51
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Deng Z, Yuan B, Yang K. Cardiolipin Selectively Binds to the Interface of VsSemiSWEET and Regulates Its Dimerization. J Phys Chem Lett 2021; 12:1940-1946. [PMID: 33591759 DOI: 10.1021/acs.jpclett.1c00022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipid-regulated oligomerization of membrane proteins plays a critical role in many cell-transduction pathways. However, molecular details of such processes are often hard to define experimentally. Here we reveal the key role of interfacial cardiolipin in regulating the functional dimerization of VsSemiSWEET (one of the smallest transporters) using molecular dynamics simulations. Four binding sites for cardiolipins are identified by calculating the spatiotemporal density distribution of cardiolipins and the free energy surface. Two types of dimerization modes (i.e., arm-to-body and body-to-body) are observed in the assembly process of VsSemiSWEET protomers. Binding of enough cardiolipin molecules at the dimer interface on the cytoplasmic side is found to be crucial in adjusting the monomer-dimer equilibrium and regulating the formation of functional dimers with proper conformation. Our results provide useful information on the relationship between lipid binding and functional dimerization of VsSemiSWEET and are helpful to understand the molecular mechanism of biological function of sugar transporters.
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Affiliation(s)
- Zhixiong Deng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P.R. China
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52
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Szczepaniak J, Press C, Kleanthous C. The multifarious roles of Tol-Pal in Gram-negative bacteria. FEMS Microbiol Rev 2021; 44:490-506. [PMID: 32472934 PMCID: PMC7391070 DOI: 10.1093/femsre/fuaa018] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
In the 1960s several groups reported the isolation and preliminary genetic mapping of
Escherichia coli strains tolerant towards the
action of colicins. These pioneering studies kick-started two new fields in bacteriology;
one centred on how bacteriocins like colicins exploit the Tol (or more commonly Tol-Pal)
system to kill bacteria, the other on the physiological role of this cell
envelope-spanning assembly. The following half century has seen significant advances in
the first of these fields whereas the second has remained elusive, until recently. Here,
we review work that begins to shed light on Tol-Pal function in Gram-negative bacteria.
What emerges from these studies is that Tol-Pal is an energised system with fundamental,
interlinked roles in cell division – coordinating the re-structuring of peptidoglycan at
division sites and stabilising the connection between the outer membrane and underlying
cell wall. This latter role is achieved by Tol-Pal exploiting the proton motive force to
catalyse the accumulation of the outer membrane peptidoglycan associated lipoprotein Pal
at division sites while simultaneously mobilising Pal molecules from around the cell.
These studies begin to explain the diverse phenotypic outcomes of tol-pal
mutations, point to other cell envelope roles Tol-Pal may have and raise many new
questions.
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Affiliation(s)
- Joanna Szczepaniak
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Cara Press
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
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53
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Hatton NE, Baumann CG, Fascione MA. Developments in Mannose-Based Treatments for Uropathogenic Escherichia coli-Induced Urinary Tract Infections. Chembiochem 2021; 22:613-629. [PMID: 32876368 PMCID: PMC7894189 DOI: 10.1002/cbic.202000406] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/28/2020] [Indexed: 12/16/2022]
Abstract
During their lifetime almost half of women will experience a symptomatic urinary tract infection (UTI) with a further half experiencing a relapse within six months. Currently UTIs are treated with antibiotics, but increasing antibiotic resistance rates highlight the need for new treatments. Uropathogenic Escherichia coli (UPEC) is responsible for the majority of symptomatic UTI cases and thus has become a key pathological target. Adhesion of type one pilus subunit FimH at the surface of UPEC strains to mannose-saturated oligosaccharides located on the urothelium is critical to pathogenesis. Since the identification of FimH as a therapeutic target in the late 1980s, a substantial body of research has been generated focusing on the development of FimH-targeting mannose-based anti-adhesion therapies. In this review we will discuss the design of different classes of these mannose-based compounds and their utility and potential as UPEC therapeutics.
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Affiliation(s)
- Natasha E. Hatton
- York Structural Biology Lab, Department of ChemistryUniversity of YorkHeslington RoadYorkYO10 5DDUK
| | | | - Martin A. Fascione
- York Structural Biology Lab, Department of ChemistryUniversity of YorkHeslington RoadYorkYO10 5DDUK
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54
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Lundquist K, Billings E, Bi M, Wellnitz J, Noinaj N. The assembly of β-barrel membrane proteins by BAM and SAM. Mol Microbiol 2020; 115:425-435. [PMID: 33314350 DOI: 10.1111/mmi.14666] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Indexed: 12/31/2022]
Abstract
Gram-negative bacteria, mitochondria, and chloroplasts all possess an outer membrane populated with a host of β-barrel outer-membrane proteins (βOMPs). These βOMPs play crucial roles in maintaining viability of their hosts, and therefore, it is essential to understand the biogenesis of this class of membrane proteins. In recent years, significant structural and functional advancements have been made toward elucidating this process, which is mediated by the β-barrel assembly machinery (BAM) in Gram-negative bacteria, and by the sorting and assembly machinery (SAM) in mitochondria. Structures of both BAM and SAM have now been reported, allowing a comparison and dissection of the two machineries, with other studies reporting on functional aspects of each. Together, these new insights provide compelling support for the proposed budding mechanism, where each nascent βOMP forms a hybrid-barrel intermediate with BAM/SAM in route to its biogenesis into the membrane. Here, we will review these recent studies and highlight their contributions toward understanding βOMP biogenesis in Gram-negative bacteria and in mitochondria. We will also weigh the evidence supporting each of the two leading mechanistic models for how BAM/SAM function, and offer an outlook on future studies within the field.
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Affiliation(s)
- Karl Lundquist
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Evan Billings
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Maxine Bi
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - James Wellnitz
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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55
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Iadanza MG, Schiffrin B, White P, Watson MA, Horne JE, Higgins AJ, Calabrese AN, Brockwell DJ, Tuma R, Kalli AC, Radford SE, Ranson NA. Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs. Commun Biol 2020; 3:766. [PMID: 33318620 PMCID: PMC7736308 DOI: 10.1038/s42003-020-01419-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022] Open
Abstract
The β-barrel assembly machinery (BAM) catalyses the folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria by mechanisms that remain unclear. Here, we present an ensemble of cryoEM structures of the E. coli BamABCDE (BAM) complex in lipid nanodiscs, determined using multi-body refinement techniques. These structures, supported by single-molecule FRET measurements, describe a range of motions in the BAM complex, mostly localised within the periplasmic region of the major subunit BamA. The β-barrel domain of BamA is in a 'lateral open' conformation in all of the determined structures, suggesting that this is the most energetically favourable species in this bilayer. Strikingly, the BAM-containing lipid nanodisc is deformed, especially around BAM's lateral gate. This distortion is also captured in molecular dynamics simulations, and provides direct structural evidence for the lipid 'disruptase' activity of BAM, suggested to be an important part of its functional mechanism.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew A Watson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Anna J Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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56
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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57
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Veith PD, Gorasia DG, Reynolds EC. Towards defining the outer membrane proteome of Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:25-36. [PMID: 33124778 DOI: 10.1111/omi.12320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/18/2023]
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobic pathogen found in subgingival plaque associated with progressive periodontitis. Proteins associated with the outer membrane (OM) of Gram-negative pathogens are particularly important for understanding virulence and for developing vaccines. The aim of this study was to establish a reliable list of outer membrane associated proteins (Omps) for this organism. Starting with a list of 99 experimentally determined Omps, several bioinformatics tools were used to predict a further 52 proteins, leading to a predicted OM proteome of 151 proteins. The tools used included databases of protein families, prediction of OM β-barrels and structural homology. The list includes 33 T9SS cargo proteins, 43 lipoproteins and 66 OM β-barrel proteins with some overlap between categories. The proteins are discussed both in these structural categories as well as their various functions in OM biogenesis, nutrient acquisition, protein secretion, adhesion and efflux. Proteins that were previously shown to be part of large complexes are highlighted and cross reference is provided to a previous major study of protein localization in P. gingivalis. Finally, proteins were also scored according to their level of conservation within the Bacteroidales taxon. Low scores were shown to correlate with virulence factors and may be predictive of novel virulence factors.
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Affiliation(s)
- Paul D Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Dhana G Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
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58
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Alvira S, Watkins DW, Troman LA, Allen WJ, Lorriman JS, Degliesposti G, Cohen EJ, Beeby M, Daum B, Gold VAM, Skehel JM, Collinson I. Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis. eLife 2020; 9:e60669. [PMID: 33146611 PMCID: PMC7695460 DOI: 10.7554/elife.60669] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
The outer-membrane of Gram-negative bacteria is critical for surface adhesion, pathogenicity, antibiotic resistance and survival. The major constituent - hydrophobic β-barrel Outer-Membrane Proteins (OMPs) - are first secreted across the inner-membrane through the Sec-translocon for delivery to periplasmic chaperones, for example SurA, which prevent aggregation. OMPs are then offloaded to the β-Barrel Assembly Machinery (BAM) in the outer-membrane for insertion and folding. We show the Holo-TransLocon (HTL) - an assembly of the protein-channel core-complex SecYEG, the ancillary sub-complex SecDF, and the membrane 'insertase' YidC - contacts BAM through periplasmic domains of SecDF and YidC, ensuring efficient OMP maturation. Furthermore, the proton-motive force (PMF) across the inner-membrane acts at distinct stages of protein secretion: (1) SecA-driven translocation through SecYEG and (2) communication of conformational changes via SecDF across the periplasm to BAM. The latter presumably drives efficient passage of OMPs. These interactions provide insights of inter-membrane organisation and communication, the importance of which is becoming increasingly apparent.
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Affiliation(s)
- Sara Alvira
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Luca A Troman
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - William J Allen
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - James S Lorriman
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Gianluca Degliesposti
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Eli J Cohen
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Bertram Daum
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- College of Life and Environmental Sciences, University of ExeterExeterUnited Kingdom
| | - Vicki AM Gold
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- College of Life and Environmental Sciences, University of ExeterExeterUnited Kingdom
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ian Collinson
- School of Biochemistry, University of BristolBristolUnited Kingdom
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59
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Inoue Y, Suzuki R, Murata I, Nomura H, Isshiki Y, Kanamoto I. Evaluation of Antibacterial Activity Expression of the Hinokitiol/Cyclodextrin Complex Against Bacteria. ACS OMEGA 2020; 5:27180-27187. [PMID: 33134678 PMCID: PMC7594135 DOI: 10.1021/acsomega.0c03222] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/06/2020] [Indexed: 05/12/2023]
Abstract
The purpose of this study was to assess the antimicrobial activity of a solid dispersion prepared by mixing and grinding hinokitiol (HT) with α-cyclodextrin (αCD), β-cyclodextrin (βCD), or γ-cyclodextrin (γCD). Antimicrobial activity was evaluated by calculating the minimum inhibitory concentration (MIC) and evaluating the change in the number of bacteria over time. The test microbes used were two Gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus), two Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa), and two fungi (Candida albicans and Aspergillus brasiliensis). Calculation of the MIC value of HT using the agar dilution method revealed that the MIC of HT/CD inclusion complexes was lower than that of HT alone. HT irreversibly inhibited the growth of microorganisms in a short amount of time. HT/CD complexes retained the antimicrobial activity of HT as a result of including HT in a CD complex. These results suggest that inclusion of HT, an antimicrobial component, using CDs could lead to appropriate control of the drug release rate and efficient display of antimicrobial activity.
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Affiliation(s)
- Yutaka Inoue
- Laboratory
of Drug Safety Management, Faculty of Pharmacy and Pharmaceutical
Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
- . Tel: +81-49-271-7317. Fax: +81-49-271-7317
| | - Rina Suzuki
- Laboratory
of Drug Safety Management, Faculty of Pharmacy and Pharmaceutical
Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
| | - Isamu Murata
- Laboratory
of Drug Safety Management, Faculty of Pharmacy and Pharmaceutical
Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
| | - Harue Nomura
- Department
of Microbiology, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
| | - Yasunori Isshiki
- Department
of Microbiology, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
| | - Ikuo Kanamoto
- Laboratory
of Drug Safety Management, Faculty of Pharmacy and Pharmaceutical
Sciences, Josai University, 1-1 Keyakidai, Sakado-shi, Saitama 3500295, Japan
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60
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Chekli Y, Peron-Cane C, Dell'Arciprete D, Allemand JF, Li C, Ghigo JM, Gautier A, Lebreton A, Desprat N, Beloin C. Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST. Sci Rep 2020; 10:15791. [PMID: 32978420 PMCID: PMC7519654 DOI: 10.1038/s41598-020-72498-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
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Affiliation(s)
- Yankel Chekli
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Caroline Peron-Cane
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Dario Dell'Arciprete
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
| | - Jean-François Allemand
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chenge Li
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
- Institut Universitaire de France, Paris, France
| | - Alice Lebreton
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- INRAE, IBENS, 75005, Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France.
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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61
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Native Cell Environment Constrains Loop Structure in the Escherichia coli Cobalamin Transporter BtuB. Biophys J 2020; 119:1550-1557. [PMID: 32946767 DOI: 10.1016/j.bpj.2020.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 11/23/2022] Open
Abstract
The extracellular loops of bacterial outer membrane (OM) transporters are thought to sample a range of conformations in the apo state but to undergo a gating motion and assume a more defined conformation upon the binding of substrate. Here, we use pulse electron paramagnetic resonance to examine the conformations of the extracellular loops of BtuB, the Escherichia coli TonB-dependent vitamin B12 transporter, in whole cells. Unlike previous measurements carried out in vitro, the loops assume well-defined configurations in situ that closely match the in surfo crystal structures. Moreover, there is no evidence that the loops undergo significant gating motions upon the binding of substrate. The results demonstrate that the structure of BtuB is dependent upon an intact native OM environment, in which a critical component is likely to be the extracellular lipopolysaccharide. In general, this work indicates that measurements on OM proteins in reconstituted membrane systems may not reflect the native state of the protein in vivo.
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62
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Cao P, Wall D. The Fluidity of the Bacterial Outer Membrane Is Species Specific: Bacterial Lifestyles and the Emergence of a Fluid Outer Membrane. Bioessays 2020; 42:e1900246. [PMID: 32363627 PMCID: PMC7392792 DOI: 10.1002/bies.201900246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/23/2020] [Indexed: 01/17/2023]
Abstract
The outer membrane (OM) is an essential barrier that guards Gram-negative bacteria from diverse environmental insults. Besides functioning as a chemical gatekeeper, the OM also contributes towards the strength and stiffness of cells and allows them to sustain mechanical stress. Largely influenced by studies of Escherichia coli, the OM is viewed as a rigid barrier where OM proteins and lipopolysaccharides display restricted mobility. Here the discussion is extended to other bacterial species, with a focus on Myxococcus xanthus. In contrast to the rigid OM paradigm, myxobacteria possess a relatively fluid OM. It is concluded that the fluidity of the OM varies across environmental species, which is likely linked to their evolution and adaptation to specific ecological niches. Importantly, a fluid OM can endow bacteria with distinct functions for cell-cell and cell-environment interactions.
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Affiliation(s)
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA
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63
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Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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64
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Jansen KB, Inns PG, Housden NG, Hopper JTS, Kaminska R, Lee S, Robinson CV, Bayley H, Kleanthous C. Bifurcated binding of the OmpF receptor underpins import of the bacteriocin colicin N into Escherichia coli. J Biol Chem 2020; 295:9147-9156. [PMID: 32398259 PMCID: PMC7335789 DOI: 10.1074/jbc.ra120.013508] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/04/2020] [Indexed: 11/14/2022] Open
Abstract
Colicins are Escherichia coli-specific bacteriocins that translocate across the outer bacterial membrane by a poorly understood mechanism. Group A colicins typically parasitize the proton-motive force-linked Tol system in the inner membrane via porins after first binding an outer membrane protein receptor. Recent studies have suggested that the pore-forming group A colicin N (ColN) instead uses lipopolysaccharide as a receptor. Contrary to this prevailing view, using diffusion-precipitation assays, native state MS, isothermal titration calorimetry, single-channel conductance measurements in planar lipid bilayers, and in vivo fluorescence imaging, we demonstrate here that ColN uses OmpF both as its receptor and translocator. This dual function is achieved by ColN having multiple distinct OmpF-binding sites, one located within its central globular domain and another within its disordered N terminus. We observed that the ColN globular domain associates with the extracellular surface of OmpF and that lipopolysaccharide (LPS) enhances this binding. Approximately 90 amino acids of ColN then translocate through the porin, enabling the ColN N terminus to localize within the lumen of an OmpF subunit from the periplasmic side of the membrane, a binding mode reminiscent of that observed for the nuclease colicin E9. We conclude that bifurcated engagement of porins is intrinsic to the import mechanism of group A colicins.
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Affiliation(s)
| | | | | | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sejeong Lee
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Hagan Bayley
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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65
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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66
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Nyenhuis DA, Nilaweera TD, Niblo JK, Nguyen NQ, DuBay KH, Cafiso DS. Evidence for the Supramolecular Organization of a Bacterial Outer-Membrane Protein from In Vivo Pulse Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc 2020; 142:10715-10722. [PMID: 32452197 DOI: 10.1021/jacs.0c01754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the outer membrane of Gram-negative bacteria, membrane proteins are thought to be organized into domains or islands that play a role in the segregation, movement, and turnover of membrane components. However, there is presently limited information on the structure of these domains or the molecular interactions that mediate domain formation. In the present work, the Escherichia coli outer membrane vitamin B12 transporter, BtuB, was spin-labeled, and double electron-electron resonance was used to measure the distances between proteins in intact cells. These data together with Monte Carlo simulations provide evidence for the presence of specific intermolecular contacts between BtuB monomers that could drive the formation of string-like oligomers. Moreover, the EPR data provide evidence for the location of the interacting interfaces and indicate that lipopolysaccharide mediates the contacts between BtuB monomers.
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67
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Carballo-Pacheco M, Nicholson MD, Lilja EE, Allen RJ, Waclaw B. Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications. PLoS Comput Biol 2020; 16:e1007930. [PMID: 32469859 PMCID: PMC7307788 DOI: 10.1371/journal.pcbi.1007930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/22/2020] [Accepted: 05/06/2020] [Indexed: 11/19/2022] Open
Abstract
Phenotypic delay-the time delay between genetic mutation and expression of the corresponding phenotype-is generally neglected in evolutionary models, yet recent work suggests that it may be more common than previously assumed. Here, we use computer simulations and theory to investigate the significance of phenotypic delay for the evolution of bacterial resistance to antibiotics. We consider three mechanisms which could potentially cause phenotypic delay: effective polyploidy, dilution of antibiotic-sensitive molecules and accumulation of resistance-enhancing molecules. We find that the accumulation of resistant molecules is relevant only within a narrow parameter range, but both the dilution of sensitive molecules and effective polyploidy can cause phenotypic delay over a wide range of parameters. We further investigate whether these mechanisms could affect population survival under drug treatment and thereby explain observed discrepancies in mutation rates estimated by Luria-Delbrück fluctuation tests. While the effective polyploidy mechanism does not affect population survival, the dilution of sensitive molecules leads both to decreased probability of survival under drug treatment and underestimation of mutation rates in fluctuation tests. The dilution mechanism also changes the shape of the Luria-Delbrück distribution of mutant numbers, and we show that this modified distribution provides an improved fit to previously published experimental data.
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Affiliation(s)
| | - Michael D. Nicholson
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Elin E. Lilja
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J. Allen
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, United Kingdom
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68
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Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae. mBio 2020; 11:mBio.00603-20. [PMID: 32291303 PMCID: PMC7157821 DOI: 10.1128/mbio.00603-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is a pathogen of humans with high rates of mortality and a recognized global rise in incidence of carbapenem-resistant K. pneumoniae (CRKP). The outer membrane of K. pneumoniae forms a permeability barrier that modulates the ability of antibiotics to reach their intracellular target. OmpK35, OmpK36, OmpK37, OmpK38, PhoE, and OmpK26 are porins in the outer membrane of K. pneumoniae, demonstrated here to have a causative relationship to drug resistance phenotypes in a physiological context. The data highlight that currently trialed combination treatments with a carbapenem and β-lactamase inhibitors could be effective on porin-deficient K. pneumoniae. Together with structural data, the results reveal the role of outer membrane proteome remodeling in antimicrobial resistance of K. pneumoniae and point to the role of extracellular loops, not channel parameters, in drug permeation. This significant finding warrants care in the development of phage therapies for K. pneumoniae infections, given the way porin expression will be modulated to confer phage-resistant—and collateral drug-resistant—phenotypes in K. pneumoniae. In Gram-negative bacteria, the permeability of the outer membrane governs rates of antibiotic uptake and thus the efficacy of antimicrobial treatment. Hydrophilic drugs like β-lactam antibiotics depend on diffusion through pore-forming outer membrane proteins to reach their intracellular targets. In this study, we investigated the distribution of porin genes in more than 2,700 Klebsiella isolates and found a widespread loss of OmpK35 functionality, particularly in those strains isolated from clinical environments. Using a defined set of outer-membrane-remodeled mutants, the major porin OmpK35 was shown to be largely responsible for β-lactam permeation. Sequence similarity network analysis characterized the porin protein subfamilies and led to discovery of a new porin family member, OmpK38. Structure-based comparisons of OmpK35, OmpK36, OmpK37, OmpK38, and PhoE showed near-identical pore frameworks but defining differences in the sequence characteristics of the extracellular loops. Antibiotic sensitivity profiles of isogenic Klebsiella pneumoniae strains, each expressing a different porin as its dominant pore, revealed striking differences in the antibiotic permeability characteristics of each channel in a physiological context. Since K. pneumoniae is a nosocomial pathogen with high rates of antimicrobial resistance and concurrent mortality, these experiments elucidate the role of porins in conferring specific drug-resistant phenotypes in a global context, informing future research to combat antimicrobial resistance in K. pneumoniae.
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69
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Szczepaniak J, Holmes P, Rajasekar K, Kaminska R, Samsudin F, Inns PG, Rassam P, Khalid S, Murray SM, Redfield C, Kleanthous C. The lipoprotein Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism. Nat Commun 2020; 11:1305. [PMID: 32161270 PMCID: PMC7066135 DOI: 10.1038/s41467-020-15083-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/13/2020] [Indexed: 11/24/2022] Open
Abstract
Coordination of outer membrane constriction with septation is critical to faithful division in Gram-negative bacteria and vital to the barrier function of the membrane. This coordination requires the recruitment of the peptidoglycan-binding outer-membrane lipoprotein Pal at division sites by the Tol system. Here, we show that Pal accumulation at Escherichia coli division sites is a consequence of three key functions of the Tol system. First, Tol mobilises Pal molecules in dividing cells, which otherwise diffuse very slowly due to their binding of the cell wall. Second, Tol actively captures mobilised Pal molecules and deposits them at the division septum. Third, the active capture mechanism is analogous to that used by the inner membrane protein TonB to dislodge the plug domains of outer membrane TonB-dependent nutrient transporters. We conclude that outer membrane constriction is coordinated with cell division by active mobilisation-and-capture of Pal at division septa by the Tol system.
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Affiliation(s)
| | - Peter Holmes
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Karthik Rajasekar
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Evotec SE, 112-114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Firdaus Samsudin
- Department of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | | | - Patrice Rassam
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Laboratoire de Bioimagerie et Pathologie, UMR 7021, CNRS, Université de Strasbourg, Faculté de pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Syma Khalid
- Department of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, 35043, Marburg, Germany
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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70
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Domínguez-Medina CC, Pérez-Toledo M, Schager AE, Marshall JL, Cook CN, Bobat S, Hwang H, Chun BJ, Logan E, Bryant JA, Channell WM, Morris FC, Jossi SE, Alshayea A, Rossiter AE, Barrow PA, Horsnell WG, MacLennan CA, Henderson IR, Lakey JH, Gumbart JC, López-Macías C, Bavro VN, Cunningham AF. Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface. Nat Commun 2020; 11:851. [PMID: 32051408 PMCID: PMC7015928 DOI: 10.1038/s41467-020-14655-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/23/2020] [Indexed: 11/28/2022] Open
Abstract
Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs. The O-antigen of LPS is known to limit the binding of antibody to bacterial surface antigens. Here the AUs show that the chemical and physical structure of the O-antigen are central factors in limiting the exposure of surface antigens to antibodies during Salmonella infection, thus defining their protective qualities.
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Affiliation(s)
- C Coral Domínguez-Medina
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marisol Pérez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.,Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Anna E Schager
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jennifer L Marshall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Charlotte N Cook
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Saeeda Bobat
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Byeong Jae Chun
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta GA, 30332, USA
| | - Erin Logan
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Will M Channell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Areej Alshayea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - William G Horsnell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, Western Cape, 7925, South Africa
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Constantino López-Macías
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre "Siglo XXI" Mexican Institute for Social Security, Mexico City, Mexico
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
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71
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Rojas ER. The Mechanical Properties of Bacteria and Why they Matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:1-14. [PMID: 32894474 DOI: 10.1007/978-3-030-46886-6_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
I review recent techniques to measure the mechanical properties of bacterial cells and their subcellular components, and then discuss what these techniques have revealed about the constitutive mechanical properties of whole bacterial cells and subcellular material, as well as the molecular basis for these properties.
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Affiliation(s)
- Enrique R Rojas
- Department of Biology, New York University, New York, NY, USA.
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72
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Abstract
Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.
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Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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73
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Łapińska U, Glover G, Capilla-Lasheras P, Young AJ, Pagliara S. Bacterial ageing in the absence of external stressors. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180442. [PMID: 31587633 PMCID: PMC6792439 DOI: 10.1098/rstb.2018.0442] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/03/2022] Open
Abstract
Evidence of ageing in the bacterium Escherichia coli was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in E. coli in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the 'maternal old pole' progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Urszula Łapińska
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Georgina Glover
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Pablo Capilla-Lasheras
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Andrew J. Young
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Stefano Pagliara
- Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
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74
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Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T, Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T. The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane. Cell Rep 2019; 23:2782-2794. [PMID: 29847806 DOI: 10.1016/j.celrep.2018.04.093] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/05/2018] [Accepted: 04/23/2018] [Indexed: 01/28/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is essential for localization of surface proteins on bacterial cells, but the mechanism by which it functions is unclear. We developed a direct stochastic optical reconstruction microscopy (dSTORM) methodology to view the BAM complex in situ. Single-cell analysis showed that discrete membrane precincts housing several BAM complexes are distributed across the E. coli surface, with a nearest neighbor distance of ∼200 nm. The auxiliary lipoprotein subunit BamB was crucial for this spatial distribution, and in situ crosslinking shows that BamB makes intimate contacts with BamA and BamB in neighboring BAM complexes within the precinct. The BAM complex precincts swell when outer membrane protein synthesis is maximal, visual proof that the precincts are active in protein assembly. This nanoscale interrogation of the BAM complex in situ suggests a model whereby bacterial outer membranes contain highly organized assembly precincts to drive integral protein assembly.
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Affiliation(s)
- Sachith D Gunasinghe
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Takuya Shiota
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Christopher J Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Keith E Schulze
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Chaille T Webb
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Alex J Fulcher
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Iain D Hay
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Thomas Naderer
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Donna R Whelan
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Kirstin D Elgass
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Hudson Institute of Medical Research, Clayton, VIC 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
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75
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Wu R, Stephenson R, Gichaba A, Noinaj N. The big BAM theory: An open and closed case? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183062. [PMID: 31520605 DOI: 10.1016/j.bbamem.2019.183062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
The β-barrel assembly machinery (BAM) is responsible for the biogenesis of outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria. These OMPs have a membrane-embedded domain consisting of a β-barrel fold which can vary from 8 to 36 β-strands, with each serving a diverse role in the cell such as nutrient uptake and virulence. BAM was first identified nearly two decades ago, but only recently has the molecular structure of the full complex been reported. Together with many years of functional characterization, we have a significantly clearer depiction of BAM's structure, the intra-complex interactions, conformational changes that BAM may undergo during OMP biogenesis, and the role chaperones may play. But still, despite advances over the past two decades, the mechanism for BAM-mediated OMP biogenesis remains elusive. Over the years, several theories have been proposed that have varying degrees of support from the literature, but none has of yet been conclusive enough to be widely accepted as the sole mechanism. We will present a brief history of BAM, the recent work on the structures of BAM, and a critical analysis of the current theories for how it may function.
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Affiliation(s)
- Runrun Wu
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert Stephenson
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Abigail Gichaba
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
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Nilaweera TD, Nyenhuis DA, Nakamoto RK, Cafiso DS. Disulfide Chaperone Knockouts Enable In Vivo Double Spin Labeling of an Outer Membrane Transporter. Biophys J 2019; 117:1476-1484. [PMID: 31582182 DOI: 10.1016/j.bpj.2019.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022] Open
Abstract
Recent advances in the application of electron paramagnetic resonance spectroscopy have demonstrated that it is possible to obtain structural information on bacterial outer membrane (OM) proteins in intact cells from extracellularly labeled cysteines. However, in the Escherichia coli OM B12 transport protein, BtuB, the double labeling of many cysteine pairs is not possible in a wild-type K12-derived E. coli strain. It has also not yet been possible to selectively label single or paired cysteines that face the periplasmic space. Here, we demonstrate that the inability to produce reactive cysteine residues in pairs is a result of the disulfide bond formation system, which functions to oxidize pairs of free-cysteine residues. Mutant strains that are dsbA or dsbB null facilitate labeling pairs of cysteines. Moreover, we demonstrate that the double labeling of sites on the periplasmic-facing surface of BtuB is possible using a dsbA null strain. BtuB is found to exhibit different structures and structural changes in the cell than it does in isolated OMs or reconstituted systems, and the ability to label and perform electron paramagnetic resonance in cells is expected to be applicable to a range of other bacterial OM proteins.
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Affiliation(s)
- Thushani D Nilaweera
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David A Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
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Establishment of a Protein Concentration Gradient in the Outer Membrane Requires Two Diffusion-Limiting Mechanisms. J Bacteriol 2019; 201:JB.00177-19. [PMID: 31209077 DOI: 10.1128/jb.00177-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/12/2019] [Indexed: 11/20/2022] Open
Abstract
OmpA-like proteins are involved in the stabilization of the outer membrane, resistance to osmotic stress, and pathogenesis. In Caulobacter crescentus, OmpA2 forms a physiologically relevant concentration gradient that forms by an uncharacterized mechanism, in which the gradient orientation depends on the position of the gene locus. This suggests that OmpA2 is synthesized and translocated to the periplasm close to the position of the gene and that the gradient forms by diffusion of the protein from this point. To further understand how the OmpA2 gradient is established, we determined the localization and mobility of the full protein and of its two structural domains. We show that OmpA2 does not diffuse and that both domains are required for gradient formation. The C-terminal domain binds tightly to the cell wall and the immobility of the full protein depends on the binding of this domain to the peptidoglycan; in contrast, the N-terminal membrane β-barrel diffuses slowly. Our results support a model in which once OmpA2 is translocated to the periplasm, the N-terminal membrane β-barrel is required for an initial fast restriction of diffusion until the position of the protein is stabilized by the binding of the C-terminal domain to the cell wall. The implications of these results on outer membrane protein diffusion and organization are discussed.IMPORTANCE Protein concentration gradients play a relevant role in the organization of the bacterial cell. The Caulobacter crescentus protein OmpA2 forms an outer membrane polar concentration gradient. To understand the molecular mechanism that determines the formation of this gradient, we characterized the mobility and localization of the full protein and of its two structural domains an integral outer membrane β-barrel and a periplasmic peptidoglycan binding domain. Each domain has a different role in the formation of the OmpA2 gradient, which occurs in two steps. We also show that the OmpA2 outer membrane β-barrel can diffuse, which is in contrast to what has been reported previously for several integral outer membrane proteins in Escherichia coli, suggesting a different organization of the outer membrane proteins.
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78
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Cao P, Wall D. Direct visualization of a molecular handshake that governs kin recognition and tissue formation in myxobacteria. Nat Commun 2019; 10:3073. [PMID: 31300643 PMCID: PMC6626042 DOI: 10.1038/s41467-019-11108-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Many organisms regulate their social life through kin recognition, but the underlying mechanisms are poorly understood. Here, we use a social bacterium, Myxococcus xanthus, to investigate kin recognition at the molecular level. By direct visualization of a cell surface receptor, TraA, we show how these myxobacteria identify kin and transition towards multicellularity. TraA is fluid on the cell surface, and homotypic interactions between TraA from juxtaposed cells trigger the receptors to coalesce, representing a ‘molecular handshake’. Polymorphisms within TraA govern social recognition such that receptors cluster only between individuals bearing compatible alleles. TraA clusters, which resemble eukaryotic gap junctions, direct the robust exchange of cellular goods that allows heterogeneous populations to transition towards homeostasis. This work provides a conceptual framework for how microbes use a fluid outer membrane receptor to recognize and assemble kin cells into a cooperative multicellular community that resembles a tissue. Many organisms, including the bacterium Myxococcus xanthus, regulate their social life through kin recognition. Here, Cao and Wall show that these bacteria use a polymorphic and fluid cell-surface receptor to recognize and assemble kin cells into a cooperative multicellular community that resembles a tissue.
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Affiliation(s)
- Pengbo Cao
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA.
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79
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Joseph B, Jaumann EA, Sikora A, Barth K, Prisner TF, Cafiso DS. In situ observation of conformational dynamics and protein ligand-substrate interactions in outer-membrane proteins with DEER/PELDOR spectroscopy. Nat Protoc 2019; 14:2344-2369. [PMID: 31278399 PMCID: PMC6886689 DOI: 10.1038/s41596-019-0182-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/18/2019] [Indexed: 12/01/2022]
Abstract
Observing structure and conformational dynamics of membrane proteins at high-resolution in their native environments is challenging because of the lack of suitable techniques. We have developed an approach for high-precision distance measurements in the nanometer range for outer membrane proteins (OMPs) in intact E. coli and native membranes. OMPs in Gram-negative bacteria rarely have reactive cysteines. This enables in-situ labeling of engineered cysteines with a methanethiosulfonate functionalized nitroxide spin label (MTSL) with minimal background signals. Following overexpression of the target protein, spin labeling is performed with E. coli or isolated outer membranes (OM) under selective conditions. The interspin distances are measured in-situ using pulsed electron-electron double resonance spectroscopy (PELDOR or DEER). The residual background signals, which are problematic for in-situ structural biology, contributes specifically to the intermolecular part of the signal and can be selectively removed to extract the desired interspin distance distribution. The initial cloning stage can take 5–7 d and the subsequent protein expression, OM isolation, spin labeling, PELDOR experiment, and the data analysis typically take 4–5 d. The described protocol provides a general strategy for observing protein-ligand/substrate interactions, oligomerization, and conformational dynamics of OMPs in the native OM and intact E. coli. EDITORIAL SUMMARY This protocol describes how to label bacterial outer membrane proteins with spin labels to study conformational changes and their interaction with ligands and substrates in native membranes and cells using Pulsed Electron-Electron Double Resonance (PELDOR or DEER) spectroscopy. TWEET A new protocol for studying conformational changes and ligand/substrate interactions of bacterial outer membrane proteins in-situ. COVER TEASER Studying membrane protein conformations in-situ
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Affiliation(s)
- Benesh Joseph
- Institute of Biophysics, Department of Physics, University of Frankfurt, Frankfurt am Main, Germany. .,Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany.
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
| | - Katja Barth
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
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80
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 419] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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81
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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82
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Hatlem D, Trunk T, Linke D, Leo JC. Catching a SPY: Using the SpyCatcher-SpyTag and Related Systems for Labeling and Localizing Bacterial Proteins. Int J Mol Sci 2019; 20:E2129. [PMID: 31052154 PMCID: PMC6539128 DOI: 10.3390/ijms20092129] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/05/2023] Open
Abstract
The SpyCatcher-SpyTag system was developed seven years ago as a method for protein ligation. It is based on a modified domain from a Streptococcus pyogenes surface protein (SpyCatcher), which recognizes a cognate 13-amino-acid peptide (SpyTag). Upon recognition, the two form a covalent isopeptide bond between the side chains of a lysine in SpyCatcher and an aspartate in SpyTag. This technology has been used, among other applications, to create covalently stabilized multi-protein complexes, for modular vaccine production, and to label proteins (e.g., for microscopy). The SpyTag system is versatile as the tag is a short, unfolded peptide that can be genetically fused to exposed positions in target proteins; similarly, SpyCatcher can be fused to reporter proteins such as GFP, and to epitope or purification tags. Additionally, an orthogonal system called SnoopTag-SnoopCatcher has been developed from an S. pneumoniae pilin that can be combined with SpyCatcher-SpyTag to produce protein fusions with multiple components. Furthermore, tripartite applications have been produced from both systems allowing the fusion of two peptides by a separate, catalytically active protein unit, SpyLigase or SnoopLigase. Here, we review the current state of the SpyCatcher-SpyTag and related technologies, with a particular emphasis on their use in vaccine development and in determining outer membrane protein localization and topology of surface proteins in bacteria.
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Affiliation(s)
- Daniel Hatlem
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Thomas Trunk
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Dirk Linke
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Jack C Leo
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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83
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Atanaskovic I, Kleanthous C. Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria. Front Microbiol 2019; 10:646. [PMID: 31001227 PMCID: PMC6455109 DOI: 10.3389/fmicb.2019.00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteriocins of Gram-negative bacteria are typically multi-domain proteins that target and kill bacteria of the same or closely related species. There is increasing interest in protein bacteriocin import; from a fundamental perspective to understand how folded proteins are imported into bacteria and from an applications perspective as species-specific antibiotics to combat multidrug resistant bacteria. In order to translocate across the cell envelope and cause cell death, protein bacteriocins hijack nutrient uptake pathways. Their import is energized by parasitizing intermembrane protein complexes coupled to the proton motive force, which delivers a toxic domain into the cell. A plethora of genetic, structural, biochemical, and biophysical methods have been applied to find cell envelope components involved in bacteriocin import since their discovery almost a century ago. Here, we review the various approaches that now exist for investigating how protein bacteriocins translocate into Gram-negative bacteria and highlight areas of research that will need methodological innovations to fully understand this process. We also highlight recent studies demonstrating how bacteriocins can be used to probe organization and architecture of the Gram-negative cell envelope itself.
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Affiliation(s)
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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84
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Vassen V, Valotteau C, Feuillie C, Formosa-Dague C, Dufrêne YF, De Bolle X. Localized incorporation of outer membrane components in the pathogen Brucella abortus. EMBO J 2019; 38:e100323. [PMID: 30635335 PMCID: PMC6396147 DOI: 10.15252/embj.2018100323] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/21/2022] Open
Abstract
The zoonotic pathogen Brucella abortus is part of the Rhizobiales, which are alpha-proteobacteria displaying unipolar growth. Here, we show that this bacterium exhibits heterogeneity in its outer membrane composition, with clusters of rough lipopolysaccharide co-localizing with the essential outer membrane porin Omp2b, which is proposed to allow facilitated diffusion of solutes through the porin. We also show that the major outer membrane protein Omp25 and peptidoglycan are incorporated at the new pole and the division site, the expected growth sites. Interestingly, lipopolysaccharide is also inserted at the same growth sites. The absence of long-range diffusion of main components of the outer membrane could explain the apparent immobility of the Omp2b clusters, as well as unipolar and mid-cell localizations of newly incorporated outer membrane proteins and lipopolysaccharide. Unipolar growth and limited mobility of surface structures also suggest that new surface variants could arise in a few generations without the need of diluting pre-existing surface antigens.
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Affiliation(s)
- Victoria Vassen
- Research Unit in Biology of Microorganisms (URBM), Narilis University of Namur (UNamur), Namur, Belgium
| | - Claire Valotteau
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Cécile Feuillie
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Cécile Formosa-Dague
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavre, Belgium
| | - Xavier De Bolle
- Research Unit in Biology of Microorganisms (URBM), Narilis University of Namur (UNamur), Namur, Belgium
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85
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Sharp C, Boinett C, Cain A, Housden NG, Kumar S, Turner K, Parkhill J, Kleanthous C. O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli. J Bacteriol 2019; 201:e00545-18. [PMID: 30510143 PMCID: PMC6351738 DOI: 10.1128/jb.00545-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
The outer membrane of Gram-negative bacteria presents a significant barrier for molecules entering the cell. Nevertheless, colicins, which are antimicrobial proteins secreted by Escherichia coli, can target other E. coli cells by binding to cell surface receptor proteins and activating their import, resulting in cell death. Previous studies have documented high rates of nonspecific resistance (insensitivity) of various E. coli strains toward colicins that is independent of colicin-specific immunity and is instead associated with lipopolysaccharide (LPS) in the outer membrane. This observation poses a contradiction: why do E. coli strains have colicin-expressing plasmids, which are energetically costly to retain, if cells around them are likely to be naturally insensitive to the colicin they produce? Here, using a combination of transposon sequencing and phenotypic microarrays, we show that colicin insensitivity of uropathogenic E. coli sequence type 131 (ST131) is dependent on the production of its O-antigen but that minor changes in growth conditions render the organism sensitive toward colicins. The reintroduction of O-antigen into E. coli K-12 demonstrated that it is the density of O-antigen that is the dominant factor governing colicin insensitivity. We also show, by microscopy of fluorescently labelled colicins, that growth conditions affect the degree of occlusion by O-antigen of outer membrane receptors but not the clustered organization of receptors. The result of our study demonstrate that environmental conditions play a critical role in sensitizing E. coli toward colicins and that O-antigen in LPS is central to this role.IMPORTANCEEscherichia coli infections can be a major health burden, especially with the organism becoming increasingly resistant to "last-resort" antibiotics such as carbapenems. Although colicins are potent narrow-spectrum antimicrobials with potential as future antibiotics, high levels of naturally occurring colicin insensitivity have been documented which could limit their efficacy. We identify O-antigen-dependent colicin insensitivity in a clinically relevant uropathogenic E. coli strain and show that this insensitivity can be circumvented by minor changes to growth conditions. The results of our study suggest that colicin insensitivity among E. coli organisms has been greatly overestimated, and as a consequence, colicins could in fact be effective species-specific antimicrobials targeting pathogenic E. coli such as uropathogenic E. coli (UPEC).
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Affiliation(s)
- Connor Sharp
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Amy Cain
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Macquarie University, Sydney, Australia
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sandip Kumar
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Keith Turner
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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86
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Paulino J, Pang X, Hung I, Zhou HX, Cross TA. Influenza A M2 Channel Clustering at High Protein/Lipid Ratios: Viral Budding Implications. Biophys J 2019; 116:1075-1084. [PMID: 30819568 DOI: 10.1016/j.bpj.2019.01.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/21/2019] [Accepted: 01/30/2019] [Indexed: 11/27/2022] Open
Abstract
Protein dynamics in crowded environments is important for understanding protein functions in vivo and is especially relevant for membrane proteins because of the roles of protein-protein interactions in membrane protein functions and their regulation. Here, using solid-state NMR spectroscopy in combination with coarse-grained molecular dynamics simulations, we report that the rotational correlation time for the transmembrane domain of the influenza A M2 proton channel in lipid bilayers increases dramatically at an elevated protein/lipid ratio. This increase is attributable to persistent protein-protein interactions, thus revealing for the first time, to the best of our knowledge, extensive cluster formation of the M2 tetrameric channel. Such clustering appears to have direct biological relevance during budding of the nascent influenza virus, which does not use the endosomal sorting complexes required for transport machinery. Indeed, initial coarse-grained molecular dynamics simulations of the longer M2 construct known as the conductance domain suggest clustering-induced membrane curvature formation.
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Affiliation(s)
- Joana Paulino
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Xiaodong Pang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
| | - Ivan Hung
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Huan-Xiang Zhou
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois
| | - Timothy A Cross
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida; National High Magnetic Field Laboratory, Tallahassee, Florida; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida.
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Robinson JA. Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria. Front Chem 2019; 7:45. [PMID: 30788339 PMCID: PMC6372539 DOI: 10.3389/fchem.2019.00045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.
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Affiliation(s)
- John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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88
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Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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89
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Complement Susceptibility in Relation to Genome Sequence of Recent Klebsiella pneumoniae Isolates from Thai Hospitals. mSphere 2018; 3:3/6/e00537-18. [PMID: 30404929 PMCID: PMC6222052 DOI: 10.1128/msphere.00537-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The capacity to resist the bactericidal action of complement (C') is a strong but poorly understood virulence trait in Klebsiella spp. Killing requires activation of one or more C' pathways, assembly of C5b-9 membrane attack complexes (MACs) on the surface of the outer membrane (OM), and penetration of MACs into the target bilayer. We interrogated whole-genome sequences of 164 Klebsiella isolates from three tertiary hospitals in Thailand for genes encoding surface-located macromolecules considered to play a role in determination of C' resistance. Most isolates (154/164) were identified as Klebsiella pneumoniae, and the collection conformed to previously established population structures and antibiotic resistance patterns. The distribution of sequence types (STs) and capsular (K) types were also typical of global populations. The majority (64%) of isolates were resistant to C', and the remainder were either rapidly or slowly killed. All isolates carried genes encoding capsular polysaccharides (K antigens), which have been strongly linked to C' resistance. In contrast to previous reports, there were no differences in the amount of capsule produced by C'-resistant isolates compared to C'-susceptible isolates, nor was there any correlation between serum reactivity and the presence of hypermucoviscous capsules. Similarly, there were no correlations between the presence of genes specifying lipopolysaccharide O-side chains or major OM proteins. Some virulence factors were found more frequently in C'-resistant isolates but were considered to reflect clonal ST expansion. Thus, no single gene accounts for the C' resistance of the isolates sequenced in this study.IMPORTANCE Multidrug-resistant Klebsiella pneumoniae is responsible for an increasing proportion of nosocomial infections, and emerging hypervirulent K. pneumoniae clones now cause severe community-acquired infections in otherwise healthy individuals. These bacteria are adept at circumventing immune defenses, and most survive and grow in serum; their capacity to avoid C'-mediated destruction is correlated with their invasive potential. Killing of Gram-negative bacteria occurs following activation of the C' cascades and stable deposition of C5b-9 MACs onto the OM. For Klebsiella, studies with mutants and conjugants have invoked capsules, lipopolysaccharide O-side chains, and OM proteins as determinants of C' resistance, although the precise roles of the macromolecules are unclear. In this study, we sequenced 164 Klebsiella isolates with different C' susceptibilities to identify genes involved in resistance. We conclude that no single OM constituent can account for resistance, which is likely to depend on biophysical properties of the target bilayer.
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90
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Vetterli SU, Zerbe K, Müller M, Urfer M, Mondal M, Wang SY, Moehle K, Zerbe O, Vitale A, Pessi G, Eberl L, Wollscheid B, Robinson JA. Thanatin targets the intermembrane protein complex required for lipopolysaccharide transport in Escherichia coli. SCIENCE ADVANCES 2018; 4:eaau2634. [PMID: 30443594 PMCID: PMC6235536 DOI: 10.1126/sciadv.aau2634] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/16/2018] [Indexed: 05/31/2023]
Abstract
With the increasing resistance of many Gram-negative bacteria to existing classes of antibiotics, identifying new paradigms in antimicrobial discovery is an important research priority. Of special interest are the proteins required for the biogenesis of the asymmetric Gram-negative bacterial outer membrane (OM). Seven Lpt proteins (LptA to LptG) associate in most Gram-negative bacteria to form a macromolecular complex spanning the entire envelope, which transports lipopolysaccharide (LPS) molecules from their site of assembly at the inner membrane to the cell surface, powered by adenosine 5'-triphosphate hydrolysis in the cytoplasm. The periplasmic protein LptA comprises the protein bridge across the periplasm, which connects LptB2FGC at the inner membrane to LptD/E anchored in the OM. We show here that the naturally occurring, insect-derived antimicrobial peptide thanatin targets LptA and LptD in the network of periplasmic protein-protein interactions required to assemble the Lpt complex, leading to the inhibition of LPS transport and OM biogenesis in Escherichia coli.
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Affiliation(s)
- Stefan U. Vetterli
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Katja Zerbe
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maik Müller
- Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Matthias Urfer
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Milon Mondal
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Shuang-Yan Wang
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kerstin Moehle
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alessandra Vitale
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - John A. Robinson
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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91
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González-Rivera C, Khara P, Awad D, Patel R, Li YG, Bogisch M, Christie PJ. Two pKM101-encoded proteins, the pilus-tip protein TraC and Pep, assemble on the Escherichia coli cell surface as adhesins required for efficient conjugative DNA transfer. Mol Microbiol 2018; 111:96-117. [PMID: 30264928 DOI: 10.1111/mmi.14141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 01/10/2023]
Abstract
Mobile genetic elements (MGEs) encode type IV secretion systems (T4SSs) known as conjugation machines for their transmission between bacterial cells. Conjugation machines are composed of an envelope-spanning translocation channel, and those functioning in Gram-negative species additionally elaborate an extracellular pilus to initiate donor-recipient cell contacts. We report that pKM101, a self-transmissible MGE functioning in the Enterobacteriaceae, has evolved a second target cell attachment mechanism. Two pKM101-encoded proteins, the pilus-tip adhesin TraC and a protein termed Pep, are exported to the cell surface where they interact and also form higher order complexes appearing as distinct foci or patches around the cell envelope. Surface-displayed TraC and Pep are required for an efficient conjugative transfer, 'extracellular complementation' potentially involving intercellular protein transfer, and activation of a Pseudomonas aeruginosa type VI secretion system. Both proteins are also required for bacteriophage PRD1 infection. TraC and Pep are exported across the outer membrane by a mechanism potentially involving the β-barrel assembly machinery. The pKM101 T4SS, thus, deploys alternative routing pathways for the delivery of TraC to the pilus tip or both TraC and Pep to the cell surface. We propose that T4SS-encoded, pilus-independent attachment mechanisms maximize the probability of MGE propagation and might be widespread among this translocation superfamily.
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Affiliation(s)
- Christian González-Rivera
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Dominik Awad
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Roosheel Patel
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | | | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
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92
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Distribution of mechanical stress in the Escherichia coli cell envelope. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2566-2575. [PMID: 30278180 DOI: 10.1016/j.bbamem.2018.09.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/14/2018] [Accepted: 09/26/2018] [Indexed: 01/05/2023]
Abstract
The cell envelope in Gram-negative bacteria comprises two distinct membranes with a cell wall between them. There has been a growing interest in understanding the mechanical adaptation of this cell envelope to the osmotic pressure (or turgor pressure), which is generated by the difference in the concentration of solutes between the cytoplasm and the external environment. However, it remains unexplored how the cell wall, the inner membrane (IM), and the outer membrane (OM) effectively protect the cell from this pressure by bearing the resulting surface tension, thus preventing the formation of inner membrane bulges, abnormal cell morphology, spheroplasts and cell lysis. In this study, we have used molecular dynamics (MD) simulations combined with experiments to resolve how and to what extent models of the IM, OM, and cell wall respond to changes in surface tension. We calculated the area compressibility modulus of all three components in simulations from tension-area isotherms. Experiments on monolayers mimicking individual leaflets of the IM and OM were also used to characterize their compressibility. While the membranes become softer as they expand, the cell wall exhibits significant strain stiffening at moderate to high tensions. We integrate these results into a model of the cell envelope in which the OM and cell wall share the tension at low turgor pressure (0.3 atm) but the tension in the cell wall dominates at high values (>1 atm).
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93
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Lessen HJ, Fleming PJ, Fleming KG, Sodt AJ. Building Blocks of the Outer Membrane: Calculating a General Elastic Energy Model for β-Barrel Membrane Proteins. J Chem Theory Comput 2018; 14:4487-4497. [PMID: 29979594 PMCID: PMC6191857 DOI: 10.1021/acs.jctc.8b00377] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The outer membranes of Gram negative bacteria are the first points of contact these organisms make with their environment. Understanding how composition determines the mechanical properties of this essential barrier is of paramount importance. Therefore, we developed a new computational method to measure the elasticity of transmembrane proteins found in the outer membrane. Using all-atom molecular dynamics simulations of these proteins, we apply a set of external forces to mechanically stress the transmembrane β-barrels. Our results from four representative β-barrels show that outer membrane proteins display elastic properties that are approximately 70 to 190 times stiffer than neat lipid membranes. These findings suggest that outer membrane β-barrels are a significant source of mechanical stability in bacteria. Our all-atom approach further reveals that resistance to radial stress is encoded by a general mechanism that includes stretching of backbone hydrogen bonds and tilting of β-strands with respect to the bilayer normal. This computational framework facilitates an increased theoretical understanding of how varying lipid and protein amounts affect the mechanical properties of the bacterial outer membrane.
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Affiliation(s)
- Henry J. Lessen
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Patrick J. Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Karen G. Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Alexander J. Sodt
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
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94
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Liquid crystalline bacterial outer membranes are critical for antibiotic susceptibility. Proc Natl Acad Sci U S A 2018; 115:E7587-E7594. [PMID: 30037998 DOI: 10.1073/pnas.1803975115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is a robust, impermeable, asymmetric bilayer of outer lipopolysaccharides (LPSs) and inner phospholipids containing selective pore proteins which confer on it the properties of a molecular sieve. This structure severely limits the variety of antibiotic molecules effective against Gram-negative pathogens and, as antibiotic resistance has increased, so has the need to solve the OM permeability problem. Polymyxin B (PmB) represents those rare antibiotics which act directly on the OM and which offer a distinct starting point for new antibiotic development. Here we investigate PmB's interactions with in vitro OM models and show how the physical state of the lipid matrix of the OM is a critical factor in regulating the interaction with the antimicrobial peptide. Using neutron reflectometry and infrared spectroscopy, we reveal the structural and chemical changes induced by PmB on OM models of increasing complexity. In particular, only a tightly packed model reproduced the temperature-controlled disruption of the asymmetric lipid bilayer by PmB observed in vivo. By measuring the order of outer-leaflet LPS and inner-leaflet phospholipids, we show that PmB insertion is dependent on the phase transition of LPS from the gel to the liquid crystalline state. The demonstration of a lipid phase transition in the physiological temperature range also supports the hypothesis that bacteria grown at different temperatures adapt their LPS structures to maintain a homeoviscous OM.
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95
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Chavent M, Duncan AL, Rassam P, Birkholz O, Hélie J, Reddy T, Beliaev D, Hambly B, Piehler J, Kleanthous C, Sansom MSP. How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins. Nat Commun 2018; 9:2846. [PMID: 30030429 PMCID: PMC6054660 DOI: 10.1038/s41467-018-05255-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/15/2018] [Indexed: 01/07/2023] Open
Abstract
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs. In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, Toulouse, 31400, France
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401, Illkirch, France
| | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,SEMMLE, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Theoretical Biology and Biophysics, T-6, Los Alamos National Laboratory, Los Alamos, NM, 87525, USA
| | - Dmitry Beliaev
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Ben Hambly
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
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96
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Housden NG, Rassam P, Lee S, Samsudin F, Kaminska R, Sharp C, Goult JD, Francis ML, Khalid S, Bayley H, Kleanthous C. Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm. Biochemistry 2018; 57:4374-4381. [PMID: 29949342 PMCID: PMC6093495 DOI: 10.1021/acs.biochem.8b00621] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein
bacteriocins are potent narrow spectrum antibiotics that
exploit outer membrane porins to kill bacteria by poorly understood
mechanisms. Here, we determine how colicins, bacteriocins specific
for Escherichia coli, engage the trimeric porin OmpF
to initiate toxin entry. The N-terminal ∼80 residues of the
nuclease colicin ColE9 are intrinsically unstructured and house two
OmpF binding sites (OBS1 and OBS2) that reside within the pores of
OmpF and which flank an epitope that binds periplasmic TolB. Using
a combination of molecular dynamics simulations, chemical trimerization,
isothermal titration calorimetry, fluorescence microscopy, and single
channel recording planar lipid bilayer measurements, we show that
this arrangement is achieved by OBS2 binding from the extracellular
face of OmpF, while the interaction of OBS1 occurs from the periplasmic
face of OmpF. Our study shows how the narrow pores of oligomeric porins
are exploited by colicin disordered regions for direction-specific
binding, which ensures the constrained presentation of an activating
signal within the bacterial periplasm.
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Affiliation(s)
- Nicholas G Housden
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Patrice Rassam
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Sejeong Lee
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K
| | - Firdaus Samsudin
- Department of Chemistry , University of Southampton , University Road , Southampton SO17 1BJ , U.K
| | - Renata Kaminska
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Connor Sharp
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Jonathan D Goult
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Marie-Louise Francis
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Syma Khalid
- Department of Chemistry , University of Southampton , University Road , Southampton SO17 1BJ , U.K
| | - Hagan Bayley
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K
| | - Colin Kleanthous
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
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97
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Rojas ER, Billings G, Odermatt PD, Auer GK, Zhu L, Miguel A, Chang F, Weibel DB, Theriot JA, Huang KC. The outer membrane is an essential load-bearing element in Gram-negative bacteria. Nature 2018; 559:617-621. [PMID: 30022160 PMCID: PMC6089221 DOI: 10.1038/s41586-018-0344-3] [Citation(s) in RCA: 317] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Gram-negative bacteria possess a complex cell envelope that consists of a plasma membrane, a peptidoglycan cell wall and an outer membrane. The envelope is a selective chemical barrier1 that defines cell shape2 and allows the cell to sustain large mechanical loads such as turgor pressure3. It is widely believed that the covalently cross-linked cell wall underpins the mechanical properties of the envelope4,5. Here we show that the stiffness and strength of Escherichia coli cells are largely due to the outer membrane. Compromising the outer membrane, either chemically or genetically, greatly increased deformation of the cell envelope in response to stretching, bending and indentation forces, and induced increased levels of cell lysis upon mechanical perturbation and during L-form proliferation. Both lipopolysaccharides and proteins contributed to the stiffness of the outer membrane. These findings overturn the prevailing dogma that the cell wall is the dominant mechanical element within Gram-negative bacteria, instead demonstrating that the outer membrane can be stiffer than the cell wall, and that mechanical loads are often balanced between these structures.
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Affiliation(s)
- Enrique R Rojas
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pascal D Odermatt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - George K Auer
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lillian Zhu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Amanda Miguel
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Weibel
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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98
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Birkholz O, Burns JR, Richter CP, Psathaki OE, Howorka S, Piehler J. Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials. Nat Commun 2018; 9:1521. [PMID: 29670084 PMCID: PMC5906680 DOI: 10.1038/s41467-018-02905-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023] Open
Abstract
Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores’ tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology. DNA nanopores can span lipid bilayers but how they interact with lipids is not known. Here the authors establish at single-molecule level the insertion mechanism and show that DNA nanopores can locally cluster and remodel membranes, and stabilize autonomously formed lipid nanotubes.
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Zinchuk V, Grossenbacher‐Zinchuk O. Mobile Quantitative Colocalization Analysis of Fluorescence Microscopy Images. ACTA ACUST UNITED AC 2018; 78:4.37.1-4.37.12. [DOI: 10.1002/cpcb.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vadim Zinchuk
- Department of Neurobiology and Anatomy, Kochi University Faculty of Medicine Kochi Japan
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Translocation of lipoproteins to the surface of gram negative bacteria. Curr Opin Struct Biol 2018; 51:73-79. [PMID: 29579694 DOI: 10.1016/j.sbi.2018.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 11/21/2022]
Abstract
The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of bacterial stress response, and have been extensively studied as vaccine antigens. The aim of this review is to summarize the recent studies that have investigated the biosynthetic and translocation pathways used by different bacterial species to deliver SLPs to the surface. We will specifically focus on Slam, a novel outer membrane protein first discovered in pathogenic Neisseria sp., that is involved in translocation of SLPs across the outer membrane.
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