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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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2
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Outer membrane permeability: Antimicrobials and diverse nutrients bypass porins in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2021; 118:2107644118. [PMID: 34326266 PMCID: PMC8346889 DOI: 10.1073/pnas.2107644118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel antibiotics are urgently needed to resolve the current antimicrobial resistance crisis. For critical pathogens, drug entry through the cell envelope is one of the major challenges in the development of effective novel antibiotics. Envelope proteins forming water-filled channels, so-called porins, are commonly thought to be essential for entry of hydrophilic molecules, but we show here for the critical pathogen Pseudomonas aeruginosa that almost all antibiotics and diverse hydrophilic nutrients bypass porins and instead permeate directly through the outer membrane lipid bilayer. However, carboxylate groups hinder bilayer penetration, and Pseudomonas thus needs porins for efficient utilization of carboxylate-containing nutrients such as succinate. The major porin-independent entry route might open opportunities for facilitating drug delivery into bacteria. Gram-negative bacterial pathogens have an outer membrane that restricts entry of molecules into the cell. Water-filled protein channels in the outer membrane, so-called porins, facilitate nutrient uptake and are thought to enable antibiotic entry. Here, we determined the role of porins in a major pathogen, Pseudomonas aeruginosa, by constructing a strain lacking all 40 identifiable porins and 15 strains carrying only a single unique type of porin and characterizing these strains with NMR metabolomics and antimicrobial susceptibility assays. In contrast to common assumptions, all porins were dispensable for Pseudomonas growth in rich medium and consumption of diverse hydrophilic nutrients. However, preferred nutrients with two or more carboxylate groups such as succinate and citrate permeated poorly in the absence of porins. Porins provided efficient translocation pathways for these nutrients with broad and overlapping substrate selectivity while efficiently excluding all tested antibiotics except carbapenems, which partially entered through OprD. Porin-independent permeation of antibiotics through the outer-membrane lipid bilayer was hampered by carboxylate groups, consistent with our nutrient data. Together, these results challenge common assumptions about the role of porins by demonstrating porin-independent permeation of the outer-membrane lipid bilayer as a major pathway for nutrient and drug entry into the bacterial cell.
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Hawley KL, Montezuma-Rusca JM, Delgado KN, Singh N, Uversky VN, Caimano MJ, Radolf JD, Luthra A. Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine. J Bacteriol 2021; 203:e0008221. [PMID: 33972353 PMCID: PMC8407342 DOI: 10.1128/jb.00082-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
Treponema pallidum, an obligate human pathogen, has an outer membrane (OM) whose physical properties, ultrastructure, and composition differ markedly from those of phylogenetically distant Gram-negative bacteria. We developed structural models for the outer membrane protein (OMP) repertoire (OMPeome) of T. pallidum Nichols using solved Gram-negative structures, computational tools, and small-angle X-ray scattering (SAXS) of selected recombinant periplasmic domains. The T. pallidum "OMPeome" harbors two "stand-alone" proteins (BamA and LptD) involved in OM biogenesis and four paralogous families involved in the influx/efflux of small molecules: 8-stranded β-barrels, long-chain-fatty-acid transporters (FadLs), OM factors (OMFs) for efflux pumps, and T. pallidum repeat proteins (Tprs). BamA (TP0326), the central component of a β-barrel assembly machine (BAM)/translocation and assembly module (TAM) hybrid, possesses a highly flexible polypeptide-transport-associated (POTRA) 1-5 arm predicted to interact with TamB (TP0325). TP0515, an LptD ortholog, contains a novel, unstructured C-terminal domain that models inside the β-barrel. T. pallidum has four 8-stranded β-barrels, each containing positively charged extracellular loops that could contribute to pathogenesis. Three of five FadL-like orthologs have a novel α-helical, presumptively periplasmic C-terminal extension. SAXS and structural modeling further supported the bipartite membrane topology and tridomain architecture of full-length members of the Tpr family. T. pallidum's two efflux pumps presumably extrude noxious small molecules via four coexpressed OMFs with variably charged tunnels. For BamA, LptD, and OMFs, we modeled the molecular machines that deliver their substrates into the OM or external milieu. The spirochete's extended families of OM transporters collectively confer a broad capacity for nutrient uptake. The models also furnish a structural road map for vaccine development. IMPORTANCE The unusual outer membrane (OM) of T. pallidum, the syphilis spirochete, is the ultrastructural basis for its well-recognized capacity for invasiveness, immune evasion, and persistence. In recent years, we have made considerable progress in identifying T. pallidum's repertoire of OMPs. Here, we developed three-dimensional (3D) models for the T. pallidum Nichols OMPeome using structural modeling, bioinformatics, and solution scattering. The OM contains three families of OMP transporters, an OMP family involved in the extrusion of noxious molecules, and two "stand-alone" proteins involved in OM biogenesis. This work represents a major advance toward elucidating host-pathogen interactions during syphilis; understanding how T. pallidum, an extreme auxotroph, obtains a wide array of biomolecules from its obligate human host; and developing a vaccine with global efficacy.
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Affiliation(s)
- Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
| | - Jairo M. Montezuma-Rusca
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases, UConn Health, Farmington, Connecticut, USA
| | | | - Navreeta Singh
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Melissa J. Caimano
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Justin D. Radolf
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Schubeis T, Schwarzer TS, Le Marchand T, Stanek J, Movellan KT, Castiglione K, Pintacuda G, Andreas LB. Resonance assignment of the outer membrane protein AlkL in lipid bilayers by proton-detected solid-state NMR. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:295-300. [PMID: 32607893 DOI: 10.1007/s12104-020-09964-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Most commonly small outer membrane proteins, possessing between 8 and 12 β-strands, are not involved in transport but fulfill diverse functions such as cell adhesion or binding of ligands. An intriguing exception are the 8-stranded β-barrel proteins of the OmpW family, which are implicated in the transport of small molecules. A representative example is AlkL from Pseudomonas putida GPoI, which functions as a passive importer of hydrophobic molecules. This role is of high interest with respect to both fundamental biological understanding and industrial applications in biocatalysis, since this protein is frequently utilized in biotransformation of alkanes. While the transport function of AlkL is generally accepted, a controversy in the transport mechanism still exists. In order to address this, we are pursuing a structural study of recombinantly produced AlkL reconstituted in lipid bilayers using solid-state NMR spectroscopy. In this manuscript we present 1H, 13C and 15N chemical shift assignments obtained via a suite of 3D experiments employing high magnetic fields (1 GHz and 800 MHz) and the latest magic-angle spinning (MAS) approaches at fast (60-111) kHz rates. We additionally analyze the secondary structure prediction in comparison with those of published structures of homologous proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Kumar Tekwani Movellan
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Institute of Bioprocess Engineering, FAU Erlangen-Nürnberg, Paul-Gordan Str. 3, 91052, Erlangen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proc Natl Acad Sci U S A 2020; 117:21014-21021. [PMID: 32817429 PMCID: PMC7474606 DOI: 10.1073/pnas.2002598117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Here we show how AlkL, a minimalistic outer-membrane protein from oil-consuming bacteria, exploits dynamics of extracellular loops to channel substrate across the polysaccharide barrier and into the hydrophobic interior of the outer membrane. This work represents a unique example of a side-by-side atomic-level structure determination by solution NMR in detergents and by solid-state NMR in lipid bilayers, which critically demonstrates the importance of a lipid environment to investigate function. Corroborating our experimental measurements, molecular-dynamics simulations capture substrate transit via lateral openings. The capacity to unravel membrane protein function under near-native conditions, fueled by the latest method developments, opens up a new frontier for their investigation, and provides thereby for improved fundamental insights into biological processes. The protein AlkL is known to increase permeability of the outer membrane of bacteria for hydrophobic molecules, yet the mechanism of transport has not been determined. Differing crystal and NMR structures of homologous proteins resulted in a controversy regarding the degree of structure and the role of long extracellular loops. Here we solve this controversy by determining the de novo NMR structure in near-native lipid bilayers, and by accessing structural dynamics relevant to hydrophobic substrate permeation through molecular-dynamics simulations and by characteristic NMR relaxation parameters. Dynamic lateral exit sites large enough to accommodate substrates such as carvone or octane occur through restructuring of a barrel extension formed by the extracellular loops.
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Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
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Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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Molecular characterization of the outer membrane of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183151. [DOI: 10.1016/j.bbamem.2019.183151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/28/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
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Otero-Asman JR, Quesada JM, Jim KK, Ocampo-Sosa A, Civantos C, Bitter W, Llamas MA. The extracytoplasmic function sigma factor σ VreI is active during infection and contributes to phosphate starvation-induced virulence of Pseudomonas aeruginosa. Sci Rep 2020; 10:3139. [PMID: 32081993 PMCID: PMC7035377 DOI: 10.1038/s41598-020-60197-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The extracytoplasmic function sigma factor σVreI of the human pathogen Pseudomonas aeruginosa promotes transcription of potential virulence determinants, including secretion systems and secreted proteins. Its activity is modulated by the VreR anti-σ factor that inhibits the binding of σVreI to the RNA polymerase in the absence of a (still unknown) inducing signal. The vreI-vreR genes are expressed under inorganic phosphate (Pi) starvation, a physiological condition often encountered in the host that increases P. aeruginosa pathogenicity. However, whether or not σVreI is active in vivo during infection and contributes to the Pi starvation-induced virulence of this pathogen has not been analyzed yet. Using zebrafish embryos and a human alveolar basal epithelial cell line as P. aeruginosa hosts, we demonstrate in this work that σVreI is active during infection and that lack of σVreI considerably reduces the Pi starvation-induced virulence of this pathogen. Surprisingly, lack of the σVreI inhibitor, the VreR anti-σ factor, also diminishes the virulence of P. aeruginosa. By transcriptomic analyses we show that VreR modulates gene expression not only in a σVreI-dependent but also in a σVreI-independent manner. This includes potential virulence determinants and transcriptional regulators that could be responsible for the reduced virulence of the ΔvreR mutant.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Kin K Jim
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centers, location VU University, Amsterdam, The Netherlands
| | - Alain Ocampo-Sosa
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Sanitaria Valdecilla, Santander, Spain
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centers, location VU University, Amsterdam, The Netherlands
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Beaton A, Lood C, Cunningham-Oakes E, MacFadyen A, Mullins AJ, Bestawy WE, Botelho J, Chevalier S, Coleman S, Dalzell C, Dolan SK, Faccenda A, Ghequire MGK, Higgins S, Kutschera A, Murray J, Redway M, Salih T, da Silva AC, Smith BA, Smits N, Thomson R, Woodcock S, Welch M, Cornelis P, Lavigne R, van Noort V, Tucker NP. Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS Microbiol Lett 2019; 365:4951603. [PMID: 29579234 PMCID: PMC5909648 DOI: 10.1093/femsle/fny069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/21/2018] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.
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Affiliation(s)
- Ainsley Beaton
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium.,Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Edward Cunningham-Oakes
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff CF10 3AX, UK
| | - Alison MacFadyen
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK
| | - Alex J Mullins
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff CF10 3AX, UK
| | - Walid El Bestawy
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228 Porto 4050-313, Portugal
| | - Sylvie Chevalier
- Laboratoire Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen, 55, rue St Germain, Evreux 27000, France
| | - Shannon Coleman
- Lower Mall Research Station, University of British Columbia, 2259 Lower Mall, Vancouver, BC V6T 1Z4, Canada
| | - Chloe Dalzell
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Stephen K Dolan
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alberto Faccenda
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Steven Higgins
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Alexander Kutschera
- Department of Phytopathology, Center of Life and Food Sciences, Technical University of Munich, Weihenstephan D-85354, Germany
| | - Jordan Murray
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Martha Redway
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Talal Salih
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Ana C da Silva
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Brian A Smith
- School of Plant Sciences, The University of Arizona, P.O. Box 210036, Forbes Building, 303 Tucson, Arizona 85721-0036, USA
| | - Nathan Smits
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Ryan Thomson
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Stuart Woodcock
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Pierre Cornelis
- Laboratoire Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen, 55, rue St Germain, Evreux 27000, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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11
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Hays JM, Kieber MK, Li JZ, Han JI, Columbus L, Kasson PM. Refinement of Highly Flexible Protein Structures using Simulation‐Guided Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jennifer M. Hays
- Departments of Biomedical Engineering and Molecular Physiology University of Virginia Box 800886 Charlottesvile VA 22908 USA
| | - Marissa K. Kieber
- Department of Chemistry University of Virginia Charlottesville VA 22908 USA
| | - Jason Z. Li
- Department of Chemistry University of Virginia Charlottesville VA 22908 USA
| | - Ji In Han
- Department of Chemistry University of Virginia Charlottesville VA 22908 USA
| | - Linda Columbus
- Department of Chemistry University of Virginia Charlottesville VA 22908 USA
| | - Peter M. Kasson
- Departments of Biomedical Engineering and Molecular Physiology University of Virginia Box 800886 Charlottesvile VA 22908 USA
- Science for Life Laboratory Program in Molecular Biophysics Uppsala University Uppsala 75124 Sweden
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Najbauer EE, Movellan KT, Schubeis T, Schwarzer T, Castiglione K, Giller K, Pintacuda G, Becker S, Andreas LB. Probing Membrane Protein Insertion into Lipid Bilayers by Solid-State NMR. Chemphyschem 2018; 20:302-310. [PMID: 30452110 DOI: 10.1002/cphc.201800793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Determination of the environment surrounding a protein is often key to understanding its function and can also be used to infer the structural properties of the protein. By using proton-detected solid-state NMR, we show that reduced spin diffusion within the protein under conditions of fast magic-angle spinning, high magnetic field, and sample deuteration allows the efficient measurement of site-specific exposure to mobile water and lipids. We demonstrate this site specificity on two membrane proteins, the human voltage dependent anion channel, and the alkane transporter AlkL from Pseudomonas putida. Transfer from lipids is observed selectively in the membrane spanning region, and an average lipid-protein transfer rate of 6 s-1 was determined for residues protected from exchange. Transfer within the protein, as tracked in the 15 N-1 H 2D plane, was estimated from initial rates and found to be in a similar range of about 8 to 15 s-1 for several resolved residues, explaining the site specificity.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280/CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, Villeurbanne, France
| | - Tom Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, D-85748, Garching, Germany
| | - Kathrin Castiglione
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
| | - Karin Giller
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280/CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, Villeurbanne, France
| | - Stefan Becker
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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13
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Hays JM, Kieber MK, Li JZ, Han JI, Columbus L, Kasson PM. Refinement of Highly Flexible Protein Structures using Simulation-Guided Spectroscopy. Angew Chem Int Ed Engl 2018; 57:17110-17114. [PMID: 30395378 DOI: 10.1002/anie.201810462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/22/2018] [Indexed: 11/06/2022]
Abstract
Highly flexible proteins present a special challenge for structure determination because they are multi-structured yet not disordered, so their conformational ensembles are essential for understanding function. Because spectroscopic measurements of multiple conformational populations often provide sparse data, experiment selection is a limiting factor in conformational refinement. A molecular simulations- and information-theory based approach to select which experiments best refine conformational ensembles has been developed. This approach was tested on three flexible proteins. For proteins where a clear mechanistic hypothesis exists, experiments that test this hypothesis were systematically identified. When available data did not yield such mechanistic hypotheses, experiments that significantly outperform structure-guided approaches in conformational refinement were identified. This approach offers a particular advantage when refining challenging, underdetermined protein conformational ensembles.
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Affiliation(s)
- Jennifer M Hays
- Departments of Biomedical Engineering and Molecular Physiology, University of Virginia, Box 800886, Charlottesvile, VA, 22908, USA
| | - Marissa K Kieber
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jason Z Li
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ji In Han
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22908, USA
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22908, USA
| | - Peter M Kasson
- Departments of Biomedical Engineering and Molecular Physiology, University of Virginia, Box 800886, Charlottesvile, VA, 22908, USA.,Science for Life Laboratory, Program in Molecular Biophysics, Uppsala University, Uppsala, 75124, Sweden
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14
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Schwarzer TS, Klermund L, Wang G, Castiglione K. Membrane functionalization of polymersomes: alleviating mass transport limitations by integrating multiple selective membrane transporters for the diffusion of chemically diverse molecules. NANOTECHNOLOGY 2018; 29:44LT01. [PMID: 30124436 DOI: 10.1088/1361-6528/aadb7e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recently, the interest in polymersomes as nanoreactors for synthetic applications has increased due to interesting proof-of-concept studies, indicating a versatile use of polymeric vesicles to compartmentalize complex reaction cascades. However, the low permeability of polymeric membranes and the requirement for a controlled mass transport across the compartment boundaries have posed a major limitation to the broad applicability of polymersomes for synthetic reactions. Current advances in the functional integration of membrane proteins (MPs) into poly(2-dimethylsiloxane)-based membranes have allowed the selective increase of the permeability for a controlled mass transport of the desired compounds across the membrane. Herein we demonstrate that polymer membranes are capable of harboring different MPs to alleviate the mass transport limitations of chemically diverse molecules, thereby enabling complex cascade reactions to be performed within the nanoreactors. The ability to functionalize the polymer membrane with multiple, highly selective MPs allows a reduction in mass transport limitations without abandoning compartmentalization of the reaction space on a low molecular mass level. As the model reaction, a two enzyme system consisting of a ketoreductase (KR) and a formate dehydrogenase was studied. For the transport of the hydrophobic substrate and product of the KR, the MPs AlkL, OmpW, OprG and TodX were investigated. For the transport of formate, OmpF, PhoE and FocA were used. AlkL showed the highest integration efficiency (39%) and a maximum of 120 AlkL molecules were successfully inserted into each polymersome. The highest channel-specific effects on the mass transfer were achieved using TodX and PhoE, respectively. The combination of both proteins led to an improvement of the space-time yield of the product (S)-pentafluorophenyl ethanol by 2.32-fold compared to nanoreactors without MPs.
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Affiliation(s)
- Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, D-85748 Garching, Germany
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15
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Sanganna Gari RR, Seelheim P, Marsh B, Kiessling V, Creutz CE, Tamm LK. Quaternary structure of the small amino acid transporter OprG from Pseudomonas aeruginosa. J Biol Chem 2018; 293:17267-17277. [PMID: 30237175 DOI: 10.1074/jbc.ra118.004461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/13/2018] [Indexed: 02/01/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that causes nosocomial infections. The P. aeruginosa outer membrane contains specific porins that enable substrate uptake, with the outer membrane protein OprG facilitating transport of small, uncharged amino acids. However, the pore size of an eight-stranded β-barrel monomer of OprG is too narrow to accommodate even the smallest transported amino acid, glycine, raising the question of how OprG facilitates amino acid uptake. Pro-92 of OprG is critically important for amino acid transport, with a P92A substitution inhibiting transport and the NMR structure of this variant revealing that this substitution produces structural changes in the barrel rim and restricts loop motions. OprG may assemble into oligomers in the outer membrane (OM) whose subunit interfaces could form a transport channel. Here, we explored the contributions of the oligomeric state and the extracellular loops to OprG's function. Using chemical cross-linking to determine the oligomeric structures of both WT and P92A OprG in native outer membranes and atomic force microscopy, and single-molecule fluorescence of the purified proteins reconstituted into lipid bilayers, we found that both protein variants form oligomers, supporting the notion that subunit interfaces in the oligomer could provide a pathway for amino acid transport. Furthermore, performing transport assays with loop-deleted OprG variants, we found that these variants also can transport small amino acids, indicating that the loops are not solely responsible for substrate transport. We propose that OprG functions as an oligomer and that conformational changes in the barrel-loop region might be crucial for its activity.
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Affiliation(s)
| | - Patrick Seelheim
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
| | - Brendan Marsh
- the Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 OWA, United Kingdom
| | - Volker Kiessling
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
| | - Carl E Creutz
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908 and
| | - Lukas K Tamm
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
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16
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Travers T, Wang KJ, López CA, Gnanakaran S. Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes. Res Microbiol 2018; 169:414-424. [DOI: 10.1016/j.resmic.2018.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/21/2018] [Indexed: 01/12/2023]
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17
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Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley MGJ, Orange N, Dufour A, Cornelis P. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev 2017; 41:698-722. [PMID: 28981745 DOI: 10.1093/femsre/fux020] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Josselin Bodilis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Laboratoire de Biotechnologie et Chimie Marines EA 3884, Université de Bretagne-Sud (UEB), 56321 Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, University of Rouen, Normandy University, 27000 Evreux, France
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18
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Guilbaud M, Bruzaud J, Bouffartigues E, Orange N, Guillot A, Aubert-Frambourg A, Monnet V, Herry JM, Chevalier S, Bellon-Fontaine MN. Proteomic Response of Pseudomonas aeruginosa PAO1 Adhering to Solid Surfaces. Front Microbiol 2017; 8:1465. [PMID: 28824592 PMCID: PMC5541441 DOI: 10.3389/fmicb.2017.01465] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/20/2017] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is a pathogenic micro-organism responsible for many hospital-acquired infections. It is able to adhere to solid surfaces and develop an immobilized community or so-called biofilm. Many studies have been focusing on the use of specific materials to prevent the formation of these biofilms, but the reactivity of the bacteria in contact to surfaces remains unknown. The aim of this study was to evaluate the impact of the abiotic surface on the physiology of adherent bacteria. Three different materials, stainless steel (SS), glass (G), and polystyrene (PS) that were relevant to industrial or medical environments were characterized at the physicochemical level in terms of their hydrophobicity and roughness. We showed that SS was moderately hydrophilic and rough, potentially containing crevices, G was hydrophilic and smooth while PS was hydrophobic and smooth. We further showed that P. aeruginosa cells were more likely able to adhere to SS and G rather than PS surfaces under our experimental conditions. The physiological response of P. aeruginosa when adhering to each of these materials was then evaluated by global proteomic analysis. The abundance of 70 proteins was shown to differ between the materials suggesting that their abundance was modified as a function of the material to which bacteria adhered. Our data lead to enabling the identification of abundance patterns that appeared to be specific to a given surface. Taken together, our data showed that P. aeruginosa is capable of sensing and responding to a surface probably via specific programmes to adapt its physiological response accordingly.
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Affiliation(s)
- Morgan Guilbaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Jérôme Bruzaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Emeline Bouffartigues
- Laboratoire de Microbiologie, Signaux et Microenvironnement, Normandie Université, Université de Rouen-NormandieRouen, France
| | - Nicole Orange
- Laboratoire de Microbiologie, Signaux et Microenvironnement, Normandie Université, Université de Rouen-NormandieRouen, France
| | - Alain Guillot
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Anne Aubert-Frambourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Véronique Monnet
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Jean-Marie Herry
- Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Sylvie Chevalier
- Laboratoire de Microbiologie, Signaux et Microenvironnement, Normandie Université, Université de Rouen-NormandieRouen, France
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19
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NMR as a tool to investigate the structure, dynamics and function of membrane proteins. Nat Struct Mol Biol 2017; 23:468-74. [PMID: 27273629 DOI: 10.1038/nsmb.3226] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
Membrane-protein NMR occupies a unique niche for determining structures, assessing dynamics, examining folding, and studying the binding of lipids, ligands and drugs to membrane proteins. However, NMR analyses of membrane proteins also face special challenges that are not encountered with soluble proteins, including sample preparation, size limitation, spectral crowding and sparse data accumulation. This Perspective provides a snapshot of current achievements, future opportunities and possible limitations in this rapidly developing field.
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20
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Schwarzer TS, Hermann M, Krishnan S, Simmel FC, Castiglione K. Preparative refolding of small monomeric outer membrane proteins. Protein Expr Purif 2017; 132:171-181. [DOI: 10.1016/j.pep.2017.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/16/2016] [Accepted: 01/31/2017] [Indexed: 12/13/2022]
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21
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Kucharska I, Liang B, Ursini N, Tamm LK. Molecular Interactions of Lipopolysaccharide with an Outer Membrane Protein from Pseudomonas aeruginosa Probed by Solution NMR. Biochemistry 2016; 55:5061-72. [PMID: 27532487 DOI: 10.1021/acs.biochem.6b00630] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen causing pneumonias that are particularly severe in cystic fibrosis and immunocompromised patients. The outer membrane (OM) of P. aeruginosa is much less permeable to nutrients and other chemical compounds than that of Escherichia coli. The low permeability of the OM, which also contributes to Pseudomonas' significant antibiotic resistance, is augmented by the presence of the outer membrane protein H (OprH). OprH directly interacts with lipopolysaccharides (LPS) that constitute the outer leaflet of the OM and thus contributes to the structural stability of the OM. In this study, we used solution NMR spectroscopy to characterize the interactions between LPS and OprH in molecular detail. NMR chemical shift perturbations observed upon the addition of LPS to OprH in DHPC micelles indicate that this interaction is predominantly electrostatic and localized to the extracellular loops 2 and 3 and a number of highly conserved basic residues near the extracellular barrel rim of OprH. Single-site mutations of these residues were not enough to completely abolish binding, but OprH with cumulative mutations of Lys70, Arg72, and Lys103 no longer binds LPS. The dissociation constant (∼200 μM) measured by NMR is sufficient to efficiently bind LPS to OprH in the OM. This work highlights that solution NMR is suitable to study specific interactions of lipids with integral membrane proteins and provides a detailed molecular model for the interaction of LPS with OprH; i.e., an interaction that contributes to the integrity of the OM of P. aeruginosa under low divalent cation and antibiotic stress conditions. These methods should thus be useful for screening antibiotics that might disrupt OprH-LPS interactions and thereby increase the permeability of the OM of P. aeruginosa.
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Affiliation(s)
- Iga Kucharska
- Center for Membrane and Cell Physiology and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Charlottesville, Virginia 22908, United States
| | - Binyong Liang
- Center for Membrane and Cell Physiology and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Charlottesville, Virginia 22908, United States
| | - Nicholas Ursini
- Center for Membrane and Cell Physiology and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Charlottesville, Virginia 22908, United States
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine , Charlottesville, Virginia 22908, United States
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22
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Wu X, Ren G, Gunning WT, Weaver DA, Kalinoski AL, Khuder SA, Huntley JF. FmvB: A Francisella tularensis Magnesium-Responsive Outer Membrane Protein that Plays a Role in Virulence. PLoS One 2016; 11:e0160977. [PMID: 27513341 PMCID: PMC4981453 DOI: 10.1371/journal.pone.0160977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/26/2016] [Indexed: 02/06/2023] Open
Abstract
Francisella tularensis is the causative agent of the lethal disease tularemia. Despite decades of research, little is understood about why F. tularensis is so virulent. Bacterial outer membrane proteins (OMPs) are involved in various virulence processes, including protein secretion, host cell attachment, and intracellular survival. Many pathogenic bacteria require metals for intracellular survival and OMPs often play important roles in metal uptake. Previous studies identified three F. tularensis OMPs that play roles in iron acquisition. In this study, we examined two previously uncharacterized proteins, FTT0267 (named fmvA, for Francisellametal and virulence) and FTT0602c (fmvB), which are homologs of the previously studied F. tularensis iron acquisition genes and are predicted OMPs. To study the potential roles of FmvA and FmvB in metal acquisition and virulence, we first examined fmvA and fmvB expression following pulmonary infection of mice, finding that fmvB was upregulated up to 5-fold during F. tularensis infection of mice. Despite sequence homology to previously-characterized iron-acquisition genes, FmvA and FmvB do not appear to be involved iron uptake, as neither fmvA nor fmvB were upregulated in iron-limiting media and neither ΔfmvA nor ΔfmvB exhibited growth defects in iron limitation. However, when other metals were examined in this study, magnesium-limitation significantly induced fmvB expression, ΔfmvB was found to express significantly higher levels of lipopolysaccharide (LPS) in magnesium-limiting medium, and increased numbers of surface protrusions were observed on ΔfmvB in magnesium-limiting medium, compared to wild-type F. tularensis grown in magnesium-limiting medium. RNA sequencing analysis of ΔfmvB revealed the potential mechanism for increased LPS expression, as LPS synthesis genes kdtA and wbtA were significantly upregulated in ΔfmvB, compared with wild-type F. tularensis. To provide further evidence for the potential role of FmvB in magnesium uptake, we demonstrated that FmvB was outer membrane-localized. Finally, ΔfmvB was found to be attenuated in mice and cytokine analyses revealed that ΔfmvB-infected mice produced lower levels of pro-inflammatory cytokines, including GM-CSF, IL-3, and IL-10, compared with mice infected with wild-type F. tularensis. Taken together, although the function of FmvA remains unknown, FmvB appears to play a role in magnesium uptake and F. tularensis virulence. These results may provide new insights into the importance of magnesium for intracellular pathogens.
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Affiliation(s)
- Xiaojun Wu
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Guoping Ren
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - William T. Gunning
- Department of Pathology and Electron Microscopy Facility, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - David A. Weaver
- Department of Surgery and Advanced Microscopy and Imaging Center, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Andrea L. Kalinoski
- Department of Surgery and Advanced Microscopy and Imaging Center, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Sadik A. Khuder
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
| | - Jason F. Huntley
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States of America
- * E-mail:
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23
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Artificial membranes for membrane protein purification, functionality and structure studies. Biochem Soc Trans 2016; 44:877-82. [DOI: 10.1042/bst20160054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method.
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