CNRS - Lyon 1 University UMR 5086, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Christine Jaxel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Team, CNRS - Lyon 1 University UMR 5086, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Manuel Garrigos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Orlowski
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nadège Jamin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, CNRS - Lyon 1 University UMR 5086, Institut de Biologie et Chimie des Protéines, Lyon, France.
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, CNRS - Lyon 1 University UMR 5086, Institut de Biologie et Chimie des Protéines, Lyon, France.
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20
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Oepen K, Özbek H, Schüffler A, Liermann JC, Thines E, Schneider D. Myristic Acid Inhibits the Activity of the Bacterial ABC Transporter BmrA. Int J Mol Sci 2021; 22:ijms222413565. [PMID: 34948362 PMCID: PMC8707315 DOI: 10.3390/ijms222413565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are conserved in all kingdoms of life, where they transport substrates against a concentration gradient across membranes. Some ABC transporters are known to cause multidrug resistances in humans and are able to transport chemotherapeutics across cellular membranes. Similarly, BmrA, the ABC transporter of Bacillus subtilis, is involved in excretion of certain antibiotics out of bacterial cells. Screening of extract libraries isolated from fungi revealed that the C14 fatty acid myristic acid has an inhibitory effect on the BmrA ATPase as well as the transport activity. Thus, a natural membrane constituent inhibits the BmrA activity, a finding with physiological consequences as to the activity and regulation of ABC transporter activities in biological membranes.
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Affiliation(s)
- Kristin Oepen
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
| | - Hüseyin Özbek
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
| | - Anja Schüffler
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
| | - Johannes C. Liermann
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
- Institute of Molecular Physiology, Johannes Gutenberg-University, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
- Institute of Molecular Physiology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-39-25833
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21
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Patel H, Wu ZX, Chen Y, Bo L, Chen ZS. Drug resistance: from bacteria to cancer. MOLECULAR BIOMEDICINE 2021; 2:27. [PMID: 35006446 PMCID: PMC8607383 DOI: 10.1186/s43556-021-00041-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
The phenomenon of drug resistance has been a hindrance to therapeutic medicine since the late 1940s. There is a plethora of factors and mechanisms contributing to progression of drug resistance. From prokaryotes to complex cancers, drug resistance is a prevailing issue in clinical medicine. Although there are numerous factors causing and influencing the phenomenon of drug resistance, cellular transporters contribute to a noticeable majority. Efflux transporters form a huge family of proteins and are found in a vast number of species spanning from prokaryotes to complex organisms such as humans. During the last couple of decades, various approaches in analyses of biochemistry and pharmacology of transporters have led us to understand much more about drug resistance. In this review, we have discussed the structure, function, potential causes, and mechanisms of multidrug resistance in bacteria as well as cancers.
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Affiliation(s)
- Harsh Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, NY, 11439, USA
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, NY, 11439, USA
| | - Yanglu Chen
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Letao Bo
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, NY, 11439, USA
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York, NY, 11439, USA.
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22
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ALTINIŞIK F, ATAŞ B, AVCI FG. Evaluation of silibinin as an efflux pump inhibitor in Bacillus subtilis. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2021. [DOI: 10.21448/ijsm.865031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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23
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The forgotten sugar: A review on multifarious applications of melezitose. Carbohydr Res 2021; 500:108248. [PMID: 33529787 DOI: 10.1016/j.carres.2021.108248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022]
Abstract
Although, 187 years elapsed after the discovery of melezitose, it is a high time to deduce some solid applications as there are only 13 more years left to celebrate a double century of this sugar. The forgotten sugar has multifarious applications; it is used as a metabolic marker to differentiate melezitose fermenting microorganisms, as a carbon source to culture specific microorganisms, as a potential surfactant and excipient to stabilize pharmaceuticals, as a lyoprotectant or cryoprotectant for several industrial applications, as an edibility enhancer in food industry, as a hair smoothening agent in cosmetic industry, and provide protective & nourishing effects in fisheries and aquaculture industries. In entomological research, it is used to study niche differentiation, increased longevity of insects and also as a biocontrol agent. This review brings out the best possible applications of melezitose and present in the form of a mnemonic to remember this forgotten sugar.
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24
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Rismondo J, Schulz LM. Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes. Microorganisms 2021; 9:microorganisms9010163. [PMID: 33450852 PMCID: PMC7828314 DOI: 10.3390/microorganisms9010163] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 12/24/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.
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25
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Serçinoğlu O, Senturk D, Altinisik Kaya FE, Avci FG, Frlan R, Tomašič T, Ozbek P, Orelle C, Jault JM, Sariyar Akbulut B. Identification of novel inhibitors of the ABC transporter BmrA. Bioorg Chem 2020; 105:104452. [PMID: 33212311 DOI: 10.1016/j.bioorg.2020.104452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/23/2020] [Accepted: 11/01/2020] [Indexed: 01/02/2023]
Abstract
The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bacterial efflux pumps in antibiotic resistance has directed research efforts to the identification of novel efflux pump inhibitors that can be used alongside antibiotics in clinical settings. Here, we aimed to find potential inhibitors of the archetypical ATP-binding cassette (ABC) efflux pump BmrA of Bacillus subtilis via virtual screening of the Mu.Ta.Lig. Chemotheca small molecule library. Molecular docking calculations targeting the nucleotide-binding domain of BmrA were performed using AutoDock Vina. Following a further drug-likeness filtering step based on Lipinski's Rule of Five, top 25 scorers were identified. These ligands were then clustered into separate groups based on their contact patterns with the BmrA nucleotide-binding domain. Six ligands with distinct contact patterns were used for further in vitro inhibition assays based on intracellular ethidium bromide accumulation. Using this methodology, we identified two novel inhibitors of BmrA from the Chemotheca small molecule library.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Fener 53100, Rize, Turkey
| | - Duygu Senturk
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | | | - Fatma Gizem Avci
- Department of Bioengineering, Uskudar University, Uskudar 34662, Istanbul, Turkey
| | - Rok Frlan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
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ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter. Molecules 2020; 25:molecules25225268. [PMID: 33198135 PMCID: PMC7698047 DOI: 10.3390/molecules25225268] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases.
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Feng Z, Liu D, Liu Z, Liang Y, Wang Y, Liu Q, Liu Z, Zang Z, Cui Y. Cloning and Functional Characterization of Putative Escherichia coli ABC Multidrug Efflux Transporter YddA. J Microbiol Biotechnol 2020; 30:982-995. [PMID: 32347079 PMCID: PMC9728188 DOI: 10.4014/jmb.2003.03003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
A putative multidrug efflux gene, yddA, was cloned from the Escherichia coli K-12 strain. A drugsensitive strain of E. coli missing the main multidrug efflux pump AcrB was constructed as a host and the yddA gene was knocked out in wild-type (WT) and drug-sensitive E. coliΔacrB to study the yddA function. Sensitivity to different substrates of WT E.coli, E. coliΔyddA, E. coliΔacrB and E. coliΔacrBΔyddA strains was compared with minimal inhibitory concentration (MIC) assays and fluorescence tests. MIC assay and fluorescence test results showed that YddA protein was a multidrug efflux pump that exported multiple substrates. Three inhibitors, ortho-vanadate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and reserpine, were used in fluorescence tests. Ortho-vanadate and reserpine significantly inhibited the efflux and increased accumulation of ethidium bromide and norfloxacin, while CCCP had no significant effect on YddA-regulated efflux. The results indicated that YddA relies on energy released from ATP hydrolysis to transfer the substrates and YddA is an ABC-type multidrug exporter. Functional study of unknown ATP-binding cassette (ABC) superfamily transporters in the model organism E. coli is conducive to discovering new multidrug resistance-reversal targets and providing references for studying other ABC proteins of unknown function.
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Affiliation(s)
- Zhenyue Feng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ziwen Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Qingpeng Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yudong Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,Corresponding author Phone/Fax: +459-6031177 E-mail:
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Songkiatisak P, Ding F, Cherukuri PK, Xu XHN. Size-Dependent Inhibitory Effects of Antibiotic Nanocarriers on Filamentation of E. coli. NANOSCALE ADVANCES 2020; 2:2135-2145. [PMID: 33791510 PMCID: PMC8009294 DOI: 10.1039/c9na00697d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 06/12/2023]
Abstract
Multidrug membrane transporters exist in both prokaryotic and eukaryotic cells, which causes multidrug resistance (MDR) and urgent need of new and more effective therapeutic agencies. In this study, we used three different sized antibiotic nanocarriers to study their mode of actions and their size-dependent inhibitory effects against Escherichia coli (E. coli). The antibiotic nanocarriers (AgMUNH-Oflx NPs) with 8.6×102, 9.4×103 and 6.5×105 Oflx molecules per nanoparticle (NP) were prepared by functionalizing the Ag NPs (2.4 ± 0.7, 13.0 ± 3.1 and 92.6 ± 4.4 nm) with a monolayer of 11-amino-1-undecanethiol (MUNH2) and covalently linking ofloxacin (Oflx) with the amine group of AgMUNH2 NPs, respectively. We designed a modified cell culture medium for nanocarriers to be stable (non-aggregated) over 18 h of cell culture, which enables us to quantitatively study their size and dose dependent inhibitory effects against E. coli. We found that inhibitory effects of Oflx against E. coli highly depend upon dose of Oflx and size of nanocarriers, showing that the equal amount of Oflx delivered by the largest nanocarriers (92.6 ± 4.4 nm) were the most potent with the lowest minimum inhibitory concentration (MIC50) and created the longest and highest percentage of filamentous cells, while the smallest nanocarriers (2.4 ± 0.7) were the least potent with the highest MIC50 and produced the shortest and lowest percentage of filamentous cells. Interestingly, the same amount of Oflx on 2.4 ± 0.7 nm nanocarriers showed the 2x higher MIC and created the 2x shorter filamentous cells than free Oflx, while the Oflx on 13.0 ± 3.1 and 92.6 ± 4.4 nm nanocarriers exhibited 2x and 6x lower MICs, and produced 2x and 3x longer filamentous cell than free Oflx, respectively. Notably, three sized AgMUNH2 NPs (absence of Oflx) showed negligible inhibitory effects and did not create filamentous cells. The results show that the filamentation of E. coli highly depends upon the sizes of nanocarriers, which leads to the size-dependent inhibitory effects of nanocarriers against E. coli.
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Affiliation(s)
- Preeyaporn Songkiatisak
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Feng Ding
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Pavan Kumar Cherukuri
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Xiao-Hong Nancy Xu
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
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Ertekin O, Kutnu M, Taşkin AA, Demir M, Karataş AY, Özcengiz G. Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis. J Microbiol 2020; 58:297-313. [DOI: 10.1007/s12275-020-9064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 12/11/2019] [Accepted: 12/24/2019] [Indexed: 11/24/2022]
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30
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Cherukuri P, Songkiatisak P, Ding F, Jault JM, Xu XHN. Antibiotic Drug Nanocarriers for Probing of Multidrug ABC Membrane Transporter of Bacillus subtilis. ACS OMEGA 2020; 5:1625-1633. [PMID: 32010837 PMCID: PMC6990642 DOI: 10.1021/acsomega.9b03698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Multidrug membrane transporters can extrude a wide range of substrates, which cause multidrug resistance and ineffective treatment of diseases. In this study, we used three different sized antibiotic drug nanocarriers to study their size-dependent inhibitory effects against Bacillus subtilis. We functionalized 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm silver nanoparticles (Ag NPs) with a monolayer of 11-amino-1-undecanethiol and covalently linked them with antibiotics (ofloxacin, Oflx). The labeling ratios of antibiotics with NPs are 8.6 × 102, 9.4 × 103, and 6.5 × 105 Oflx molecules per NP, respectively. We designed cell culture medium in which both BmrA and ΔBmrA cells grew and functioned normally while ensuring the stabilities of nanocarriers (nonaggregation). These approaches allow us to quantitatively study the dependence of their inhibitory effect against two isogenic strains of B. subtilis, WT (normal expression of BmrA) and ΔBmrA (deletion of bmrA), upon the NP size, antibiotic dose, and BmrA expression. Our results show that the inhibitory effects of nanocarriers highly depend on NP size and antibiotic dose. The same amount of Oflx on 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm nanocarriers shows the 3× lower, nearly the same, and 10× higher inhibitory effects than that of free Oflx, against both WT and ΔBmrA, respectively. Control experiments of the respective sized AgMUNH2 NPs (absence of Oflx) show insignificant inhibitory effects toward both strains. Taken together, the results show multiple factors, such as labeling ratios, multivalent effects, and pharmacodynamics (Oflx localization and distribution), which might play the roles in the size-dependent inhibitory effects on the growth of both WT and ΔBmrA strains. Interestingly, the inhibitory effects of nanocarriers are independent of the expression of BmrA, which could be attributed to the higher efflux of nanocarriers by other membrane transporters in both strains.
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Affiliation(s)
- Pavan
Kumar Cherukuri
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Preeyaporn Songkiatisak
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Feng Ding
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Jean-Michel Jault
- UMR5086
CNRS/UCBLyon I, MMSB-IBCP, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Xiao-Hong Nancy Xu
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
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31
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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32
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Avci FG, Atas B, Aksoy CS, Kurpejovic E, Gulsoy Toplan G, Gurer C, Guillerminet M, Orelle C, Jault JM, Sariyar Akbulut B. Repurposing bioactive aporphine alkaloids as efflux pump inhibitors. Fitoterapia 2019; 139:104371. [PMID: 31629051 DOI: 10.1016/j.fitote.2019.104371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 01/13/2023]
Abstract
Extrusion of drugs or drug-like compounds through bacterial efflux pumps is a serious health issue that leads to loss in drug efficacy. Combinatorial therapies of low-efficacy drugs with efflux pump inhibitors may help to restore the activities of such drugs. In this quest, natural products are attractive molecules, since in addition to their wide range of bioactivities they may inhibit efflux pumps. The current work repurposed the bioactive alkaloid roemerine as a potential efflux pump inhibitor. In Bacillus subtilis, both Bmr and BmrA, belonging to the major facilitator and the ATP-binding cassette superfamilies, respectively, were found to be inhibited by roemerine. Scanning electron microscopy and RNA-Seq analyses showed that it potentiated the effect of berberine. Growth rates and checkerboard assays confirmed the synergy of roemerine and berberine and that roemerine prevented berberine efflux by inhibiting Bmr. Transport assays with inverted membrane vesicles prepared from Escherichia coli overexpressing BmrA showed that increasing roemerine concentration decreased the transport of doxorubicin, the BmrA substrate, confirming that roemerine may also be considered as an inhibitor of BmrA. Thus, these findings suggest that conjugation of roemerine to substrates of efflux pumps, Bmr and BmrA, may help to potentiate the activity of their drug substrates.
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Affiliation(s)
- Fatma Gizem Avci
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey.
| | - Basak Atas
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey.
| | - Cemile Selin Aksoy
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey
| | - Eldin Kurpejovic
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey
| | - Gizem Gulsoy Toplan
- Department of Pharmacognosy, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
| | - Caglayan Gurer
- Department of Pharmacognosy, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
| | - Maxime Guillerminet
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
| | - Cedric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
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33
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Lowrence RC, Subramaniapillai SG, Ulaganathan V, Nagarajan S. Tackling drug resistance with efflux pump inhibitors: from bacteria to cancerous cells. Crit Rev Microbiol 2019; 45:334-353. [PMID: 31248314 DOI: 10.1080/1040841x.2019.1607248] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drug resistance is a serious concern in a clinical setting jeopardizing treatment for both infectious agents and cancers alike. The wide-spread emergence of multi-drug resistant (MDR) phenotypes from bacteria to cancerous cells necessitates the need to target resistance mechanisms and prevent the emergence of resistant mutants. Drug efflux seems to be one of the preferred approaches embraced by both microbial and mammalian cells alike, to thwart the action of chemotherapeutic agents thereby leading to a drug resistant phenotype. Relative to microbes, which predominantly employs proton motive force (PMF) powered, Major Facilitator Superfamily (MFS)/Resistance Nodulation and Division (RND) classes of efflux pumps to efflux drugs, cancerous cells preferentially use ATP fuelled ATP binding cassette (ABC) transporters to extrude chemotherapeutic agents. The prevalence, evolutionary characteristics and overlapping functions of ABC transporters have been highlighted in this review. Additionally, we outline the role of ABC pumps in conferring MDR phenotype to both bacteria and cancerous cells and underscore the importance of efflux pump inhibitors (EPI) to mitigate drug resistance. Based on the literature reports and analysis, we reason out feasibility of employing bacteria as a tool to screen for EPI's targeting ABC pumps of cancerous cells.
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Affiliation(s)
- Rene Christena Lowrence
- a Department of Molecular Biology and Biotechnology, University of Sheffield , Sheffield , UK
| | | | | | - Saisubramanian Nagarajan
- c Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University , Thanjavur , India
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34
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Functional Reconstitution of HlyB, a Type I Secretion ABC Transporter, in Saposin-A Nanoparticles. Sci Rep 2019; 9:8436. [PMID: 31182729 PMCID: PMC6558041 DOI: 10.1038/s41598-019-44812-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/23/2019] [Indexed: 11/08/2022] Open
Abstract
Type I secretion systems (T1SS) are ubiquitous transport machineries in Gram-negative bacteria. They comprise a relatively simple assembly of three membrane-localised proteins: an inner-membrane complex composed of an ABC transporter and a membrane fusion protein, and a TolC-like outer membrane component. T1SS transport a wide variety of substrates with broad functional diversity. The ABC transporter hemolysin B (HlyB), for example, is part of the hemolysin A-T1SS in Escherichia coli. In contrast to canonical ABC transporters, an accessory domain, a C39 peptidase-like domain (CLD), is located at the N-terminus of HlyB and is essential for secretion. In this study, we have established an optimised purification protocol for HlyB and the subsequent reconstitution employing the saposin-nanoparticle system. We point out the negative influence of free detergent on the basal ATPase activity of HlyB, studied the influence of a lysolipid or lipid matrix on activity and present functional studies with the full-length substrate proHlyA in its folded and unfolded states, which both have a stimulatory effect on the ATPase activity.
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35
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Lacabanne D, Orelle C, Lecoq L, Kunert B, Chuilon C, Wiegand T, Ravaud S, Jault JM, Meier BH, Böckmann A. Flexible-to-rigid transition is central for substrate transport in the ABC transporter BmrA from Bacillus subtilis. Commun Biol 2019; 2:149. [PMID: 31044174 PMCID: PMC6488656 DOI: 10.1038/s42003-019-0390-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/15/2019] [Indexed: 01/15/2023] Open
Abstract
ATP-binding-cassette (ABC) transporters are molecular pumps that translocate molecules across the cell membrane by switching between inward-facing and outward-facing states. To obtain a detailed understanding of their mechanism remains a challenge to structural biology, as these proteins are notoriously difficult to study at the molecular level in their active, membrane-inserted form. Here we use solid-state NMR to investigate the multidrug ABC transporter BmrA reconstituted in lipids. We identify the chemical-shift differences between the inward-facing, and outward-facing state induced by ATP:Mg2+:Vi addition. Analysis of an X-loop mutant, for which we show that ATPase and transport activities are uncoupled, reveals an incomplete transition to the outward-facing state upon ATP:Mg2+:Vi addition, notably lacking the decrease in dynamics of a defined set of residues observed in wild-type BmrA. This suggests that this stiffening is required for an efficient transmission of the conformational changes to allow proper transport of substrate by the pump.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stéphanie Ravaud
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
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36
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Gulamhussein AA, Meah D, Soja DD, Fenner S, Saidani Z, Akram A, Lallie S, Mathews A, Painter C, Liddar MK, Mohammed Z, Chiu LK, Sumar SS, Healy H, Hussain N, Patel JH, Hall SC, Dafforn TR, Rothnie AJ. Examining the stability of membrane proteins within SMALPs. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Mathieu K, Javed W, Vallet S, Lesterlin C, Candusso MP, Ding F, Xu XN, Ebel C, Jault JM, Orelle C. Functionality of membrane proteins overexpressed and purified from E. coli is highly dependent upon the strain. Sci Rep 2019; 9:2654. [PMID: 30804404 PMCID: PMC6390180 DOI: 10.1038/s41598-019-39382-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Overexpression of correctly folded membrane proteins is a fundamental prerequisite for functional and structural studies. One of the most commonly used expression systems for the production of membrane proteins is Escherichia coli. While misfolded proteins typically aggregate and form inclusions bodies, membrane proteins that are addressed to the membrane and extractable by detergents are generally assumed to be properly folded. Accordingly, GFP fusion strategy is often used as a fluorescent proxy to monitor their expression and folding quality. Here we investigated the functionality of two different multidrug ABC transporters, the homodimer BmrA from Bacillus subtilis and the heterodimer PatA/PatB from Streptococcus pneumoniae, when produced in several E. coli strains with T7 expression system. Strikingly, while strong expression in the membrane of several strains could be achieved, we observed drastic differences in the functionality of these proteins. Moreover, we observed a general trend in which mild detergents mainly extract the population of active transporters, whereas a harsher detergent like Fos-choline 12 could solubilize transporters irrespective of their functionality. Our results suggest that the amount of T7 RNA polymerase transcripts may indirectly but notably impact the structure and activity of overexpressed membrane proteins, and advise caution when using GFP fusion strategy.
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Affiliation(s)
- Khadija Mathieu
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Waqas Javed
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Sylvain Vallet
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Christian Lesterlin
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Marie-Pierre Candusso
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Feng Ding
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Xiaohong Nancy Xu
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Christine Ebel
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Jean-Michel Jault
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
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Breyton C, Javed W, Vermot A, Arnaud CA, Hajjar C, Dupuy J, Petit-Hartlein I, Le Roy A, Martel A, Thépaut M, Orelle C, Jault JM, Fieschi F, Porcar L, Ebel C. Assemblies of lauryl maltose neopentyl glycol (LMNG) and LMNG-solubilized membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:939-957. [PMID: 30776334 DOI: 10.1016/j.bbamem.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Laurylmaltose neopentylglycol (LMNG) bears two linked hydrophobic chains of equal length and two hydrophilic maltoside groups. It arouses a strong interest in the field of membrane protein biochemistry, since it was shown to efficiently solubilize and stabilize membrane proteins often better than the commonly used dodecylmaltopyranoside (DDM), and to allow structure determination of some challenging membrane proteins. However, LMNG was described to form large micelles, which could be unfavorable for structural purposes. We thus investigated its auto-assemblies and the association state of different membrane proteins solubilized in LMNG by analytical ultracentrifugation, size exclusion chromatography coupled to light scattering, centrifugation on sucrose gradient and/or small angle scattering. At high concentrations (in the mM range), LMNG forms long rods, and it stabilized the membrane proteins investigated herein, i.e. a bacterial multidrug transporter, BmrA; a prokaryotic analogous of the eukaryotic NADPH oxidases, SpNOX; an E. coli outer membrane transporter, FhuA; and the halobacterial bacteriorhodopsin, bR. BmrA, in the Apo and the vanadate-inhibited forms showed reduced kinetics of limited proteolysis in LMNG compared to DDM. Both SpNOX and BmrA display an increased specific activity in LMNG compared to DDM. The four proteins form LMNG complexes with their usual quaternary structure and with usual amount of bound detergent. No heterogeneous complexes related to the large micelle size of LMNG alone were observed. In conditions where LMNG forms assemblies of large size, FhuA crystals diffracting to 4.0 Å were obtained by vapor diffusion. LMNG large micelle size thus does not preclude membrane protein homogeneity and crystallization.
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Affiliation(s)
- Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Waqas Javed
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France; University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Christine Hajjar
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Jérôme Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Isabelle Petit-Hartlein
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Anne Martel
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Lionel Porcar
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France.
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Abriouel H, Lavilla Lerma L, Pérez Montoro B, Alonso E, Knapp CW, Caballero Gómez N, Gálvez A, Benomar N. Efficacy of "HLE"-a multidrug efflux-pump inhibitor-as a disinfectant against surface bacteria. ENVIRONMENTAL RESEARCH 2018; 165:133-139. [PMID: 29704774 DOI: 10.1016/j.envres.2018.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/14/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
We evaluated the efficacy of a new disinfectant product, HLE, to inhibit multiple species of planktonic and biofilm bacterial cultures. The HLE disinfectant comprised of EDTA, lactic acid and hydrogen peroxide, and our data indicated that the disinfectant had effective antimicrobial and anti-biofilm activity even at low concentrations (0.15% to 0.4% HLE, v/v). Furthermore, the HLE disinfectant destabilized biofilm structures eradicated them due to the synergistic effect of EDTA and both antimicrobials (lactic acid and hydrogen peroxide), as revealed by confocal laser scanning microscopy. Additionally, sub-inhibitory concentrations of HLE disinfectant, with EDTA as an efflux pump inhibitor, inhibited the expression of multidrug EfrAB, NorE and MexCD efflux pumps in both planktonic and biofilm cultures. This could provide an alternative way to disinfect surfaces to avoid spreading multi-drug resistant strains in the food chain and the environment by decreasing efflux pump expression and consequently reducing the antibiotic selective pressure caused by systemic antibiotics and disinfectant use.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain.
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
| | - Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
| | - Esther Alonso
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability, and Public Health; Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Edif. B3, 23071 Jaén, Spain
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40
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Browning LM, Lee KJ, Cherukuri PK, Huang T, Songkiatisak P, Warren S, Xu XHN. Single gold nanoparticle plasmonic spectroscopy for study of chemical-dependent efflux function of single ABC transporters of single live Bacillus subtilis cells. Analyst 2018; 143:1599-1608. [PMID: 29488517 PMCID: PMC5869163 DOI: 10.1039/c7an01787a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) membrane transporters serve as self-defense transport apparatus in many living organisms and they can selectively extrude a wide variety of substrates, leading to multidrug resistance (MDR). The detailed molecular mechanisms remain elusive. Single nanoparticle plasmonic spectroscopy highly depends upon their sizes, shapes, chemical and surface properties. In our previous studies, we have used the size-dependent plasmonic spectra of single silver nanoparticles (Ag NPs) to study the real-time efflux kinetics of the ABC (BmrA) transporter and MexAB-OprM transporter in single live cells (Gram-positive and Gram-negative bacterium), respectively. In this study, we prepared and used purified, biocompatible and stable (non-aggregated) gold nanoparticles (Au NPs) (12.4 ± 0.9 nm) to study the efflux kinetics of single BmrA membrane transporters of single live Bacillus subtillis cells, aiming to probe chemical dependent efflux functions of BmrA transporters and their potential chemical sensing capability. Similar to those observed using Ag NPs, accumulation of the intracellular Au NPs in single live cells (WT and ΔBmrA) highly depends upon the cellular expression of BmrA and the NP concentration (0.7 and 1.4 nM). The lower accumulation of intracellular Au NPs in WT (normal expression of BmrA) than ΔBmrA (deletion of bmrA) indicates that BmrA extrudes the Au NPs out of the WT cells. The accumulation of Au NPs in the cells increases with NP concentration, suggesting that the Au NPs most likely passively diffuse into the cells, similar to antibiotics. The result demonstrates that such small Au NPs can serve as imaging probes to study the efflux function of the BmrA membrane transporter in single live cells. Furthermore, the dependence of the accumulation rate of intracellular Au NPs in single live cells upon the expression of BmrA and the concentration of the NPs is about twice higher than that of the same sized Ag NPs. This interesting finding suggests the chemical-dependent efflux kinetics of BmrA and that BmrA could distinguish nearly identical sized Au NPs from Ag NPs and might possess chemical sensing machinery.
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Affiliation(s)
- Lauren M Browning
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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41
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Orelle C, Durmort C, Mathieu K, Duchêne B, Aros S, Fenaille F, André F, Junot C, Vernet T, Jault JM. A multidrug ABC transporter with a taste for GTP. Sci Rep 2018; 8:2309. [PMID: 29396536 PMCID: PMC5797166 DOI: 10.1038/s41598-018-20558-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/19/2018] [Indexed: 01/26/2023] Open
Abstract
During the evolution of cellular bioenergetics, many protein families have been fashioned to match the availability and replenishment in energy supply. Molecular motors and primary transporters essentially need ATP to function while proteins involved in cell signaling or translation consume GTP. ATP-Binding Cassette (ABC) transporters are one of the largest families of membrane proteins gathering several medically relevant members that are typically powered by ATP hydrolysis. Here, a Streptococcus pneumoniae ABC transporter responsible for fluoroquinolones resistance in clinical settings, PatA/PatB, is shown to challenge this concept. It clearly favors GTP as the energy supply to expel drugs. This preference is correlated to its ability to hydrolyze GTP more efficiently than ATP, as found with PatA/PatB reconstituted in proteoliposomes or nanodiscs. Importantly, the ATP and GTP concentrations are similar in S. pneumoniae supporting the physiological relevance of GTP as the energy source of this bacterial transporter.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Claire Durmort
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
| | - Khadija Mathieu
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Benjamin Duchêne
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sandrine Aros
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François Fenaille
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication (LSOD), Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Christophe Junot
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - Thierry Vernet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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42
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Lacabanne D, Lends A, Danis C, Kunert B, Fogeron ML, Jirasko V, Chuilon C, Lecoq L, Orelle C, Chaptal V, Falson P, Jault JM, Meier BH, Böckmann A. Gradient reconstitution of membrane proteins for solid-state NMR studies. JOURNAL OF BIOMOLECULAR NMR 2017; 69:81-91. [PMID: 28900789 DOI: 10.1007/s10858-017-0135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR. NMR spectra recorded on a sample produced by GRecon showed a highly similar fingerprint as those recorded previously on samples reconstituted by dialysis. GRecon sample preparation presents a gain in time of nearly an order of magnitude for reconstitution, and shall represent a valuable alternative in solid-state NMR membrane protein sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Alons Lends
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Clément Danis
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vlastimil Jirasko
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France.
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43
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Jones PM, George AM. How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer. J Chem Theory Comput 2017; 13:1712-1722. [PMID: 28240893 DOI: 10.1021/acs.jctc.6b00839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
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44
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Spengler G, Kincses A, Gajdács M, Amaral L. New Roads Leading to Old Destinations: Efflux Pumps as Targets to Reverse Multidrug Resistance in Bacteria. Molecules 2017; 22:molecules22030468. [PMID: 28294992 PMCID: PMC6155429 DOI: 10.3390/molecules22030468] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 01/05/2023] Open
Abstract
Multidrug resistance (MDR) has appeared in response to selective pressures resulting from the incorrect use of antibiotics and other antimicrobials. This inappropriate application and mismanagement of antibiotics have led to serious problems in the therapy of infectious diseases. Bacteria can develop resistance by various mechanisms and one of the most important factors resulting in MDR is efflux pump-mediated resistance. Because of the importance of the efflux-related multidrug resistance the development of new therapeutic approaches aiming to inhibit bacterial efflux pumps is a promising way to combat bacteria having over-expressed MDR efflux systems. The definition of an efflux pump inhibitor (EPI) includes the ability to render the bacterium increasingly more sensitive to a given antibiotic or even reverse the multidrug resistant phenotype. In the recent years numerous EPIs have been developed, although so far their clinical application has not yet been achieved due to their in vivo toxicity and side effects. In this review, we aim to give a short overview of efflux mediated resistance in bacteria, EPI compounds of plant and synthetic origin, and the possible methods to investigate and screen EPI compounds in bacterial systems.
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Affiliation(s)
- Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Annamária Kincses
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Márió Gajdács
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Leonard Amaral
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
- Travel Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal.
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45
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Quantification of Detergents Complexed with Membrane Proteins. Sci Rep 2017; 7:41751. [PMID: 28176812 PMCID: PMC5297245 DOI: 10.1038/srep41751] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 01/20/2023] Open
Abstract
Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies.
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46
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Lacabanne D, Kunert B, Gardiennet C, Meier BH, Bo Ckmann A. Sample Preparation for Membrane Protein Structural Studies by Solid-State NMR. Methods Mol Biol 2017; 1635:345-358. [PMID: 28755379 DOI: 10.1007/978-1-4939-7151-0_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Conformational studies of membrane proteins remain a challenge in the field of structural biology, and in particular the investigation of the proteins in a native-like lipid environment. Solid-state NMR presents a valuable opportunity for this, and we present here three critical steps in the solid-state NMR sample preparation, i.e., membrane reconstitution of the protein in native lipids, rotor filling, and sample quality assessment, at the example of the Bacillus subtilis ATP-binding cassette transporter BmrA.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France
| | - Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France.,CRM2, UMR 7036, CNRS, Université de Lorraine, 54506, Vandoeuvre-lès-Nancy, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Bo Ckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS - Université de Lyon, 7 Passage du Vercors, 69367, Lyon, France.
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47
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Membrane protein extraction and purification using styrene–maleic acid (SMA) copolymer: effect of variations in polymer structure. Biochem J 2016; 473:4349-4360. [DOI: 10.1042/bcj20160723] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The use of styrene–maleic acid (SMA) copolymers to extract and purify transmembrane proteins, while retaining their native bilayer environment, overcomes many of the disadvantages associated with conventional detergent-based procedures. This approach has huge potential for the future of membrane protein structural and functional studies. In this investigation, we have systematically tested a range of commercially available SMA polymers, varying in both the ratio of styrene and maleic acid and in total size, for the ability to extract, purify and stabilise transmembrane proteins. Three different membrane proteins (BmrA, LeuT and ZipA), which vary in size and shape, were used. Our results show that several polymers, can be used to extract membrane proteins, comparably to conventional detergents. A styrene:maleic acid ratio of either 2:1 or 3:1, combined with a relatively small average molecular mass (7.5–10 kDa), is optimal for membrane extraction, and this appears to be independent of the protein size, shape or expression system. A subset of polymers were taken forward for purification, functional and stability tests. Following a one-step affinity purification, SMA 2000 was found to be the best choice for yield, purity and function. However, the other polymers offer subtle differences in size and sensitivity to divalent cations that may be useful for a variety of downstream applications.
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48
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Browning LM, Lee KJ, Nallathamby PD, Cherukuri PK, Huang T, Warren S, Xu XHN. Single Nanoparticle Plasmonic Spectroscopy for Study of Charge-Dependent Efflux Function of Multidrug ABC Transporters of Single Live Bacillus subtilis Cells. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:21007-21016. [PMID: 29662596 PMCID: PMC5899213 DOI: 10.1021/acs.jpcc.6b03313] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Multidrug membrane transporters can selectively extrude a wide variety of structurally and functionally unrelated substrates, and they are responsible for ineffective treatment of a wide range of diseases (e.g., infection and cancer). Their underlying molecular mechanisms remain elusive. In this study, we functionalized Ag NPs (11 nm in diameter) with two biocompatible peptides (CALNNK, CALNNE) to prepare positively and negatively charged Ag-peptide NPs (Ag-CALNNK NPs+ζ, Ag-CALNNE NPs-4ζ), respectively. We used them as photostable plasmonic imaging probes to study charge-dependent efflux kinetics of BmrA (ABC) membrane transporter of single live Bacillus (B.) subtilis cells. Two strains of the cells, normal expression of BmrA (WT) or devoid of BmrA (ΔBmrA), were used to study the charge-dependent efflux kinetics of single NPs upon the expression of BmrA. The NPs (1.4 nM) were stable (non-aggregated) in a PBS buffer and biocompatible to the cells. We found the high dependent accumulation of the intracellular NPs in both WT and ΔBmrA upon the charge and concentration of NPs. Notably, the accumulation rates of the positively charged NPs in single live WT cells are nearly identical to those in ΔBmrA cells, showing independence upon the expression of BmrA. In contrast, the accumulation rates of the negatively charged NPs in WT are much lower than in ΔBmrA, showing high dependence upon the expression of BmrA and suggesting that BmrA extrude the negatively charged NPs, but not positively charged NPs, out of the WT. The accumulation of positively charged NPs in both WT and ΔBmrA increases nearly proportionally to the NP concentration. The accumulation of negatively charged NPs in ΔBmrA, but not in WT, also increases nearly proportionally to the NP concentration. These results suggest that both negatively and positively charged NPs enter the cells via passive diffusion driven by concentration gradients across the cellular membrane, and BmrA can only extrude the negatively charged NPs out of the WT. This study shows that single NP plasmon spectroscopy can serve as a powerful tool to identify single plasmonic NPs and to probe the charge-dependent efflux kinetics and function of single membrane transporters in single live cells in real time.
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Affiliation(s)
- Lauren M. Browning
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Kerry J. Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Prakash D. Nallathamby
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Pavan K. Cherukuri
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Tao Huang
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Seth Warren
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | - Xiao-Hong Nancy Xu
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
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Interdomain regulation of the ATPase activity of the ABC transporter haemolysin B from Escherichia coli. Biochem J 2016; 473:2471-83. [DOI: 10.1042/bcj20160154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/07/2016] [Indexed: 12/27/2022]
Abstract
Type 1 secretion systems (T1SS) transport a wide range of substrates across both membranes of Gram-negative bacteria and are composed of an outer membrane protein, a membrane fusion protein and an ABC (ATP-binding cassette) transporter. The ABC transporter HlyB (haemolysin B) is part of a T1SS catalysing the export of the toxin HlyA in E. coli. HlyB consists of the canonical transmembrane and nucleotide-binding domains. Additionally, HlyB contains an N-terminal CLD (C39-peptidase-like domain) that interacts with the transport substrate, but its functional relevance is still not precisely defined. In the present paper, we describe the purification and biochemical characterization of detergent-solubilized HlyB in the presence of its transport substrate. Our results exhibit a positive co-operativity in ATP hydrolysis. We characterized further the influence of the CLD on kinetic parameters by using an HlyB variant lacking the CLD (HlyB∆CLD). The biochemical parameters of HlyB∆CLD revealed an increased basal maximum velocity but no change in substrate-binding affinity in comparison with full-length HlyB. We also assigned a distinct interaction of the CLD and a transport substrate (HlyA1), leading to an inhibition of HlyB hydrolytic activity at low HlyA1 concentrations. At higher HlyA1 concentrations, we observed a stimulation of the hydrolytic activities of both HlyB and HlyB∆CLD, which was completely independent of the interaction of HlyA1 with the CLD. Notably, all observed effects on ATPase activity, which were also analysed in detail by mass spectrometry, were independent of the HlyA1 secretion signal. These results assign an interdomain regulatory role for the CLD modulating the hydrolytic activity of HlyB.
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Overexpression, Membrane Preparation, and Purification of a Typical Multidrug ABC Transporter BmrA. Methods Mol Biol 2016. [PMID: 27485334 DOI: 10.1007/978-1-4939-3637-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The production and purification is normally the first step in any biophysical or biochemical study of a new target protein. For membrane proteins, due to their generally low expression levels and hydrophobic properties this is often a major hurdle. Some multidrug transporters are members of one of the largest families of membrane proteins, the ABC ("ATP-binding cassette"), and are responsible for the uptake and export of a wide variety of molecules. This can lead to resistance when those molecules are antibiotics or chemotherapy drugs. To better understand their role in multidrug resistance pure and active protein is required. Here we outline a protocol to produce a highly pure and functionally active multidrug transporter BmrA that is suitable for use in biophysical and biochemical studies. We show that BmrA can be heterologously overexpressed in huge amount in E. coli and extracted from the membrane in a functionally active form.
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