1
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Hanson SE, Dowdy T, Larion M, Doyle MT, Bernstein HD. The patatin-like protein PlpD forms structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane. Nat Commun 2024; 15:4389. [PMID: 38782915 PMCID: PMC11116518 DOI: 10.1038/s41467-024-48756-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we find that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.
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Affiliation(s)
- Sarah E Hanson
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
- Sydney Infectious Diseases Institute and School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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2
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Prudhomme N, Pastora R, Thomson S, Zheng E, Sproule A, Krieger JR, Murphy JP, Overy DP, Cossar D, McLean MD, Geddes-McAlister J. Bacterial growth-mediated systems remodelling of Nicotiana benthamiana defines unique signatures of target protein production in molecular pharming. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38516995 DOI: 10.1111/pbi.14342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
The need for therapeutics to treat a plethora of medical conditions and diseases is on the rise and the demand for alternative approaches to mammalian-based production systems is increasing. Plant-based strategies provide a safe and effective alternative to produce biological drugs but have yet to enter mainstream manufacturing at a competitive level. Limitations associated with batch consistency and target protein production levels are present; however, strategies to overcome these challenges are underway. In this study, we apply state-of-the-art mass spectrometry-based proteomics to define proteome remodelling of the plant following agroinfiltration with bacteria grown under shake flask or bioreactor conditions. We observed distinct signatures of bacterial protein production corresponding to the different growth conditions that directly influence the plant defence responses and target protein production on a temporal axis. Our integration of proteomic profiling with small molecule detection and quantification reveals the fluctuation of secondary metabolite production over time to provide new insight into the complexities of dual system modulation in molecular pharming. Our findings suggest that bioreactor bacterial growth may promote evasion of early plant defence responses towards Agrobacterium tumefaciens (updated nomenclature to Rhizobium radiobacter). Furthermore, we uncover and explore specific targets for genetic manipulation to suppress host defences and increase recombinant protein production in molecular pharming.
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Affiliation(s)
- Nicholas Prudhomme
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | - Sarah Thomson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Edison Zheng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | | | - J Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - David P Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doug Cossar
- PlantForm Corporation Canada, Toronto, ON, Canada
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3
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Elery ZK, Myers-Morales T, Phillips ED, Garcia EC. Relaxed specificity of BcpB transporters mediates interactions between Burkholderia cepacia complex contact-dependent growth inhibition systems. mSphere 2023; 8:e0030323. [PMID: 37498085 PMCID: PMC10449530 DOI: 10.1128/msphere.00303-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/11/2023] [Indexed: 07/28/2023] Open
Abstract
Belonging to the two-partner secretion family of proteins, contact-dependent growth inhibition (CDI) systems mediate interbacterial antagonism among closely related Gram-negative bacteria. The toxic portion of a large surface protein, BcpA/CdiA, is delivered to the cytoplasm of neighboring cells where it inhibits growth. Translocation of the antibacterial polypeptide out of the producing cell requires an associated outer membrane transporter, BcpB/CdiB. Some bacteria, including many Burkholderia species, encode multiple distinct CDI systems, but whether there is interaction between these systems is largely unknown. Using Burkholderia cepacia complex species as a model, here we show that related BcpB transporters exhibit considerable secretion flexibility and can secrete both cognate and non-cognate BcpA substrates. We also identified an additional unique Burkholderia dolosa CDI system capable of mediating interbacterial competition and demonstrated that its BcpB transporter has similar relaxed substrate specificity. Our results showed that two BcpB transporters (BcpB-2 and BcpB-3) were able to secrete all four of the B. dolosa BcpA toxins, while one transporter (BcpB-1) appeared unable to secrete even its cognate BcpA substrate under the tested conditions. This flexibility provided a competitive advantage, as strains lacking the full repertoire of BcpB proteins had decreased CDI activity. Similar results were obtained in Burkholderia multivorans, suggesting that secretion flexibility may be a conserved feature of Burkholderia CDI systems. Together these findings suggest that the interaction between distinct CDI systems enhances the efficiency of bacterial antagonism. IMPORTANCE The Burkholderia cepacia complex (Bcc) is a group of related opportunistic bacterial pathogens that occupy a diverse range of ecological niches and exacerbate disease in patients with underlying conditions. Contact-dependent growth inhibition (CDI) system proteins, produced by Gram-negative bacteria, contain antagonistic properties that allow for intoxication of closely related neighboring bacteria via a secreted protein, BcpA. Multiple unique CDI systems can be found in the same bacterial strain, and here we show that these distinct systems interact in several Bcc species. Our findings suggest that the interaction between CDI system proteins is important for interbacterial toxicity. Understanding the mechanism of interplay between CDI systems provides further insight into the complexity of bacterial antagonism. Moreover, since many bacterial species are predicted to encode multiple CDI systems, this study suggests that interactions between these distinct systems likely contribute to the overall competitive fitness of these species.
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Affiliation(s)
- Zaria K. Elery
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | | | - Erica D. Phillips
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Erin C. Garcia
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
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4
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Hanson SE, Doyle MT, Bernstein HD. The patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537245. [PMID: 37333265 PMCID: PMC10274916 DOI: 10.1101/2023.04.17.537245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we found that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.
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Affiliation(s)
- Sarah E. Hanson
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Harris D. Bernstein
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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5
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Sicoli G, Konijnenberg A, Guérin J, Hessmann S, Del Nero E, Hernandez-Alba O, Lecher S, Rouaut G, Müggenburg L, Vezin H, Cianférani S, Sobott F, Schneider R, Jacob-Dubuisson F. Large-Scale Conformational Changes of FhaC Provide Insights Into the Two-Partner Secretion Mechanism. Front Mol Biosci 2022; 9:950871. [PMID: 35936790 PMCID: PMC9355242 DOI: 10.3389/fmolb.2022.950871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
The Two-Partner secretion pathway mediates protein transport across the outer membrane of Gram-negative bacteria. TpsB transporters belong to the Omp85 superfamily, whose members catalyze protein insertion into, or translocation across membranes without external energy sources. They are composed of a transmembrane β barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Here we used an integrative approach combining in vivo assays, mass spectrometry, nuclear magnetic resonance and electron paramagnetic resonance techniques suitable to detect minor states in heterogeneous populations, to explore transient conformers of the TpsB transporter FhaC. This revealed substantial, spontaneous conformational changes on a slow time scale, with parts of the POTRA2 domain approaching the lipid bilayer and the protein’s surface loops. Specifically, our data indicate that an amphipathic POTRA2 β hairpin can insert into the β barrel. We propose that these motions enlarge the channel and initiate substrate secretion. Our data propose a solution to the conundrum how TpsB transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | | | - Jérémy Guérin
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Elise Del Nero
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Sophie Lecher
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Guillaume Rouaut
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Linn Müggenburg
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Hervé Vezin
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert Schneider
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
| | - Françoise Jacob-Dubuisson
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
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6
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Doyle MT, Bernstein HD. Function of the Omp85 Superfamily of Outer Membrane Protein Assembly Factors and Polypeptide Transporters. Annu Rev Microbiol 2022; 76:259-279. [PMID: 35650668 DOI: 10.1146/annurev-micro-033021-023719] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Omp85 protein superfamily is found in the outer membrane (OM) of all gram-negative bacteria and eukaryotic organelles of bacterial origin. Members of the family catalyze both the membrane insertion of β-barrel proteins and the translocation of proteins across the OM. Although the mechanism(s) by which these proteins function is unclear, striking new insights have emerged from recent biochemical and structural studies. In this review we discuss the entire Omp85 superfamily but focus on the function of the best-studied member, BamA, which is an essential and highly conserved component of the bacterial barrel assembly machinery (BAM). Because BamA has multiple functions that overlap with those of other Omp85 proteins, it is likely the prototypical member of the Omp85 superfamily. Furthermore, BamA has become a protein of great interest because of the recent discovery of small-molecule inhibitors that potentially represent an important new class of antibiotics. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; ,
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7
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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8
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Dautin N. Folding Control in the Path of Type 5 Secretion. Toxins (Basel) 2021; 13:341. [PMID: 34064645 PMCID: PMC8151025 DOI: 10.3390/toxins13050341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.
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Affiliation(s)
- Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005 Paris, France
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9
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Guérin J, Buchanan SK. Protein import and export across the bacterial outer membrane. Curr Opin Struct Biol 2021; 69:55-62. [PMID: 33901701 DOI: 10.1016/j.sbi.2021.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/09/2021] [Accepted: 03/21/2021] [Indexed: 01/06/2023]
Abstract
The bacterial outer membrane forms an impermeable barrier to the environment, but a wide variety of substances must cross it without compromising the membrane. Perhaps, the most fascinating transport phenomenon is the import and export of very large protein toxins using relatively small β-barrel proteins residing in the outer membrane. Progress has been made on three systems in recent years that shed light on this process. In this review, we summarize bacteriocin (toxin) import using TonB-dependent transporters and protein secretion by autotransporters and two partner secretion systems.
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Affiliation(s)
- Jérémy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, 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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10
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Chu Y, Wang Z, Weigold S, Norrell D, Fan E. TtOmp85, a single Omp85 member protein functions as a β-barrel protein insertase and an autotransporter translocase without any accessory proteins. Biochem Biophys Res Commun 2021; 552:73-77. [PMID: 33743350 DOI: 10.1016/j.bbrc.2021.03.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
The biogenesis of outer membrane proteins requires the function of β-barrel assembly machinery (BAM), whose function is highly conserved while its composition is variable. The Escherichia coli BAM is composed of five subunits, while Thermus thermophilus seems to contain a single BAM protein, named TtOmp85. To search for the primitive form of a functional BAM, we investigated and compared the function of TtOmp85 and E. coli BAM by use of a reconstitution assay that examines the integration of OmpA and BamA from E. coli and TtoA from T. thermophilus, as well as the translocation of the E. coli Ag43. Our results show that a single TtOmp85 protein can substitute for the collective function of the five subunits constituting E. coli BAM.
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Affiliation(s)
- Yindi Chu
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100005, Beijing, China
| | - Zhe Wang
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100005, Beijing, China
| | - Sebastian Weigold
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Straße 17, 79104, Freiburg im Breisgau, Germany
| | - Derrick Norrell
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Straße 17, 79104, Freiburg im Breisgau, Germany
| | - Enguo Fan
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100005, Beijing, China; Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Stefan-Meier-Straße 17, 79104, Freiburg im Breisgau, Germany; College of Life Sciences, Linyi University, Linyi, 276005, China.
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11
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Doyle MT, Bernstein HD. BamA forms a translocation channel for polypeptide export across the bacterial outer membrane. Mol Cell 2021; 81:2000-2012.e3. [PMID: 33705710 DOI: 10.1016/j.molcel.2021.02.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/05/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022]
Abstract
The β-barrel assembly machine (BAM) integrates β-barrel proteins into the outer membrane (OM) of Gram-negative bacteria. An essential BAM subunit (BamA) catalyzes integration by promoting the formation of a hybrid-barrel intermediate state between its own β-barrel domain and that of its client proteins. Here we show that in addition to catalyzing the integration of β-barrel proteins, BamA functions as a polypeptide export channel. In vivo structural mapping via intermolecular disulfide crosslinking showed that the extracellular "passenger" domain of a member of the "autotransporter" superfamily of virulence factors traverses the OM through the BamA β-barrel lumen. Furthermore, we demonstrate that a highly conserved residue within autotransporter β-barrels is required to position the passenger inside BamA to initiate translocation and that during translocation, the passenger stabilizes the hybrid-barrel state. Our results not only establish a new function for BamA but also unify the divergent functions of BamA and other "Omp85" superfamily transporters.
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Affiliation(s)
- Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harris David 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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12
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Diederichs KA, Buchanan SK, Botos I. Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria. J Mol Biol 2021; 433:166894. [PMID: 33639212 PMCID: PMC8292188 DOI: 10.1016/j.jmb.2021.166894] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/20/2023]
Abstract
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.
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Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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13
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Guerin J, Botos I, Zhang Z, Lundquist K, Gumbart JC, Buchanan SK. Structural insight into toxin secretion by contact-dependent growth inhibition transporters. eLife 2020; 9:58100. [PMID: 33089781 PMCID: PMC7644211 DOI: 10.7554/elife.58100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial contact-dependent growth inhibition (CDI) systems use a type Vb secretion mechanism to export large CdiA toxins across the outer membrane by dedicated outer membrane transporters called CdiB. Here, we report the first crystal structures of two CdiB transporters from Acinetobacter baumannii and Escherichia coli. CdiB transporters adopt a TpsB fold, containing a 16-stranded transmembrane β-barrel connected to two periplasmic domains. The lumen of the CdiB pore is occluded by an N-terminal α-helix and the conserved extracellular loop 6; these two elements adopt different conformations in the structures. We identified a conserved DxxG motif located on strand β1 that connects loop 6 through different networks of interactions. Structural modifications of DxxG induce rearrangement of extracellular loops and alter interactions with the N-terminal α-helix, preparing the system for α-helix ejection. Using structural biology, functional assays, and molecular dynamics simulations, we show how the barrel pore is primed for CdiA toxin secretion.
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Affiliation(s)
- Jeremy Guerin
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
| | - Istvan Botos
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
| | - Zijian Zhang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
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14
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Ruhe ZC, Low DA, Hayes CS. Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery. Annu Rev Microbiol 2020; 74:497-520. [PMID: 32680451 DOI: 10.1146/annurev-micro-020518-115638] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
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15
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Exolysin (ExlA) from Pseudomonas aeruginosa Punctures Holes into Target Membranes Using a Molten Globule Domain. J Mol Biol 2020; 432:4466-4480. [DOI: 10.1016/j.jmb.2020.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
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16
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Structure of the mitochondrial import gate reveals distinct preprotein paths. Nature 2019; 575:395-401. [PMID: 31600774 DOI: 10.1038/s41586-019-1680-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/30/2019] [Indexed: 11/08/2022]
Abstract
The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins1-4. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex5-9 at 3.8-Å resolution. The structure reveals the high-resolution architecture of the translocator consisting of two Tom40 β-barrel channels and α-helical transmembrane subunits, providing insight into critical features that are conserved in all eukaryotes1-3. Each Tom40 β-barrel is surrounded by small TOM subunits, and tethered by two Tom22 subunits and one phospholipid. The N-terminal extension of Tom40 forms a helix inside the channel; mutational analysis reveals its dual role in early and late steps in the biogenesis of intermembrane-space proteins in cooperation with Tom5. Each Tom40 channel possesses two precursor exit sites. Tom22, Tom40 and Tom7 guide presequence-containing preproteins to the exit in the middle of the dimer, whereas Tom5 and the Tom40 N extension guide preproteins lacking a presequence to the exit at the periphery of the dimer.
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17
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Bacterial outer membrane proteins assemble via asymmetric interactions with the BamA β-barrel. Nat Commun 2019; 10:3358. [PMID: 31350400 PMCID: PMC6659671 DOI: 10.1038/s41467-019-11230-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
The integration of β-barrel proteins into the bacterial outer membrane (OM) is catalysed by the β-barrel assembly machinery (BAM). The central BAM subunit (BamA) itself contains a β-barrel domain that is essential for OM protein biogenesis, but its mechanism of action is unknown. To elucidate its function, here we develop a method to trap a native Escherichia coli β-barrel protein bound stably to BamA at a late stage of assembly in vivo. Using disulfide-bond crosslinking, we find that the first β-strand of a laterally ‘open’ form of the BamA β-barrel forms a rigid interface with the C-terminal β-strand of the substrate. In contrast, the lipid-facing surface of the last two BamA β-strands forms weaker, conformationally heterogeneous interactions with the first β-strand of the substrate that likely represent intermediate assembly states. Based on our results, we propose that BamA promotes the membrane integration of partially folded β-barrels by a ‘swing’ mechanism. The integration of β-barrel proteins into the bacterial outer membrane (OM) is catalysed by the β-barrel assembly machinery (BAM). Here authors develop a method to trap an E. coli β-barrel protein bound stably to BamA at a late stage of assembly in vivo which provides insights BamA mediated membrane integration.
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18
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Meuskens I, Saragliadis A, Leo JC, Linke D. Type V Secretion Systems: An Overview of Passenger Domain Functions. Front Microbiol 2019; 10:1163. [PMID: 31214135 PMCID: PMC6555100 DOI: 10.3389/fmicb.2019.01163] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteria secrete proteins for different purposes such as communication, virulence functions, adhesion to surfaces, nutrient acquisition, or growth inhibition of competing bacteria. For secretion of proteins, Gram-negative bacteria have evolved different secretion systems, classified as secretion systems I through IX to date. While some of these systems consist of multiple proteins building a complex spanning the cell envelope, the type V secretion system, the subject of this review, is rather minimal. Proteins of the Type V secretion system are often called autotransporters (ATs). In the simplest case, a type V secretion system consists of only one polypeptide chain with a β-barrel translocator domain in the membrane, and an extracellular passenger or effector region. Depending on the exact domain architecture of the protein, type V secretion systems can be further separated into sub-groups termed type Va through e, and possibly another recently identified subtype termed Vf. While this classification works well when it comes to the architecture of the proteins, this is not the case for the function(s) of the secreted passenger. In this review, we will give an overview of the functions of the passengers of the different AT classes, shedding more light on the variety of functions carried out by type V secretion systems.
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Affiliation(s)
| | | | | | - Dirk Linke
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
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19
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Abstract
Bacteria use a variety of mechanisms to translocate proteins from the cytoplasm, where they are synthesized, to the cell surface or extracellular environment or directly into other cells, where they perform their ultimate functions. Type V secretion systems (T5SS) use β-barrel transporter domains to export passenger domains across the outer membranes of Gram-negative bacteria. Distinct among T5SS are type Vb or two-partner secretion (TPS) systems in which the transporter and passenger are separate proteins, necessitating a mechanism for passenger-translocator recognition in the periplasm and providing the potential for reuse of the translocator. This review describes current knowledge of the TPS translocation mechanism, using Bordetella filamentous hemagglutinin (FHA) and its transporter FhaC as a model. We present the hypothesis that the TPS pathway may be a general mechanism for contact-dependent delivery of toxins to target cells.
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20
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Ganesan I, Theg SM. Structural considerations of folded protein import through the chloroplast TOC/TIC translocons. FEBS Lett 2019; 593:565-572. [PMID: 30775779 DOI: 10.1002/1873-3468.13342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 11/11/2022]
Abstract
Protein import into chloroplasts is carried out by the protein translocons at the outer and inner envelope membranes (TOC and TIC). Detailed structures for these translocons are lacking, with only a low-resolution TOC complex structure available. Recently, we showed that the TOC/TIC translocons can import folded proteins, a rather unique feat for a coupled double membrane system. We also determined the maximum functional TOC/TIC pore size to be 30-35 Å. Here, we discuss how such large pores could form and compare the structural dynamics of the pore-forming Toc75 subunit to its bacterial/mitochondrial Omp85 family homologs. We put forward structural models that can be empirically tested and also briefly review the pore dynamics of other protein translocons with known structures.
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Affiliation(s)
- Iniyan Ganesan
- Department of Plant Biology, University of California Davis, CA, USA
| | - Steven M Theg
- Department of Plant Biology, University of California Davis, CA, USA
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21
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Abstract
Type V, or "autotransporter," secretion is a term used to refer to several simple protein export pathways that are found in a wide range of Gram-negative bacteria. Autotransporters are generally single polypeptides that consist of an extracellular ("passenger") domain and a β barrel domain that anchors the protein to the outer membrane (OM). Although it was originally proposed that the passenger domain is secreted through a channel formed solely by the covalently linked β barrel domain, experiments performed primarily on the type Va, or "classical," autotransporter pathway have challenged this hypothesis. Several lines of evidence strongly suggest that both the secretion of the passenger domain and the membrane integration of the β barrel domain are catalyzed by the barrel assembly machinery (Bam) complex, a conserved hetero-oligomer that plays an essential role in the assembly of most integral OM proteins. The secretion reaction appears to be driven at least in part by the folding of the passenger domain in the extracellular space. Although many aspects of autotransporter biogenesis remain to be elucidated, it will be especially interesting to determine whether the different classes of proteins that fall under the type V rubric-most of which have not been examined in detail-are assembled by the same basic mechanism as classical autotransporters.
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22
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A Proposed Chaperone of the Bacterial Type VI Secretion System Functions To Constrain a Self-Identity Protein. J Bacteriol 2018; 200:JB.00688-17. [PMID: 29555703 DOI: 10.1128/jb.00688-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/15/2018] [Indexed: 01/01/2023] Open
Abstract
The bacterium Proteus mirabilis can communicate identity through the secretion of the self-identity protein IdsD via the type VI secretion (T6S) system. IdsD secretion is essential for self-versus-nonself recognition behaviors in these populations. Here we provide an answer to the unresolved question of how the activity of a T6S substrate, such as IdsD, is regulated before secretion. We demonstrate that IdsD is found in clusters that form independently of the T6S machinery and activity. We show that the IdsC protein, which is a member of the proposed DUF4123 chaperone family, is essential for the maintenance of these clusters and of the IdsD protein itself. We provide evidence that amino acid disruptions in IdsC are sufficient to disrupt IdsD secretion but not IdsD localization into subcellular clusters, strongly supporting the notion that IdsC functions in at least two different ways: maintaining IdsD levels and secreting IdsD. We propose that IdsC, and likely other DUF4123-containing proteins, functions to regulate T6S substrates in the donor cell both by maintaining protein levels and by mediating secretion at the T6S machinery.IMPORTANCE Understanding the subcellular dynamics of self-identity proteins is crucial for developing models of self-versus-nonself recognition. We directly addressed how a bacterium restricts self-identity information before cell-cell exchange. We resolved two conflicting models for type VI secretion (T6S) substrate regulation by focusing on the self-identity protein IdsD. One model is that a cognate immunity protein binds the substrate, inhibiting activity before transport. Another model proposes that DUF4123 proteins act as chaperones in the donor cell, but no detailed molecular mechanism was previously known. We resolve this discrepancy and propose a model wherein a chaperone couples IdsD sequestration with its localization. Such a molecular mechanism restricts the communication of identity, and possibly other T6S substrates, in producing cells.
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23
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Höhr AIC, Lindau C, Wirth C, Qiu J, Stroud DA, Kutik S, Guiard B, Hunte C, Becker T, Pfanner N, Wiedemann N. Membrane protein insertion through a mitochondrial β-barrel gate. Science 2018; 359:359/6373/eaah6834. [PMID: 29348211 DOI: 10.1126/science.aah6834] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/12/2017] [Accepted: 12/14/2017] [Indexed: 11/02/2022]
Abstract
The biogenesis of mitochondria, chloroplasts, and Gram-negative bacteria requires the insertion of β-barrel proteins into the outer membranes. Homologous Omp85 proteins are essential for membrane insertion of β-barrel precursors. It is unknown if precursors are threaded through the Omp85-channel interior and exit laterally or if they are translocated into the membrane at the Omp85-lipid interface. We have mapped the interaction of a precursor in transit with the mitochondrial Omp85-channel Sam50 in the native membrane environment. The precursor is translocated into the channel interior, interacts with an internal loop, and inserts into the lateral gate by β-signal exchange. Transport through the Omp85-channel interior followed by release through the lateral gate into the lipid phase may represent a basic mechanism for membrane insertion of β-barrel proteins.
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Affiliation(s)
- Alexandra I C Höhr
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christophe Wirth
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Jian Qiu
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - David A Stroud
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stephan Kutik
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, 91190 Gif-sur-Yvette, France
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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24
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Ranava D, Caumont-Sarcos A, Albenne C, Ieva R. Bacterial machineries for the assembly of membrane-embedded β-barrel proteins. FEMS Microbiol Lett 2018; 365:4961134. [DOI: 10.1093/femsle/fny087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/03/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- David Ranava
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Cécile Albenne
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Raffaele Ieva
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
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25
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Translocation of lipoproteins to the surface of gram negative bacteria. Curr Opin Struct Biol 2018; 51:73-79. [PMID: 29579694 DOI: 10.1016/j.sbi.2018.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 11/21/2022]
Abstract
The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of bacterial stress response, and have been extensively studied as vaccine antigens. The aim of this review is to summarize the recent studies that have investigated the biosynthetic and translocation pathways used by different bacterial species to deliver SLPs to the surface. We will specifically focus on Slam, a novel outer membrane protein first discovered in pathogenic Neisseria sp., that is involved in translocation of SLPs across the outer membrane.
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26
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Guérin J, Bigot S, Schneider R, Buchanan SK, Jacob-Dubuisson F. Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions. Front Cell Infect Microbiol 2017; 7:148. [PMID: 28536673 PMCID: PMC5422565 DOI: 10.3389/fcimb.2017.00148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022] Open
Abstract
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
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Affiliation(s)
- Jeremy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, Centre National de La Recherche Scientifique UMR 5086-Université Lyon 1, Institute of Biology and Chemistry of ProteinsLyon, France
| | - Robert Schneider
- NMR and Molecular Interactions, Université de Lille, Centre National de La Recherche Scientifique, UMR 8576-Unité de Glycobiologie Structurale et FonctionnelleLille, France
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Françoise Jacob-Dubuisson
- Université de Lille, Centre National de La Recherche Scientifique, Institut National de La Santé et de La Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-Centre d'Infection et d'Immunité de LilleLille, France
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27
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Hooda Y, Lai CCL, Judd A, Buckwalter CM, Shin HE, Gray-Owen SD, Moraes TF. Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. Nat Microbiol 2016; 1:16009. [DOI: 10.1038/nmicrobiol.2016.9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
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28
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Affiliation(s)
- Dejana Mokranjac
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians University, 82152 Martinsried, Germany
| | - Walter Neupert
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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29
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Scheller EV, Cotter PA. Bordetella filamentous hemagglutinin and fimbriae: critical adhesins with unrealized vaccine potential. Pathog Dis 2015; 73:ftv079. [PMID: 26416077 DOI: 10.1093/femspd/ftv079] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2015] [Indexed: 02/06/2023] Open
Abstract
Pertussis, or whooping cough, is a highly contagious respiratory disease that is caused by the Gram-negative bacterium Bordetella pertussis, which is transmitted exclusively from human to human. While vaccination against B. pertussis has been successful, replacement of the whole cell vaccine with an acellular component vaccine has correlated with reemergence of the disease, especially in adolescents and infants. Based on their presumed importance in mediating adherence to host tissues, filamentous hemagglutinin (FHA) and fimbria (FIM) were selected as components of most acellular pertussis vaccines. In this review, we describe the biogenesis of FHA and FIM, recent data that show that these factors do, in fact, play critical roles in adherence to respiratory epithelium, and evidence that they also contribute to persistence in the lower respiratory tract by modulating the host immune response. We also discuss shortcomings of whole cell and acellular pertussis vaccines and the possibility that FHA and FIM could serve as effective protective antigens in next-generation vaccines.
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Affiliation(s)
- Erich V Scheller
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC 27599-7290, USA
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30
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Contact-Dependent Growth Inhibition (CDI) and CdiB/CdiA Two-Partner Secretion Proteins. J Mol Biol 2015; 427:3754-65. [PMID: 26388411 DOI: 10.1016/j.jmb.2015.09.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
Bacteria have developed several strategies to communicate and compete with one another in complex environments. One important mechanism of inter-bacterial competition is contact-dependent growth inhibition (CDI), in which Gram-negative bacteria use CdiB/CdiA two-partner secretion proteins to suppress the growth of neighboring target cells. CdiB is an Omp85 outer-membrane protein that exports and assembles CdiA exoproteins onto the inhibitor cell surface. CdiA binds to receptors on susceptible bacteria and subsequently delivers its C-terminal toxin domain (CdiA-CT) into the target cell. CDI systems also encode CdiI immunity proteins, which specifically bind to the CdiA-CT and neutralize its toxin activity, thereby protecting CDI(+) cells from auto-inhibition. Remarkably, CdiA-CT sequences are highly variable between bacteria, as are the corresponding CdiI immunity proteins. Variations in CDI toxin/immunity proteins suggest that these systems function in bacterial self/non-self recognition and thereby play an important role in microbial communities. In this review, we discuss recent advances in the biochemistry, structural biology and physiology of CDI.
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31
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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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Ruhe ZC, Townsley L, Wallace AB, King A, Van der Woude MW, Low DA, Yildiz FH, Hayes CS. CdiA promotes receptor-independent intercellular adhesion. Mol Microbiol 2015; 98:175-92. [PMID: 26135212 DOI: 10.1111/mmi.13114] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 01/02/2023]
Abstract
CdiB/CdiA proteins mediate inter-bacterial competition in a process termed contact-dependent growth inhibition (CDI). Filamentous CdiA exoproteins extend from CDI(+) cells and bind specific receptors to deliver toxins into susceptible target bacteria. CDI has also been implicated in auto-aggregation and biofilm formation in several species, but the contribution of CdiA-receptor interactions to these multi-cellular behaviors has not been examined. Using Escherichia coli isolate EC93 as a model, we show that cdiA and bamA receptor mutants are defective in biofilm formation, suggesting a prominent role for CdiA-BamA mediated cell-cell adhesion. However, CdiA also promotes auto-aggregation in a BamA-independent manner, indicating that the exoprotein possesses an additional adhesin activity. Cells must express CdiA in order to participate in BamA-independent aggregates, suggesting that adhesion could be mediated by homotypic CdiA-CdiA interactions. The BamA-dependent and BamA-independent interaction domains map to distinct regions within the CdiA filament. Thus, CdiA orchestrates a collective behavior that is independent of its growth-inhibition activity. This adhesion should enable 'greenbeard' discrimination, in which genetically unrelated individuals cooperate with one another based on a single shared trait. This kind-selective social behavior could provide immediate fitness benefits to bacteria that acquire the systems through horizontal gene transfer.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Loni Townsley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Adam B Wallace
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Andrew King
- Centre for Immunology and Infection, Hull York Medical School and the Department of Biology, University of York, York, YO10 5DD, UK
| | - Marjan W Van der Woude
- Centre for Immunology and Infection, Hull York Medical School and the Department of Biology, University of York, York, YO10 5DD, UK
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106-9625, USA
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33
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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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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: 39] [Impact Index Per Article: 4.3] [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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35
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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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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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