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Niu L, Gao M, Ren H, De X, Jiang Z, Zhou X, Liu R, Li H, Duan H, Zhang C, Wang F, Ge J. A novel bacterium-like particles platform displaying antigens by new anchoring proteins induces efficacious immune responses. Front Microbiol 2024; 15:1395837. [PMID: 38841059 PMCID: PMC11150769 DOI: 10.3389/fmicb.2024.1395837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Bacterium-like particles (BLP) are the peptidoglycan skeleton particles of lactic acid bacteria, which have high safety, mucosal delivery efficiency, and adjuvant effect. It has been widely used in recent years in the development of vaccines. Existing anchoring proteins for BLP surfaces are few in number, so screening and characterization of new anchoring proteins are necessary. In this research, we created the OACD (C-terminal domain of Escherichia coli outer membrane protein A) to serve as an anchoring protein on the surface of BLP produced by the immunomodulatory bacteria Levilactobacillus brevis 23017. We used red fluorescent protein (RFP) to demonstrate the novel surface display system's effectiveness, stability, and ability to be adapted to a wide range of lactic acid bacteria. Furthermore, this study employed this surface display method to develop a novel vaccine (called COB17) by using the multi-epitope antigen of Clostridium perfringens as the model antigen. The vaccine can induce more than 50% protection rate against C. perfringens type A challenge in mice immunized with a single dose and has been tested through three routes. The vaccine yields protection rates of 75% for subcutaneous, 50% for intranasal, and 75% for oral immunization. Additionally, it elicits a strong mucosal immune response, markedly increasing levels of specific IgG, high-affinity IgG, specific IgA, and SIgA antibodies. Additionally, we used protein anchors (PA) and OACD simultaneous to show several antigens on the BLP surface. The discovery of novel BLP anchoring proteins may expand the possibilities for creating mucosal immunity subunit vaccines. Additionally, it may work in concert with PA to provide concepts for the creation of multivalent or multiple vaccines that may be used in clinical practice to treat complex illnesses.
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Affiliation(s)
- Lingdi Niu
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- National Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mingchun Gao
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hongkun Ren
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xinqi De
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zhigang Jiang
- National Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyao Zhou
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Runhang Liu
- National Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hai Li
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Haoyuan Duan
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Chuankun Zhang
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Fang Wang
- National Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junwei Ge
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Liu BD, Akbar R, Oliverio A, Thapa K, Wang X, Fan GC. BACTERIAL EXTRACELLULAR VESICLES IN THE REGULATION OF INFLAMMATORY RESPONSE AND HOST-MICROBE INTERACTIONS. Shock 2024; 61:175-188. [PMID: 37878470 PMCID: PMC10921997 DOI: 10.1097/shk.0000000000002252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
ABSTRACT Extracellular vesicles (EVs) are a new revelation in cross-kingdom communication, with increasing evidence showing the diverse roles of bacterial EVs (BEVs) in mammalian cells and host-microbe interactions. Bacterial EVs include outer membrane vesicles released by gram-negative bacteria and membrane vesicles generated from gram-positive bacteria. Recently, BEVs have drawn attention for their potential as biomarkers and therapeutic tools because they are nano-sized and can deliver bacterial cargo into host cells. Importantly, exposure to BEVs significantly affects various physiological and pathological responses in mammalian cells. Herein, we provide a comprehensive overview of the various effects of BEVs on host cells (i.e., immune cells, endothelial cells, and epithelial cells) and inflammatory/infectious diseases. First, the biogenesis and purification methods of BEVs are summarized. Next, the mechanisms and pathways identified by BEVs that stimulate either proinflammatory or anti-inflammatory responses are highlighted. In addition, we discuss the mechanisms by which BEVs regulate host-microbe interactions and their effects on the immune system. Finally, this review focuses on the contribution of BEVs to the pathogenesis of sepsis/septic shock and their therapeutic potential for the treatment of sepsis.
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Affiliation(s)
- Benjamin D. Liu
- Department of Chemistry and Biochemistry, The Ohio State University College of Arts and Sciences, Columbus, OH, 43210, USA
| | - Rubab Akbar
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Anna Oliverio
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kajol Thapa
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaohong Wang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Hermansen S, Ryoo D, Orwick-Rydmark M, Saragliadis A, Gumbart JC, Linke D. The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of Escherichia coli. Front Mol Biosci 2022; 9:918480. [PMID: 35911955 PMCID: PMC9329534 DOI: 10.3389/fmolb.2022.918480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. It is perforated by outer membrane proteins (OMPs) that function most often as diffusion pores, but sometimes also as parts of larger cellular transport complexes, structural components of the cell wall, or even as enzymes. These OMPs often have large loops that protrude into the extracellular environment, which have promise for biotechnological applications and as therapeutic targets. Thus, understanding how modifications to these loops affect OMP stability and folding is critical for their efficient application. In this work, the small outer membrane protein OmpX was used as a model system to quantify the effects of loop insertions on OMP folding and stability. The insertions were varied according to both hydrophobicity and size, and their effects were determined by assaying folding into detergent micelles in vitro by SDS-PAGE and in vivo by isolating the outer membrane of cells expressing the constructs. The different insertions were also examined in molecular dynamics simulations to resolve how they affect OmpX dynamics in its native outer membrane. The results indicate that folding of OMPs is affected by both the insert length and by its hydrophobic character. Small insertions sometimes even improved the folding efficiency of OmpX, while large hydrophilic inserts reduced it. All the constructs that were found to fold in vitro could also do so in their native environment. One construct that could not fold in vitro was transported to the OM in vivo, but remained unfolded. Our results will help to improve the design and efficiency of recombinant OMPs used for surface display.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Ryoo
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, United States
| | - Marcella Orwick-Rydmark
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Athanasios Saragliadis
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- *Correspondence: Dirk Linke,
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Chang CM, Awanye AM, Marsay L, Dold C, Pollard AJ, Rollier CS, Feavers IM, Maiden MC, Derrick JP. Application of a Neisseria meningitidis antigen microarray to identify candidate vaccine proteins from a human Phase I clinical trial. Vaccine 2022; 40:3835-3842. [DOI: 10.1016/j.vaccine.2022.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
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Hsu SH, Yang CW. Insight into the Structure, Functions, and Dynamics of the Leptospira Outer Membrane Proteins with the Pathogenicity. MEMBRANES 2022; 12:membranes12030300. [PMID: 35323775 PMCID: PMC8951592 DOI: 10.3390/membranes12030300] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023]
Abstract
Leptospirosis is a widespread zoonosis that frequently occurs in tropical and subtropical countries. Leptospira enters the host through wounds or mucous membranes and spreads to the whole body through the blood, causing systemic infection. Kidneys are the preferential site where Leptospira accumulates, especially in the renal interstitium and renal tubule epithelial cells. Clinical symptoms in humans include high fever, jaundice, renal failure, and severe multiple-organ failure (Weil’s syndrome). Surface-exposed antigens are located at the outermost layer of Leptospira and these potential virulence factors are likely involved in primary host-pathogen interactions, adhesion, and/or invasion. Using the knockout/knockdown techniques to the evaluation of pathogenicity in the virulence factor are the most direct and effective methods and many virulence factors are evaluated including lipopolysaccharides (LPS), Leptospira lipoprotein 32 (LipL32), Leptospira ompA domain protein 22 (Loa22), LipL41, LipL71, Leptospira immunoglobulin-like repeat A (LigA), LigB, and LipL21. In this review, we will discuss the structure, functions, and dynamics of these virulence factors and the roles of these virulence factors in Leptospira pathogenicity. In addition, a protein family with special Leucine-rich repeat (LRR) will also be discussed for their vital role in Leptospira pathogenicity. Finally, these surface-exposed antigens are discussed in the application of the diagnosis target for leptospirosis and compared with the serum microscope agglutination test (MAT), the gold standard for leptospirosis.
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de Jonge EF, van Boxtel R, Balhuizen MD, Haagsman HP, Tommassen J. Pal depletion results in hypervesiculation and affects cell morphology and outer-membrane lipid asymmetry in bordetellae. Res Microbiol 2022; 173:103937. [DOI: 10.1016/j.resmic.2022.103937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 10/18/2022]
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de Jonge EF, Balhuizen MD, van Boxtel R, Wu J, Haagsman HP, Tommassen J. Heat shock enhances outer-membrane vesicle release in Bordetella spp. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100009. [PMID: 34841303 PMCID: PMC8610307 DOI: 10.1016/j.crmicr.2020.100009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/05/2020] [Indexed: 01/06/2023] Open
Abstract
Pertussis, also known as whooping cough, is caused by the Gram-negative bacterium Bordetella pertussis, an obligate human pathogen. Despite high vaccination rates in high-income countries, resurgence of pertussis cases is an occurring problem that urges the necessity of developing an improved vaccine. Likewise, the efficacy of vaccines for Bordetella bronchiseptica, which causes similar disease in pigs and companion animals, is debatable. A promising approach for novel vaccines is the use of outer membrane vesicles (OMVs). However, spontaneous OMV (sOMV) release by Bordetella spp. is too low for cost-effective vaccine production. Therefore, we investigated the influence of growth in various media commonly used for culturing Bordetella in the Bvg+, i.e. virulent, phase and of a heat shock applied to inactivate the cells on OMV production. Inactivation of the bacterial cells at 56 °C before OMV isolation greatly enhanced OMV release in both Bordetella spp. without causing significant cell lysis. The growth medium used barely affected the efficiency of OMV release but did affect the protein pattern of the OMVs. Differences were found to be related, at least in part, to different availability of the nutrient metals iron and zinc in the media and include expression of potentially relevant vaccine antigens, such as the receptors FauA and ZnuD. The protein content of OMVs released by heat shock was comparable to that of sOMVs as determined by SDS-PAGE and Western blot analysis, and their heat-modifiable electrophoretic mobility suggests that also protein conformation is unaffected. However, significant differences were noticed between the protein content of OMVs and that of a purified outer membrane fraction, with two major outer membrane proteins, porin OmpP and the peptidoglycan-associated RmpM, being underrepresented in the OMVs. Altogether, these results indicate that the application of a heat shock is potentially an important step in the development of cost-effective, OMV-based vaccines for both Bordetella spp.
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Affiliation(s)
- Eline F. de Jonge
- Section Molecular Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Melanie D. Balhuizen
- Section Molecular Host Defence, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Ria van Boxtel
- Section Molecular Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Jianjun Wu
- Section Molecular Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Henk P. Haagsman
- Section Molecular Host Defence, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jan Tommassen
- Section Molecular Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
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Arenas J, Catón L, van den Hoeven T, de Maat V, Cruz Herrero J, Tommassen J. The outer-membrane protein MafA of Neisseria meningitidis constitutes a novel protein secretion pathway specific for the fratricide protein MafB. Virulence 2021; 11:1701-1715. [PMID: 33315509 PMCID: PMC7738311 DOI: 10.1080/21505594.2020.1851940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MafB proteins are toxins secreted by Neisseria spp. which are involved in interbacterial competition. Their secretion mechanism has so far not been elucidated. Each strain can produce several MafB variants. On the chromosome, the mafB genes are localized on genomic islands also containing mafA genes. MafA proteins have a role in virulence with reported activities in adhesion and transcytosis of pathogenic Neisseria, a priori unrelated to MafB activities. In this study, we investigated the possible involvement of MafA in the transport of MafB across the outer membrane of Neisseria meningitidis. In wild-type strains, proteolytic fragments of MafB proteins were detected in the extracellular medium. In the absence of MafA, secretion was abrogated, and, in the case of MafBI, full-length and truncated polypeptides were detected inside the cells and inside outer-membrane vesicles. MafBI secretion required its cognate MafA, whereas MafBIII could use any MafA. Heterologous expression in Escherichia coli showed that MafBIII is transported to a cell-surface-exposed, i.e. protease-accessible, location in a MafA-dependent way. MafA itself was found to be localized to the outer membrane, forming large oligomeric complexes. As homologs were found in diverse bacteria, the Maf system represents a new protein secretion system in Gram-negative bacteria.
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Affiliation(s)
- Jesús Arenas
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands.,Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza , Zaragoza, Spain
| | - Laura Catón
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands
| | - Tom van den Hoeven
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands
| | - Vincent de Maat
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands
| | - Juan Cruz Herrero
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands
| | - Jan Tommassen
- Section Molecular Microbiology, Department of Biology, Utrecht University , Utrecht, Netherlands
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Crisan CV, Chandrashekar H, Everly C, Steinbach G, Hill SE, Yunker PJ, Lieberman RR, Hammer BK. A New Contact Killing Toxin Permeabilizes Cells and Belongs to a Broadly Distributed Protein Family. mSphere 2021; 6:e0031821. [PMID: 34287011 PMCID: PMC8386463 DOI: 10.1128/msphere.00318-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/21/2021] [Indexed: 01/12/2023] Open
Abstract
Vibrio cholerae is an aquatic Gram-negative bacterium that causes severe diarrheal cholera disease when ingested by humans. To eliminate competitor cells in both the external environment and inside hosts, V. cholerae uses the type VI secretion system (T6SS). The T6SS is a macromolecular contact-dependent weapon employed by many Gram-negative bacteria to deliver cytotoxic proteins into adjacent cells. In addition to canonical T6SS gene clusters encoded by all sequenced V. cholerae isolates, strain BGT49 encodes another locus, which we named auxiliary (Aux) cluster 4. The Aux 4 cluster is located on a mobile genetic element and can be used by killer cells to eliminate both V. cholerae and Escherichia coli cells in a T6SS-dependent manner. A putative toxin encoded in the cluster, which we name TpeV (type VI permeabilizing effector Vibrio), shares no homology to known proteins and does not contain motifs or domains indicative of function. Ectopic expression of TpeV in the periplasm of E. coli permeabilizes cells and disrupts the membrane potential. Using confocal microscopy, we confirm that susceptible target cells become permeabilized when competed with killer cells harboring the Aux 4 cluster. We also determine that tpiV, the gene located immediately downstream of tpeV, encodes an immunity protein that neutralizes the toxicity of TpeV. Finally, we show that TpeV homologs are broadly distributed across important human, animal, and plant pathogens and are localized in proximity to other T6SS genes. Our results suggest that TpeV is a toxin that belongs to a large family of T6SS proteins. IMPORTANCE Bacteria live in polymicrobial communities where competition for resources and space is essential for survival. Proteobacteria use the T6SS to eliminate neighboring cells and cause disease. However, the mechanisms by which many T6SS toxins kill or inhibit susceptible target cells are poorly understood. The sequence of the TpeV toxin that we describe here is unlike any previously described protein. We demonstrate that it has antimicrobial activity by permeabilizing cells, eliminating membrane potentials, and causing severe cytotoxicity. TpeV homologs are found near known T6SS genes in human, animal, and plant bacterial pathogens, indicating that the toxin is a representative member of a broadly distributed protein family. We propose that TpeV-like toxins contribute to the fitness of many bacteria. Finally, since antibiotic resistance is a critical global health threat, the discovery of new antimicrobial mechanisms could lead to the development of new treatments against resistant strains.
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Affiliation(s)
- Cristian V. Crisan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Harshini Chandrashekar
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Catherine Everly
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gabi Steinbach
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Shannon E. Hill
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter J. Yunker
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel R. Lieberman
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Brian K. Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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Chen Y, Vargas SM, Smith TC, Karna SLR, MacMackin Ingle T, Wozniak KL, Wormley FL, Seshu J. Borrelia peptidoglycan interacting Protein (BpiP) contributes to the fitness of Borrelia burgdorferi against host-derived factors and influences virulence in mouse models of Lyme disease. PLoS Pathog 2021; 17:e1009535. [PMID: 33882111 PMCID: PMC8092773 DOI: 10.1371/journal.ppat.1009535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 05/03/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
The Peptidoglycan (PG) cell wall of the Lyme disease (LD) spirochete, Borrelia burgdorferi (Bb), contributes to structural and morphological integrity of Bb; is a persistent antigen in LD patients; and has a unique pentapeptide with L-Ornithine as the third amino acid that cross-links its glycan polymers. A borrelial homolog (BB_0167) interacted specifically with borrelilal PG via its peptidoglycan interacting motif (MHELSEKRARAIGNYL); was localized to the protoplasmic cylinder of Bb; and was designated as Borrelia peptidoglycan interacting Protein (BpiP). A bpiP mutant displayed no defect under in vitro growth conditions with similar levels of several virulence-related proteins. However, the burden of bpiP mutant in C3H/HeN mice at day 14, 28 and 62 post-infection was significantly lower compared to control strains. No viable bpiP mutant was re-isolated from any tissues at day 62 post-infection although bpiP mutant was able to colonize immunodeficient SCID at day 28 post-infection. Acquisition or transmission of bpiP mutant by Ixodes scapularis larvae or nymphs respectively, from and to mice, was significantly lower compared to control strains. Further analysis of bpiP mutant revealed increased sensitivity to vancomycin, osmotic stress, lysosomal extracts, human antimicrobial peptide cathelicidin-LL37, complement-dependent killing in the presence of day 14 post-infection mouse serum and increased internalization of CFSC-labeled bpiP mutant by macrophages and dendritic cells compared to control strains. These studies demonstrate the importance of accessory protein/s involved in sustaining integrity of PG and cell envelope during different phases of Bb infection.
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Affiliation(s)
- Yue Chen
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Sean M. Vargas
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Trever C. Smith
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Sai Lakshmi Rajasekhar Karna
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Taylor MacMackin Ingle
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Karen L. Wozniak
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Floyd L. Wormley
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Janakiram Seshu
- South Texas Center for Emerging Infectious Diseases (STCEID) and Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
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12
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Rey M, Dhenin J, Kong Y, Nouchikian L, Filella I, Duchateau M, Dupré M, Pellarin R, Duménil G, Chamot-Rooke J. Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions. Anal Chem 2021; 93:4166-4174. [DOI: 10.1021/acs.analchem.0c04430] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Martial Rey
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Jonathan Dhenin
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Youxin Kong
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Lucienne Nouchikian
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Isaac Filella
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Guillaume Duménil
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
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13
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Abstract
Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host-cell recognition, biofilm formation, regulation of OM stability, permeability and antibiotic resistance. OmpA members are two-domain proteins with an N-terminal eight-stranded β-barrel domain with four external loops (ELs) interacting with the environment, and a C-terminal periplasmic domain binding non-covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic and multilocus sequence analyses from 975 strains/isolates of the Acinetobacter calcoaceticus/Acinetobacter baumannii complex (ACB), 946 from A. baumannii, to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) in A. baumannii, encompassing 52 different alleles coding for 23 different proteins. Polymorphisms were concentrated in five regions corresponding to the four ELs and the C-terminal end, and provided evidence for intra-genic recombination. ompA variants were not randomly distributed across the A. baumannii phylogeny, with the most frequent V1(lct)a1 allele found in most clonal complex 2 (CC2) strains and the second most frequent V2(lct)a1 allele in the majority of CC1 strains. Evidence was found for assortative exchanges of ompA alleles not only between separate A. baumannii lineages, but also different ACB species. The overall results have implications for A. baumannii evolution, epidemiology, virulence and vaccine design.
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Affiliation(s)
- Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
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14
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Trinh NTT, Tran HQ, Van Dong Q, Cambillau C, Roussel A, Leone P. Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment. Sci Rep 2020; 10:7384. [PMID: 32355178 PMCID: PMC7192894 DOI: 10.1038/s41598-020-64115-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Porphyromonas gingivalis, the major human pathogen associated to periodontal diseases, utilizes the Bacteroidetes-specific type IX secretion system (T9SS) to export virulence factors. PorE is a periplasmic multi-domain lipoprotein associated to the outer membrane that was recently identified as essential for T9SS function. Little is known on T9SS at the structural level, and in particular its interaction with peptidoglycan. This prompted us to carry out structural studies on PorE full length as well as on its four isolated domains. Here we report the crystal structure of the C-terminal OmpA_C-like putative peptidoglycan-binding domain at 1.55 Å resolution. An electron density volume was identified in the protein cleft, making it possible to build a naturally-occurring peptidoglycan fragment. This result suggests that PorE interacts with peptidoglycan and that PorE could anchor T9SS to the cell wall.
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Affiliation(s)
- Nhung Thi Trang Trinh
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Faculty of Medical Technology, PHENIKAA University, Yen Nghia, Ha Dong, Hanoi 12116, Vietnam.,PHENIKAA Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, No. 167 Hoang Ngan, Trung Hoa, Cau Giay, Hanoi 11313, Vietnam
| | - Hieu Quang Tran
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Quyen Van Dong
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam.,University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Philippe Leone
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France. .,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.
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15
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Awanye AM, Chang CM, Wheeler JX, Chan H, Marsay L, Dold C, Rollier CS, Bird LE, Nettleship JE, Owens RJ, Pollard AJ, Derrick JP. Immunogenicity profiling of protein antigens from capsular group B Neisseria meningitidis. Sci Rep 2019; 9:6843. [PMID: 31048732 PMCID: PMC6497663 DOI: 10.1038/s41598-019-43139-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/11/2019] [Indexed: 11/29/2022] Open
Abstract
Outer membrane vesicle (OMV)- based vaccines have been used to provide strain-specific protection against capsular group B Neisseria meningitidis infections, but the full breadth of the immune response against the components of the OMV has not been established. Sera from adults vaccinated with an OMV vaccine were used to screen 91 outer membrane proteins (OMPs) incorporated in an antigen microarray panel. Antigen-specific IgG levels were quantified pre-vaccination, and after 12 and 18 weeks. These results were compared with IgG levels from mice vaccinated with the same OMV vaccine. The repertoires of highly responding antigens in humans and mice overlapped, but were not identical. The highest responding antigens to human IgG comprised four integral OMPs (PorA, PorB, OpcA and PilQ), a protein which promotes the stability of PorA and PorB (RmpM) and two lipoproteins (BamC and GNA1162). These observations will assist in evaluating the role of minor antigen components within OMVs in providing protection against meningococcal infection. In addition, the relative dominance of responses to integral OMPs in humans emphasizes the importance of this subclass and points to the value of maintaining conformational epitopes from integral membrane proteins in vaccine formulations.
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Affiliation(s)
- Amaka M Awanye
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Chun-Mien Chang
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Jun X Wheeler
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Hannah Chan
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Leanne Marsay
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Louise E Bird
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Joanne E Nettleship
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Raymond J Owens
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Jeremy P Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK.
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16
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Sikora AE, Wierzbicki IH, Zielke RA, Ryner RF, Korotkov KV, Buchanan SK, Noinaj N. Structural and functional insights into the role of BamD and BamE within the β-barrel assembly machinery in Neisseria gonorrhoeae. J Biol Chem 2018; 293:1106-1119. [PMID: 29229778 PMCID: PMC5787791 DOI: 10.1074/jbc.ra117.000437] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/18/2017] [Indexed: 12/22/2022] Open
Abstract
The β-barrel assembly machinery (BAM) is a conserved multicomponent protein complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Given its role in the production of OMPs for survival and pathogenesis, BAM represents an attractive target for the development of therapeutic interventions, including drugs and vaccines against multidrug-resistant bacteria such as Neisseria gonorrhoeae The first structure of BamA, the central component of BAM, was from N. gonorrhoeae, the etiological agent of the sexually transmitted disease gonorrhea. To aid in pharmaceutical targeting of BAM, we expanded our studies to BamD and BamE within BAM of this clinically relevant human pathogen. We found that the presence of BamD, but not BamE, is essential for gonococcal viability. However, BamE, but not BamD, was cell-surface-displayed under native conditions; however, in the absence of BamE, BamD indeed becomes surface-exposed. Loss of BamE altered cell envelope composition, leading to slower growth and an increase in both antibiotic susceptibility and formation of membrane vesicles containing greater amounts of vaccine antigens. Both BamD and BamE are expressed in diverse gonococcal isolates, under host-relevant conditions, and throughout different phases of growth. The solved structures of Neisseria BamD and BamE share overall folds with Escherichia coli proteins but contain differences that may be important for function. Together, these studies highlight that, although BAM is conserved across Gram-negative bacteria, structural and functional differences do exist across species, which may be leveraged in the development of species-specific therapeutics in the effort to combat multidrug resistance.
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Affiliation(s)
- Aleksandra E Sikora
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330,
| | - Igor H Wierzbicki
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Ryszard A Zielke
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Rachael F Ryner
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536
| | - Susan K Buchanan
- NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - 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, Indiana 47907
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17
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Liew CW, Hynson RM, Ganuelas LA, Shah-Mohammadi N, Duff AP, Kojima S, Homma M, Lee LK. Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem Biophys Res Commun 2017; 495:1614-1619. [PMID: 29197577 DOI: 10.1016/j.bbrc.2017.11.194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/18/2023]
Abstract
The bacterial flagellar motor drives the rotation of helical flagellar filaments to propel bacteria through viscous media. It consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica (MotBC2) and Vibrio alginolyticus (PomBC5) have previously been elucidated. Here, we use small-angle X-ray scattering (SAXS). We show that unlike MotBC2, the dimeric conformation of the PomBC5 in solution differs to its crystal structure, and explore the functional relevance by characterising gain-of-function mutants as well as wild-type constructs of various lengths. These provide new insight into the conformational diversity of flagellar motor PGB domains and experimental verification of their overall topology.
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Affiliation(s)
- C W Liew
- School of Medical Sciences, The University of New South Wales, Australia
| | - R M Hynson
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - L A Ganuelas
- School of Medical Sciences, The University of New South Wales, Australia
| | - N Shah-Mohammadi
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - A P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - S Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - M Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - L K Lee
- School of Medical Sciences, The University of New South Wales, Australia; Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
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18
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Samsudin F, Boags A, Piggot TJ, Khalid S. Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall. Biophys J 2017; 113:1496-1504. [PMID: 28978443 DOI: 10.1016/j.bpj.2017.08.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/13/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli are protected by a complex cell envelope. The development of novel therapeutics against these bacteria necessitates a molecular level understanding of the structure-dynamics-function relationships of the various components of the cell envelope. We use atomistic MD simulations to reveal the details of covalent and noncovalent protein interactions that link the outer membrane to the aqueous periplasmic region. We show that the Braun's lipoprotein tilts and bends, and thereby lifts the cell wall closer to the outer membrane. Both monomers and dimers of the outer membrane porin OmpA can interact with peptidoglycan in the presence of Braun's lipoprotein, but in the absence of the latter, only dimers of OmpA show a propensity to form contacts with peptidoglycan. Our study provides a glimpse of how the molecular components of the bacterial cell envelope interact with each other to mediate cell wall attachment in E. coli.
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Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
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19
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Chan JM, Dillard JP. Attention Seeker: Production, Modification, and Release of Inflammatory Peptidoglycan Fragments in Neisseria Species. J Bacteriol 2017; 199:e00354-17. [PMID: 28674065 PMCID: PMC5637178 DOI: 10.1128/jb.00354-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Maintenance of the structural macromolecule peptidoglycan (PG), which involves regulated cycles of PG synthesis and PG degradation, is pivotal for cellular integrity and survival. PG fragments generated from the degradation process are usually efficiently recycled by Gram-negative bacteria. However, Neisseria gonorrhoeae and a limited number of Gram-negative bacteria release PG fragments in amounts sufficient to induce host tissue inflammation and damage during an infection. Due to limited redundancy in PG-modifying machineries and genetic tractability, N. gonorrhoeae serves as a great model organism for the study of biological processes related to PG. This review summarizes the generation, modification, and release of inflammatory PG molecules by N. gonorrhoeae and related species and discusses these findings in the context of understanding bacterial physiology and pathogenesis.
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Affiliation(s)
- Jia Mun Chan
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph P Dillard
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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20
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Vaccination with a recombinant OprL fragment induces a Th17 response and confers serotype-independent protection against Pseudomonas aeruginosa infection in mice. Clin Immunol 2017; 183:354-363. [PMID: 28970186 DOI: 10.1016/j.clim.2017.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/06/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
Abstract
Pseudomonas aeruginosa (PA) is the major causative agent of nosocomial infection. Despite of adequate use of antibiotics, it still represents a major challenge in controlling PA infection. The local pulmonary Th17 response plays an important protective role against PA infection. And the Th17-mediated protection is antibody independent, so we hypothesized that it would be an optimal strategy of a vaccine for PA control to induce an effective Th17 response. Herein we report the successful production of a recombinant fragment of the OprL (reOprL) of PA. Purified reOprL forms homogeneous monomers in solution and vaccination with reOprL elicited a remarkable Th17 response. In addition, reOprL vaccination conferred effective serotype-independent protection against PA infection, which relied on the Th17 response. Our data suggest that reOprL is a good candidate for the future development of Th17 immunity based PA vaccines.
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21
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Ortiz-Suarez ML, Samsudin F, Piggot TJ, Bond PJ, Khalid S. Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations. Biophys J 2017; 111:1692-1702. [PMID: 27760356 PMCID: PMC5071624 DOI: 10.1016/j.bpj.2016.09.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/30/2016] [Accepted: 09/06/2016] [Indexed: 12/02/2022] Open
Abstract
OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers. The N-terminal domains were embedded in an asymmetric model of the outer membrane, with lipopolysaccharide molecules in the outer leaflet and phospholipids in the inner leaflet. Our results reveal a large dimerization interface within the membrane environment, ensuring that the dimer is stable over the course of the simulations. The linker is flexible, expanding and contracting to pull the globular C-terminal domain up toward the membrane or push it down toward the periplasm, suggesting a possible mechanism for providing mechanical stability to the cell. The external loops were more stabilized than was observed in previous studies due to the extensive dimerization interface and presence of lipopolysaccharide molecules in our outer-membrane model, which may have functional consequences in terms of OmpA adhesion to host cells. In addition, the pore-gating behavior of the protein was modulated compared with previous observations, suggesting a possible role for dimerization in channel regulation.
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Affiliation(s)
- Maite L Ortiz-Suarez
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Peter J Bond
- Bioinformatics Institute (A(∗)STAR), Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Syma Khalid
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom.
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22
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Tan K, Deatherage Kaiser BL, Wu R, Cuff M, Fan Y, Bigelow L, Jedrzejczak RP, Adkins JN, Cort JR, Babnigg G, Joachimiak A. Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi. Protein Sci 2017; 26:1738-1748. [PMID: 28580643 DOI: 10.1002/pro.3209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 11/10/2022]
Abstract
Salmonella enterica serovar Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel transmembrane domain and a C-terminal domain (OmpACTD ). The OmpACTD and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM. Here we present the first crystal structures of the OmpACTD from two pathogens: S. typhimurium (STOmpACTD ) in open and closed forms and causative agent of Lyme Disease Borrelia burgdorferi (BbOmpACTD ), in closed form. In the open form of STOmpACTD , an aspartate residue from a long β2-α3 loop points into the binding pocket, suggesting that an anion group such as a carboxylate group from PG is favored at the binding site. In the closed form of STOmpACTD and in the structure of BbOmpACTD , a sulfate group from the crystallization buffer is tightly bound at the binding site. The differences between the closed and open forms of STOmpACTD , suggest a large conformational change that includes an extension of α3 helix by ordering a part of β2-α3 loop. We propose that the sulfate anion observed in these structures mimics the carboxylate group of PG when bound to STOmpACTD suggesting PG-anchoring mechanism. In addition, the binding of PG or a ligand mimic may enhance dimerization of STOmpACTD , or possibly that of full length STOmpA.
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Affiliation(s)
- Kemin Tan
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
| | | | - Ruiying Wu
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Marianne Cuff
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Yao Fan
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Robert P Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637
| | - Joshua N Adkins
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
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23
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Yeo KJ, Lee WC, Lee S, Hwang E, Park JS, Choi IG, Kim SI, Lee JC, Jeon YH, Cheong C, Kim HY. d-Stereoisomer preference of the OmpA-like domain of Pal in peptidoglycan of Acinetobacter baumannii. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S. OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment. Structure 2016; 24:2227-2235. [PMID: 27866852 DOI: 10.1016/j.str.2016.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/16/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022]
Abstract
The envelope of Gram-negative bacteria is highly complex, containing separate outer and inner membranes and an intervening periplasmic space encompassing a peptidoglycan (PGN) cell wall. The PGN scaffold is anchored non-covalently to the outer membrane via globular OmpA-like domains of various proteins. We report atomically detailed simulations of PGN bound to OmpA in three different states, including the isolated C-terminal domain (CTD), the full-length monomer, or the complete full-length dimeric form. Comparative analysis of dynamics of OmpA CTD from different bacteria helped to identify a conserved PGN-binding mode. The dynamics of full-length OmpA, embedded within a realistic representation of the outer membrane containing full-rough (Ra) lipopolysaccharide, phospholipids, and cardiolipin, suggested how the protein may provide flexible mechanical support to the cell wall. An accurate model of the heterogeneous bacterial cell envelope should facilitate future efforts to develop antibacterial agents.
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Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Maite L Ortiz-Suarez
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Peter J Bond
- Bioinformatics Institute (A(∗)STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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The relationship between capsular type and OmpA of Pasteurella multocida is associated with the outcome of disease. Microb Pathog 2016; 101:68-75. [PMID: 27838388 DOI: 10.1016/j.micpath.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 02/05/2023]
Abstract
The genes encoding OmpA of Pasteurella multocida recovered from diseased and apparently healthy animals have been characterized. The nucleotide sequence revealed ORFs of 1047-1077 bp encoding proteins of 349-360 amino acids. Domain analysis of OmpA showed signal peptide, N-terminal ompA domain and C-terminal ligand binding domain. The transmembrane topology of OmpA showed short turns at the periplasmic end and longer irregular loops at the extracellular end. The phylogenetic analysis based on OmpA showed affiliation of isolates to 7 groups representing different alleles. The identical segments in OmpA also suggested assortative recombination within classes IV, V and VI of distinct lineages. Principal component analysis separated isolates into groups based on capsular type and PmompA alleles. The alleles belonging to class VI exclusively associated with capsular type A, whereas class I-IV were associated with capsular type B. PmompA alleles in class V were recorded in both serogroups. PmompA6.1, 6.4 were distributed among strains with capsular type A, and PmompA6.2 and 6.3 among capsular type B. Despite internal OmpA variabilty, restrictive and well defined distribution was seen amongst P. multocida. A definitive association of "OmpA-capsular type" was observed with clinical status of animals. A cohort of pasteurellae comprising of OmpA(I-IV)-capB was recovered from diseased animals and OmpA(VI)-capA from healthy subjects. This study concludes that P. multocida with serogroup A and B from healthy and diseased animals represent distinct clusters also differentiated based on their OmpA-types and OmpA-capsular type relationship possibly determine the virulence and disease outcome.
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The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains. PLoS One 2016; 11:e0166274. [PMID: 27832149 PMCID: PMC5104382 DOI: 10.1371/journal.pone.0166274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/25/2016] [Indexed: 02/03/2023] Open
Abstract
Treponema pallidum subspecies pallidum is the causative agent of syphilis, a chronic, multistage, systemic infection that remains a major global health concern. The molecular mechanisms underlying T. pallidum pathogenesis are incompletely understood, partially due to the phylogenetic divergence of T. pallidum. One aspect of T. pallidum that differentiates it from conventional Gram-negative bacteria, and is believed to play an important role in pathogenesis, is its unusual cell envelope ultrastructure; in particular, the T. pallidum peptidoglycan layer is chemically distinct, thinner and more distal to the outer membrane. Established functional roles for peptidoglycan include contributing to the structural integrity of the cell envelope and stabilization of the flagellar motor complex, which are typically mediated by the OmpA domain-containing family of proteins. To gain insight into the molecular mechanisms that govern peptidoglycan binding and cell envelope biogenesis in T. pallidum we report here the structural characterization of the putative OmpA-like domain-containing protein, Tp0624. Analysis of the 1.70 Å resolution Tp0624 crystal structure reveals a multi-modular architecture comprised of three distinct domains including a C-terminal divergent OmpA-like domain, which we show is unable to bind the conventional peptidoglycan component diaminopimelic acid, and a previously uncharacterized tandem domain unit. Intriguingly, bioinformatic analysis indicates that the three domains together are found in all orthologs from pathogenic treponemes, but are not observed together in genera outside Treponema. These findings provide the first structural insight into a multi-modular treponemal protein containing an OmpA-like domain and its potential role in peptidoglycan coordination and stabilization of the T. pallidum cell envelope.
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PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System. PLoS One 2016; 11:e0164313. [PMID: 27711252 PMCID: PMC5053529 DOI: 10.1371/journal.pone.0164313] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/22/2016] [Indexed: 01/10/2023] Open
Abstract
Porphyromonas gingivalis utilises the Bacteroidetes-specific type IX secretion system (T9SS) to export proteins across the outer membrane (OM), including virulence factors such as the gingipains. The secreted proteins have a conserved carboxy-terminal domain essential for type IX secretion that is cleaved upon export. In P. gingivalis the T9SS substrates undergo glycosylation with anionic lipopolysaccharide (A-LPS) and are attached to the OM. In this study, comparative analyses of 24 Bacteroidetes genomes identified ten putative novel components of the T9SS in P. gingivalis, one of which was PG1058. Computer modelling of the PG1058 structure predicted a novel N- to C-terminal architecture comprising a tetratricopeptide repeat (TPR) domain, a β-propeller domain, a carboxypeptidase regulatory domain-like fold (CRD) and an OmpA_C-like putative peptidoglycan binding domain. Inactivation of pg1058 in P. gingivalis resulted in loss of both colonial pigmentation and surface-associated proteolytic activity; a phenotype common to T9SS mutants. Immunoblot and LC-MS/MS analyses of subcellular fractions revealed T9SS substrates accumulated within the pg1058 mutant periplasm whilst whole-cell ELISA showed the Kgp gingipain was absent from the cell surface, confirming perturbed T9SS function. Immunoblot, TEM and whole-cell ELISA analyses indicated A-LPS was produced and present on the pg1058 mutant cell surface although it was not linked to T9SS substrate proteins. This indicated that PG1058 is crucial for export of T9SS substrates but not for the translocation of A-LPS. PG1058 is a predicted lipoprotein and was localised to the periplasmic side of the OM using whole-cell ELISA, immunoblot and LC-MS/MS analyses of subcellular fractions. The structural prediction and localisation of PG1058 suggests that it may have a role as an essential scaffold linking the periplasmic and OM components of the T9SS.
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Ishikawa M, Yoshimoto S, Hayashi A, Kanie J, Hori K. Discovery of a novel periplasmic protein that forms a complex with a trimeric autotransporter adhesin and peptidoglycan. Mol Microbiol 2016; 101:394-410. [PMID: 27074146 DOI: 10.1111/mmi.13398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/06/2016] [Indexed: 12/01/2022]
Abstract
Trimeric autotransporter adhesins (TAAs), fibrous proteins on the cell surface of Gram-negative bacteria, have attracted attention as virulence factors. However, little is known about the mechanism of their biogenesis. AtaA, a TAA of Acinetobacter sp. Tol 5, confers nonspecific, high adhesiveness to bacterial cells. We identified a new gene, tpgA, which forms a single operon with ataA and encodes a protein comprising two conserved protein domains identified by Pfam: an N-terminal SmpA/OmlA domain and a C-terminal OmpA_C-like domain with a peptidoglycan (PGN)-binding motif. Cell fractionation and a pull-down assay showed that TpgA forms a complex with AtaA, anchoring it to the outer membrane (OM). Isolation of total PGN-associated proteins showed TpgA binding to PGN. Disruption of tpgA significantly decreased the adhesiveness of Tol 5 because of a decrease in surface-displayed AtaA, suggesting TpgA involvement in AtaA secretion. This is reminiscent of SadB, which functions as a specific chaperone for SadA, a TAA in Salmonella species; however, SadB anchors to the inner membrane, whereas TpgA anchors to the OM through AtaA. The genetic organization encoding the TAA-TpgA-like protein cassette can be found in diverse Gram-negative bacteria, suggesting a common contribution of TpgA homologues to TAA biogenesis.
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Affiliation(s)
- Masahito Ishikawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Shogo Yoshimoto
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Ayumi Hayashi
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Junichi Kanie
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
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Maharjan S, Saleem M, Feavers IM, Wheeler JX, Care R, Derrick JP. Dissection of the function of the RmpM periplasmic protein from Neisseria meningitidis. Microbiology (Reading) 2016; 162:364-375. [DOI: 10.1099/mic.0.000227] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Sunil Maharjan
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, EN6 3QGUK
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PTUK
| | - Muhammad Saleem
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PTUK
| | - Ian M. Feavers
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, EN6 3QGUK
| | - Jun X. Wheeler
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, EN6 3QGUK
| | - Rory Care
- National Institute for Biological Standards and Control, South Mimms, Hertfordshire, EN6 3QGUK
| | - Jeremy P. Derrick
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PTUK
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Wang H, Li Q, Fang Y, Yu S, Tang B, Na L, Yu B, Zou Q, Mao X, Gu J. Biochemical and functional characterization of the periplasmic domain of the outer membrane protein A from enterohemorrhagic Escherichia coli. Microbiol Res 2015; 182:109-15. [PMID: 26686619 DOI: 10.1016/j.micres.2015.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/01/2015] [Accepted: 10/10/2015] [Indexed: 11/25/2022]
Abstract
Outer membrane protein A (OmpA) plays multiple roles in the physiology and pathogenesis of the zoonotic pathogen enterohemorrhagic Escherichia coli (EHEC). The N-terminus of OmpA forms a transmembrane domain (OmpA™), and the roles of this domain in bacterial pathogenesis have been well studied. However, how its C-terminal domain (OmpAper), which is located at the periplasmic space in the bacterial membrane, contributes to virulence remains unclear. Herein, we report that OmpAper forms a dimer and binds to peptidoglycan in vitro. Furthermore, OmpAper is responsible for bacterial resistance to acidic conditions, high osmotic pressure and high SDS environments. In addition, OmpAper contributes to the adhesion of bacteria to HeLa cells in vitro and ex vivo. These results provide an additional understanding of the role of OmpA in EHEC physiology and pathogenesis.
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Affiliation(s)
- Haiguang Wang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Qian Li
- Department of Clinical Microbiology and Immunology, Southwest Hospital & College of Medical Laboratory Science, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Fang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Shu Yu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Bin Tang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Li Na
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Bo Yu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Xuhu Mao
- Department of Clinical Microbiology and Immunology, Southwest Hospital & College of Medical Laboratory Science, Third Military Medical University, Chongqing, People's Republic of China.
| | - Jiang Gu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China.
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Zaccai NR, Sandlin CW, Hoopes JT, Curtis JE, Fleming PJ, Fleming KG, Krueger S. Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins. Methods Enzymol 2015; 566:159-210. [PMID: 26791979 PMCID: PMC4913355 DOI: 10.1016/bs.mie.2015.06.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archaeal prefoldins and the mitochondrial Tim chaperones, that is the α-helical "tentacles" extend from a β-strand "body" to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis, and structure modeling.
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Affiliation(s)
- Nathan R Zaccai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clifford W Sandlin
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - James T Hoopes
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Joseph E Curtis
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Patrick J Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Susan Krueger
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA.
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Teixeira AF, de Morais ZM, Kirchgatter K, Romero EC, Vasconcellos SA, Nascimento ALTO. Features of two new proteins with OmpA-like domains identified in the genome sequences of Leptospira interrogans. PLoS One 2015; 10:e0122762. [PMID: 25849456 PMCID: PMC4388678 DOI: 10.1371/journal.pone.0122762] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/13/2015] [Indexed: 12/12/2022] Open
Abstract
Leptospirosis is an acute febrile disease caused by pathogenic spirochetes of the genus Leptospira. It is considered an important re-emerging infectious disease that affects humans worldwide. The knowledge about the mechanisms by which pathogenic leptospires invade and colonize the host remains limited since very few virulence factors contributing to the pathogenesis of the disease have been identified. Here, we report the identification and characterization of two new leptospiral proteins with OmpA-like domains. The recombinant proteins, which exhibit extracellular matrix-binding properties, are called Lsa46 - LIC13479 and Lsa77 - LIC10050 (Leptospiral surface adhesins of 46 and 77 kDa, respectively). Attachment of Lsa46 and Lsa77 to laminin was specific, dose dependent and saturable, with KD values of 24.3 ± 17.0 and 53.0 ± 17.5 nM, respectively. Lsa46 and Lsa77 also bind plasma fibronectin, and both adhesins are plasminogen (PLG)-interacting proteins, capable of generating plasmin (PLA) and as such, increase the proteolytic ability of leptospires. The proteins corresponding to Lsa46 and Lsa77 are present in virulent L. interrogans L1-130 and in saprophyte L. biflexa Patoc 1 strains, as detected by immunofluorescence. The adhesins are recognized by human leptospirosis serum samples at the onset and convalescent phases of the disease, suggesting that they are expressed during infection. Taken together, our data could offer valuable information to the understanding of leptospiral pathogenesis.
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Affiliation(s)
- Aline F. Teixeira
- Centro de Biotecnologia, Instituto Butantan, Sao Paulo, SP, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia,Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Zenaide M. de Morais
- Laboratório de Zoonoses Bacterianas, Faculdade de Medicina Veterinária e Zootecnia, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Karin Kirchgatter
- Nucleo de Estudos em Malária, Superintendência de Controle de Endemias - Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Eliete C. Romero
- Centro de Bacteriologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | - Silvio A. Vasconcellos
- Laboratório de Zoonoses Bacterianas, Faculdade de Medicina Veterinária e Zootecnia, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Ana Lucia T. O. Nascimento
- Centro de Biotecnologia, Instituto Butantan, Sao Paulo, SP, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia,Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
- * E-mail:
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Døvling Kaspersen J, Moestrup Jessen C, Stougaard Vad B, Skipper Sørensen E, Kleiner Andersen K, Glasius M, Pinto Oliveira CL, Otzen DE, Pedersen JS. Low-Resolution Structures of OmpA⋅DDM Protein-Detergent Complexes. Chembiochem 2014; 15:2113-24. [DOI: 10.1002/cbic.201402162] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 11/07/2022]
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Ishida H, Garcia-Herrero A, Vogel HJ. The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3014-24. [PMID: 25135663 DOI: 10.1016/j.bbamem.2014.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/21/2023]
Abstract
Gram-negative bacteria such as Escherichia coli are surrounded by two membranes with a thin peptidoglycan (PG)-layer located in between them in the periplasmic space. The outer membrane protein A (OmpA) is a 325-residue protein and it is the major protein component of the outer membrane of E. coli. Previous structure determinations have focused on the N-terminal fragment (residues 1-171) of OmpA, which forms an eight stranded transmembrane β-barrel in the outer membrane. Consequently it was suggested that OmpA is composed of two independently folded domains in which the N-terminal β-barrel traverses the outer membrane and the C-terminal domain (residues 180-325) adopts a folded structure in the periplasmic space. However, some reports have proposed that full-length OmpA can instead refold in a temperature dependent manner into a single domain forming a larger transmembrane pore. Here, we have determined the NMR solution structure of the C-terminal periplasmic domain of E. coli OmpA (OmpA(180-325)). Our structure reveals that the C-terminal domain folds independently into a stable globular structure that is homologous to the previously reported PG-associated domain of Neisseria meningitides RmpM. Our results lend credence to the two domain structure model and a PG-binding function for OmpA, and we could indeed localize the PG-binding site on the protein through NMR chemical shift perturbation experiments. On the other hand, we found no evidence for binding of OmpA(180-325) with the TonB protein. In addition, we have also expressed and purified full-length OmpA (OmpA(1-325)) to study the structure of the full-length protein in micelles and nanodiscs by NMR spectroscopy. In both membrane mimetic environments, the recombinant OmpA maintains its two domain structure that is connected through a flexible linker. A series of temperature-dependent HSQC experiments and relaxation dispersion NMR experiments detected structural destabilization in the bulge region of the periplasmic domain of OmpA above physiological temperatures, which may induce dimerization and play a role in triggering the previously reported larger pore formation.
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Affiliation(s)
- Hiroaki Ishida
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Alicia Garcia-Herrero
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Koeberling O, Ispasanie E, Hauser J, Rossi O, Pluschke G, Caugant DA, Saul A, MacLennan CA. A broadly-protective vaccine against meningococcal disease in sub-Saharan Africa based on Generalized Modules for Membrane Antigens (GMMA). Vaccine 2014; 32:2688-95. [DOI: 10.1016/j.vaccine.2014.03.068] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/19/2014] [Accepted: 03/20/2014] [Indexed: 12/01/2022]
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Bos MP, Grijpstra J, Tommassen-van Boxtel R, Tommassen J. Involvement of Neisseria meningitidis lipoprotein GNA2091 in the assembly of a subset of outer membrane proteins. J Biol Chem 2014; 289:15602-10. [PMID: 24755216 DOI: 10.1074/jbc.m113.539510] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
GNA2091 of Neisseria meningitidis is a lipoprotein of unknown function that is included in the novel 4CMenB vaccine. Here, we investigated the biological function and the subcellular localization of the protein. We demonstrate that GNA2091 functions in the assembly of outer membrane proteins (OMPs) because its absence resulted in the accumulation of misassembled OMPs. Cell fractionation and protease accessibility experiments showed that the protein is localized at the periplasmic side of the outer membrane. Pulldown experiments revealed that it is not stably associated with the β-barrel assembly machinery, the previously identified complex for OMP assembly. Thus, GNA2091 constitutes a novel outer membrane-based lipoprotein required for OMP assembly. Furthermore, its location at the inner side of the outer membrane indicates that protective immunity elicited by this antigen cannot be due to bactericidal or opsonic activity of antibodies.
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Affiliation(s)
- Martine P Bos
- From the Department of Molecular Microbiology, Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jan Grijpstra
- From the Department of Molecular Microbiology, Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Ria Tommassen-van Boxtel
- From the Department of Molecular Microbiology, Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jan Tommassen
- From the Department of Molecular Microbiology, Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
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Marcoux J, Politis A, Rinehart D, Marshall DP, Wallace MI, Tamm LK, Robinson CV. Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA. Structure 2014; 22:781-90. [PMID: 24746938 DOI: 10.1016/j.str.2014.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/26/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
The transmembrane domain of the outer membrane protein A (OmpA) from Escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. However, full-length OmpA resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. Here we use site-directed mutagenesis and mass spectrometry of different constructs of OmpA, released in the gas phase from detergent micelles, to define the minimal region encompassing the C-terminal dimer interface. Combining knowledge of the location of the dimeric interface with molecular modeling and ion mobility data allows us to propose a low-resolution model for the full-length OmpA dimer. Our model of the dimer is in remarkable agreement with experimental ion mobility data, with none of the unfolding or collapse observed for full-length monomeric OmpA, implying that dimer formation stabilizes the overall structure and prevents collapse of the flexible linker that connects the two domains.
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Affiliation(s)
- Julien Marcoux
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Argyris Politis
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Dennis Rinehart
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David P Marshall
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Mark I Wallace
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK.
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Identification of an outer membrane lipoprotein involved in nasopharyngeal colonization by Moraxella catarrhalis in an animal model. Infect Immun 2014; 82:2287-99. [PMID: 24643539 DOI: 10.1128/iai.01745-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Colonization of the human nasopharynx by Moraxella catarrhalis is presumed to involve attachment of this bacterium to the mucosa. DNA microarray analysis was used to determine whether attachment of M. catarrhalis to human bronchial epithelial (HBE) cells in vitro affected gene expression in this bacterium. Attachment affected expression of at least 454 different genes, with 163 being upregulated and 291 being downregulated. Among the upregulated genes was one (ORF113) previously annotated as encoding a protein with some similarity to outer membrane protein A (OmpA). The protein encoded by ORF113 was predicted to have a signal peptidase II cleavage site, and globomycin inhibition experiments confirmed that this protein was indeed a lipoprotein. The ORF113 protein also contained a predicted peptidoglycan-binding domain in its C-terminal half. The use of mutant and recombinant M. catarrhalis strains confirmed that the ORF113 protein was present in outer membrane preparations, and this protein was also shown to be at least partially exposed on the bacterial cell surface. A mutant unable to produce the ORF113 protein showed little or no change in its growth rate in vitro, in its ability to attach to HBE cells in vitro, or in its autoagglutination characteristics, but it did exhibit a reduced ability to survive in the chinchilla nasopharynx. This is the first report of a lipoprotein essential to the ability of M. catarrhalis to persist in an animal model.
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40
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Leuzzi R, Nesta B, Monaci E, Cartocci E, Serino L, Soriani M, Rappuoli R, Pizza M. Neisseria gonorrhoeae PIII has a role on NG1873 outer membrane localization and is involved in bacterial adhesion to human cervical and urethral epithelial cells. BMC Microbiol 2013; 13:251. [PMID: 24206788 PMCID: PMC4226279 DOI: 10.1186/1471-2180-13-251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/07/2013] [Indexed: 11/20/2022] Open
Abstract
Background Protein PIII is one of the major outer membrane proteins of Neisseria gonorrhoeae, 95% identical to RmpM (reduction modifiable protein M) or class 4 protein of Neisseria meningitidis. RmpM is known to be a membrane protein associated by non-covalent bonds to the peptidoglycan layer and interacting with PorA/PorB porin complexes resulting in the stabilization of the bacterial membrane. The C-terminal domain of PIII (and RmpM) is highly homologous to members of the OmpA family, known to have a role in adhesion/invasion in many bacterial species. The contribution of PIII in the membrane architecture and its role in the interaction with epithelial cells has never been investigated. Results We generated a ΔpIII knock-out mutant strain and evaluated the effects of the loss of PIII expression on bacterial morphology and on outer membrane composition. Deletion of the pIII gene does not cause any alteration in bacterial morphology or sensitivity to detergents. Moreover, the expression profile of the main membrane proteins remains the same for the wild-type and knock-out strains, with the exception of the NG1873 which is not exported to the outer membrane and accumulates in the inner membrane in the ΔpIII knock-out mutant strain. We also show that purified PIII protein is able to bind human cervical and urethral cells and that the ΔpIII knock-out mutant strain has a lower ability to adhere to human cervical and urethral cells. Conclusion Here we demonstrated that the PIII protein does not play a key structural role in the membrane organization of gonococcus and does not induce major effects on the expression of the main outer membrane proteins. However, in the PIII knock-out strain, the NG1873 protein is not localized in the outer membrane as it is in the wild-type strain suggesting a possible interaction of PIII with NG1873. The evidence that PIII binds to human epithelial cells derived from the female and male genital tract highlights a possible role of PIII in the virulence of gonococcus and suggests that the structural homology to OmpA is conserved also at functional level.
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Affiliation(s)
| | | | | | | | | | | | | | - Mariagrazia Pizza
- Novartis Vaccines and Diagnostics, S,r,L, Via Fiorentina 1, Siena 53100, Italy.
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Hung MC, Christodoulides M. The biology of Neisseria adhesins. BIOLOGY 2013; 2:1054-109. [PMID: 24833056 PMCID: PMC3960869 DOI: 10.3390/biology2031054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 01/15/2023]
Abstract
Members of the genus Neisseria include pathogens causing important human diseases such as meningitis, septicaemia, gonorrhoea and pelvic inflammatory disease syndrome. Neisseriae are found on the exposed epithelia of the upper respiratory tract and the urogenital tract. Colonisation of these exposed epithelia is dependent on a repertoire of diverse bacterial molecules, extending not only from the surface of the bacteria but also found within the outer membrane. During invasive disease, pathogenic Neisseriae also interact with immune effector cells, vascular endothelia and the meninges. Neisseria adhesion involves the interplay of these multiple surface factors and in this review we discuss the structure and function of these important molecules and the nature of the host cell receptors and mechanisms involved in their recognition. We also describe the current status for recently identified Neisseria adhesins. Understanding the biology of Neisseria adhesins has an impact not only on the development of new vaccines but also in revealing fundamental knowledge about human biology.
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Affiliation(s)
- Miao-Chiu Hung
- Neisseria Research, Molecular Microbiology, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD, UK.
| | - Myron Christodoulides
- Neisseria Research, Molecular Microbiology, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD, UK.
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Comparative proteome analysis of spontaneous outer membrane vesicles and purified outer membranes of Neisseria meningitidis. J Bacteriol 2013; 195:4425-35. [PMID: 23893116 DOI: 10.1128/jb.00625-13] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Outer membrane vesicles (OMVs) of Gram-negative bacteria receive increasing attention because of various biological functions and their use as vaccines. However, the mechanisms of OMV release and selective sorting of proteins into OMVs remain unclear. Comprehensive quantitative proteome comparisons between spontaneous OMVs (SOMVs) and the outer membrane (OM) have not been conducted so far. Here, we established a protocol for metabolic labeling of neisserial proteins with (15)N. SOMV and OM proteins labeled with (15)N were used as an internal standard for proteomic comparison of the SOMVs and OMs of two different strains. This labeling approach, coupled with high-sensitivity mass spectrometry, allowed us to comprehensively unravel the proteome of the SOMVs and OMs. We quantified the relative distribution of 155 proteins between SOMVs and the OM. Complement regulatory proteins, autotransporters, proteins involved in iron and zinc acquisition, and a two-partner secretion system were enriched in SOMVs. The highly abundant porins PorA and PorB and proteins connecting the OM with peptidoglycan or the inner membrane, such as RmpM, MtrE, and PilQ, were depleted in SOMVs. Furthermore, the three lytic transglycosylases MltA, MltB, and Slt were less abundant in SOMVs. In conclusion, SOMVs are likely to be released from surface areas with a low local abundance of membrane-anchoring proteins and lytic transglycosylases. The enrichment of complement regulatory proteins, autotransporters, and trace metal binding and transport proteins needs to be explored in the context of the pathogenesis of meningococcal disease.
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43
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Confer AW, Ayalew S. The OmpA family of proteins: Roles in bacterial pathogenesis and immunity. Vet Microbiol 2013; 163:207-22. [DOI: 10.1016/j.vetmic.2012.08.019] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022]
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Verhoeven GS, Dogterom M, den Blaauwen T. Absence of long-range diffusion of OmpA in E. coli is not caused by its peptidoglycan binding domain. BMC Microbiol 2013; 13:66. [PMID: 23522061 PMCID: PMC3637615 DOI: 10.1186/1471-2180-13-66] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/18/2013] [Indexed: 11/15/2022] Open
Abstract
Background It is widely believed that integral outer membrane (OM) proteins in bacteria are able to diffuse laterally in the OM. However, stable, immobile proteins have been identified in the OM of Escherichia coli. In explaining the observations, a hypothesized interaction of the immobilized OM proteins with the underlying peptidoglycan (PG) cell wall played a prominent role. Results OmpA is an abundant outer membrane protein in E. coli containing a PG-binding domain. We use FRAP to investigate whether OmpA is able to diffuse laterally over long-range (> ~100 nm) distances in the OM. First, we show that OmpA, containing a PG binding domain, does not exhibit long-range lateral diffusion in the OM. Then, to test whether PG interaction was required for this immobilization, we genetically removed the PG binding domain and repeated the FRAP experiment. To our surprise, this did not increase the mobility of the protein in the OM. Conclusions OmpA exhibits an absence of long-range (> ~100 nm) diffusion in the OM that is not caused by its PG binding domain. Therefore, other mechanisms are needed to explain this observation, such as the presence of physical barriers in the OM, or strong interactions with other elements in the cell envelope.
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45
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Abstract
The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and mediate a rapid bacterial invasion into host cells in a phosphate-sensitive manner. To gain insights into this structure-function relationship we analysed PorBIA by X-ray crystallography in the presence of phosphate and ATP. The structure of PorBIA in the complex solved at a resolution of 3.3 Å (1 Å=0.1 nm) displays a surplus of positive charges inside the channel. ATP ligand-binding in the channel is co-ordinated by the positively charged residues of the channel interior. These residues ligate the aromatic, sugar and pyrophosphate moieties of the ligand. Two phosphate ions were observed in the structure, one of which clamped by two arginine residues (Arg92 and Arg124) localized at the extraplasmic channel exit. A short β-bulge in β2-strand together with the long L3 loop narrow the barrel diameter significantly and further support substrate specificity through hydrogen bond interactions. Interestingly the structure also comprised a small peptide as a remnant of a periplasmic protein which physically links porin molecules to the peptidoglycan network. To test the importance of Arg92 on bacterial invasion the residue was mutated. In vivo assays of bacteria carrying a R92S mutation confirmed the importance of this residue for host-cell invasion. Furthermore systematic sequence and structure comparisons of PorBIA from Neisseriaceae indicated Arg92 to be unique in disseminating N. gonorrhoeae thereby possibly distinguishing invasion-promoting porins from other neisserial porins.
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46
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Freixeiro P, Diéguez-Casal E, Costoya L, Seijo B, Ferreirós CM, Criado MT, Sánchez S. Study of the stability of proteoliposomes as vehicles for vaccines against Neisseria meningitidis based on recombinant porin complexes. Int J Pharm 2013; 443:1-8. [DOI: 10.1016/j.ijpharm.2012.12.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/21/2012] [Accepted: 12/30/2012] [Indexed: 11/29/2022]
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47
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van de Waterbeemd B, Zomer G, van den Ijssel J, van Keulen L, Eppink MH, van der Ley P, van der Pol LA. Cysteine depletion causes oxidative stress and triggers outer membrane vesicle release by Neisseria meningitidis; implications for vaccine development. PLoS One 2013; 8:e54314. [PMID: 23372704 PMCID: PMC3553081 DOI: 10.1371/journal.pone.0054314] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/11/2012] [Indexed: 12/13/2022] Open
Abstract
Outer membrane vesicles (OMV) contain immunogenic proteins and contribute to in vivo survival and virulence of bacterial pathogens. The first OMV vaccines successfully stopped Neisseria meningitidis serogroup B outbreaks but required detergent-extraction for endotoxin removal. Current vaccines use attenuated endotoxin, to preserve immunological properties and allow a detergent-free process. The preferred process is based on spontaneously released OMV (sOMV), which are most similar to in vivo vesicles and easier to purify. The release mechanism however is poorly understood resulting in low yield. This study with N. meningitidis demonstrates that an external stimulus, cysteine depletion, can trigger growth arrest and sOMV release in sufficient quantities for vaccine production (±1500 human doses per liter cultivation). Transcriptome analysis suggests that cysteine depletion impairs iron-sulfur protein assembly and causes oxidative stress. Involvement of oxidative stress is confirmed by showing that addition of reactive oxygen species during cysteine-rich growth also triggers vesiculation. The sOMV in this study are similar to vesicles from natural infection, therefore cysteine-dependent vesiculation is likely to be relevant for the in vivo pathogenesis of N. meningitidis.
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Affiliation(s)
- Bas van de Waterbeemd
- Vaccinology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Freixeiro P, Diéguez-Casal E, Costoya L, Marzoa J, Ferreirós CM, Criado MT, Sánchez S. High resolution clear native electrophoresis (hrCNE) allows a detailed analysis of the heterotrimeric structure of recombinant Neisseria meningitidis porins inserted into liposomes. J Proteome Res 2013; 12:777-84. [PMID: 23259616 DOI: 10.1021/pr3008573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three recombinant proteins of Neisseria meningitidis, rPorB, rPorA, and rRmpM, were purified and incorporated into liposomes prepared by dialysis-extrusion. The protein complexes formed using different combinations of recombinant proteins were studied by high resolution clear native electrophoresis (hrCNE) and 2-D hrCNE/SDS-PAGE, analyzing the influence of the stoichiometry of the two porins in the formation of complexes and comparing them with native porin complexes present in OMVs from five different N. meningitidis strains. Insertion of the recombinant proteins into liposomes allowed a complete refolding of porin complexes, and the electrophoretic analyses showed that, when the three recombinant proteins are present, the pattern of porin complexes obtained is similar to that observed in native OMVs. We could show homocomplexes of each individual porin and PorA/PorB, RmpM/PorB, and PorA/PorB/RmpM heterocomplexes. Our results suggest that RmpM binds only to PorB, confirm the trimeric structure of N. meningitidis pores, and demonstrate that insertion into liposomes restores the native structure of porin complexes.
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Affiliation(s)
- Paula Freixeiro
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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System specificity of the TpsB transporters of coexpressed two-partner secretion systems of Neisseria meningitidis. J Bacteriol 2012; 195:788-97. [PMID: 23222722 DOI: 10.1128/jb.01355-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The two-partner secretion (TPS) systems of Gram-negative bacteria consist of a large secreted exoprotein (TpsA) and a transporter protein (TpsB) located in the outer membrane. TpsA targets TpsB for transport across the membrane via its ∼30-kDa TPS domain located at its N terminus, and this domain is also the minimal secretory unit. Neisseria meningitidis genomes encode up to five TpsAs and two TpsBs. Sequence alignments of TPS domains suggested that these are organized into three systems, while there are two TpsBs, which raised questions on their system specificity. We show here that the TpsB2 transporter of Neisseria meningitidis is able to secrete all types of TPS domains encoded in N. meningitidis and the related species Neisseria lactamica but not domains of Haemophilus influenzae and Pseudomonas aeruginosa. In contrast, the TpsB1 transporter seemed to be specific for its cognate N. meningitidis system and did not secrete the TPS domains of other meningococcal systems. However, TpsB1 did secrete the TPS2b domain of N. lactamica, which is related to the meningococcal TPS2 domains. Apparently, the secretion depends on specific sequences within the TPS domain rather than the overall TPS domain structure.
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50
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Webb CT, Heinz E, Lithgow T. Evolution of the β-barrel assembly machinery. Trends Microbiol 2012; 20:612-20. [DOI: 10.1016/j.tim.2012.08.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/10/2012] [Accepted: 08/14/2012] [Indexed: 11/29/2022]
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