1
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Seyfert C, Müller AV, Walsh DJ, Birkelbach J, Kany AM, Porten C, Yuan B, Krug D, Herrmann J, Marlovits TC, Hirsch AKH, Müller R. New Genetically Engineered Derivatives of Antibacterial Darobactins Underpin Their Potential for Antibiotic Development. J Med Chem 2023; 66:16330-16341. [PMID: 38093695 PMCID: PMC10726357 DOI: 10.1021/acs.jmedchem.3c01660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Biosynthetic engineering of bicyclic darobactins, selectively sealing the lateral gate of the outer membrane protein BamA, leads to active analogues, which are up to 128-fold more potent against Gram-negative pathogens compared to native counterparts. Because of their excellent antibacterial activity, darobactins represent one of the most promising new antibiotic classes of the past decades. Here, we present a series of structure-driven biosynthetic modifications of our current frontrunner, darobactin 22 (D22), to investigate modifications at the understudied positions 2, 4, and 5 for their impact on bioactivity. Novel darobactins were found to be highly active against critical pathogens from the WHO priority list. Antibacterial activity data were corroborated by dissociation constants with BamA. The most active derivatives D22 and D69 were subjected to ADMET profiling, showing promising features. We further evaluated D22 and D69 for bioactivity against multidrug-resistant clinical isolates and found them to have strong activity.
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Affiliation(s)
- Carsten
E. Seyfert
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Alison V. Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Danica J. Walsh
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Joy Birkelbach
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Andreas M. Kany
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Christoph Porten
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Biao Yuan
- Institute
of Structural and Systems Biology and Centre for Structural Systems
Biology (CSSB), University Medical Center
Hamburg-Eppendorf (UKE), Hamburg 22607, Germany
- Deutsches
Elektronen-Synchrotron Zentrum (DESY), Hamburg 22607, Germany
- Centre for
Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Daniel Krug
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Jennifer Herrmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
| | - Thomas C. Marlovits
- Institute
of Structural and Systems Biology and Centre for Structural Systems
Biology (CSSB), University Medical Center
Hamburg-Eppendorf (UKE), Hamburg 22607, Germany
- Deutsches
Elektronen-Synchrotron Zentrum (DESY), Hamburg 22607, Germany
- Centre for
Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Anna K. H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
- Helmholtz
International Lab for Anti-Infectives, Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre
for Infection Research (HZI) and Saarland University Department of
Pharmacy, Saarbrücken 66123, Germany
- German
Centre for Infection Research (DZIF),
partner site, Hannover, Braunschweig 38124, Germany
- Helmholtz
International Lab for Anti-Infectives, Saarbrücken 66123, Germany
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2
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Yuan B, Scholz J, Wald J, Thuenauer R, Hennell James R, Ellenberg I, Windhorst S, Faix J, Marlovits TC. Structural basis for subversion of host cell actin cytoskeleton during Salmonella infection. Sci Adv 2023; 9:eadj5777. [PMID: 38064550 PMCID: PMC10708208 DOI: 10.1126/sciadv.adj5777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Secreted bacterial type III secretion system (T3SS) proteins are essential for successful infection by many human pathogens. Both T3SS translocator SipC and effector SipA are critical for Salmonella infection by subversion of the host cell cytoskeleton, but the precise molecular interplay between them remains unknown. Here, using cryo-electron microscopy, we show that SipA binds along the F-actin grooves with a unique binding pattern. SipA stabilizes F-actin through charged interface residues and appears to prevent inorganic phosphate release through closure of the "back door" of adenosine 5'-triphosphate pocket. We also show that SipC enhances the binding of SipA to F-actin, thus demonstrating that a sequential presence of T3SS proteins in host cells is associated with a sequence of infection events-starting with actin nucleation, filament growth, and stabilization. Together, our data explain the coordinated interplay of a precisely tuned and highly effective mechanism during Salmonella infection and provide a blueprint for interfering with Salmonella effectors acting on actin.
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Affiliation(s)
- Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Jonas Scholz
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Roland Thuenauer
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Technology Platform Light Microscopy (TPLM), University of Hamburg, Hamburg, Germany
- Technology Platform Microscopy and Image Analysis (TP MIA), Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Rory Hennell James
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Irina Ellenberg
- University Medical Center Hamburg-Eppendorf (UKE), Institute for Biochemistry and Signal Transduction, Hamburg, Germany
| | - Sabine Windhorst
- University Medical Center Hamburg-Eppendorf (UKE), Institute for Biochemistry and Signal Transduction, Hamburg, Germany
| | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Thomas C. Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
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3
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Simonis A, Kreer C, Albus A, Rox K, Yuan B, Holzmann D, Wilms JA, Zuber S, Kottege L, Winter S, Meyer M, Schmitt K, Gruell H, Theobald SJ, Hellmann AM, Meyer C, Ercanoglu MS, Cramer N, Munder A, Hallek M, Fätkenheuer G, Koch M, Seifert H, Rietschel E, Marlovits TC, van Koningsbruggen-Rietschel S, Klein F, Rybniker J. Discovery of highly neutralizing human antibodies targeting Pseudomonas aeruginosa. Cell 2023; 186:5098-5113.e19. [PMID: 37918395 DOI: 10.1016/j.cell.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023]
Abstract
Drug-resistant Pseudomonas aeruginosa (PA) poses an emerging threat to human health with urgent need for alternative therapeutic approaches. Here, we deciphered the B cell and antibody response to the virulence-associated type III secretion system (T3SS) in a cohort of patients chronically infected with PA. Single-cell analytics revealed a diverse B cell receptor repertoire directed against the T3SS needle-tip protein PcrV, enabling the production of monoclonal antibodies (mAbs) abrogating T3SS-mediated cytotoxicity. Mechanistic studies involving cryoelectron microscopy identified a surface-exposed C-terminal PcrV epitope as the target of highly neutralizing mAbs with broad activity against drug-resistant PA isolates. These anti-PcrV mAbs were as effective as treatment with conventional antibiotics in vivo. Our study reveals that chronically infected patients represent a source of neutralizing antibodies, which can be exploited as therapeutics against PA.
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Affiliation(s)
- Alexander Simonis
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50937 Cologne, Germany.
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Alexandra Albus
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Biao Yuan
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany; Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany; Deutsches Elektronen-Synchrotron Zentrum (DESY), 22607 Hamburg, Germany
| | - Dmitriy Holzmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Joana A Wilms
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sylvia Zuber
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lisa Kottege
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sandra Winter
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Meike Meyer
- CF Centre, Pediatric Pulmonology and Allergology, University Children's Hospital Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Centre for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Kristin Schmitt
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Anna-Maria Hellmann
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Department of Experimental Pediatric Oncology, University Children's Hospital Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christina Meyer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Meryem Seda Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nina Cramer
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
| | - Antje Munder
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, 30625 Hannover, Germany
| | - Michael Hallek
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50937 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50937 Cologne, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany
| | - Ernst Rietschel
- CF Centre, Pediatric Pulmonology and Allergology, University Children's Hospital Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Centre for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Thomas C Marlovits
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany; Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany; Deutsches Elektronen-Synchrotron Zentrum (DESY), 22607 Hamburg, Germany
| | - Silke van Koningsbruggen-Rietschel
- CF Centre, Pediatric Pulmonology and Allergology, University Children's Hospital Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Centre for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Florian Klein
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50937 Cologne, Germany; Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50937 Cologne, Germany.
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4
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Wald J, Marlovits TC. Holliday junction branch migration driven by AAA+ ATPase motors. Curr Opin Struct Biol 2023; 82:102650. [PMID: 37604043 DOI: 10.1016/j.sbi.2023.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 08/23/2023]
Abstract
Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research.
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Affiliation(s)
- Jiri Wald
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany.
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5
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Genthe E, Miletic S, Tekkali I, Hennell James R, Marlovits TC, Heuser P. PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms. J Struct Biol 2023; 215:107990. [PMID: 37364763 DOI: 10.1016/j.jsb.2023.107990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/31/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram averaging (STA) pipelines. In this paper, we introduce a deep learning framework called PickYOLO to tackle this problem. PickYOLO is a super-fast, universal particle detector based on the deep-learning real-time object recognition system YOLO (You Only Look Once), and tested on single particles, filamentous structures, and membrane-embedded particles. After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles with high yield and reliability at a rate of 0.24-3.75 s per tomogram. PickYOLO can automatically detect number of particles comparable to those manually selected by experienced microscopists. This makes PickYOLO a valuable tool to substantially reduce the time and manual effort needed to analyse cryoET data for STA, greatly aiding in high-resolution cryoET structure determination.
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Affiliation(s)
- Erik Genthe
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sean Miletic
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Indira Tekkali
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Rory Hennell James
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Thomas C Marlovits
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.
| | - Philipp Heuser
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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6
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Reggiano G, Lugmayr W, Farrell D, Marlovits TC, DiMaio F. Residue-level error detection in cryoelectron microscopy models. Structure 2023; 31:860-869.e4. [PMID: 37253357 PMCID: PMC10330749 DOI: 10.1016/j.str.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/01/2023]
Abstract
Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local backbone errors in protein structures built into cryo-EM maps by combining local fit-to-density with deep-learning-derived structural information. MEDIC is validated on a set of 28 structures that were subsequently solved to higher resolutions, where we identify the differences between low- and high-resolution structures with 68% precision and 60% recall. We additionally use this model to fix over 100 errors in 12 deposited structures and to identify errors in 4 refined AlphaFold predictions with 80% precision and 60% recall. As modelers more frequently use deep learning predictions as a starting point for refinement and rebuilding, MEDIC's ability to handle errors in structures derived from hand-building and machine learning methods makes it a powerful tool for structural biologists.
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Affiliation(s)
- Gabriella Reggiano
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Wolfgang Lugmayr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany; CSSB Centre for Structural Systems Biology, Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | | | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany; CSSB Centre for Structural Systems Biology, Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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7
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Seyfert CE, Porten C, Yuan B, Deckarm S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits TC, Herrmann J, Müller R. Darobactins Exhibiting Superior Antibiotic Activity by Cryo-EM Structure Guided Biosynthetic Engineering. Angew Chem Int Ed Engl 2023; 62:e202214094. [PMID: 36308277 PMCID: PMC10107326 DOI: 10.1002/anie.202214094] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Over recent decades, the pipeline of antibiotics acting against Gram-negative bacteria is running dry, as most discovered candidate antibiotics suffer from insufficient potency, pharmacokinetic properties, or toxicity. The darobactins, a promising new small peptide class of drug candidates, bind to novel antibiotic target BamA, an outer membrane protein. Previously, we reported that biosynthetic engineering in a heterologous host generated novel darobactins with enhanced antibacterial activity. Here we utilize an optimized purification method and present cryo-EM structures of the Bam complex with darobactin 9 (D9), which served as a blueprint for the biotechnological generation of twenty new darobactins including halogenated analogs. The newly engineered darobactin 22 binds more tightly to BamA and outperforms the favorable activity profile of D9 against clinically relevant pathogens such as carbapenem-resistant Acinetobacter baumannii up to 32-fold, without observing toxic effects.
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Affiliation(s)
- Carsten E Seyfert
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Christoph Porten
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Selina Deckarm
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Fabian Panter
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Chantal D Bader
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Janetta Coetzee
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Felix Deschner
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Kamaleddin H M E Tehrani
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Paul G Higgins
- Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Harald Seifert
- Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Jennifer Herrmann
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
| | - Rolf Müller
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy at, Saarland University Campus Building E8.1, 66123 Saarbrücken (Germany).,German Centre for Infection Research (DZIF), partnersite Hannover-Braunschweig, Germany
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8
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Lugmayr W, Kotov V, Goessweiner-Mohr N, Wald J, DiMaio F, Marlovits TC. StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Nat Protoc 2023; 18:239-264. [PMID: 36323866 DOI: 10.1038/s41596-022-00757-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/08/2022] [Indexed: 01/13/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes.
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Affiliation(s)
- Wolfgang Lugmayr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria
| | - Vadim Kotov
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Evotec SE, Hamburg, Germany
| | - Nikolaus Goessweiner-Mohr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Johannes Kepler University, Institute of Biophysics, Linz, Austria
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria
| | - Frank DiMaio
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany. .,CSSB Centre for Structural Systems Biology, Hamburg, Germany. .,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany. .,Research Institute of Molecular Pathology (IMP), Vienna, Austria. .,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.
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9
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Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC. Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration. Nature 2022; 609:630-639. [PMID: 36002576 PMCID: PMC9477746 DOI: 10.1038/s41586-022-05121-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 07/18/2022] [Indexed: 12/12/2022]
Abstract
The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life1. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, which assemble together with the RuvA-Holliday junction complex to energize the strand-exchange reaction2. Despite its importance for chromosome maintenance, the structure and mechanism by which this complex facilitates branch migration are unknown. Here, using time-resolved cryo-electron microscopy, we obtained structures of the ATP-hydrolysing RuvAB complex in seven distinct conformational states, captured during assembly and processing of a Holliday junction. Five structures together resolve the complete nucleotide cycle and reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange and context-specific conformational changes in RuvB. Coordinated motions in a converter formed by DNA-disengaged RuvB subunits stimulate hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, which generates the pulling force driving the branch migration. We show that RuvB motors rotate together with the DNA substrate, which, together with a progressing nucleotide cycle, forms the mechanistic basis for DNA recombination by continuous branch migration. Together, our data decipher the molecular principles of homologous recombination by the RuvAB complex, elucidate discrete and sequential transition-state intermediates for chemo-mechanical coupling of hexameric AAA+ motors and provide a blueprint for the design of state-specific compounds targeting AAA+ motors.
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Affiliation(s)
- Jiri Wald
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Centre for Structural Systems Biology, Hamburg, Germany.
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Dirk Fahrenkamp
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Centre for Structural Systems Biology, Hamburg, Germany.
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
| | - Nikolaus Goessweiner-Mohr
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- Institute of Biophysics, Johannes Kepler University (JKU), Linz, Austria
| | - Wolfgang Lugmayr
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Luciano Ciccarelli
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- GlaxoSmithKline Vaccines, Siena, Italy
| | - Oliver Vesper
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Thomas C Marlovits
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Centre for Structural Systems Biology, Hamburg, Germany.
- Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
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10
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Bergeron JRC, Marlovits TC. Cryo-EM of the injectisome and type III secretion systems. Curr Opin Struct Biol 2022; 75:102403. [PMID: 35724552 PMCID: PMC10114087 DOI: 10.1016/j.sbi.2022.102403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 11/25/2022]
Abstract
Double-membrane-spanning protein complexes, such as the T3SS, had long presented an intractable challenge for structural biology. As a consequence, until a few years ago, our molecular understanding of this fascinating complex was limited to composite models, consisting of structures of isolated domains, positioned within the overall complex. Most of the membrane-embedded components remained completely uncharacterized. In recent years, the emergence of cryo-electron microscopy (cryo-EM) as a method for determining protein structures to high resolution, has be transformative to our capacity to understand the architecture of this complex, and its mechanism of substrate transport. In this review, we summarize the recent structures of the various T3SS components, determined by cryo-EM, and highlight the regions of the complex that remain to be characterized. We also discuss the recent structural insights into the mechanism of effector transport through the T3SS. Finally, we highlight some of the challenges that remain to be tackled.
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Affiliation(s)
- Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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11
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Killer M, Wald J, Pieprzyk J, Marlovits TC, Löw C. Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes. Sci Adv 2021; 7:eabk3259. [PMID: 34730990 PMCID: PMC8565842 DOI: 10.1126/sciadv.abk3259] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body.
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Affiliation(s)
- Maxime Killer
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Faculty of Biosciences, Im Neuenheimer Feld 234, D-69120 Heidelberg, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestrasse 85, D-22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Joanna Pieprzyk
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestrasse 85, D-22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
- Corresponding author.
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12
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Kotov V, Lunelli M, Wald J, Kolbe M, Marlovits TC. Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies. Biochem Biophys Rep 2021; 27:101039. [PMID: 34258394 PMCID: PMC8254080 DOI: 10.1016/j.bbrep.2021.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/26/2021] [Indexed: 12/02/2022] Open
Abstract
Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.
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Affiliation(s)
- Vadim Kotov
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Michele Lunelli
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- Department of Structural Infection Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Kolbe
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- Department of Structural Infection Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Rothenbaumchaussee 19, 20148 Hamburg, Germany
- Corresponding author. Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany.
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
- Corresponding author. Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany.
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13
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Bunduc CM, Fahrenkamp D, Wald J, Ummels R, Bitter W, Houben ENG, Marlovits TC. Structure and dynamics of a mycobacterial type VII secretion system. Nature 2021; 593:445-448. [PMID: 33981042 PMCID: PMC8131196 DOI: 10.1038/s41586-021-03517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/06/2021] [Indexed: 11/20/2022]
Abstract
Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year1. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope2,3. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP5 protease. A trimer of MycP5 caps a central periplasmic dome-like chamber that is formed by three EccB5 dimers, with the proteolytic sites of MycP5 facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP5 show disruption of the EccB5 periplasmic assembly and increased flexibility, which highlights the importance of MycP5 for complex integrity. Beneath the EccB5-MycP5 chamber, dimers of the EccC5 ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC5 domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.
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Affiliation(s)
- Catalin M Bunduc
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dirk Fahrenkamp
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Edith N G Houben
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Hamburg, Germany.
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany.
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14
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Miletic S, Fahrenkamp D, Goessweiner-Mohr N, Wald J, Pantel M, Vesper O, Kotov V, Marlovits TC. Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation. Nat Commun 2021; 12:1546. [PMID: 33750771 PMCID: PMC7943601 DOI: 10.1038/s41467-021-21143-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
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Affiliation(s)
- Sean Miletic
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Fahrenkamp
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Nikolaus Goessweiner-Mohr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Maurice Pantel
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Oliver Vesper
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Vadim Kotov
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany. .,Centre for Structural Systems Biology (CSSB), Hamburg, Germany. .,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany. .,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria. .,Research Institute of Molecular Pathology (IMP), Vienna, Austria.
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15
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Kotov V, Mlynek G, Vesper O, Pletzer M, Wald J, Teixeira‐Duarte CM, Celia H, Garcia‐Alai M, Nussberger S, Buchanan SK, Morais‐Cabral JH, Loew C, Djinovic‐Carugo K, Marlovits TC. In-depth interrogation of protein thermal unfolding data with MoltenProt. Protein Sci 2021; 30:201-217. [PMID: 33140490 PMCID: PMC7737771 DOI: 10.1002/pro.3986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/06/2023]
Abstract
Protein stability is a key factor in successful structural and biochemical research. However, the approaches for systematic comparison of protein stability are limited by sample consumption or compatibility with sample buffer components. Here we describe how miniaturized measurement of intrinsic tryptophan fluorescence (NanoDSF assay) in combination with a simplified description of protein unfolding can be used to interrogate the stability of a protein sample. We demonstrate that improved protein stability measures, such as apparent Gibbs free energy of unfolding, rather than melting temperature Tm , should be used to rank the results of thermostability screens. The assay is compatible with protein samples of any composition, including protein complexes and membrane proteins. Our data analysis software, MoltenProt, provides an easy and robust way to perform characterization of multiple samples. Potential applications of MoltenProt and NanoDSF include buffer and construct optimization for X-ray crystallography and cryo-electron microscopy, screening for small-molecule binding partners and comparison of effects of point mutations.
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Affiliation(s)
- Vadim Kotov
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Oliver Vesper
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Marina Pletzer
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Celso M. Teixeira‐Duarte
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Herve Celia
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Maria Garcia‐Alai
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular SystemsUniversity of StuttgartStuttgartGermany
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - João H. Morais‐Cabral
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Christian Loew
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Kristina Djinovic‐Carugo
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
- Department of Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
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16
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Banger A, Sindram J, Otten M, Kania J, Wilms D, Strzelczyk A, Miletic S, Marlovits TC, Karg M, Hartmann L. Synthesis and self-assembly of amphiphilic precision glycomacromolecules. Polym Chem 2021. [DOI: 10.1039/d1py00422k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Amphiphilic precision glycomacromolecules (APG) are synthesized using solid-phase synthesis and studied for their self-assembly behavior and as inhibitors of bacterial adhesion.
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Affiliation(s)
- Alexander Banger
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Julian Sindram
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marius Otten
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jessica Kania
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dimitri Wilms
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alexander Strzelczyk
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Sean Miletic
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Thomas C. Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Matthias Karg
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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17
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Abstract
The type III secretion system (T3SS) is an essential virulence factor of many pathogenic bacterial species including Salmonella, Yersinia, Shigella and enteropathogenic Escherichia coli (EPEC). It is an intricate molecular machine that spans the bacterial membranes and injects effector proteins into target host cells, enabling bacterial infection. The T3SS needle complex comprises of proteinaceous rings supporting a needle filament which extends out into the extracellular environment. It serves as the central conduit for translocating effector proteins. Multiple laboratories have dedicated a remarkable effort to decipher the structure and function of the needle complex. A combination of structural biology techniques such as cryo-electron microscopy (cryoEM), X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and computer modelling have been utilized to study different structural components at progressively higher resolutions. This chapter will provide an overview of the structural details of the T3SS needle complex, shedding light on this essential component of this fascinating bacterial system.
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Affiliation(s)
- Sean Miletic
- Center for Structural Systems Biology, Institute for Structural and Systems Biology, Universitätsklinikum Hamburg-Eppendorf, 85 Notkestraße, Hamburg, 22607, Germany
| | | | - Thomas C Marlovits
- Center for Structural Systems Biology, Institute for Structural and Systems Biology, Universitätsklinikum Hamburg-Eppendorf, 85 Notkestraße, Hamburg, 22607, Germany.
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18
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Mlynek G, Nagy M, Kostan J, Kotov V, Marlovits TC, Djinovic-Carugo K. High-throughput stability screening of integral membrane proteins. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319095044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Beckham KSH, Ciccarelli L, Bunduc CM, Mertens HDT, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AHA, Houben ENG. Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis. Nat Microbiol 2017; 2:17047. [DOI: 10.1038/nmicrobiol.2017.47] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022]
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20
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Dietsche T, Tesfazgi Mebrhatu M, Brunner MJ, Abrusci P, Yan J, Franz-Wachtel M, Schärfe C, Zilkenat S, Grin I, Galán JE, Kohlbacher O, Lea S, Macek B, Marlovits TC, Robinson CV, Wagner S. Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. PLoS Pathog 2016; 12:e1006071. [PMID: 27977800 PMCID: PMC5158082 DOI: 10.1371/journal.ppat.1006071] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/17/2016] [Indexed: 02/04/2023] Open
Abstract
Bacterial type III protein secretion systems inject effector proteins into eukaryotic host cells in order to promote survival and colonization of Gram-negative pathogens and symbionts. Secretion across the bacterial cell envelope and injection into host cells is facilitated by a so-called injectisome. Its small hydrophobic export apparatus components SpaP and SpaR were shown to nucleate assembly of the needle complex and to form the central “cup” substructure of a Salmonella Typhimurium secretion system. However, the in vivo placement of these components in the needle complex and their function during the secretion process remained poorly defined. Here we present evidence that a SpaP pentamer forms a 15 Å wide pore and provide a detailed map of SpaP interactions with the export apparatus components SpaQ, SpaR, and SpaS. We further refine the current view of export apparatus assembly, consolidate transmembrane topology models for SpaP and SpaR, and present intimate interactions of the periplasmic domains of SpaP and SpaR with the inner rod protein PrgJ, indicating how export apparatus and needle filament are connected to create a continuous conduit for substrate translocation. Many Gram-negative bacteria use type III secretion systems to inject bacterial proteins into eukaryotic host cells in order to promote their own survival and colonization. These systems are large molecular machines with the ability to transport proteins across three cell membranes in one step. It is believed that the only gated barrier of these systems lies in the bacterial cytoplasmic membrane but it was unclear so far how this gate looks like and of which components it is composed. Here we present evidence based on in depth biochemical and genetic characterization that an assembly of five SpaP proteins forms this gate in the cytoplasmic membrane of the type III secretion system of Salmonella pathogenicity island 1. We further show that one subunit each of the proteins SpaQ, SpaR, and SpaS are closely associated to the SpaP gate and may function in the gating mechanism, and that the protein PrgJ is attached to this gate on the outside to connect it to the hollow needle filament projecting towards the host cell. Our findings elucidate a hitherto ill-defined aspect of type III secretion systems and may help to develop novel antiinfective therapies targeting these virulence-associated molecular devices.
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Affiliation(s)
- Tobias Dietsche
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany
| | - Mehari Tesfazgi Mebrhatu
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany
| | - Matthias J. Brunner
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE) and German Electron Synchrotron Centre (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Patrizia Abrusci
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jun Yan
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | | | - Susann Zilkenat
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany
| | - Iwan Grin
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany
| | - Jorge E. Galán
- Yale University School of Medicine, Department of Microbial Pathogenesis, New Haven, Connecticut, United States of America
| | - Oliver Kohlbacher
- University of Tübingen, Center for BioinformaticsTübingen, Germany
- Max Planck Institute for Developmental Biology, Biomolecular Interactions, Tübingen, Germany
| | - Susan Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Boris Macek
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | - Thomas C. Marlovits
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE) and German Electron Synchrotron Centre (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Samuel Wagner
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner-site Tübingen, Tübingen, Germany
- * E-mail:
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21
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Hornung P, Troc P, Malvezzi F, Maier M, Demianova Z, Zimniak T, Litos G, Lampert F, Schleiffer A, Brunner M, Mechtler K, Herzog F, Marlovits TC, Westermann S. A cooperative mechanism drives budding yeast kinetochore assembly downstream of CENP-A. ACTA ACUST UNITED AC 2014; 206:509-24. [PMID: 25135934 PMCID: PMC4137059 DOI: 10.1083/jcb.201403081] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During kinetochore assembly in budding yeast, the key steps of CENP-A recognition and outer kinetochore recruitment are executed through different yeast CCAN subunits, potentially protecting against inappropriate kinetochore assembly. Kinetochores are megadalton-sized protein complexes that mediate chromosome–microtubule interactions in eukaryotes. How kinetochore assembly is triggered specifically on centromeric chromatin is poorly understood. Here we use biochemical reconstitution experiments alongside genetic and structural analysis to delineate the contributions of centromere-associated proteins to kinetochore assembly in yeast. We show that the conserved kinetochore subunits Ame1CENP-U and Okp1CENP-Q form a DNA-binding complex that associates with the microtubule-binding KMN network via a short Mtw1 recruitment motif in the N terminus of Ame1. Point mutations in the Ame1 motif disrupt kinetochore function by preventing KMN assembly on chromatin. Ame1–Okp1 directly associates with the centromere protein C (CENP-C) homologue Mif2 to form a cooperative binding platform for outer kinetochore assembly. Our results indicate that the key assembly steps, CENP-A recognition and outer kinetochore recruitment, are executed through different yeast constitutive centromere-associated network subunits. This two-step mechanism may protect against inappropriate kinetochore assembly similar to rate-limiting nucleation steps used by cytoskeletal polymers.
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Affiliation(s)
- Peter Hornung
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Paulina Troc
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Francesca Malvezzi
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael Maier
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Zuzana Demianova
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Tomasz Zimniak
- Department of Biochemistry, Gene Center, Ludwig-Maximilians Universität München, 81377 Munich, Germany
| | - Gabriele Litos
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Fabienne Lampert
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Matthias Brunner
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria Center for Structural Systems Biology, University Medical Center Eppendorf-Hamburg, 20246 Hamburg, Germany Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Franz Herzog
- Department of Biochemistry, Gene Center, Ludwig-Maximilians Universität München, 81377 Munich, Germany
| | - Thomas C Marlovits
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria Center for Structural Systems Biology, University Medical Center Eppendorf-Hamburg, 20246 Hamburg, Germany Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Stefan Westermann
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
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22
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Galán JE, Lara-Tejero M, Marlovits TC, Wagner S. Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells. Annu Rev Microbiol 2014; 68:415-38. [PMID: 25002086 DOI: 10.1146/annurev-micro-092412-155725] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. These effector proteins modulate a variety of cellular functions for the pathogen's benefit. One of these protein-delivery machines is the type III secretion system (T3SS). T3SSs are widespread in nature and are encoded not only by bacteria pathogenic to vertebrates or plants but also by bacteria that are symbiotic to plants or insects. A central component of T3SSs is the needle complex, a supramolecular structure that mediates the passage of the secreted proteins across the bacterial envelope. Working in conjunction with several cytoplasmic components, the needle complex engages specific substrates in sequential order, moves them across the bacterial envelope, and ultimately delivers them into eukaryotic cells. The central role of T3SSs in pathogenesis makes them great targets for novel antimicrobial strategies.
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Affiliation(s)
- Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536;
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23
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Abstract
Type-3 secretion systems are sophisticated syringe-like nanomachines present in many animal and plant Gram-negative pathogens. They are capable of translocating an arsenal of specific bacterial toxins (effector proteins) from the prokaryotic cytoplasm across the three biological membranes directly into the eukaryotic cytosol, some of which modulate host cell mechanisms for the benefit of the pathogen. They populate a particular biological niche, which is maintained by specific, pathogen-dependent effectors. In contrast, the needle complex, which is the central component of this specialized protein delivery machine, is structurally well-conserved. It is a large supramolecular cylindrical structure composed of multiple copies of a relatively small subset of proteins, is embedded in the bacterial membranes and protrudes from the pathogen's surface with a needle filament. A central channel traverses the entire needle complex, and serves as a hollow conduit for proteins destined to travel this secretion pathway. In the past few years, there has been a tremendous increase in an understanding on both the structural and the mechanistic level. This review will thus focus on new insights of this remarkable molecular machine.
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Affiliation(s)
- Agata Kosarewicz
- Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria
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24
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Fernandez-Rodriguez J, Marlovits TC. Induced heterodimerization and purification of two target proteins by a synthetic coiled-coil tag. Protein Sci 2012; 21:511-9. [PMID: 22362668 DOI: 10.1002/pro.2035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 01/23/2012] [Indexed: 11/09/2022]
Abstract
A synthetic de novo designed heterodimeric coiled-coil was used to copurify two target fluorescent proteins, Venus and enhanced cyan fluorescent protein (ECFP). The coiled-coil consists of two 21-amino acid repetitive sequences, (EIAALEK)(3) and (KIAALKE)(3), named E3 and K3, respectively. These sequences were fused to the C-termini of ECFP or Venus followed by either a strep- or a his-tag, respectively, for affinity purification. Mixed lysates of Venus-K3 and ECFP-E3 were subjected to consecutive affinity purification and showed highly specific association between the coiled-coil pair by SDS-PAGE, gel filtration, isothermal titration calorimetry (ITC), and fluorescence resonance energy transfer (FRET). The tagged proteins eluted as heterodimers at the concentrations tested. FRET analysis further showed that the coiled-coil pair was stable in buffers commonly used for protein purification, including those containing high salt concentration and detergent. This study shows that the E3/K3 pair is very well suited for the copurification of two target proteins expressed in vivo because of its high specificity: it forms exclusively heterodimers in solution, it does not interact with any cellular proteins and it is stable under different buffer conditions.
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25
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Abstract
Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.
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Affiliation(s)
- Oliver Schraidt
- Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria
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26
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Khan AG, Pickl-Herk A, Gajdzik L, Marlovits TC, Fuchs R, Blaas D. Entry of a heparan sulphate-binding HRV8 variant strictly depends on dynamin but not on clathrin, caveolin, and flotillin. Virology 2011; 412:55-67. [DOI: 10.1016/j.virol.2010.12.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 10/22/2010] [Accepted: 12/22/2010] [Indexed: 02/08/2023]
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27
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Galkin VE, Schmied WH, Schraidt O, Marlovits TC, Egelman EH. The structure of the Salmonella typhimurium type III secretion system needle shows divergence from the flagellar system. J Mol Biol 2010; 396:1392-7. [PMID: 20060835 DOI: 10.1016/j.jmb.2010.01.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/22/2009] [Accepted: 01/01/2010] [Indexed: 01/16/2023]
Abstract
The type III secretion system (T3SS) is essential for the infectivity of many pathogenic Gram-negative bacteria. The T3SS contains proteins that form a channel in the inner and outer bacterial membranes, as well as an extracellular needle that is used for transporting and injecting effector proteins into a host cell. The homology between the T3SS and the bacterial flagellar system has been firmly established, based upon both sequence similarities between respective proteins in the two systems and the structural homology of higher-order assemblies. It has previously been shown that the Shigella flexneri needle has a helical symmetry of approximately 5.6 subunits/turn, which is quite similar to that of the most intensively studied flagellar filament (from Salmonella typhimurium), which has approximately 5.5 subunits/turn. We now show that the Sa. typhimurium needle, expected by homology arguments to be more similar to the Sa. typhimurium flagellar filament than is the needle from Shigella, actually has approximately 6.3 subunits/turn. It is not currently understood how host cell contact, made at the tip of the needle, is communicated to the secretory system at the base. In contrast to the Sa. typhimurium flagellar filament, which shows a nearly crystalline order, the Sa. typhimurium needle has a highly variable symmetry, which could be used to transmit information about host cell contact.
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Affiliation(s)
- Vitold E Galkin
- Department of Biochemistry and Molecular Genetics, University of Virginia Medical School, Charlottesville, VA 22908-0733, USA
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28
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Marlovits TC, Kubori T, Lara-Tejero M, Thomas D, Unger VM, Galán JE. Assembly of the inner rod determines needle length in the type III secretion injectisome. Nature 2006; 441:637-40. [PMID: 16738660 DOI: 10.1038/nature04822] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 04/19/2006] [Indexed: 11/09/2022]
Abstract
Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion machine, which mediates the transfer of bacterial virulence proteins into host cells. A central component of this nanomachine is the needle complex or injectisome, an organelle associated with the bacterial envelope that is composed of a multi-ring base, an inner rod, and a protruding needle. Assembly of this organelle proceeds in sequential steps that require the reprogramming of the secretion machine. Here we provide evidence that, in Salmonella typhimurium, completion of the assembly of the inner rod determines the size of the needle substructure. Assembly of the inner rod, which is regulated by the InvJ protein, triggers conformational changes on the cytoplasmic side of the injectisome, reprogramming the secretion apparatus to stop secretion of the needle protein.
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Affiliation(s)
- Thomas C Marlovits
- Section of Microbial Pathogenesis, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, Connecticut 06536, USA
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29
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Abstract
Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, the needle complex, and its assembly precursor, the bacterial envelope-anchored base. Both the base and the fully assembled needle complex adopted multiple oligomeric states in vivo, and needle assembly was accompanied by recruitment of the protein PrgJ as a structural component of the base. Moreover, conformational changes during needle assembly created scaffolds for anchoring both PrgJ and the needle substructure and may provide the basis for substrate-specificity switching during type III secretion.
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Affiliation(s)
- Thomas C. Marlovits
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520–8024, USA
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Tomoko Kubori
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Anand Sukhan
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Dennis R. Thomas
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Jorge E. Galán
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Vinzenz M. Unger
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520–8024, USA
- †To whom correspondence should be addressed., E-mail:
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Marlovits TC, Haase W, Herrmann C, Aller SG, Unger VM. The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria. Proc Natl Acad Sci U S A 2002; 99:16243-8. [PMID: 12446835 PMCID: PMC138596 DOI: 10.1073/pnas.242338299] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G proteins are critical for the regulation of membrane protein function and signal transduction. Nevertheless, coupling between G proteins and membrane proteins with multiple membrane-spanning domains has so far been observed only in higher organisms. Here we show that the polytopic membrane protein FeoB, which is essential for Fe(II) uptake in bacteria, contains a guanine-nucleotide-specific nucleotide binding site. We identify the G4-motif, NXXD, responsible for guanine nucleotide specificity, and show that GTP hydrolysis occurs very slowly. In contrast to typical G proteins, the association and dissociation of GDP were found to be faster than for GTP, suggesting that in the absence of additional factors, FeoB's G protein domain may exist mostly in the GTP-bound form. Furthermore, the binding of GTP is required for efficient Fe(II) uptake through the FeoB-dependent system. Notably, even in bacteria, this covalent linkage between a G protein and a polytopic membrane protein appears, to our knowledge, to be unique. These findings raise the intriguing question whether FeoB represents a primordial archetype of G protein-regulated membrane proteins.
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Affiliation(s)
- Thomas C Marlovits
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, P.O. Box 208024, New Haven, CT 06520-8024, USA
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Ronacher B, Marlovits TC, Moser R, Blaas D. Expression and folding of human very-low-density lipoprotein receptor fragments: neutralization capacity toward human rhinovirus HRV2. Virology 2000; 278:541-50. [PMID: 11118376 DOI: 10.1006/viro.2000.0636] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Minor group human rhinoviruses (HRVs) use members of the low-density lipoprotein receptor family for cell entry. To investigate the utility of receptor fragments as viral inhibitors, various polypeptide segments derived from the ligand binding domain of human very-low-density lipoprotein receptor (VLDLR) were expressed in a soluble form in bacteria. Whereas none of the fragments was active in virus binding immediately after recovery from the cell lysates, constructs encompassing complement type repeats 1-3, 1-6, and 1-8 spontaneously acquired virus binding activity by incubation at 4 degrees C in buffer containing Ca(2+) ions and lacking any redox system. When immobilized receptor-associated protein (RAP), a specific chaperone for VLDLR, was present during the incubation, the yield of protein active in ligand binding was substantially increased. A VLDLR fragment with repeats 4-6 failed to bind virus; however, it bound RAP. Bacterial expression of truncated VLDLR 1-3 at high yield, easy purification, and folding together with high inhibitory activity toward HRV2 makes this protein a promising starting point for the development of an oligopeptide-based antiviral agent. Using sucrose density gradient centrifugation, we demonstrate the formation of virus-receptor complexes. The recombinant receptors can thus be used for structure determination by electron cryo-microscopy.
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Affiliation(s)
- B Ronacher
- Vienna Biocenter (VBC), Institute of Medical Biochemistry, University of Vienna, Dr. Bohr Gasse 9/3, Vienna, A-1030, Austria
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Hewat EA, Neumann E, Conway JF, Moser R, Ronacher B, Marlovits TC, Blaas D. The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view. EMBO J 2000; 19:6317-25. [PMID: 11101504 PMCID: PMC305862 DOI: 10.1093/emboj/19.23.6317] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human rhinovirus serotype 2 (HRV2) belongs to the minor group of HRVs that bind to members of the LDL-receptor family including the very low density lipoprotein (VLDL)-receptor (VLDL-R). We have determined the structures of the complex between HRV2 and soluble fragments of the VLDL-R to 15 A resolution by cryo-electron microscopy. The receptor fragments, which include the first three ligand-binding repeats of the VLDL-R (V1-3), bind to the small star-shaped dome on the icosahedral 5-fold axis. This is in sharp contrast to the major group of HRVs where the receptor site for ICAM-1 is located at the base of a depression around each 5-fold axis. Homology models of the three domains of V1-3 were used to explore the virus-receptor interaction. The footprint of VLDL-R on the viral surface covers the BC- and HI-loops on VP1.
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Affiliation(s)
- E A Hewat
- Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble, France
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Abstract
A fragment of the human low-density lipoprotein receptor encompassing the seven ligand-binding repeats fused to a C-terminal oligo-His tag was expressed in Sf9 insect cells. The melittin signal sequence encoded in the baculovirus vector led to secretion of the protein into the cell supernatant in a soluble form. The receptor fragment bound its natural ligand beta-migrating very-low-density lipoprotein and human rhinovirus serotype 2 in non-reducing ligand blots. Infection of all minor group human rhinovirus serotypes investigated was inhibited by the presence of the receptor fragment during viral challenge of HeLa cells. Infection is inhibited by aggregation of the virions.
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Affiliation(s)
- T C Marlovits
- Institute of Biochemistry, University of Vienna, Austria
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Verdaguer N, Marlovits TC, Bravo J, Stuart DI, Blaas D, Fita I. Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2). Acta Crystallogr D Biol Crystallogr 1999; 55:1459-61. [PMID: 10417415 DOI: 10.1107/s0907444999006137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group P2(1), diffracted at least to 2.8 A resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 A resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 A, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 A, diffracted to high resolution (beyond 1.8 A) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.
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Affiliation(s)
- N Verdaguer
- Centre d'Investigació i Desenvolupament (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
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Marlovits TC, Abrahamsberg C, Blaas D. Soluble LDL minireceptors. Minimal structure requirements for recognition of minor group human rhinovirus. J Biol Chem 1998; 273:33835-40. [PMID: 9837974 DOI: 10.1074/jbc.273.50.33835] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Soluble human low density lipoprotein minireceptors with less than seven ligand binding repeats (as are present in the native membrane receptor) were expressed in Sf9 insect cells with a hexa-His tag fused to the C terminus. The recombinant truncated proteins were affinity purified from the tissue culture supernatants by Ni-NTA column chromatography. Minireceptors with more than two repeats bound to rabbit beta very low density lipoprotein and could thus be further purified by affinity chromatography. Binding and cell protection assays indicated that two ligand binding repeats are sufficient for attachment of minor group human rhinoviruses to immobilized receptors, whereas at least three ligand binding repeats are required to protect HeLa cells against viral infection.
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Affiliation(s)
- T C Marlovits
- Institute of Biochemistry, University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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Abstract
The large family of human rhinoviruses, the main causative agents of the common cold, is divided into the major and the minor group based on receptor specificity. Major group viruses attach to intercellular adhesion molecule 1 (ICAM-1), a member of the immunoglobulin superfamily, whereas minor group viruses use low-density lipoprotein receptors (LDLR) for cell entry. During early attempts aimed at isolating the minor group receptor, we discovered that a protein with virus binding activity was released from HeLa cells upon incubation with buffer at 37 degreesC (F. Hofer, B. Berger, M. Gruenberger, H. Machat, R. Dernick, U. Tessmer, E. Kuechler, and D. Blaas, J. Gen. Virol. 73:627-632, 1992). In light of the recent discovery of several new members of the LDLR family, we reinvestigated the nature of this protein and present evidence for its being derived from the human very-low density lipoprotein receptor (VLDLR). A soluble VLDLR fragment encompassing the eight complement type repeats and representing the N-terminal part of the receptor was then expressed in the baculovirus system; both the shed protein and the recombinant soluble VLDLR bind minor group viruses and inhibit viral infection of HeLa cells in a concentration-dependent manner.
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Affiliation(s)
- T C Marlovits
- Institute of Biochemistry, Medical Faculty, A-1030 Vienna, Austria
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Marlovits TC, Zechmeister T, Gruenberger M, Ronacher B, Schwihla H, Blaas D. Recombinant soluble low density lipoprotein receptor fragment inhibits minor group rhinovirus infection in vitro. FASEB J 1998; 12:695-703. [PMID: 9619448 DOI: 10.1096/fasebj.12.9.695] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A fragment of the low density lipoprotein receptor encompassing the seven ligand binding repeats was expressed in Sf9 insect cells as a fusion protein with a carboxyl-terminally linked hexa-his tag by using a baculovirus vector. Up to 10 mg/l of the fusion protein was secreted into the medium. The material was soluble in the absence of detergent and active in binding beta very low density lipoprotein and a member of the minor group of human rhinoviruses (HRV2) in ligand blots from sodium dodecyl sulfate-polyacrylamide gels run under nonreducing conditions. The receptor fragment specifically inhibits viral infection of HeLa cells by minor group HRVs in a concentration-dependent manner. Viral infectivity is neutralized by aggregation.
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Affiliation(s)
- T C Marlovits
- Institute of Biochemistry, University of Vienna, Austria
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Abstract
The structure of a complex between human rhinovirus 2 (HRV2) and the Fab fragment of neutralizing monoclonal antibody (MAb) 3B10 has been determined to 25-A resolution by cryoelectron microscopy and three-dimensional reconstruction techniques. The footprint of 3B10 on HRV2 is very similar to that of neutralizing MAb 8F5, which binds bivalently across the icosahedral twofold axis. However, the 3B10 Fab fragment (Fab-3B10) is bound in an orientation, inclined at approximately 45 degrees to the surface of the virus capsid, which is compatible only with monovalent binding of the antibody. The canyon around the fivefold axis is not directly obstructed by the bound Fab. The X-ray structures of a closely related HRV (HRV1A) and a Fab fragment were fitted to the density maps of the HRV2-Fab-3B10 complex obtained by cryoelectron microscope techniques. The footprint of 3B10 on the viral surface is largely on VP2 but also covers the VP3 loop centered on residue 3064 and the VP1 loop centered on residue 1267. MAb 3B10 can interact directly with VP2 residue 2164, the site of an escape mutation on VP2, and with VP1 residues 1264 to 1267, the site of a deletion escape mutation. Deletion of these residues shortens the VP1 loop, moving it away from the MAb binding site. All structural and biochemical evidence indicates that MAb 3B10 binds to a conformation epitope on HRV2.
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Affiliation(s)
- E A Hewat
- Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France.
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