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Hoffmann T, Tych KM, Crosskey T, Schiffrin B, Brockwell DJ, Dougan L. Rapid and Robust Polyprotein Production Facilitates Single-Molecule Mechanical Characterization of β-Barrel Assembly Machinery Polypeptide Transport Associated Domains. ACS NANO 2015; 9:8811-21. [PMID: 26284289 DOI: 10.1021/acsnano.5b01962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule force spectroscopy by atomic force microscopy exploits the use of multimeric protein constructs, namely, polyproteins, to decrease the impact of nonspecific interactions, to improve data accumulation, and to allow the accommodation of benchmarking reference domains within the construct. However, methods to generate such constructs are either time- and labor-intensive or lack control over the length or the domain sequence of the obtained construct. Here, we describe an approach that addresses both of these shortcomings that uses Gibson assembly (GA) to generate a defined recombinant polyprotein rapidly using linker sequences. To demonstrate the feasibility of this approach, we used GA to make a polyprotein composed of alternating domains of I27 and TmCsp, (I27-TmCsp)3-I27)(GA), and showed the mechanical fingerprint, mechanical strength, and pulling speed dependence are the same as an analogous polyprotein constructed using the classical approach. After this benchmarking, we exploited this approach to facilitiate the mechanical characterization of POTRA domain 2 of BamA from E. coli (EcPOTRA2) by assembling the polyprotein (I27-EcPOTRA2)3-I27(GA). We show that, as predicted from the α + β topology, EcPOTRA2 domains are mechanically robust over a wide range of pulling speeds. Furthermore, we identify a clear correlation between mechanical robustness and brittleness for a range of other α + β proteins that contain the structural feature of proximal terminal β-strands in parallel geometry. We thus demonstrate that the GA approach is a powerful tool, as it circumvents the usual time- and labor-intensive polyprotein production process and allows for rapid production of new constructs for single-molecule studies. As shown for EcPOTRA2, this approach allows the exploration of the mechanical properties of a greater number of proteins and their variants. This improves our understanding of the relationship between structure and mechanical strength, increasing our ability to design proteins with tailored mechanical properties.
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Affiliation(s)
- Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Thomas Crosskey
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Bob Schiffrin
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
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52
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Wimmer MR, Woods CN, Adamczak KJ, Glasgow EM, Novak WRP, Grilley DP, Weaver TM. Sequential unfolding of the hemolysin two-partner secretion domain from Proteus mirabilis. Protein Sci 2015; 24:1841-55. [PMID: 26350294 DOI: 10.1002/pro.2791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 01/07/2023]
Abstract
Protein secretion is a major contributor to Gram-negative bacterial virulence. Type Vb or two-partner secretion (TPS) pathways utilize a membrane bound β-barrel B component (TpsB) to translocate large and predominantly virulent exoproteins (TpsA) through a nucleotide independent mechanism. We focused our studies on a truncated TpsA member termed hemolysin A (HpmA265), a structurally and functionally characterized TPS domain from Proteus mirabilis. Contrary to the expectation that the TPS domain of HpmA265 would denature in a single cooperative transition, we found that the unfolding follows a sequential model with three distinct transitions linking four states. The solvent inaccessible core of HpmA265 can be divided into two different regions. The C-proximal region contains nonpolar residues and forms a prototypical hydrophobic core as found in globular proteins. The N-proximal region of the solvent inaccessible core, however, contains polar residues. To understand the contributions of the hydrophobic and polar interiors to overall TPS domain stability, we conducted unfolding studies on HpmA265 and site-specific mutants of HpmA265. By correlating the effect of individual site-specific mutations with the sequential unfolding results we were able to divide the HpmA265 TPS domain into polar core, nonpolar core, and C-terminal subdomains. Moreover, the unfolding studies provide quantitative evidence that the folding free energy for the polar core subdomain is more favorable than for the nonpolar core and C-terminal subdomains. This study implicates the hydrogen bonds shared among these conserved internal residues as a primary means for stabilizing the N-proximal polar core subdomain.
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Affiliation(s)
- Megan R Wimmer
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
| | - Christopher N Woods
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
| | - Kyle J Adamczak
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
| | - Evan M Glasgow
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
| | - Walter R P Novak
- Department of Chemistry, Wabash College, Crawfordsville, Indiana, 47933
| | - Daniel P Grilley
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
| | - Todd M Weaver
- Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, La Crosse, Wisconsin, 54601
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53
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Probing the conformation of FhaC with small-angle neutron scattering and molecular modeling. Biophys J 2015; 107:185-96. [PMID: 24988353 DOI: 10.1016/j.bpj.2014.05.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 04/20/2014] [Accepted: 05/05/2014] [Indexed: 11/22/2022] Open
Abstract
Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120-160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins.
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54
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Guérin J, Saint N, Baud C, Meli AC, Etienne E, Locht C, Vezin H, Jacob-Dubuisson F. Dynamic interplay of membrane-proximal POTRA domain and conserved loop L6 in Omp85 transporter FhaC. Mol Microbiol 2015; 98:490-501. [PMID: 26192332 DOI: 10.1111/mmi.13137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 12/30/2022]
Abstract
Omp85 transporters mediate protein insertion into, or translocation across, membranes. They have a conserved architecture, with POTRA domains that interact with substrate proteins, a 16-stranded transmembrane β barrel, and an extracellular loop, L6, folded back in the barrel pore. Here using electrophysiology, in vivo biochemical approaches and electron paramagnetic resonance, we show that the L6 loop of the Omp85 transporter FhaC changes conformation and modulates channel opening. Those conformational changes involve breaking the conserved interaction between the tip of L6 and the inner β-barrel wall. The membrane-proximal POTRA domain also exchanges between several conformations, and the binding of FHA displaces this equilibrium. We further demonstrate a dynamic, physical communication between the POTRA domains and L6, which must take place via the β barrel. Our findings thus link all three essential components of Omp85 transporters and indicate that they operate in a concerted fashion in the transport cycle.
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Affiliation(s)
- Jeremy Guérin
- Institut Pasteur de Lille, CIIL, 1 rue Calmette, 59019, Lille Cedex, France.,Université de Lille, 1 rue G. Lefebvre, 59000, Lille, France.,CNRS UMR 8204, 2 rue des Canonniers, 59046, Lille, France.,INSERM U1019, 6 rue Pr. Laguesse, 59045, Lille, France
| | - Nathalie Saint
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR9214, 371 av. G. Giraud, 34295, Montpellier cedex 05, France
| | - Catherine Baud
- Institut Pasteur de Lille, CIIL, 1 rue Calmette, 59019, Lille Cedex, France.,Université de Lille, 1 rue G. Lefebvre, 59000, Lille, France.,CNRS UMR 8204, 2 rue des Canonniers, 59046, Lille, France.,INSERM U1019, 6 rue Pr. Laguesse, 59045, Lille, France
| | - Albano C Meli
- PhyMedExp, University of Montpellier, INSERM U1046, CNRS UMR9214, 371 av. G. Giraud, 34295, Montpellier cedex 05, France
| | - Emilien Etienne
- Aix-Marseille Université, CNRS, BIP (UMR 7281), 31 chemin J. Aiguier, 13402, Marseille cedex 20, France
| | - Camille Locht
- Institut Pasteur de Lille, CIIL, 1 rue Calmette, 59019, Lille Cedex, France.,Université de Lille, 1 rue G. Lefebvre, 59000, Lille, France.,CNRS UMR 8204, 2 rue des Canonniers, 59046, Lille, France.,INSERM U1019, 6 rue Pr. Laguesse, 59045, Lille, France
| | - Hervé Vezin
- Université de Lille, 1 rue G. Lefebvre, 59000, Lille, France.,CNRS UMR8516, Bat. C4, 59658, Villeneuve d'Ascq, France
| | - Françoise Jacob-Dubuisson
- Institut Pasteur de Lille, CIIL, 1 rue Calmette, 59019, Lille Cedex, France.,Université de Lille, 1 rue G. Lefebvre, 59000, Lille, France.,CNRS UMR 8204, 2 rue des Canonniers, 59046, Lille, France.,INSERM U1019, 6 rue Pr. Laguesse, 59045, Lille, France
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55
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Villarino Romero R, Osicka R, Sebo P. Filamentous hemagglutinin of Bordetella pertussis: a key adhesin with immunomodulatory properties? Future Microbiol 2015; 9:1339-60. [PMID: 25517899 DOI: 10.2217/fmb.14.77] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The filamentous hemagglutinin of pathogenic Bordetellae is a prototype of a large two-partner-system-secreted and β-structure-rich bacterial adhesin. It exhibits several binding activities that may facilitate bacterial adherence to airway mucosa and host phagocytes in the initial phases of infection. Despite three decades of research on filamentous hemagglutinin, there remain many questions on its structure-function relationships, integrin interactions and possible immunomodulatory signaling capacity. Here we review the state of knowledge on this important virulence factor and acellular pertussis vaccine component. Specific emphasis is placed on outstanding questions that are yet to be answered.
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Affiliation(s)
- Rodrigo Villarino Romero
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
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56
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Browning DF, Bavro VN, Mason JL, Sevastsyanovich YR, Rossiter AE, Jeeves M, Wells TJ, Knowles TJ, Cunningham AF, Donald JW, Palmer T, Overduin M, Henderson IR. Cross-species chimeras reveal BamA POTRA and β-barrel domains must be fine-tuned for efficient OMP insertion. Mol Microbiol 2015; 97:646-59. [PMID: 25943387 PMCID: PMC4950039 DOI: 10.1111/mmi.13052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BAM is a conserved molecular machine, the central component of which is BamA. Orthologues of BamA are found in all Gram-negative bacteria, chloroplasts and mitochondria where it is required for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the outer membrane. BamA binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains at its N-terminus. The C-terminus of BamA folds into a β-barrel domain, which tethers BamA to the outer membrane and is involved in OMP insertion. BamA orthologues are found in all Gram-negative bacteria and appear to function in a species-specific manner. Here we investigate the nature of this species-specificity by examining whether chimeric Escherichia coli BamA fusion proteins, carrying either the β-barrel or POTRA domains from various BamA orthologues, can functionally replace E. coli BamA. We demonstrate that the β-barrel domains of many BamA orthologues are functionally interchangeable. We show that defects in the orthologous POTRA domains can be rescued by compensatory mutations within the β-barrel. These data reveal that the POTRA and barrel domains must be precisely aligned to ensure efficient OMP insertion.
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Affiliation(s)
- Douglas F Browning
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jessica L Mason
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Wells
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - James W Donald
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tracy Palmer
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michael Overduin
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
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57
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Vimala A, Ramakrishnan C, Gromiha MM. Identifying a potential receptor for the antibacterial peptide of sponge Axinella donnani endosymbiont. Gene 2015; 566:166-74. [PMID: 25939848 DOI: 10.1016/j.gene.2015.04.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/03/2015] [Accepted: 04/15/2015] [Indexed: 11/30/2022]
Abstract
Marine sponges and their associated bacteria are rich sources of novel secondary metabolites with therapeutic usefulness. In our earlier work, we have identified a novel antibacterial peptide from the marine sponge Axinella donnani endosymbiotic bacteria. In this work, we have carried out a comparative genomic analysis and identified a set of 60 proteins as probable receptor which is common in all the strains. The analysis on binding substrate showed that β barrel assembly machinery (BamA) of the outer membrane protein 85 (omp85) superfamily is a potential receptor protein for the antibacterial peptide. It plays a central role in OMP biogenesis, especially in cell viability. Further, the triplet and quartet motifs RGF and YGDG, respectively in L6 loop are conserved over all the strains and these conserved residues interact with antibacterial peptide to inhibit the BamA function, which is essential for OMP biogenesis.
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Affiliation(s)
- A Vimala
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 Tamilnadu, India.
| | - C Ramakrishnan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 Tamilnadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 Tamilnadu, India.
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58
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Conserved Omp85 lid-lock structure and substrate recognition in FhaC. Nat Commun 2015; 6:7452. [PMID: 26058369 PMCID: PMC4490367 DOI: 10.1038/ncomms8452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 05/09/2015] [Indexed: 11/11/2022] Open
Abstract
Omp85 proteins mediate translocation of polypeptide substrates across and into cellular membranes. They share a common architecture comprising substrate-interacting POTRA domains, a C-terminal 16-stranded β-barrel pore and two signature motifs located on the inner barrel wall and at the tip of the extended L6 loop. The observation of two distinct conformations of the L6 loop in the available Omp85 structures previously suggested a functional role of conformational changes in L6 in the Omp85 mechanism. Here we present a 2.5 Å resolution structure of a variant of the Omp85 secretion protein FhaC, in which the two signature motifs interact tightly and form the conserved ‘lid lock'. Reanalysis of previous structural data shows that L6 adopts the same, conserved resting state position in all available Omp85 structures. The FhaC variant structure further reveals a competitive mechanism for the regulation of substrate binding mediated by the linker to the N-terminal plug helix H1. The fundamental processes of protein insertion and translocation at the outer membrane are mediated by Omp85 proteins. Here the authors report structures of the translocase FhaC, showing that the critical L6 loop adopts a conformation similar to that of related insertases; establishing a common structural basis for Omp85 function.
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59
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Bernstein HD. Looks can be deceiving: recent insights into the mechanism of protein secretion by the autotransporter pathway. Mol Microbiol 2015; 97:205-15. [PMID: 25881492 DOI: 10.1111/mmi.13031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/14/2022]
Abstract
Autotransporters are a large superfamily of cell surface proteins produced by Gram-negative bacteria that consist of an N-terminal extracellular domain ('passenger domain') and a C-terminal β-barrel domain that resides in the outer membrane (OM). Although it was originally proposed that the passenger domain is translocated across the OM through a channel formed exclusively by the covalently linked β-barrel domain, this idea has been strongly challenged by a variety of observations. Recent experimental results have suggested a new model in which both the translocation of the passenger domain and the membrane integration of the β-barrel domain are facilitated by the Bam complex, a highly conserved heteroligomer that plays a general role in OM protein assembly. Other factors, including periplasmic chaperones and inner membrane proteins, have also recently been implicated in the biogenesis of at least some members of the autotransporter superfamily. New results have raised intriguing questions about the energetics of the secretion reaction and the relationship between the assembly of autotransporters and the assembly of other classes of OM proteins. Concomitantly, new mechanistic and structural insights have expanded the utility of the autotransporter pathway for the surface display of heterologous peptides and proteins of interest.
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Affiliation(s)
- Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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60
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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61
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Noinaj N, Rollauer SE, Buchanan SK. The β-barrel membrane protein insertase machinery from Gram-negative bacteria. Curr Opin Struct Biol 2015; 31:35-42. [PMID: 25796031 PMCID: PMC4476940 DOI: 10.1016/j.sbi.2015.02.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/06/2015] [Accepted: 02/23/2015] [Indexed: 12/25/2022]
Abstract
The outer membranes (OM) of Gram-negative bacteria contain a host of β-barrel outer membrane proteins (OMPs) which serve many functions for cell survival and virulence. The biogenesis of these OMPs is mediated by the β-barrel assembly machinery (BAM) complex which is composed of five components including the essential core component called BamA that mediates the insertase function within the OM. The crystal structure of BamA has recently been reported from three different species, including a full-length structure from Neisseria gonorrhoeae. Mutagenesis and functional studies identified several conformational changes within BamA that are required for function, providing a significant advancement towards unraveling exactly how BamA and the BAM complex are able to fold and insert new OMPs in the OM.
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Affiliation(s)
- Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Sarah E Rollauer
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States.
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62
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Dunn JP, Kenedy MR, Iqbal H, Akins DR. Characterization of the β-barrel assembly machine accessory lipoproteins from Borrelia burgdorferi. BMC Microbiol 2015; 15:70. [PMID: 25887384 PMCID: PMC4377024 DOI: 10.1186/s12866-015-0411-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 12/26/2022] Open
Abstract
Background Like all diderm bacteria studied to date, Borrelia burgdorferi possesses a β-barrel assembly machine (BAM) complex. The bacterial BAM complexes characterized thus far consist of an essential integral outer membrane protein designated BamA and one or more accessory proteins. The accessory proteins are typically lipid-modified proteins anchored to the inner leaflet of the outer membrane through their lipid moieties. We previously identified and characterized the B. burgdorferi BamA protein in detail and more recently identified two lipoproteins encoded by open reading frames bb0324 and bb0028 that associate with the borrelial BamA protein. The role(s) of the BAM accessory lipoproteins in B. burgdorferi is currently unknown. Results Structural modeling of B. burgdorferi BB0028 revealed a distinct β-propeller fold similar to the known structure for the E. coli BAM accessory lipoprotein BamB. Additionally, the structural model for BB0324 was highly similar to the known structure of BamD, which is consistent with the prior finding that BB0324 contains tetratricopeptide repeat regions similar to other BamD orthologs. Consistent with BB0028 and BB0324 being BAM accessory lipoproteins, mutants lacking expression of each protein were found to exhibit altered membrane permeability and enhanced sensitivity to various antimicrobials. Additionally, BB0028 mutants also exhibited significantly impaired in vitro growth. Finally, immunoprecipitation experiments revealed that BB0028 and BB0324 each interact specifically and independently with BamA to form the BAM complex in B. burgdorferi. Conclusions Combined structural studies, functional assays, and co-immunoprecipitation experiments confirmed that BB0028 and BB0324 are the respective BamB and BamD orthologs in B. burgdorferi, and are important in membrane integrity and/or outer membrane protein localization. The borrelial BamB and BamD proteins both interact specifically and independently with BamA to form a tripartite BAM complex in B. burgdorferi. A working model has been developed to further analyze outer membrane biogenesis and outer membrane protein transport in this pathogenic spirochete.
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Affiliation(s)
- Joshua P Dunn
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Henna Iqbal
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Darrin R Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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63
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Structural determinants of the interaction between the TpsA and TpsB proteins in the Haemophilus influenzae HMW1 two-partner secretion system. J Bacteriol 2015; 197:1769-80. [PMID: 25777673 DOI: 10.1128/jb.00039-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 02/26/2015] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED The two-partner secretion (TPS) pathway in Gram-negative bacteria consists of a TpsA exoprotein and a cognate TpsB outer membrane pore-forming translocator protein. Previous work has demonstrated that the TpsA protein contains an N-terminal TPS domain that plays an important role in targeting the TpsB protein and is required for secretion. The nontypeable Haemophilus influenzae HMW1 and HMW2 adhesins are homologous proteins that are prototype TpsA proteins and are secreted by the HMW1B and HMW2B TpsB proteins. In the present study, we sought to define the structural determinants of HMW1 interaction with HMW1B during the transport process and while anchored to the bacterial surface. Modeling of HMW1B revealed an N-terminal periplasmic region that contains two polypeptide transport-associated (POTRA) domains and a C-terminal membrane-localized region that forms a pore. Biochemical studies demonstrated that HMW1 engages HMW1B via interaction between the HMW1 TPS domain and the HMW1B periplasmic region, specifically, the predicted POTRA1 and POTRA2 domains. Subsequently, HMW1 is shuttled to the HMW1B pore, facilitated by the N-terminal region, the middle region, and the NPNG motif in the HMW1 TPS domain. Additional analysis revealed that the interaction between HMW1 and HMW1B is highly specific and is dependent upon the POTRA domains and the pore-forming domain of HMW1B. Further studies established that tethering of HMW1 to the surface-exposed region of HMW1B is dependent upon the external loops of HMW1B formed by residues 267 to 283 and residues 324 to 330. These observations may have broad relevance to proteins secreted by the TPS pathway. IMPORTANCE Secretion of HMW1 involves a recognition event between the extended form of the HMW1 propiece and the HMW1B POTRA domains. Our results identify specific interactions between the HMW1 propiece and the periplasmic HMW1B POTRA domains. The results also suggest that the process of HMW1 translocation involves at least two discrete steps, including initial interaction between the HMW1 propiece and the HMW1B POTRA domains and then a separate translocation event. We have also discovered that the HMW1B pore itself appears to influence the translocation process. These observations extend our knowledge of the two-partner secretion system and may be broadly relevant to other proteins secreted by the TPS pathway.
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Garnett JA, Muhl D, Douse CH, Hui K, Busch A, Omisore A, Yang Y, Simpson P, Marchant J, Waksman G, Matthews S, Filloux A. Structure-function analysis reveals that the Pseudomonas aeruginosa Tps4 two-partner secretion system is involved in CupB5 translocation. Protein Sci 2015; 24:670-87. [PMID: 25641651 PMCID: PMC4420518 DOI: 10.1002/pro.2640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 01/11/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium, synonymous with cystic fibrosis patients, which can cause chronic infection of the lungs. This pathogen is a model organism to study biofilms: a bacterial population embedded in an extracellular matrix that provide protection from environmental pressures and lead to persistence. A number of Chaperone-Usher Pathways, namely CupA-CupE, play key roles in these processes by assembling adhesive pili on the bacterial surface. One of these, encoded by the cupB operon, is unique as it contains a nonchaperone-usher gene product, CupB5. Two-partner secretion (TPS) systems are comprised of a C-terminal integral membrane β-barrel pore with tandem N-terminal POTRA (POlypeptide TRansport Associated) domains located in the periplasm (TpsB) and a secreted substrate (TpsA). Using NMR we show that TpsB4 (LepB) interacts with CupB5 and its predicted cognate partner TpsA4 (LepA), an extracellular protease. Moreover, using cellular studies we confirm that TpsB4 can translocate CupB5 across the P. aeruginosa outer membrane, which contrasts a previous observation that suggested the CupB3 P-usher secretes CupB5. In support of our findings we also demonstrate that tps4/cupB operons are coregulated by the RocS1 sensor suggesting P. aeruginosa has developed synergy between these systems. Furthermore, we have determined the solution-structure of the TpsB4-POTRA1 domain and together with restraints from NMR chemical shift mapping and in vivo mutational analysis we have calculated models for the entire TpsB4 periplasmic region in complex with both TpsA4 and CupB5 secretion motifs. The data highlight specific residues for TpsA4/CupB5 recognition by TpsB4 in the periplasm and suggest distinct roles for each POTRA domain.
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Affiliation(s)
- James A Garnett
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom; Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
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Abstract
The outer membranes of gram-negative bacteria contain integral membrane proteins, most of which are of β-barrel structure, and critical for bacterial survival. These β-barrel proteins rely on the β-barrel assembly machinery (BAM) complex for their integration into the outer membrane as folded species. The central and essential subunit of the BAM complex, BamA, is a β-barrel protein conserved in all gram-negative bacteria and also found in eukaryotic organelles derived from bacterial endosymbionts. In Escherichia coli, BamA docks with four peripheral lipoproteins, BamB, BamC, BamD and BamE, partner subunits that add to the function of the BAM complex in outer membrane protein biogenesis. By way of introduction to this volume, we provide an overview of the work that has illuminated the mechanism by which the BAM complex drives β-barrel assembly. The protocols and methodologies associated with these studies as well as the challenges encountered and their elegant solutions are discussed in subsequent chapters.
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66
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Gruss F, Hiller S, Maier T. Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA. Methods Mol Biol 2015; 1329:259-70. [PMID: 26427691 DOI: 10.1007/978-1-4939-2871-2_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
TamA is an Omp85 protein involved in autotransporter assembly in the outer membrane of Escherichia coli. It comprises a C-terminal 16-stranded transmembrane β-barrel as well as three periplasmic POTRA domains, and is a challenging target for structure determination. Here, we present a method for crystal structure determination of TamA, including recombinant expression in E. coli, detergent extraction, chromatographic purification, and bicelle crystallization in combination with seeding. As a result, crystals in space group P21212 are obtained, which diffract to 2.3 Å resolution. This protocol also serves as a template for structure determination of other outer membrane proteins, in particular of the Omp85 family.
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Affiliation(s)
- Fabian Gruss
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
| | - Timm Maier
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
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Simmerman RF, Dave AM, Bruce BD. Structure and function of POTRA domains of Omp85/TPS superfamily. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:1-34. [PMID: 24411168 DOI: 10.1016/b978-0-12-800097-7.00001-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Omp85/TPS (outer-membrane protein of 85 kDa/two-partner secretion) superfamily is a ubiquitous and major class of β-barrel proteins. This superfamily is restricted to the outer membranes of gram-negative bacteria, mitochondria, and chloroplasts. The common architecture, with an N-terminus consisting of repeats of soluble polypeptide-transport-associated (POTRA) domains and a C-terminal β-barrel pore is highly conserved. The structures of multiple POTRA domains and one full-length TPS protein have been solved, yet discovering roles of individual POTRA domains has been difficult. This review focuses on similarities and differences between POTRA structures, emphasizing POTRA domains in autotrophic organisms including plants and cyanobacteria. Unique roles, specific for certain POTRA domains, are examined in the context of POTRA location with respect to their attachment to the β-barrel pore, and their degree of biological dispensability. Finally, because many POTRA domains may have the ability to interact with thousands of partner proteins, possible modes of these interactions are also explored.
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Affiliation(s)
- Richard F Simmerman
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA
| | - Ashita M Dave
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA; Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.
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Abstract
The paper provides a short overview of three investigated bacterial protein toxins, colicin M (Cma) of Escherichia coli, pesticin (Pst) of Yersinia pestis and hemolysin (ShlAB) of Serratia marcescens. Cma and Pst are exceptional among colicins in that they kill bacteria by degrading the murein (peptidoglycan). Both are released into the medium and bind to specific receptor proteins in the outer membrane of sensitive E. coli cells. Subsequently they are translocated into the periplasm by an energy-consuming process using the proton motive force. For transmembrane translocation the colicins unfold and refold in the periplasm. In the case of Cma the FkpA peptidyl prolyl cis-trans isomerase/chaperone is required. ShlA is secreted and activated through ShlB in the outer membrane by a type Vb secretion mechanism.
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69
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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70
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Norell D, Heuck A, Tran-Thi TA, Götzke H, Jacob-Dubuisson F, Clausen T, Daley DO, Braun V, Müller M, Fan E. Versatile in vitro system to study translocation and functional integration of bacterial outer membrane proteins. Nat Commun 2014; 5:5396. [DOI: 10.1038/ncomms6396] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
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71
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Baud C, Guérin J, Petit E, Lesne E, Dupré E, Locht C, Jacob-Dubuisson F. Translocation path of a substrate protein through its Omp85 transporter. Nat Commun 2014; 5:5271. [PMID: 25327833 DOI: 10.1038/ncomms6271] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/16/2014] [Indexed: 11/09/2022] Open
Abstract
TpsB proteins are Omp85 superfamily members that mediate protein translocation across the outer membrane of Gram-negative bacteria. Omp85 transporters are composed of N-terminal POTRA domains and a C-terminal transmembrane β-barrel. In this work, we track the in vivo secretion path of the Bordetella pertussis filamentous haemagglutinin (FHA), the substrate of the model TpsB transporter FhaC, using site-specific crosslinking. The conserved secretion domain of FHA interacts with the POTRA domains, specific extracellular loops and strands of FhaC and the inner β-barrel surface. The interaction map indicates a funnel-like pathway, with conformationally flexible FHA entering the channel in a non-exclusive manner and exiting along a four-stranded β-sheet at the surface of the FhaC barrel. This sheet of FhaC guides the secretion domain of FHA along discrete steps of translocation and folding. This work demonstrates that the Omp85 barrel serves as a channel for translocation of substrate proteins.
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Affiliation(s)
- Catherine Baud
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Jérémy Guérin
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Emmanuelle Petit
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Elodie Lesne
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Elian Dupré
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Camille Locht
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
| | - Françoise Jacob-Dubuisson
- 1] Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue Calmette, Lille 59021, France [2] CNRS UMR8204, Lille 59021, France [3] INSERM U1019, Lille 59045, France [4] University of Lille Nord de France, Lille 59044, France
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72
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Höhr AIC, Straub SP, Warscheid B, Becker T, Wiedemann N. Assembly of β-barrel proteins in the mitochondrial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:74-88. [PMID: 25305573 DOI: 10.1016/j.bbamcr.2014.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 12/15/2022]
Abstract
Mitochondria evolved through endosymbiosis of a Gram-negative progenitor with a host cell to generate eukaryotes. Therefore, the outer membrane of mitochondria and Gram-negative bacteria contain pore proteins with β-barrel topology. After synthesis in the cytosol, β-barrel precursor proteins are first transported into the mitochondrial intermembrane space. Folding and membrane integration of β-barrel proteins depend on the mitochondrial sorting and assembly machinery (SAM) located in the outer membrane, which is related to the β-barrel assembly machinery (BAM) in bacteria. The SAM complex recognizes β-barrel proteins by a β-signal in the C-terminal β-strand that is required to initiate β-barrel protein insertion into the outer membrane. In addition, the SAM complex is crucial to form membrane contacts with the inner mitochondrial membrane by interacting with the mitochondrial contact site and cristae organizing system (MICOS) and shares a subunit with the endoplasmic reticulum-mitochondria encounter structure (ERMES) that links the outer mitochondrial membrane to the endoplasmic reticulum (ER).
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Affiliation(s)
- Alexandra I C Höhr
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian P Straub
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany; Abteilung Biochemie und Funktionelle Proteomik, Institut für Biologie II, Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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73
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Paila YD, Richardson LGL, Schnell DJ. New insights into the mechanism of chloroplast protein import and its integration with protein quality control, organelle biogenesis and development. J Mol Biol 2014; 427:1038-1060. [PMID: 25174336 DOI: 10.1016/j.jmb.2014.08.016] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 01/04/2023]
Abstract
The translocons at the outer (TOC) and the inner (TIC) envelope membranes of chloroplasts mediate the targeting and import of several thousand nucleus-encoded preproteins that are required for organelle biogenesis and homeostasis. The cytosolic events in preprotein targeting remain largely unknown, although cytoplasmic chaperones have been proposed to facilitate delivery to the TOC complex. Preprotein recognition is mediated by the TOC GTPase receptors Toc159 and Toc34. The receptors constitute a GTP-regulated switch, which initiates membrane translocation via Toc75, a member of the Omp85 (outer membrane protein 85)/TpsB (two-partner secretion system B) family of bacterial, plastid and mitochondrial β-barrel outer membrane proteins. The TOC receptor systems have diversified to recognize distinct sets of preproteins, thereby maximizing the efficiency of targeting in response to changes in gene expression during developmental and physiological events that impact organelle function. The TOC complex interacts with the TIC translocon to allow simultaneous translocation of preproteins across the envelope. Both the two inner membrane complexes, the Tic110 and 1 MDa complexes, have been implicated as constituents of the TIC translocon, and it remains to be determined how they interact to form the TIC channel and assemble the import-associated chaperone network in the stroma that drives import across the envelope membranes. This review will focus on recent developments in our understanding of the mechanisms and diversity of the TOC-TIC systems. Our goal is to incorporate these recent studies with previous work and present updated or revised models for the function of TOC-TIC in protein import.
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Affiliation(s)
- Yamuna D Paila
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
| | - Lynn G L Richardson
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
| | - Danny J Schnell
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
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74
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Sommer MS, Schleiff E. Protein targeting and transport as a necessary consequence of increased cellular complexity. Cold Spring Harb Perspect Biol 2014; 6:6/8/a016055. [PMID: 25085907 DOI: 10.1101/cshperspect.a016055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
With increasing intracellular complexity, a new cell-biological problem that is the allocation of cytoplasmically synthesized proteins to their final destinations within the cell emerged. A special challenge is thereby the translocation of proteins into or across cellular membranes. The underlying mechanisms are only in parts well understood, but it can be assumed that the course of cellular evolution had a deep impact on the design of the required molecular machines. In this article, we aim to summarize the current knowledge and concepts of the evolutionary development of protein trafficking as a necessary premise and consequence of increased cellular complexity.
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Affiliation(s)
- Maik S Sommer
- Institute for Molecular Biosciences, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany Centre of Membrane Proteomics, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
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75
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van Ulsen P, Rahman SU, Jong WS, Daleke-Schermerhorn MH, Luirink J. Type V secretion: From biogenesis to biotechnology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1592-611. [DOI: 10.1016/j.bbamcr.2013.11.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/01/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
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Heinz E, Lithgow T. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. Front Microbiol 2014; 5:370. [PMID: 25101071 PMCID: PMC4104836 DOI: 10.3389/fmicb.2014.00370] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 01/25/2023] Open
Abstract
Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins.
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Affiliation(s)
- Eva Heinz
- Department of Microbiology, Monash University Melbourne, VIC, Australia ; Victorian Bioinformatics Consortium, Monash University Melbourne, VIC, Australia
| | - Trevor Lithgow
- Department of Microbiology, Monash University Melbourne, VIC, Australia
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77
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Faure LM, Garvis S, de Bentzmann S, Bigot S. Characterization of a novel two-partner secretion system implicated in the virulence of Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2014; 160:1940-1952. [PMID: 25009238 DOI: 10.1099/mic.0.079616-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen implicated in nosocomial infection and infecting people with compromised immune systems such as cystic fibrosis patients. Although multiple genes involved in P. aeruginosa pathogenesis have been characterized, the overall mechanism of virulence is not fully understood. In this study, we identified a functional two-partner secretion (TPS) system, composed of the PdtA exoprotein and its cognate pore-forming β-barrel PdtB transporter, which is implicated in the virulence of P. aeruginosa. We found that the predicted PdtA exoprotein is related to the HMW-like adhesins subfamily TPS systems. We demonstrate here that limitation of inorganic phosphate (Pi) allows the production of PdtA protein. We show that PdtA is processed during its outer-membrane translocation, with an N-terminal domain released into the extracellular environment and a C-terminal domain associated with the outer membrane of the cell. We also obtained evidence that the transport of PdtA is strictly dependent on the production of PdtB, a result confirming that these proteins constitute a functional TPS system. Furthermore, using the Caenorhabditis elegans model of infection, we show that a pdtA mutant is less virulent than the wild-type strain.
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Affiliation(s)
- Laura M Faure
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Steve Garvis
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Sophie de Bentzmann
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Sarah Bigot
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Noinaj N, Kuszak AJ, Balusek C, Gumbart JC, Buchanan SK. Lateral opening and exit pore formation are required for BamA function. Structure 2014; 22:1055-62. [PMID: 24980798 DOI: 10.1016/j.str.2014.05.008] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
Abstract
The outer membrane of Gram-negative bacteria is replete with a host of β-barrel outer membrane proteins (OMPs). Despite serving a variety of essential functions, including immune response evasion, the exact mechanism of OMP folding and membrane insertion remains largely unclear. The β-barrel assembly machinery complex is required for OMP biogenesis. Crystal structures and molecular dynamics (MD) simulations of the central and essential component, BamA, suggest a mechanism involving lateral opening of its barrel domain. MD simulations reported here reveal an additional feature of BamA: a substrate exit pore positioned above the lateral opening site. Disulfide crosslinks that prevent lateral opening and exit pore formation result in a loss of BamA function, which can be fully rescued by the reductant tris(2-carboxyethyl)phosphine. These data provide strong evidence that lateral opening and exit pore formation are required for BamA function.
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Affiliation(s)
- Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam J Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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79
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Albrecht R, Schütz M, Oberhettinger P, Faulstich M, Bermejo I, Rudel T, Diederichs K, Zeth K. Structure of BamA, an essential factor in outer membrane protein biogenesis. ACTA ACUST UNITED AC 2014; 70:1779-89. [PMID: 24914988 DOI: 10.1107/s1399004714007482] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/03/2014] [Indexed: 11/10/2022]
Abstract
Outer membrane protein (OMP) biogenesis is an essential process for maintaining the bacterial cell envelope and involves the β-barrel assembly machinery (BAM) for OMP recognition, folding and assembly. In Escherichia coli this function is orchestrated by five proteins: the integral outer membrane protein BamA of the Omp85 superfamily and four associated lipoproteins. To unravel the mechanism underlying OMP folding and insertion, the structure of the E. coli BamA β-barrel and P5 domain was determined at 3 Å resolution. These data add information beyond that provided in the recently published crystal structures of BamA from Haemophilus ducreyi and Neisseria gonorrhoeae and are a valuable basis for the interpretation of pertinent functional studies. In an `open' conformation, E. coli BamA displays a significant degree of flexibility between P5 and the barrel domain, which is indicative of a multi-state function in substrate transfer. E. coli BamA is characterized by a discontinuous β-barrel with impaired β1-β16 strand interactions denoted by only two connecting hydrogen bonds and a disordered C-terminus. The 16-stranded barrel surrounds a large cavity which implies a function in OMP substrate binding and partial folding. These findings strongly support a mechanism of OMP biogenesis in which substrates are partially folded inside the barrel cavity and are subsequently released laterally into the lipid bilayer.
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Affiliation(s)
- Reinhard Albrecht
- Department of Protein Evolution, Max-Planck-Institut für Entwicklungsbiologie, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Monika Schütz
- Institut für Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany
| | - Philipp Oberhettinger
- Institut für Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany
| | - Michaela Faulstich
- Department for Microbiology, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivan Bermejo
- Unidad de Biofisica (CSIC-UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Vizcaya, Spain
| | - Thomas Rudel
- Department for Microbiology, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kornelius Zeth
- Department of Protein Evolution, Max-Planck-Institut für Entwicklungsbiologie, Spemannstrasse 35, 72076 Tübingen, Germany
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80
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ur Rahman S, Arenas J, Öztürk H, Dekker N, van Ulsen P. The polypeptide transport-associated (POTRA) domains of TpsB transporters determine the system specificity of two-partner secretion systems. J Biol Chem 2014; 289:19799-809. [PMID: 24872418 DOI: 10.1074/jbc.m113.544627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The two-partner secretion (TPS) systems of Gram-negative bacteria secrete large TpsA exoproteins by a dedicated TpsB transporter in the outer membrane. TpsBs contain an N-terminal module located in the periplasm that includes two polypeptide transport-associated (POTRA) domains. These are thought to initiate secretion of a TpsA by binding its N-terminal secretion signal, called the TPS domain. Neisseria meningitidis encodes up to five TpsA proteins that are secreted via only two TpsB transporters: TpsB1 and TpsB2. Of these two, the TpsB2 recognizes the TPS domains of all TpsAs, despite their sequence diversity. By contrast, the TpsB1 shows a limited recognition of a TPS domain that is shared by two TpsAs. The difference in substrate specificity of the TpsBs enabled us to investigate the role of the POTRA domains in the selection of TPS domains. We tested secretion of TPS domains or full-length TpsAs by TpsB mutants with deleted, duplicated, and exchanged POTRA domains. Exchanging the two POTRA domains of a TpsB resulted in a switch in specificity. Furthermore, exchanging a single POTRA domain showed that each of the two domains contributed to the cargo selection. Remarkably, the order of the POTRA domains could be reversed without affecting substrate selection, but this aberrant order did result in an alternatively processed secretion product. Our results suggest that secretion of a TpsA is initiated by engaging both POTRA domains of a TpsB transporter and that these select the cognate TpsAs for secretion.
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Affiliation(s)
- Sadeeq ur Rahman
- From the Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands and
| | - Jesús Arenas
- the Section of Molecular Microbiology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hülya Öztürk
- From the Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands and
| | - Nicole Dekker
- From the Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands and
| | - Peter van Ulsen
- From the Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands and
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81
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Noinaj N, Buchanan SK. FhaC takes a bow to FHA in the two-partner do-si-do. Mol Microbiol 2014; 92:1155-8. [PMID: 24798489 DOI: 10.1111/mmi.12627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2014] [Indexed: 11/30/2022]
Abstract
FhaC is an outer membrane transporter from Bordetella pertussis belonging to the two-partner secretion (TPS) pathway with its primary role being the secretion of the virulence factor filamentous haemagglutinin (FHA). FhaC serves as a model transporter of the TPS pathway and significant work has been done to characterize the role of FhaC in FHA secretion. Recent studies characterized interactions between FHA and the POTRA domains of FhaC, suggesting that secretion may involve a successive translocation mechanism mediated by β-augmentation and/or electrostatic interactions. Moreover, it was also shown that reconstituted FhaC is necessary and sufficient to transport FHA into proteoliposomes. While the crystal structure of FhaC clearly suggests a role in transport, the putative transport pore is plugged by an N-terminal α-helix (H1 helix) that occludes access by FHA. Therefore, it has been proposed that the H1 helix must be expelled from the pore in order for secretion of FHA to occur. However, this has yet to be shown experimentally. Guérin et al. (2014) report the first direct experimental evidence to show that the FhaC H1 helix is quite dynamic and exchanges between closed and open states upon interaction with FHA.
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Affiliation(s)
- Nicholas Noinaj
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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82
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Guérin J, Baud C, Touati N, Saint N, Willery E, Locht C, Vezin H, Jacob-Dubuisson F. Conformational dynamics of protein transporter FhaC: large-scale motions of plug helix. Mol Microbiol 2014; 92:1164-76. [DOI: 10.1111/mmi.12585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Jérémy Guérin
- Institut Pasteur de Lille; Center for Infection and Immunity; Lille France
- CNRS UMR8204; Lille France
- INSERM U1019; Lille France
- Univ Lille Nord de France; Lille France
| | - Catherine Baud
- Institut Pasteur de Lille; Center for Infection and Immunity; Lille France
- CNRS UMR8204; Lille France
- INSERM U1019; Lille France
- Univ Lille Nord de France; Lille France
| | | | - Nathalie Saint
- INSERM U1046; CHU A. de Villeneuve; Montpellier Cedex 05 France
| | - Eve Willery
- Institut Pasteur de Lille; Center for Infection and Immunity; Lille France
- CNRS UMR8204; Lille France
- INSERM U1019; Lille France
- Univ Lille Nord de France; Lille France
| | - Camille Locht
- Institut Pasteur de Lille; Center for Infection and Immunity; Lille France
- CNRS UMR8204; Lille France
- INSERM U1019; Lille France
- Univ Lille Nord de France; Lille France
| | | | - Françoise Jacob-Dubuisson
- Institut Pasteur de Lille; Center for Infection and Immunity; Lille France
- CNRS UMR8204; Lille France
- INSERM U1019; Lille France
- Univ Lille Nord de France; Lille France
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83
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Abstract
Bacteria secrete and harbor in their membranes a number of pore-forming proteins. Some of these are bona fide ion channels that may respond to changes in membrane tension, voltage, or pH. Others may be large translocons used for the secretion of folded or unfolded polypeptide substrates. Additionally, many secreted toxins insert into target cell membranes and form pores that either collapse membrane electrochemical gradients or provide conduits for the delivery of virulence factors. In all cases, electrophysiological approaches have yielded much progress in past decades in understanding the functional mechanisms of these pores. By monitoring the changes in current due to ion flow through the pores, these techniques are used as high-resolution tools to gather detailed information on the kinetic and permeation properties of these proteins, including those whose physiological role is not ion flux. This review highlights some of the electrophysiological studies that have advanced the field of transport by pore-forming proteins of bacterial origin.
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Affiliation(s)
- Anne H Delcour
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001;
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84
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Ni D, Wang Y, Yang X, Zhou H, Hou X, Cao B, Lu Z, Zhao X, Yang K, Huang Y. Structural and functional analysis of the β-barrel domain of BamA from Escherichia coli. FASEB J 2014; 28:2677-85. [PMID: 24619089 DOI: 10.1096/fj.13-248450] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved component. To elucidate the mechanism of BamA-mediated OMP biogenesis, we determined the crystal structure of the C-terminal transmembrane domain of BamA from Escherichia coli (EcBamA) at 2.6 Å resolution. The structure reveals 2 distinct features. First, a portion of the extracellular side of the β barrel is composed of 5 markedly short β strands, and the loops stemming from these β strands form a potential surface cavity, filled by a portion of the L6 loop that includes the conserved VRGF/Y motif found in the Omp85 family. Second, the 4 extracellular loops L3, L4, L6, and L7 of EcBamA form a dome over the barrel, stabilized by a salt-bridge interaction network. Functional data show that hydrophilic-to-hydrophobic mutations of the potential hydrophilic surface cavity and a single Arg547Ala point mutation that may destabilize the dome severely affect the function of EcBamA. Our structure of the EcBamA β barrel and structure-based mutagenesis studies suggest that the transmembrane β strands of OMP substrates may integrate into the outer membrane at the interface of the first and last β strands of the EcBamA barrel, whereas the soluble loops or domains may be transported out of the cell via the hydrophilic surface cavity on dislocation of the VRGF/Y motif of L6. In addition, the dome over the barrel may play an important role in maintaining the efficiency of OMP biogenesis.
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Affiliation(s)
- Dongchun Ni
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Public Health, Tianjin Medical University, Tianjin, China
| | - Yan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; and
| | - Xu Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Hou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baohua Cao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Lu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species and Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing, China
| | - Xinsheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species and Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing, China
| | - Kun Yang
- School of Public Health, Tianjin Medical University, Tianjin, China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China;
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85
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Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY, Tuanyok A, Mayo M, Kaestli M, Currie BJ. Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 2014; 9:e91682. [PMID: 24618705 PMCID: PMC3950250 DOI: 10.1371/journal.pone.0091682] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/14/2014] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a potentially life-threatening infectious disease affecting mammals, including humans. Melioidosis symptoms are both protean and diverse, ranging from mild, localized skin infections to more severe and often fatal presentations including pneumonia, septic shock with multiple internal abscesses and occasionally neurological involvement. Several ubiquitous virulence determinants in B. pseudomallei have already been discovered. However, the molecular basis for differential pathogenesis has, until now, remained elusive. Using clinical data from 556 Australian melioidosis cases spanning more than 20 years, we identified a Burkholderia mallei-like actin polymerization bimA(Bm) gene that is strongly associated with neurological disease. We also report that a filamentous hemagglutinin gene, fhaB3, is associated with positive blood cultures but is negatively correlated with localized skin lesions without sepsis. We show, for the first time, that variably present virulence factors play an important role in the pathogenesis of melioidosis. Collectively, our study provides a framework for assessing other non-ubiquitous bacterial virulence factors and their association with disease, such as candidate loci identified from large-scale microbial genome-wide association studies.
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Affiliation(s)
- Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Linda M. Ward
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Marcos Y. Voutsinos
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Apichai Tuanyok
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawai’i, Honolulu, Hawai’i, United States of America
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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86
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Affiliation(s)
- Bert van den Berg
- Institute for Cellular and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
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87
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Richardson LGL, Paila YD, Siman SR, Chen Y, Smith MD, Schnell DJ. Targeting and assembly of components of the TOC protein import complex at the chloroplast outer envelope membrane. FRONTIERS IN PLANT SCIENCE 2014; 5:269. [PMID: 24966864 PMCID: PMC4052903 DOI: 10.3389/fpls.2014.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/24/2014] [Indexed: 05/20/2023]
Abstract
The translocon at the outer envelope membrane of chloroplasts (TOC) initiates the import of thousands of nuclear encoded preproteins required for chloroplast biogenesis and function. The multimeric TOC complex contains two GTP-regulated receptors, Toc34 and Toc159, which recognize the transit peptides of preproteins and initiate protein import through a β-barrel membrane channel, Toc75. Different isoforms of Toc34 and Toc159 assemble with Toc75 to form structurally and functionally diverse translocons, and the composition and levels of TOC translocons is required for the import of specific subsets of coordinately expressed proteins during plant growth and development. Consequently, the proper assembly of the TOC complexes is key to ensuring organelle homeostasis. This review will focus on our current knowledge of the targeting and assembly of TOC components to form functional translocons at the outer membrane. Our analyses reveal that the targeting of TOC components involves elements common to the targeting of other outer membrane proteins, but also include unique features that appear to have evolved to specifically facilitate assembly of the import apparatus.
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Affiliation(s)
- Lynn G. L. Richardson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, AmherstMA, USA
| | - Yamuna D. Paila
- Department of Biochemistry and Molecular Biology, University of Massachusetts, AmherstMA, USA
| | - Steven R. Siman
- Department of Biology, Wilfrid Laurier University, WaterlooON, Canada
| | - Yi Chen
- Department of Biology, Wilfrid Laurier University, WaterlooON, Canada
| | - Matthew D. Smith
- Department of Biology, Wilfrid Laurier University, WaterlooON, Canada
| | - Danny J. Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, AmherstMA, USA
- *Correspondence: Danny J. Schnell, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Life Sciences Laboratories, Room N431, 240 Thatcher Way, Amherst, MA 01003-9364, USA e-mail:
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88
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Day PM, Potter D, Inoue K. Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane. FRONTIERS IN PLANT SCIENCE 2014; 5:535. [PMID: 25352854 PMCID: PMC4195282 DOI: 10.3389/fpls.2014.00535] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/19/2014] [Indexed: 05/20/2023]
Abstract
Translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75) is the core component of the chloroplast protein import machinery. It belongs to the Omp85 family whose members exist in various Gram-negative bacteria, mitochondria, and chloroplasts of eukaryotes. Chloroplasts of Viridiplantae contain another Omp85 homolog called outer envelope protein 80 (OEP80), whose exact function is unknown. In addition, the Arabidopsis thaliana genome encodes truncated forms of Toc75 and OEP80. Multiple studies have shown a common origin of the Omp85 homologs of cyanobacteria and chloroplasts but their results about evolutionary relationships among cyanobacterial Omp85 (cyanoOmp85), Toc75, and OEP80 are inconsistent. The bipartite targeting sequence-dependent sorting of Toc75 has been demonstrated but the targeting mechanisms of other chloroplast Omp85 homologs remain largely unexplored. This study was aimed to address these unresolved issues in order to further our understanding of chloroplast evolution. Sequence alignments and recently determined structures of bacterial Omp85 homologs were used to predict structures of chloroplast Omp85 homologs. The results enabled us to identify amino acid residues that may indicate functional divergence of Toc75 from cyanoOmp85 and OEP80. Phylogenetic analyses using Omp85 homologs from various cyanobacteria and chloroplasts provided strong support for the grouping of Toc75 and OEP80 sister to cyanoOmp85. However, this support was diminished when the analysis included Omp85 homologs from other bacteria and mitochondria. Finally, results of import assays using isolated chloroplasts support outer membrane localization of OEP80tr and indicate that OEP80 may carry a cleavable targeting sequence.
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Affiliation(s)
| | | | - Kentaro Inoue
- *Correspondence: Kentaro Inoue, Department of Plant Sciences, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA e-mail:
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89
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Browning DF, Matthews SA, Rossiter AE, Sevastsyanovich YR, Jeeves M, Mason JL, Wells TJ, Wardius CA, Knowles TJ, Cunningham AF, Bavro VN, Overduin M, Henderson IR. Mutational and topological analysis of the Escherichia coli BamA protein. PLoS One 2013; 8:e84512. [PMID: 24376817 PMCID: PMC3871556 DOI: 10.1371/journal.pone.0084512] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
The multi-protein β-barrel assembly machine (BAM) of Escherichia coli is responsible for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the bacterial outer membrane. An essential component of this complex is the BamA protein, which binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains in its N-terminus. The C-terminus of BamA contains a β-barrel domain, which tethers BamA to the outer membrane and is also thought to be involved in OMP insertion. Here we mutagenize BamA using linker scanning mutagenesis and demonstrate that all five POTRA domains are essential for BamA protein function in our experimental system. Furthermore, we generate a homology based model of the BamA β-barrel and test our model using insertion mutagenesis, deletion analysis and immunofluorescence to identify β-strands, periplasmic turns and extracellular loops. We show that the surface-exposed loops of the BamA β-barrel are essential.
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Affiliation(s)
- Douglas F. Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
| | - Sophie A. Matthews
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Yanina R. Sevastsyanovich
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jessica L. Mason
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Wells
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Catherine A. Wardius
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Knowles
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Adam F. Cunningham
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Overduin
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
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90
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Volokhina EB, Grijpstra J, Beckers F, Lindh E, Robert V, Tommassen J, Bos MP. Species-specificity of the BamA component of the bacterial outer membrane protein-assembly machinery. PLoS One 2013; 8:e85799. [PMID: 24376896 PMCID: PMC3869937 DOI: 10.1371/journal.pone.0085799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/02/2013] [Indexed: 11/29/2022] Open
Abstract
The BamA protein is the key component of the Bam complex, the assembly machinery for outer membrane proteins (OMP) in gram-negative bacteria. We previously demonstrated that BamA recognizes its OMP substrates in a species-specific manner in vitro. In this work, we further studied species specificity in vivo by testing the functioning of BamA homologs of the proteobacteria Neisseria meningitidis, Neisseria gonorrhoeae, Bordetella pertussis, Burkholderia mallei, and Escherichia coli in E. coli and in N. meningitidis. We found that no BamA functioned in another species than the authentic one, except for N. gonorrhoeae BamA, which fully complemented a N. meningitidis bamA mutant. E. coli BamA was not assembled into the N. meningitidis outer membrane. In contrast, the N. meningitidis BamA protein was assembled into the outer membrane of E. coli to a significant extent and also associated with BamD, an essential accessory lipoprotein of the Bam complex.Various chimeras comprising swapped N-terminal periplasmic and C-terminal membrane-embedded domains of N. meningitidis and E. coli BamA proteins were also not functional in either host, although some of them were inserted in the OM suggesting that the two domains of BamA need to be compatible in order to function. Furthermore, conformational analysis of chimeric proteins provided evidence for a 16-stranded β-barrel conformation of the membrane-embedded domain of BamA.
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Affiliation(s)
- Elena B. Volokhina
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Jan Grijpstra
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Frank Beckers
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Erika Lindh
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Viviane Robert
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Jan Tommassen
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Martine P. Bos
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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91
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Pramanik A, Könninger U, Selvam A, Braun V. Secretion and activation of the Serratia marcescens hemolysin by structurally defined ShlB mutants. Int J Med Microbiol 2013; 304:351-9. [PMID: 24462008 DOI: 10.1016/j.ijmm.2013.11.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/11/2013] [Accepted: 11/30/2013] [Indexed: 11/15/2022] Open
Abstract
The ShlA hemolysin of Serratia marcescens is secreted across the outer membrane by the ShlB protein; ShlB belongs to the two-partner secretion system (type Vb), a subfamily of the Omp85 outer membrane protein assembly and secretion superfamily. During secretion, ShlA is converted from an inactive non-hemolytic form into an active hemolytic form. The structure of ShlB is predicted to consist of the N-terminal α-helix H1, followed by the two polypeptide-transport-associated domains POTRA P1 and P2, and the β-barrel of 16 β-strands. H1 is inserted into the pore of the β-barrel in the outer membrane; P1 and P2 are located in the periplasm. To obtain insights into the secretion and activation of ShlA by ShlB, we isolated ShlB mutants impaired in secretion and/or activation. The triple H1 P1 P2 mutant did not secrete ShlA. The P1 and P2 deletion derivatives secreted reduced amounts of ShlA, of which P1 showed some hemolysis, whereas P2 was inactive. Deletion of loop 6 (L6), which is conserved among exporters of the Omp85 family, compromised activation but retained low secretion. Secretion-negative mutants generated by random mutagenesis were located in loop 6. The inactive secreted ShlA derivatives were complemented in vitro to active ShlA by an N-terminal ShlA fragment (ShlA242) secreted by ShlB. Deletion of H1 did not impair secretion of hemolytic ShlA. The study defines domains of ShlB which are important for ShlA secretion and activation.
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Affiliation(s)
- Avijit Pramanik
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Ulrich Könninger
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Arun Selvam
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Volkmar Braun
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany.
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92
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Baelen S, Dewitte F, Clantin B, Villeret V. Structure of the secretion domain of HxuA from Haemophilus influenzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1322-7. [PMID: 24316822 PMCID: PMC3855712 DOI: 10.1107/s174430911302962x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/28/2013] [Indexed: 12/25/2022]
Abstract
Haemophilus influenzae HxuA is a cell-surface protein with haem-haemopexin binding activity which is key to haem acquisition from haemopexin and thus is one of the potential sources of haem for this microorganism. HxuA is secreted by its specific transporter HxuB. HxuA/HxuB belongs to the so-called two-partner secretion systems (TPSs) that are characterized by a conserved N-terminal domain in the secreted protein which is essential for secretion. Here, the 1.5 Å resolution structure of the secretion domain of HxuA, HxuA301, is reported. The structure reveals that HxuA301 folds into a β-helix domain with two extra-helical motifs, a four-stranded β-sheet and an N-terminal cap. Comparisons with other structures of TpsA secretion domains are reported. They reveal that despite limited sequence identity, strong structural similarities are found between the β-helix motifs, consistent with the idea that the TPS domain plays a role not only in the interaction with the specific TpsB partners but also as the scaffold initiating progressive folding of the TpsA proteins at the bacterial surface.
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Affiliation(s)
- Stéphanie Baelen
- Institut de Recherche Interdisciplinaire, IRI USR 3078 CNRS–Université Lille Nord de France, Parc CNRS de la Haute Borne, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France
| | - Frédérique Dewitte
- Institut de Recherche Interdisciplinaire, IRI USR 3078 CNRS–Université Lille Nord de France, Parc CNRS de la Haute Borne, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France
| | - Bernard Clantin
- Institut de Recherche Interdisciplinaire, IRI USR 3078 CNRS–Université Lille Nord de France, Parc CNRS de la Haute Borne, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France
| | - Vincent Villeret
- Institut de Recherche Interdisciplinaire, IRI USR 3078 CNRS–Université Lille Nord de France, Parc CNRS de la Haute Borne, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France
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93
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Kumar A, Yogisharadhya R, Ramakrishnan MA, Viswas K, Shivachandra SB. Structural analysis and cross-protective efficacy of recombinant 87 kDa outer membrane protein (Omp87) of Pasteurella multocida serogroup B:2. Microb Pathog 2013; 65:48-56. [DOI: 10.1016/j.micpath.2013.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/16/2013] [Accepted: 09/26/2013] [Indexed: 01/10/2023]
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94
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Flinner N, Ellenrieder L, Stiller SB, Becker T, Schleiff E, Mirus O. Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3314-3325. [PMID: 24135058 DOI: 10.1016/j.bbamcr.2013.10.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/20/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial β-barrel proteins fulfill central functions in the outer membrane like metabolite exchange catalyzed by the voltage-dependent anion channel (VDAC) and protein biogenesis by the central components of the preprotein translocase of the outer membrane (Tom40) or of the sorting and assembly machinery (Sam50). The mitochondrial division and morphology protein Mdm10 is another essential outer membrane protein with proposed β-barrel fold, which has so far only been found in Fungi. Mdm10 is part of the endoplasmic reticulum mitochondria encounter structure (ERMES), which tethers the ER to mitochondria and associates with the SAM complex. In here, we provide evidence that Mdm10 phylogenetically belongs to the VDAC/Tom40 superfamily. Contrary to Tom40 and VDAC, Mdm10 exposes long loops towards both sides of the membrane. Analyses of single loop deletion mutants of Mdm10 in the yeast Saccharomyces cerevisiae reveal that the loops are dispensable for Mdm10 function. Sequences similar to fungal Mdm10 can be found in species from Excavates to Fungi, but neither in Metazoa nor in plants. Strikingly, the presence of Mdm10 coincides with the appearance of the other ERMES components. Mdm10's presence in both unikonts and bikonts indicates an introduction at an early time point in eukaryotic evolution.
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Affiliation(s)
- Nadine Flinner
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Enrico Schleiff
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Oliver Mirus
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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95
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Wager B, Faudry E, Wills T, Attree I, Delcour AH. Current fluctuation analysis of the PopB and PopD translocon components of the Pseudomonas aeruginosa type III secretion system. Biophys J 2013; 104:1445-55. [PMID: 23561521 DOI: 10.1016/j.bpj.2013.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 02/05/2013] [Accepted: 02/12/2013] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa is a major agent of hospital-acquired infections, and a pathogen of immunocompromised, cystic fibrosis and burn patients. It uses a type III secretion system for the injection of toxins directly into host cells, through a translocon assembled in the host cell membrane. The hydrophobic translocator subunits of this system, PopB and PopD, have membrane permeabilizing activity based on previous dye leakage experiments, but little is known about the mechanism of assembly and the pore properties of this translocon. Using electrophysiology, we have observed that an equimolar mixture of PopB and PopD induces current fluctuations in planar lipid bilayers, with a unitary conductance of 57 pS in 1 M KCl and numerous larger conductance levels. The activity depends on voltage magnitude and polarity, and increases with protein concentration and the duration of the voltage step. PopB alone is sufficient for producing current fluctuations. PopD rarely displays any transitions, but accelerates PopB onset of activity. The effects of pH, ionic strength, and lipid composition have also been explored. Our data provide new, to our knowledge, insights into the behavior of PopB and PopD by highlighting similarities with secreted pore-forming peptides, and by suggesting that PopB/PopD may form channels via the toroidal pore model. We believe that the events we report here represent the initial steps of insertion and assembly of these translocators in the membrane.
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Affiliation(s)
- Beau Wager
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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96
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The structural basis of autotransporter translocation by TamA. Nat Struct Mol Biol 2013; 20:1318-20. [DOI: 10.1038/nsmb.2689] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/11/2013] [Indexed: 01/08/2023]
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97
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Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK. Structural insight into the biogenesis of β-barrel membrane proteins. Nature 2013; 501:385-90. [PMID: 23995689 PMCID: PMC3779476 DOI: 10.1038/nature12521] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 08/01/2013] [Indexed: 11/17/2022]
Abstract
β-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex is responsible for the biogenesis of β-barrel membrane proteins, with homologous complexes found in mitochondria and chloroplasts. Here we describe the structure of BamA, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain. Three structural features speak to the mechanism by which BamA catalyzes β-barrel assembly. First, the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the β-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. And third, the β-barrel can undergo lateral opening, evocatively suggesting a route from the interior cavity in BamA into the outer membrane.
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Affiliation(s)
- Nicholas Noinaj
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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98
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Sequential unfolding of beta helical protein by single-molecule atomic force microscopy. PLoS One 2013; 8:e73572. [PMID: 24009757 PMCID: PMC3756990 DOI: 10.1371/journal.pone.0073572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/25/2013] [Indexed: 12/14/2022] Open
Abstract
The parallel βhelix is a common fold among extracellular proteins, however its mechanical properties remain unexplored. In Gram-negative bacteria, extracellular proteins of diverse functions of the large ‘TpsA’ family all fold into long βhelices. Here, single-molecule atomic force microscopy and steered molecular dynamics simulations were combined to investigate the mechanical properties of a prototypic TpsA protein, FHA, the major adhesin of Bordetella pertussis. Strong extension forces were required to fully unfold this highly repetitive protein, and unfolding occurred along a stepwise, hierarchical process. Our analyses showed that the extremities of the βhelix unfold early, while central regions of the helix are more resistant to mechanical unfolding. In particular, a mechanically resistant subdomain conserved among TpsA proteins and critical for secretion was identified. This nucleus harbors structural elements packed against the βhelix that might contribute to stabilizing the N-terminal region of FHA. Hierarchical unfolding of the βhelix in response to a mechanical stress may maintain β-helical portions that can serve as templates for regaining the native structure after stress. The mechanical properties uncovered here might apply to many proteins with β-helical or related folds, both in prokaryotes and in eukaryotes, and play key roles in their structural integrity and functions.
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99
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Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics 2013; 195:443-55. [PMID: 23934888 DOI: 10.1534/genetics.113.155861] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The essential outer membrane β-barrel protein BamA forms a complex with four lipoprotein partners BamBCDE that assembles β-barrel proteins into the outer membrane of Escherichia coli. Detailed genetic studies have shown that BamA cycles through multiple conformations during substrate assembly, suggesting that a complex network of residues may be involved in coordinating conformational changes and lipoprotein partner function. While genetic analysis of BamA has been informative, it has also been slow in the absence of a straightforward selection for mutants. Here we take a bioinformatic approach to identify candidate residues for mutagenesis using direct coupling analysis. Starting with the BamA paralog FhaC, we show that direct coupling analysis works well for large β-barrel proteins, identifying pairs of residues in close proximity in tertiary structure with a true positive rate of 0.64 over the top 50 predictions. To reduce the effects of noise, we designed and incorporated a novel structured prior into the empirical correlation matrix, dramatically increasing the FhaC true positive rate from 0.64 to 0.88 over the top 50 predictions. Our direct coupling analysis of BamA implicates residues R661 and D740 in a functional interaction. We find that the substitutions R661G and D740G each confer OM permeability defects and destabilize the BamA β-barrel. We also identify synthetic phenotypes and cross-suppressors that suggest R661 and D740 function in a similar process and may interact directly. We expect that the direct coupling analysis approach to informed mutagenesis will be particularly useful in systems lacking adequate selections and for dynamic proteins with multiple conformations.
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100
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Receptor polymorphism restricts contact-dependent growth inhibition to members of the same species. mBio 2013; 4:mBio.00480-13. [PMID: 23882017 PMCID: PMC3735181 DOI: 10.1128/mbio.00480-13] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacteria that express contact-dependent growth inhibition (CDI) systems outcompete siblings that lack immunity, suggesting that CDI mediates intercellular competition. To further explore the role of CDI in competition, we determined the target cell range of the CDIEC93 system from Escherichia coli EC93. The CdiAEC93 effector protein recognizes the widely conserved BamA protein as a receptor, yet E. coli EC93 does not inhibit other enterobacterial species. The predicted membrane topology of BamA indicates that three of its extracellular loops vary considerably between species, suggesting that loop heterogeneity may control CDI specificity. Consistent with this hypothesis, other enterobacteria are sensitized to CDIEC93 upon the expression of E. coli bamA and E. coli cells become CDIEC93 resistant when bamA is replaced with alleles from other species. Our data indicate that BamA loops 6 and 7 form the CdiAEC93-binding epitope and their variation between species restricts CDIEC93 target cell selection. Although BamA loops 6 and 7 vary dramatically between species, these regions are identical in hundreds of E. coli strains, suggesting that BamAEcoli and CdiAEC93 play a role in self-nonself discrimination. Contact-dependent growth inhibition (CDI) systems are widespread among Gram-negative bacteria, enabling them to bind to neighboring bacterial cells and deliver protein toxins that inhibit cell growth. In this study, we tested the role of CDI in interspecies competition using intestinal isolate Escherichia coli EC93 as an inhibitor cell model. Although E. coli EC93 inhibits different E. coli strains, other bacterial species from the intestine are completely resistant to CDI. We show that resistance is due to small variations in the CDI receptor that prevent other species from being recognized as target cells. CDI receptor interactions thus provide a mechanism by which bacteria can distinguish siblings and other close relatives (self) from more distant relatives or other species of bacteria (nonself). Our results provide a possible means by which antimicrobials could be directed to one or only a few related bacterial pathogens by using a specific receptor “zip code.”
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