1
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Bitter RM, Zimmerman MI, Summers BT, Pinkner JS, Dodson KW, Hultgren SJ, Yuan P. Structural basis for adhesin secretion by the outer-membrane usher in type 1 pili. Proc Natl Acad Sci U S A 2024; 121:e2410594121. [PMID: 39316053 PMCID: PMC11459180 DOI: 10.1073/pnas.2410594121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024] Open
Abstract
Gram-negative bacteria produce chaperone-usher pathway pili, which are extracellular protein fibers tipped with an adhesive protein that binds to a receptor with stereochemical specificity to determine host and tissue tropism. The outer-membrane usher protein, together with a periplasmic chaperone, assembles thousands of pilin subunits into a highly ordered pilus fiber. The tip adhesin in complex with its cognate chaperone activates the usher to allow extrusion across the outer membrane. The structural requirements to translocate the adhesin through the usher pore from the periplasm to the extracellular space remains incompletely understood. Here, we present a cryoelectron microscopy structure of a quaternary tip complex in the type 1 pilus system from Escherichia coli, which consists of the usher FimD, chaperone FimC, adhesin FimH, and the tip adapter FimF. In this structure, the usher FimD is caught in the act of secreting its cognate adhesin FimH. Comparison with previous structures depicting the adhesin either first entering or having completely exited the usher pore reveals remarkable structural plasticity of the two-domain adhesin during translocation. Moreover, a piliation assay demonstrated that the structural plasticity, enabled by a flexible linker between the two domains, is a prerequisite for adhesin translocation through the usher pore and thus pilus biogenesis. Overall, this study provides molecular details of adhesin translocation across the outer membrane and elucidates a unique conformational state adopted by the adhesin during stepwise secretion through the usher pore. This study elucidates fundamental aspects of FimH and usher dynamics critical in urinary tract infections and is leading to antibiotic-sparing therapeutics.
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Affiliation(s)
- Ryan M. Bitter
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Maxwell I. Zimmerman
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO63110
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St Louis, MO63110
| | - Brock T. Summers
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO63110
| | - Jerome S. Pinkner
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO63110
- Center for Women’s Infectious Disease Research, Washington University in St Louis, St Louis, MO63110
| | - Karen W. Dodson
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO63110
- Center for Women’s Infectious Disease Research, Washington University in St Louis, St Louis, MO63110
| | - Scott J. Hultgren
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO63110
- Center for Women’s Infectious Disease Research, Washington University in St Louis, St Louis, MO63110
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO63110
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY10029
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2
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Zyla DS, Wiegand T, Bachmann P, Zdanowicz R, Giese C, Meier BH, Waksman G, Hospenthal MK, Glockshuber R. The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Nat Commun 2024; 15:3032. [PMID: 38589417 PMCID: PMC11001860 DOI: 10.1038/s41467-024-47212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
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Affiliation(s)
- Dawid S Zyla
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Paul Bachmann
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Manuela K Hospenthal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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3
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Giese C, Puorger C, Ignatov O, Bečárová Z, Weber ME, Schärer MA, Capitani G, Glockshuber R. Stochastic chain termination in bacterial pilus assembly. Nat Commun 2023; 14:7718. [PMID: 38001074 PMCID: PMC10673952 DOI: 10.1038/s41467-023-43449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Adhesive type 1 pili from uropathogenic Escherichia coli strains are filamentous, supramolecular protein complexes consisting of a short tip fibrillum and a long, helical rod formed by up to several thousand copies of the major pilus subunit FimA. Here, we reconstituted the entire type 1 pilus rod assembly reaction in vitro, using all constituent protein subunits in the presence of the assembly platform FimD, and identified the so-far uncharacterized subunit FimI as an irreversible assembly terminator. We provide a complete, quantitative model of pilus rod assembly kinetics based on the measured rate constants of FimD-catalyzed subunit incorporation. The model reliably predicts the length distribution of assembled pilus rods as a function of the ratio between FimI and the main pilus subunit FimA and is fully consistent with the length distribution of membrane-anchored pili assembled in vivo. The results show that the natural length distribution of adhesive pili formed via the chaperone-usher pathway results from a stochastic chain termination reaction. In addition, we demonstrate that FimI contributes to anchoring the pilus to the outer membrane and report the crystal structures of (i) FimI in complex with the assembly chaperone FimC, (ii) the FimI-FimC complex bound to the N-terminal domain of FimD, and (iii) a ternary complex between FimI, FimA and FimC that provides structural insights on pilus assembly termination and pilus anchoring by FimI.
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Affiliation(s)
- Christoph Giese
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.
| | - Chasper Puorger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
- Institute for Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland, 4132, Muttenz, Switzerland
| | - Oleksandr Ignatov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
- V.I. Grishchenko Clinic of Reproductive Medicine, Blahovishchenska st.25, 61052, Kharkiv, Ukraine
| | - Zuzana Bečárová
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Marco E Weber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Martin A Schärer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
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4
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Zhou Y, Zhou Z, Zheng L, Gong Z, Li Y, Jin Y, Huang Y, Chi M. Urinary Tract Infections Caused by Uropathogenic Escherichia coli: Mechanisms of Infection and Treatment Options. Int J Mol Sci 2023; 24:10537. [PMID: 37445714 DOI: 10.3390/ijms241310537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Urinary tract infections (UTIs) are common bacterial infections that represent a severe public health problem. They are often caused by Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumonia), Proteus mirabilis (P. mirabilis), Enterococcus faecalis (E. faecalis), and Staphylococcus saprophyticus (S. saprophyticus). Among these, uropathogenic E. coli (UPEC) are the most common causative agent in both uncomplicated and complicated UTIs. The adaptive evolution of UPEC has been observed in several ways, including changes in colonization, attachment, invasion, and intracellular replication to invade the urothelium and survive intracellularly. While antibiotic therapy has historically been very successful in controlling UTIs, high recurrence rates and increasing antimicrobial resistance among uropathogens threaten to greatly reduce the efficacy of these treatments. Furthermore, the gradual global emergence of multidrug-resistant UPEC has highlighted the need to further explore its pathogenesis and seek alternative therapeutic and preventative strategies. Therefore, a thorough understanding of the clinical status and pathogenesis of UTIs and the advantages and disadvantages of antibiotics as a conventional treatment option could spark a surge in the search for alternative treatment options, especially vaccines and medicinal plants. Such options targeting multiple pathogenic mechanisms of UPEC are expected to be a focus of UTI management in the future to help combat antibiotic resistance.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
- School of Pharmaceutical Sciences, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Zuying Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
- School of Pharmaceutical Sciences, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Lin Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
- School of Pharmaceutical Sciences, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Zipeng Gong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Yueting Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Yang Jin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Yong Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
- School of Pharmaceutical Sciences, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
| | - Mingyan Chi
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
- School of Pharmaceutical Sciences, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, China
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5
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Van Eyssen SR, Samarkina A, Isbilen O, Zeden MS, Volkan E. FimH and Type 1 Pili Mediated Tumor Cell Cytotoxicity by Uropathogenic Escherichia coli In Vitro. Pathogens 2023; 12:751. [PMID: 37375441 DOI: 10.3390/pathogens12060751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/20/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Uropathogenic Escherichia coli express hairlike proteinaceous surface projections, known as chaperone-usher pathway (CUP) pili. Type 1 pili are CUP pili with well-established pathogenic properties. The FimH adhesin subunit of type 1 pili plays a key role in the pathogenesis of urinary tract infections (UTIs) as it mediates the adhesion of the bacteria to urothelial cells of the bladder. In this study, two breast cancer cell lines, MDA-MB-231 and MCF-7, were used to demonstrate the cytotoxic activities of type 1 piliated uropathogenic E. coli UTI89 on breast cancer cells in a type 1 pili and FimH-mediated manner. E. coli were grown in static and shaking conditions to induce or inhibit optimal type 1 pili biogenesis, respectively. Deletion constructs of UTI89 ΔfimH and a complemented strain (UTI89 ΔfimH/pfimH) were further utilized to genetically assess the effect of type 1 pili and FimH on cancer cell viability. After incubation with the different strains, cytotoxicity was measured using trypan blue exclusion assays. UTI89 grown statically caused significant cytotoxicity in both breast cancer cell lines whereas cytotoxicity was reduced when the cells were incubated with bacteria grown under shaking conditions. The incubation of both MDA-MB-231 and MCF-7 with UTI89 Δfim operon or ΔfimH showed a significant reduction in cytotoxicity exerted by the bacterial strains, revealing that type 1 pili expression was necessary for cytotoxicity. Complementing the ΔfimH strain with pfimH reversed the phenotype, leading to a significant increase in cytotoxicity. Incubating type 1 pili expressing bacteria with the competitive FimH inhibitor D-mannose before cancer cell treatment also led to a significant reduction in cytotoxicity on both MDA-MB-231 and MCF-7 cancer cells, compared to vehicle control or D-mannose alone, indicating the requirement for functional FimH for cytotoxicity. Overall, our results reveal that, as opposed to UTI89 lacking type 1 pili, type 1 piliated UTI89 causes significant cancer cell mortality in a FimH-mediated manner, that is decreased with D-mannose.
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Affiliation(s)
- Shelly Roselyn Van Eyssen
- Biotechnology Research Center, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
| | - Anastasia Samarkina
- Biotechnology Research Center, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
| | - Ovgu Isbilen
- Biotechnology Research Center, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
- Department of Pharmacy, Faculty of Pharmacy, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
| | - Merve Suzan Zeden
- Biotechnology Research Center, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
- Department of Microbiology, School of Biological and Chemical Sciences, University of Galway, H91TK33 Galway, Ireland
| | - Ender Volkan
- Biotechnology Research Center, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
- Department of Pharmacy, Faculty of Pharmacy, Cyprus International University, Northern Cyprus, Mersin 10, 99258 Nicosia, Turkey
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6
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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7
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Nasi GI, Georgakopoulou KI, Theodoropoulou MK, Papandreou NC, Chrysina ED, Tsiolaki PL, Iconomidou VA. Bacterial Lectin FimH and Its Aggregation Hot-Spots: An Alternative Strategy against Uropathogenic Escherichia coli. Pharmaceutics 2023; 15:pharmaceutics15031018. [PMID: 36986878 PMCID: PMC10058141 DOI: 10.3390/pharmaceutics15031018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Type I fimbriae are the main adhesive organelles of uropathogenic Escherichia coli (UPEC), consisting of four different subunits. Their component with the most important role in establishing bacterial infections is the FimH adhesin located at the fimbrial tip. This two-domain protein mediates adhesion to host epithelial cells through interaction with terminal mannoses on epithelial glycoproteins. Here, we propose that the amyloidogenic potential of FimH can be exploited for the development of therapeutic agents against Urinary Tract Infections (UTIs). Aggregation-prone regions (APRs) were identified via computational methods, and peptide-analogues corresponding to FimH lectin domain APRs were chemically synthesized and studied with the aid of both biophysical experimental techniques and molecular dynamic simulations. Our findings indicate that these peptide-analogues offer a promising set of antimicrobial candidate molecules since they can either interfere with the folding process of FimH or compete for the mannose-binding pocket.
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Affiliation(s)
- Georgia I Nasi
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Konstantina I Georgakopoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Marilena K Theodoropoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Nikos C Papandreou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Paraskevi L Tsiolaki
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Vassiliki A Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
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8
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Pakharukova N, Malmi H, Tuittila M, Dahlberg T, Ghosal D, Chang YW, Myint SL, Paavilainen S, Knight SD, Lamminmäki U, Uhlin BE, Andersson M, Jensen G, Zavialov AV. Archaic chaperone-usher pili self-secrete into superelastic zigzag springs. Nature 2022; 609:335-340. [PMID: 35853476 PMCID: PMC9452303 DOI: 10.1038/s41586-022-05095-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria1-3. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Henri Malmi
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Minna Tuittila
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Tobias Dahlberg
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Si Lhyam Myint
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sari Paavilainen
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Stefan David Knight
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Bernt Eric Uhlin
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Magnus Andersson
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anton V Zavialov
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland.
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9
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Werneburg GT. Catheter-Associated Urinary Tract Infections: Current Challenges and Future Prospects. Res Rep Urol 2022; 14:109-133. [PMID: 35402319 PMCID: PMC8992741 DOI: 10.2147/rru.s273663] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/27/2022] [Indexed: 12/15/2022] Open
Abstract
Catheter-associated urinary tract infection (CAUTI) is the most common healthcare-associated infection and cause of secondary bloodstream infections. Despite many advances in diagnosis, prevention and treatment, CAUTI remains a severe healthcare burden, and antibiotic resistance rates are alarmingly high. In this review, current CAUTI management paradigms and challenges are discussed, followed by future prospects as they relate to the diagnosis, prevention, and treatment. Clinical and translational evidence will be evaluated, as will key basic science studies that underlie preventive and therapeutic approaches. Novel diagnostic strategies and treatment decision aids under development will decrease the time to diagnosis and improve antibiotic accuracy and stewardship. These include several classes of biomarkers often coupled with artificial intelligence algorithms, cell-free DNA, and others. New preventive strategies including catheter coatings and materials, vaccination, and bacterial interference are being developed and investigated. The antibiotic pipeline remains insufficient, and new strategies for the identification of new classes of antibiotics, and rational design of small molecule inhibitor alternatives, are under development for CAUTI treatment.
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Affiliation(s)
- Glenn T Werneburg
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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10
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Hermansen S, Linke D, Leo JC. Transmembrane β-barrel proteins of bacteria: From structure to function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:113-161. [PMID: 35034717 DOI: 10.1016/bs.apcsb.2021.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The outer membrane of Gram-negative bacteria is a specialized organelle conferring protection to the cell against various environmental stresses and resistance to many harmful compounds. The outer membrane has a number of unique features, including an asymmetric lipid bilayer, the presence of lipopolysaccharides and an individual proteome. The vast majority of the integral transmembrane proteins in the outer membrane belongs to the family of β-barrel proteins. These evolutionarily related proteins share a cylindrical, anti-parallel β-sheet core fold spanning the outer membrane. The loops and accessory domains attached to the β-barrel allow for a remarkable versatility in function for these proteins, ranging from diffusion pores and transporters to enzymes and adhesins. We summarize the current knowledge on β-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Antimicrobial resistance, Omics and Microbiota Group, Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom.
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11
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Garnett JA, Atherton J. Structure Determination of Microtubules and Pili: Past, Present, and Future Directions. Front Mol Biosci 2022; 8:830304. [PMID: 35096976 PMCID: PMC8795688 DOI: 10.3389/fmolb.2021.830304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 11/30/2022] Open
Abstract
Historically proteins that form highly polymeric and filamentous assemblies have been notoriously difficult to study using high resolution structural techniques. This has been due to several factors that include structural heterogeneity, their large molecular mass, and available yields. However, over the past decade we are now seeing a major shift towards atomic resolution insight and the study of more complex heterogenous samples and in situ/ex vivo examination of multi-subunit complexes. Although supported by developments in solid state nuclear magnetic resonance spectroscopy (ssNMR) and computational approaches, this has primarily been due to advances in cryogenic electron microscopy (cryo-EM). The study of eukaryotic microtubules and bacterial pili are good examples, and in this review, we will give an overview of the technical innovations that have enabled this transition and highlight the advancements that have been made for these two systems. Looking to the future we will also describe systems that remain difficult to study and where further technical breakthroughs are required.
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Affiliation(s)
- James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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12
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Du M, Yuan Z, Werneburg GT, Henderson NS, Chauhan H, Kovach A, Zhao G, Johl J, Li H, Thanassi DG. Processive dynamics of the usher assembly platform during uropathogenic Escherichia coli P pilus biogenesis. Nat Commun 2021; 12:5207. [PMID: 34471127 PMCID: PMC8410936 DOI: 10.1038/s41467-021-25522-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/12/2021] [Indexed: 11/25/2022] Open
Abstract
Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and pyelonephritis. P pili are assembled through the conserved chaperone-usher pathway. Much of the structural and functional understanding of the chaperone-usher pathway has been gained through investigations of type 1 pili, which promote binding to the bladder and cystitis. In contrast, the structural basis for P pilus biogenesis at the usher has remained elusive. This is in part due to the flexible and variable-length P pilus tip fiber, creating structural heterogeneity, and difficulties isolating stable P pilus assembly intermediates. Here, we circumvent these hindrances and determine cryo-electron microscopy structures of the activated PapC usher in the process of secreting two- and three-subunit P pilus assembly intermediates, revealing processive steps in P pilus biogenesis and capturing new conformational dynamics of the usher assembly machine. Escherichia coli form pili structures in order to initiate infection of the urinary tract. Here, Thanassi et al., have solved the structures of pili assembly intermediates and provided insights into their biogenesis and assembly.
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Affiliation(s)
- Minge Du
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Zuanning Yuan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Glenn T Werneburg
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY, USA.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nadine S Henderson
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY, USA
| | - Hemil Chauhan
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY, USA.,SUNY Downstate College of Medicine, Brooklyn, New York, NY, USA
| | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Gongpu Zhao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Jessica Johl
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - David G Thanassi
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, NY, USA. .,Center for Infectious Diseases, Stony Brook University, Stony Brook, New York, NY, USA.
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13
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Wang X, Peterson JH, Bernstein HD. Bacterial Outer Membrane Proteins Are Targeted to the Bam Complex by Two Parallel Mechanisms. mBio 2021; 12:e00597-21. [PMID: 33947759 PMCID: PMC8262991 DOI: 10.1128/mbio.00597-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/12/2021] [Indexed: 01/23/2023] Open
Abstract
Membrane proteins that are integrated into the outer membrane of Gram-negative bacteria typically contain a unique "β barrel" structure that serves as a membrane spanning segment. A conserved "β signal" motif is located at the C terminus of the β barrel of many outer membrane proteins (OMPs), but the function of this sequence is unclear. We found that mutations in the β signal slightly delayed the assembly of three model Escherichia coli OMPs by reducing their affinity for the barrel assembly machinery (Bam) complex, a heterooligomer that catalyzes β barrel insertion, and led to the degradation of a fraction of the protein in the periplasm. Interestingly, the absence of the periplasmic chaperone SurA amplified the effect of the mutations and caused the complete degradation of the mutant proteins. In contrast, the absence of another periplasmic chaperone (Skp) suppressed the effect of the mutations and considerably enhanced the efficiency of assembly. Our results reveal the existence of two parallel OMP targeting mechanisms that rely on a cis-acting peptide (the β signal) and a trans-acting factor (SurA), respectively. Our results also challenge the long-standing view that periplasmic chaperones are redundant and provide evidence that they have specialized functions.IMPORTANCE Proteins that are embedded in the outer membrane of Gram-negative bacteria (OMPs) play an important role in protecting the cell from harmful chemicals. OMPs share a common architecture and often contain a conserved sequence motif (β motif) of unknown function. Although OMPs are escorted to the outer membrane by proteins called chaperones, the exact function of the chaperones is also unclear. Here, we show that the β motif and the chaperone SurA both target OMPs to the β barrel insertion machinery in the outer membrane. In contrast, the chaperone Skp delivers unintegrated OMPs to protein degradation complexes. Our results challenge the long-standing view that chaperones are functionally redundant and strongly suggest that they have specialized roles in OMP targeting and quality control.
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Affiliation(s)
- Xu Wang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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14
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Dufrêne YF, Viljoen A, Mignolet J, Mathelié-Guinlet M. AFM in cellular and molecular microbiology. Cell Microbiol 2021; 23:e13324. [PMID: 33710716 DOI: 10.1111/cmi.13324] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
The unique capabilities of the atomic force microscope (AFM), including super-resolution imaging, piconewton force-sensitivity, nanomanipulation and ability to work under physiological conditions, have offered exciting avenues for cellular and molecular biology research. AFM imaging has helped unravel the fine architectures of microbial cell envelopes at the nanoscale, and how these are altered by antimicrobial treatment. Nanomechanical measurements have shed new light on the elasticity, tensile strength and turgor pressure of single cells. Single-molecule and single-cell force spectroscopy experiments have revealed the forces and dynamics of receptor-ligand interactions, the nanoscale distribution of receptors on the cell surface and the elasticity and adhesiveness of bacterial pili. Importantly, recent force spectroscopy studies have demonstrated that extremely stable bonds are formed between bacterial adhesins and their cognate ligands, originating from a catch bond behaviour allowing the pathogen to reinforce adhesion under shear or tensile stress. Here, we survey how the versatility of AFM has enabled addressing crucial questions in microbiology, with emphasis on bacterial pathogens. TAKE AWAYS: AFM topographic imaging unravels the ultrastructure of bacterial envelopes. Nanomechanical mapping shows what makes cell envelopes stiff and resistant to drugs. Force spectroscopy characterises the molecular forces in pathogen adhesion. Stretching pili reveals a wealth of mechanical and adhesive responses.
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Affiliation(s)
- Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Johann Mignolet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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15
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Damalanka VC, Maddirala AR, Janetka JW. Novel approaches to glycomimetic design: development of small molecular weight lectin antagonists. Expert Opin Drug Discov 2021; 16:513-536. [PMID: 33337918 DOI: 10.1080/17460441.2021.1857721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: The direct binding of carbohydrates or those presented on glycoproteins or glycolipids to proteins is the primary effector of many biological responses. One class of carbohydrate-binding proteins, lectins are important in all forms of life. Their functions in animals include regulating cell adhesion, glycoprotein synthesis, metabolism, and mediating immune system response while in bacteria and viruses a lectin-mediated carbohydrate-protein interaction between host cells and the pathogen initiates pathogenesis of the infection.Areas covered: In this review, the authors outline the structural and functional pathogenesis of lectins from bacteria, amoeba, and humans. Mimics of a carbohydrate are referred to as glycomimetics, which are much smaller in molecular weight and are devised to mimic the key binding interactions of the carbohydrate while also allowing additional contacts with the lectin. This article emphasizes the various approaches used over the past 10-15 years in the rational design of glycomimetic ligands.Expert opinion: Medicinal chemistry efforts enabled by X-ray structural biology have identified small-molecule glycomimetic lectin antagonists that have entered or are nearing clinical trials. A common theme in these strategies is the use of biaryl ring systems to emulate the carbohydrate interactions with the lectin.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - Amarendar Reddy Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
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16
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Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. PLoS Comput Biol 2021; 17:e1008551. [PMID: 33481784 PMCID: PMC7857587 DOI: 10.1371/journal.pcbi.1008551] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/03/2021] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software program to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein.DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - João M. Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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17
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He LH, Wang H, Liu Y, Kang M, Li T, Li CC, Tong AP, Zhu YB, Song YJ, Savarino SJ, Prouty MG, Xia D, Bao R. Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis. PLoS Pathog 2020; 16:e1008848. [PMID: 33007034 PMCID: PMC7531860 DOI: 10.1371/journal.ppat.1008848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 07/30/2020] [Indexed: 02/05/2023] Open
Abstract
Colonization factor CFA/I defines the major adhesive fimbriae of enterotoxigenic Escherichia coli and mediates bacterial attachment to host intestinal epithelial cells. The CFA/I fimbria consists of a tip-localized minor adhesive subunit, CfaE, and thousands of copies of the major subunit CfaB polymerized into an ordered helical rod. Biosynthesis of CFA/I fimbriae requires the assistance of the periplasmic chaperone CfaA and outer membrane usher CfaC. Although the CfaE subunit is proposed to initiate the assembly of CFA/I fimbriae, how it performs this function remains elusive. Here, we report the establishment of an in vitro assay for CFA/I fimbria assembly and show that stabilized CfaA-CfaB and CfaA-CfaE binary complexes together with CfaC are sufficient to drive fimbria formation. The presence of both CfaA-CfaE and CfaC accelerates fimbria formation, while the absence of either component leads to linearized CfaB polymers in vitro. We further report the crystal structure of the stabilized CfaA-CfaE complex, revealing features unique for biogenesis of Class 5 fimbriae.
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Affiliation(s)
- Li-hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wang
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Yang Liu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Mei Kang
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chang-cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ai-ping Tong
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ying-jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Stephen J. Savarino
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Michael G. Prouty
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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18
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Shoji M, Shibata S, Sueyoshi T, Naito M, Nakayama K. Biogenesis of Type V pili. Microbiol Immunol 2020; 64:643-656. [DOI: 10.1111/1348-0421.12838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Mikio Shoji
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Satoshi Shibata
- Molecular Cryo‐Electron Microscopy Unit Okinawa Institute of Science and Technology Graduate University Onna Okinawa Japan
| | - Takayuki Sueyoshi
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
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19
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Jiang W, Ubhayasekera W, Breed MC, Norsworthy AN, Serr N, Mobley HLT, Pearson MM, Knight SD. MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation. PLoS Pathog 2020; 16:e1008707. [PMID: 32780778 PMCID: PMC7444556 DOI: 10.1371/journal.ppat.1008707] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/21/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Proteus mirabilis, a Gram-negative uropathogen, is a major causative agent in catheter-associated urinary tract infections (CAUTI). Mannose-resistant Proteus-like fimbriae (MR/P) are crucially important for P. mirabilis infectivity and are required for biofilm formation and auto-aggregation, as well as for bladder and kidney colonization. Here, the X-ray crystal structure of the MR/P tip adhesin, MrpH, is reported. The structure has a fold not previously described and contains a transition metal center with Zn2+ coordinated by three conserved histidine residues and a ligand. Using biofilm assays, chelation, metal complementation, and site-directed mutagenesis of the three histidines, we show that an intact metal binding site occupied by zinc is essential for MR/P fimbria-mediated biofilm formation, and furthermore, that P. mirabilis biofilm formation is reversible in a zinc-dependent manner. Zinc is also required for MR/P-dependent agglutination of erythrocytes, and mutation of the metal binding site renders P. mirabilis unfit in a mouse model of UTI. The studies presented here provide important clues as to the mechanism of MR/P-mediated biofilm formation and serve as a starting point for identifying the physiological MR/P fimbrial receptor. Many bacteria use fimbriae to adhere to surfaces, and this function is often essential for pathogens to gain a foothold in the host. In this study, we examine the major virulence-associated fimbrial protein, MrpH, of the bacterial urinary tract pathogen Proteus mirabilis. This species is particularly known for causing catheter-associated urinary tract infections, in which it forms damaging urinary stones and crystalline biofilms that can block the flow of urine through indwelling catheters. MrpH resides at the tip of mannose-resistant Proteus-like (MR/P) fimbriae and is required for MR/P-dependent adherence to surfaces. Although MR/P belongs to a well-known class of adhesive fimbriae encoded by the chaperone-usher pathway, we found that MrpH has a dramatically different structure compared with other tip-located adhesins in this family. Unexpectedly, MrpH was found to bind a zinc cation, which we show is essential for MR/P-mediated biofilm formation and adherence to red blood cells. Furthermore, MR/P-mediated adherence can be modified by controlling zinc levels. These findings have the potential to aid development of better anti-biofilm urinary catheters or other methods to prevent P. mirabilis infection of the urinary tract.
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Affiliation(s)
- Wangshu Jiang
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Wimal Ubhayasekera
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Michael C. Breed
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Allison N. Norsworthy
- Department of Microbiology, New York University School of Medicine, New York, NY, United States of America
| | - Nina Serr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Melanie M. Pearson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
- * E-mail: (MMP); (SDK)
| | - Stefan D. Knight
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
- * E-mail: (MMP); (SDK)
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20
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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21
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The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire. Cell 2020; 181:665-673.e10. [PMID: 32289252 PMCID: PMC7198977 DOI: 10.1016/j.cell.2020.03.032] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/18/2019] [Accepted: 03/13/2020] [Indexed: 01/15/2023]
Abstract
A growing number of bacteria are recognized to conduct electrons across their cell envelope, and yet molecular details of the mechanisms supporting this process remain unknown. Here, we report the atomic structure of an outer membrane spanning protein complex, MtrAB, that is representative of a protein family known to transport electrons between the interior and exterior environments of phylogenetically and metabolically diverse microorganisms. The structure is revealed as a naturally insulated biomolecular wire possessing a 10-heme cytochrome, MtrA, insulated from the membrane lipidic environment by embedding within a 26 strand β-barrel formed by MtrB. MtrAB forms an intimate connection with an extracellular 10-heme cytochrome, MtrC, which presents its hemes across a large surface area for electrical contact with extracellular redox partners, including transition metals and electrodes. The 20 hemes of a 3-component complex are arranged to move electrons across 185 Å A β-barrel and 10-heme cytochrome form an insulated transmembrane nanowire An extracellular 10-heme cytochrome has a large surface area for electron exchange The hemes of both cytochromes are packed with a maximum inter-heme distance of 8 Å
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22
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Abstract
The translocation of proteins across membranes is a fundamental cellular function. Bacteria have evolved a striking array of pathways for delivering proteins into or across cytoplasmic membranes and, when present, outer membranes. Translocated proteins can form part of the membrane landscape, reside in the periplasmic space situated between the inner and outer membranes of Gram-negative bacteria, deposit on the cell surface, or be released to the extracellular milieu or injected directly into target cells. One protein translocation system, the general secretory pathway, is conserved in all domains of life. A second, the twin-arginine translocation pathway, is also phylogenetically distributed among most bacteria and plant chloroplasts. While all cell types have evolved additional systems dedicated to the translocation of protein cargoes, the number of such systems in bacteria is now known to exceed nine. These dedicated protein translocation systems, which include the types 1 through 9 secretion systems (T1SSs-T9SSs), the chaperone-usher pathway, and type IV pilus system, are the subject of this review. Most of these systems were originally identified and have been extensively characterized in Gram-negative or diderm (two-membrane) species. It is now known that several of these systems also have been adapted to function in Gram-positive or monoderm (single-membrane) species, and at least one pathway is found only in monoderms. This review briefly summarizes the distinctive mechanistic and structural features of each dedicated pathway, as well as the shared properties, that together account for the broad biological diversity of protein translocation in bacteria.
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Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St., Houston, TX, USA.
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23
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Magala P, Klevit RE, Thomas WE, Sokurenko EV, Stenkamp RE. RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain. Proteins 2019; 88:593-603. [PMID: 31622514 DOI: 10.1002/prot.25840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/07/2019] [Accepted: 10/12/2019] [Indexed: 01/14/2023]
Abstract
FimH is a bacterial adhesin protein located at the tip of Escherichia coli fimbria that functions to adhere bacteria to host cells. Thus, FimH is a critical factor in bacterial infections such as urinary tract infections and is of interest in drug development. It is also involved in vaccine development and as a model for understanding shear-enhanced catch bond cell adhesion. To date, over 60 structures have been deposited in the Protein Data Bank showing interactions between FimH and mannose ligands, potential inhibitors, and other fimbrial proteins. In addition to providing insights about ligand recognition and fimbrial assembly, these structures provide insights into conformational changes in the two domains of FimH that are critical for its function. To gain further insights into these structural changes, we have superposed FimH's mannose binding lectin domain in all these structures and categorized the structures into five groups of lectin domain conformers using RMSD as a metric. Many structures also include the pilin domain, which anchors FimH to the fimbriae and regulates the conformation and function of the lectin domain. For these structures, we have also compared the relative orientations of the two domains. These structural analyses enhance our understanding of the conformational changes associated with FimH ligand binding and domain-domain interactions, including its catch bond behavior through allosteric action of force in bacterial adhesion.
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Affiliation(s)
- Pearl Magala
- Department of Biochemistry, University of Washington, Seattle, WA.,Biomolecular Structure Center, University of Washington, Seattle, WA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA.,Biomolecular Structure Center, University of Washington, Seattle, WA
| | - Wendy E Thomas
- Department of Bioengineering, University of Washington, Seattle, WA
| | | | - Ronald E Stenkamp
- Department of Biochemistry, University of Washington, Seattle, WA.,Biomolecular Structure Center, University of Washington, Seattle, WA.,Department of Biological Structure, University of Washington, Seattle, WA
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24
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Psonis JJ, Chahales P, Henderson NS, Rigel NW, Hoffman PS, Thanassi DG. The small molecule nitazoxanide selectively disrupts BAM-mediated folding of the outer membrane usher protein. J Biol Chem 2019; 294:14357-14369. [PMID: 31391254 PMCID: PMC6768635 DOI: 10.1074/jbc.ra119.009616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial pathogens assemble adhesive surface structures termed pili or fimbriae to initiate and sustain infection of host tissues. Uropathogenic Escherichia coli, the primary causative agent of urinary tract infections, expresses type 1 and P pili required for colonization of the bladder and kidney, respectively. These pili are assembled by the conserved chaperone-usher (CU) pathway, in which a periplasmic chaperone works together with an outer membrane (OM) usher protein to build and secrete the pilus fiber. Previously, we found that the small molecule and antiparasitic drug nitazoxanide (NTZ) inhibits CU pathway-mediated pilus biogenesis in E. coli by specifically interfering with proper maturation of the usher protein in the OM. The usher is folded and inserted into the OM by the β-barrel assembly machine (BAM) complex, which in E. coli comprises five proteins, BamA-E. Here, we show that sensitivity of the usher to NTZ is modulated by BAM expression levels and requires the BamB and BamE lipoproteins. Furthermore, a genetic screen for NTZ-resistant bacterial mutants isolated a mutation in the essential BamD lipoprotein. These findings suggest that NTZ selectively interferes with an usher-specific arm of the BAM complex, revealing new details of the usher folding pathway and BAM complex function. Evaluation of a set of NTZ derivatives identified compounds with increased potency and disclosed that NTZ's nitrothiazole ring is critical for usher inhibition. In summary, our findings indicate highly specific effects of NTZ on the usher folding pathway and have uncovered NTZ analogs that specifically decrease usher levels in the OM.
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Affiliation(s)
- John J Psonis
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Peter Chahales
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Nadine S Henderson
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Nathan W Rigel
- Department of Biology, Hofstra University, Hempstead, New York 11549
| | - Paul S Hoffman
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia 22908
| | - David G Thanassi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
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25
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Zheng W, Andersson M, Mortezaei N, Bullitt E, Egelman E. Cryo-EM structure of the CFA/I pilus rod. IUCRJ 2019; 6:815-821. [PMID: 31576215 PMCID: PMC6760452 DOI: 10.1107/s2052252519007966] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/03/2019] [Indexed: 05/04/2023]
Abstract
Enterotoxigenic Escherichia coli (ETEC) are common agents of diarrhea for travelers and a major cause of mortality in children in developing countries. To attach to intestinal cells ETEC express colonization factors, among them CFA/I, which are the most prevalent factors and are the archetypical representative of class 5 pili. The helical quaternary structure of CFA/I can be unwound under tensile force and it has been shown that this mechanical property helps bacteria to withstand shear forces from fluid motion. We report in this work the CFA/I pilus structure at 4.3 Å resolution from electron cryomicroscopy (cryo-EM) data, and report details of the donor strand complementation. The CfaB pilins modeled into the cryo-EM map allow us to identify the buried surface area between subunits, and these regions are correlated to quaternary structural stability in class 5 and chaperone-usher pili. In addition, from the model built using the EM structure we also predicted that residue 13 (proline) of the N-terminal β-strand could have a major impact on the filament's structural stability. Therefore, we used optical tweezers to measure and compare the stability of the quaternary structure of wild type CFA/I and a point-mutated CFA/I with a propensity for unwinding. We found that pili with this mutated CFA/I require a lower force to unwind, supporting our hypothesis that Pro13 is important for structural stability. The high-resolution CFA/I pilus structure presented in this work and the analysis of structural stability will be useful for the development of novel antimicrobial drugs that target adhesion pili needed for initial attachment and sustained adhesion of ETEC.
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Affiliation(s)
- Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | | | | | - Esther Bullitt
- Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Edward Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
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26
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Abstract
The chaperone-usher (CU) pathway is a conserved secretion system dedicated to the assembly of a superfamily of virulence-associated surface structures by a wide range of Gram-negative bacteria. Pilus biogenesis by the CU pathway requires two specialized assembly components: a dedicated periplasmic chaperone and an integral outer membrane assembly and secretion platform termed the usher. The CU pathway assembles a variety of surface fibers, ranging from thin, flexible filaments to rigid, rod-like organelles. Pili typically act as adhesins and function as virulence factors that mediate contact with host cells and colonization of host tissues. Pilus-mediated adhesion is critical for early stages of infection, allowing bacteria to establish a foothold within the host. Pili are also involved in modulation of host cell signaling pathways, bacterial invasion into host cells, and biofilm formation. Pili are critical for initiating and sustaining infection and thus represent attractive targets for the development of antivirulence therapeutics. Such therapeutics offer a promising alternative to broad-spectrum antibiotics and provide a means to combat antibiotic resistance and treat infection while preserving the beneficial microbiota. A number of strategies have been taken to develop antipilus therapeutics, including vaccines against pilus proteins, competitive inhibitors of pilus-mediated adhesion, and small molecules that disrupt pilus biogenesis. Here we provide an overview of the function and assembly of CU pili and describe current efforts aimed at interfering with these critical virulence structures.
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27
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Hwang S, Öster C, Chevelkov V, Giller K, Lange S, Becker S, Lange A. Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:281-291. [PMID: 31028572 PMCID: PMC6692446 DOI: 10.1007/s10858-019-00247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural dynamics. Deuterium back-exchange at labile sites of the perdeuterated, fully proton back-exchanged pili was conducted to investigate hydrogen/deuterium (H/D) exchange patterns of backbone amide protons in pre-assembled pili. We found distinct H/D exchange patterns in lateral and axial intermolecular interfaces in pili. Amide protons protected from H/D exchange in pili are mainly located in the core region of the monomeric subunit and in the lateral intermolecular interface, whereas the axial intermolecular interface and the exterior region of pili are highly exposed to H/D exchange. Additionally, we performed molecular dynamics simulations of the type 1 pilus rod and estimated the probability of H/D exchange based on hydrogen bond dynamics. The comparison of the experimental observables and simulation data provides insights into stability and mechanical properties of pili.
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Affiliation(s)
- Songhwan Hwang
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Biologie, Humboldt-Universität Zu Berlin, Berlin, Germany.
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28
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FimH-based display of functional eukaryotic proteins on bacteria surfaces. Sci Rep 2019; 9:8410. [PMID: 31182802 PMCID: PMC6557881 DOI: 10.1038/s41598-019-44883-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023] Open
Abstract
The demand for recombinant proteins for analytic and therapeutic purposes is increasing; however, most currently used bacterial production systems accumulate the recombinant proteins in the intracellular space, which requires denaturating procedures for harvesting and functional testing. We here present a novel FimH-based expression system that enables display of fully functional eukaryotic proteins while preventing technical difficulties in translocating, folding, stabilizing and isolating the displayed proteins. As examples, Gaussia Luciferase (GLuc), epidermal growth factor (EGF), transforming growth factor-α (TGF-α) and epiregulin (EPRG) were expressed as FimH fusion proteins on the surface of E. coli bacteria. The fusion proteins were functionally active and could be released from the bacterial surface by specific proteolytic cleavage into the culture supernatant allowing harvesting of the produced proteins. EGFR ligands, produced as FimH fusion proteins and released by proteolytic cleavage, bound to the EGF receptor (EGFR) on cancer cells inducing EGFR phosphorylation. In another application of the technology, GLuc-FimH expressed on the surface of bacteria was used to track tumor-infiltrating bacteria by bioluminescence imaging upon application to mice, thereby visualizing the colonization of transplanted tumors. The examples indicate that the FimH-fusion protein technology can be used in various applications that require functionally active proteins to be displayed on bacterial surfaces or released into the culture supernatant.
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29
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Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs). Folia Microbiol (Praha) 2019; 65:45-65. [DOI: 10.1007/s12223-019-00719-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022]
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30
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Meuskens I, Saragliadis A, Leo JC, Linke D. Type V Secretion Systems: An Overview of Passenger Domain Functions. Front Microbiol 2019; 10:1163. [PMID: 31214135 PMCID: PMC6555100 DOI: 10.3389/fmicb.2019.01163] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteria secrete proteins for different purposes such as communication, virulence functions, adhesion to surfaces, nutrient acquisition, or growth inhibition of competing bacteria. For secretion of proteins, Gram-negative bacteria have evolved different secretion systems, classified as secretion systems I through IX to date. While some of these systems consist of multiple proteins building a complex spanning the cell envelope, the type V secretion system, the subject of this review, is rather minimal. Proteins of the Type V secretion system are often called autotransporters (ATs). In the simplest case, a type V secretion system consists of only one polypeptide chain with a β-barrel translocator domain in the membrane, and an extracellular passenger or effector region. Depending on the exact domain architecture of the protein, type V secretion systems can be further separated into sub-groups termed type Va through e, and possibly another recently identified subtype termed Vf. While this classification works well when it comes to the architecture of the proteins, this is not the case for the function(s) of the secreted passenger. In this review, we will give an overview of the functions of the passengers of the different AT classes, shedding more light on the variety of functions carried out by type V secretion systems.
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Affiliation(s)
| | | | | | - Dirk Linke
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
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31
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Tamadonfar KO, Omattage NS, Spaulding CN, Hultgren SJ. Reaching the End of the Line: Urinary Tract Infections. Microbiol Spectr 2019; 7:10.1128/microbiolspec.bai-0014-2019. [PMID: 31172909 PMCID: PMC11314827 DOI: 10.1128/microbiolspec.bai-0014-2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
Urinary tract infections (UTIs) cause a substantial health care burden. UTIs (i) are most often caused by uropathogenic Escherichia coli (UPEC), (ii) primarily affect otherwise healthy females (50% of women will have a UTI), (iii) are associated with significant morbidity and economic impact, (iv) can become chronic, and (v) are highly recurrent. A history of UTI is a significant risk factor for a recurrent UTI (rUTI). In otherwise healthy women, an acute UTI leads to a 25 to 50% chance of rUTI within months of the initial infection. Interestingly, rUTIs are commonly caused by the same strain of E. coli that led to the initial infection, arguing that there exist host-associated reservoirs, like the gastrointestinal tract and underlying bladder tissue, that can seed rUTIs. Additionally, catheter-associated UTIs (CAUTI), caused by Enterococcus and Staphylococcus as well as UPEC, represent a major health care concern. The host's response of depositing fibrinogen at the site of infection has been found to be critical to establishing CAUTI. The Drug Resistance Index, an evaluation of antibiotic resistance, indicates that UTIs have become increasingly difficult to treat since the mid-2000s. Thus, UTIs are a "canary in the coal mine," warning of the possibility of a return to the preantibiotic era, where some common infections are untreatable with available antibiotics. Numerous alternative strategies for both the prevention and treatment of UTIs are being pursued, with a focus on the development of vaccines and small-molecule inhibitors targeting virulence factors, in the hopes of reducing the burden of urogenital tract infections in an antibiotic-sparing manner.
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Affiliation(s)
- Kevin O Tamadonfar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Natalie S Omattage
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Caitlin N Spaulding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Harvard University School of Public Health, Boston, MA 02115
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University, School of Medicine, St. Louis, MO 63110
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32
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Liu Y, Sun C, Han L, Yu Y, Zhou H, Shao Q, Lou J, Zhao Y, Huang Y. Conformational Dynamics, Intramolecular Domain Conformation Signaling, and Activation of Apo-FimD Revealed by Single-Molecule Fluorescence Resonance Energy Transfer Studies. Biochemistry 2019; 58:1931-1941. [PMID: 30888187 DOI: 10.1021/acs.biochem.9b00080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chaperone-usher secretion pathway is a conserved bacterial protein secretion system dedicated to the biogenesis of adhesive fibers. Usher, a multidomain-containing outer membrane protein, plays a central role in this process by acting as a molecular machine that recruits different chaperone-subunit complexes, catalyzes subunit polymerization, and forms a channel for secretion of the assembled subunits. While recent crystal structural studies have greatly advanced our understanding of the structure and function of ushers, the overall architecture of the full-length apo-usher, the molecular events that dictate conformational changes in usher during pilus biogenesis, and its activation by the specific chaperone-adhesin complex remain largely elusive. Using single-molecule fluorescence resonance energy transfer studies, we found that the substrate-free usher FimD (apo-FimD) adopts a contracted conformation that is distinct from its substrate-bound states; both the N-terminal domain (NTD) and the C-terminal domain (CTD) of apo-FimD are highly dynamic, and FimD coordinates its domain conformational changes via intramolecular domain conformation signaling. By combining these studies with in vitro photo-cross-linking studies, we further show that only the chaperone-bound adhesin (FimC:FimH) can be transferred to the CTD, dislocates the plug domain, and triggers conformational changes in the remaining FimD domains. Taken together, these studies delineate an overall architecture of the full-length apo-FimD, provide detailed mechanic insight into the activation of apo-FimD, and explain why FimD could adjust its conformational states to perform multiple functions in each cycle of pilus subunit addition and ensure that pilus assembly proceeds progressively in a cellular energy-free environment.
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Affiliation(s)
- Yanqing Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100101 , China
| | - Chuanqi Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100101 , China
| | - Long Han
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100101 , China
| | - Yuqi Yu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China
| | - Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
| | - Jizhong Lou
- University of Chinese Academy of Sciences , Beijing 100101 , China.,Key Laboratory of RNA Biology, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Yongfang Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100101 , China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,University of Chinese Academy of Sciences , Beijing 100101 , China
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33
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Abstract
Type 1 and P pili are important virulence factors of uropathogenic Escherichia coli, the leading cause of urinary tract infections. In this issue of Structure, Hospenthal et al. (2017) describe a near-atomic resolution cryo-EM structure of the type 1 pilus rod, providing molecular insights into rod uncoiling in two pili.
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34
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Abstract
To interact with the external environments, bacteria often display long proteinaceous appendages on their cell surface, called pili or fimbriae. These non-flagellar thread-like structures are polymers composed of covalently or non-covalently interacting repeated pilin subunits. Distinct pilus classes can be identified on basis of their assembly pathways, including chaperone-usher pili, type V pili, type IV pili, curli and fap fibers, conjugative and type IV secretion pili, as well as sortase-mediated pili. Pili play versatile roles in bacterial physiology, and can be involved in adhesion and host cell invasion, DNA and protein secretion and uptake, biofilm formation, cell motility and more. Recent advances in structure determination of components involved in the various pilus systems has enabled a better molecular understanding of their mechanisms of assembly and function. In this chapter we describe the diversity in structure, biogenesis and function of the different pilus systems found in Gram-positive and Gram-negative bacteria, and review their potential as anti-microbial targets.
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Affiliation(s)
- Magdalena Lukaszczyk
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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35
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Hospenthal MK, Waksman G. The Remarkable Biomechanical Properties of the Type 1 Chaperone-Usher Pilus: A Structural and Molecular Perspective. Microbiol Spectr 2019; 7. [PMID: 30681068 DOI: 10.1128/microbiolspec.psib-0010-2018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Indexed: 01/02/2023] Open
Abstract
Chaperone-usher (CU) pili are long, supramolecular protein fibers tethered to the surface of numerous bacterial pathogens. These virulence factors function primarily in bacterial adhesion to host tissues, but they also mediate biofilm formation. Type 1 and P pili of uropathogenic Escherichia coli (UPEC) are the two best-studied CU pilus examples, and here we primarily focus on the former. UPEC can be transmitted to the urinary tract by fecal shedding. It can then ascend up the urinary tract and cause disease by invading and colonizing host tissues of the bladder, causing cystitis, and the kidneys, causing pyelonephritis. FimH is the subunit displayed at the tip of type 1 pili and mediates adhesion to mannosylated host cells via a unique catch-bond mechanism. In response to shear forces caused by urine flow, FimH can transition from a low-affinity to high-affinity binding mode. This clever allosteric mechanism allows UPEC cells to remain tightly attached during periods of urine flow, while loosening their grip to allow dissemination through the urinary tract during urine stasis. Moreover, the bulk of a CU pilus is made up of the rod, which can reversibly uncoil in response to urine flow to evenly spread the tensile forces over the entire pilus length. We here explore the novel structural and mechanistic findings relating to the type 1 pilus FimH catch-bond and rod uncoiling and explain how they function together to enable successful attachment, spread, and persistence in the hostile urinary tract.
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Affiliation(s)
- Manuela K Hospenthal
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 7HX, United Kingdom
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London WC1E 7HX, United Kingdom
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36
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Omattage NS, Deng Z, Pinkner JS, Dodson KW, Almqvist F, Yuan P, Hultgren SJ. Structural basis for usher activation and intramolecular subunit transfer in P pilus biogenesis in Escherichia coli. Nat Microbiol 2018; 3:1362-1368. [PMID: 30275511 PMCID: PMC6258349 DOI: 10.1038/s41564-018-0255-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022]
Abstract
Chaperone-usher pathway pili are extracellular proteinaceous fibres ubiquitously found on Gram-negative bacteria, and mediate host-pathogen interactions and biofilm formation critical in pathogenesis in numerous human diseases1. During pilus assembly, an outer membrane macromolecular machine called the usher catalyses pilus biogenesis from the individual subunits that are delivered as chaperone-subunit complexes in the periplasm. The usher orchestrates pilus assembly using all five functional domains: a 24-stranded transmembrane β-barrel translocation domain, a β-sandwich plug domain, an amino-terminal periplasmic domain and two carboxy-terminal periplasmic domains (CTD1 and CTD2)2-6. Despite extensive structural and functional characterization, the mechanism by which the usher is activated to initiate pilus biogenesis is unknown. Here, we present the crystal structure of the full-length PapC usher from Escherichia coli in complex with its cognate PapDG chaperone-subunit complex in a pre-activation state, elucidating molecular details of how the usher is specifically engaged by allosteric interactions with its substrate preceding activation and how the usher facilitates the transfer of subunits from the amino-terminal periplasmic domain to the CTDs during pilus assembly. This work elucidates the intricate workings of a molecular machine that catalyses chaperone-usher pathway pilus assembly and opens the door for the development of potent inhibitors to block pilus biogenesis.
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Affiliation(s)
- Natalie S Omattage
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA
| | - Jerome S Pinkner
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Center for Microbial Research, Umeå University, Umeå, Sweden
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.
- Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA.
- Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.
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Pakharukova N, McKenna S, Tuittila M, Paavilainen S, Malmi H, Xu Y, Parilova O, Matthews S, Zavialov AV. Archaic and alternative chaperones preserve pilin folding energy by providing incomplete structural information. J Biol Chem 2018; 293:17070-17080. [PMID: 30228191 DOI: 10.1074/jbc.ra118.004170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/14/2018] [Indexed: 11/06/2022] Open
Abstract
Adhesive pili are external component of fibrous adhesive organelles and help bacteria attach to biotic or abiotic surfaces. The biogenesis of adhesive pili via the chaperone-usher pathway (CUP) is independent of external energy sources. In the classical CUP, chaperones transport assembly-competent pilins in a folded but expanded conformation. During donor-strand exchange, pilins subsequently collapse, producing a tightly packed hydrophobic core and releasing the necessary free energy to drive fiber formation. Here, we show that pilus biogenesis in non-classical, archaic, and alternative CUPs uses a different source of conformational energy. High-resolution structures of the archaic Csu-pili system from Acinetobacter baumannii revealed that non-classical chaperones employ a short donor strand motif that is insufficient to fully complement the pilin fold. This results in chaperone-bound pilins being trapped in a substantially unfolded intermediate. The exchange of this short motif with the longer donor strand from adjacent pilin provides the full steric information essential for folding, and thereby induces a large unfolded-to-folded conformational transition to drive assembly. Our findings may inform the development of anti-adhesion drugs (pilicides) to combat bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sophie McKenna
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Minna Tuittila
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sari Paavilainen
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Henri Malmi
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Yingqi Xu
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Olena Parilova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Steve Matthews
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Anton V Zavialov
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
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38
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Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD. Nature 2018; 562:444-447. [PMID: 30283140 PMCID: PMC6309448 DOI: 10.1038/s41586-018-0587-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/15/2018] [Indexed: 12/19/2022]
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Mechanical architecture and folding of E. coli type 1 pilus domains. Nat Commun 2018; 9:2758. [PMID: 30013059 PMCID: PMC6048123 DOI: 10.1038/s41467-018-05107-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 05/03/2018] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent β-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains. The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.
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40
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Wheeler NE, Gardner PP, Barquist L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genet 2018; 14:e1007333. [PMID: 29738521 PMCID: PMC5940178 DOI: 10.1371/journal.pgen.1007333] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/24/2018] [Indexed: 11/18/2022] Open
Abstract
Emerging pathogens are a major threat to public health, however understanding how pathogens adapt to new niches remains a challenge. New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiological purposes. Here, we measure the burden of atypical mutations in protein coding genes across independently evolved Salmonella enterica lineages, and use these as input to train a random forest classifier to identify strains associated with extraintestinal disease. Members of the species fall along a continuum, from pathovars which cause gastrointestinal infection and low mortality, associated with a broad host-range, to those that cause invasive infection and high mortality, associated with a narrowed host range. Our random forest classifier learned to perfectly discriminate long-established gastrointestinal and invasive serovars of Salmonella. Additionally, it was able to discriminate recently emerged Salmonella Enteritidis and Typhimurium lineages associated with invasive disease in immunocompromised populations in sub-Saharan Africa, and within-host adaptation to invasive infection. We dissect the architecture of the model to identify the genes that were most informative of phenotype, revealing a common theme of degradation of metabolic pathways in extraintestinal lineages. This approach accurately identifies patterns of gene degradation and diversifying selection specific to invasive serovars that have been captured by more labour-intensive investigations, but can be readily scaled to larger analyses.
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Affiliation(s)
- Nicole E. Wheeler
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NEW); (LB)
| | - Paul P. Gardner
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Wuerzburg, Germany
- * E-mail: (NEW); (LB)
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41
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Abstract
Nosocomial infections and infections of indwelling devices are major healthcare problems worldwide. These infections are strongly associated with the ability of pathogens to form biofilms on biotic and abiotic surfaces. Panantibiotic-resistant Acinetobacter baumannii is one of the most troublesome pathogens, capable of colonizing medical devices by means of Csu pili, an adhesive organelle that belongs to the widespread class of archaic chaperone–usher pili. Here, we report an atomic-resolution insight into the mechanism of bacterial attachment to abiotic surfaces. We show that archaic pili use a binding mechanism that enables bacterial adhesion to structurally variable substrates. The results suggest a simple and cheap solution to reduce infections of A. baumannii and related pathogens. Acinetobacter baumannii—a leading cause of nosocomial infections—has a remarkable capacity to persist in hospital environments and medical devices due to its ability to form biofilms. Biofilm formation is mediated by Csu pili, assembled via the “archaic” chaperone–usher pathway. The X-ray structure of the CsuC-CsuE chaperone–adhesin preassembly complex reveals the basis for bacterial attachment to abiotic surfaces. CsuE exposes three hydrophobic finger-like loops at the tip of the pilus. Decreasing the hydrophobicity of these abolishes bacterial attachment, suggesting that archaic pili use tip-fingers to detect and bind to hydrophobic cavities in substrates. Antitip antibody completely blocks biofilm formation, presenting a means to prevent the spread of the pathogen. The use of hydrophilic materials instead of hydrophobic plastics in medical devices may represent another simple and cheap solution to reduce pathogen spread. Phylogenetic analysis suggests that the tip-fingers binding mechanism is shared by all archaic pili carrying two-domain adhesins. The use of flexible fingers instead of classical receptor-binding cavities is presumably more advantageous for attachment to structurally variable substrates, such as abiotic surfaces.
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42
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Werneburg GT, Thanassi DG. Pili Assembled by the Chaperone/Usher Pathway in Escherichia coli and Salmonella. EcoSal Plus 2018; 8:10.1128/ecosalplus.ESP-0007-2017. [PMID: 29536829 PMCID: PMC5940347 DOI: 10.1128/ecosalplus.esp-0007-2017] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 12/12/2022]
Abstract
Gram-negative bacteria assemble a variety of surface structures, including the hair-like organelles known as pili or fimbriae. Pili typically function in adhesion and mediate interactions with various surfaces, with other bacteria, and with other types of cells such as host cells. The chaperone/usher (CU) pathway assembles a widespread class of adhesive and virulence-associated pili. Pilus biogenesis by the CU pathway requires a dedicated periplasmic chaperone and integral outer membrane protein termed the usher, which forms a multifunctional assembly and secretion platform. This review addresses the molecular and biochemical aspects of the CU pathway in detail, focusing on the type 1 and P pili expressed by uropathogenic Escherichia coli as model systems. We provide an overview of representative CU pili expressed by E. coli and Salmonella, and conclude with a discussion of potential approaches to develop antivirulence therapeutics that interfere with pilus assembly or function.
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Affiliation(s)
- Glenn T. Werneburg
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
- Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
| | - David G. Thanassi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
- Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
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43
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Translocation through the Conjugative Type IV Secretion System Requires Unfolding of Its Protein Substrate. J Bacteriol 2018; 200:JB.00615-17. [PMID: 29311273 PMCID: PMC5826034 DOI: 10.1128/jb.00615-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Bacterial conjugation, a mechanism of horizontal gene transfer, is the major means by which antibiotic resistance spreads among bacteria (1, 2). Conjugative plasmids are transferred from one bacterium to another through a type IV secretion system (T4SS) in the form of single-stranded DNA covalently attached to a protein called relaxase. The relaxase is fully functional both in a donor cell (prior to conjugation) and recipient cell (after conjugation). Here, we demonstrate that the protein substrate has to unfold for efficient translocation through the conjugative T4SS. Furthermore, we present various relaxase modifications that preserve the function of the relaxase but block substrate translocation. This study brings us a step closer to deciphering the complete mechanism of T4SS substrate translocation, which is vital for the development of new therapies against multidrug-resistant pathogenic bacteria. IMPORTANCE Conjugation is the principal means by which antibiotic resistance genes spread from one bacterium to another (1, 2). During conjugation, a covalent complex of single-stranded DNA and a protein termed relaxase is transported by a type IV secretion system. To date, it is not known whether the relaxase requires unfolding prior to transport. In this report, we use functional assays to monitor the transport of wild-type relaxase and variants containing unfolding-resistant domains and show that these domains reduce conjugation and protein transport dramatically. Mutations that lower the free energy of unfolding in these domains do not block translocation and can even promote it. We thus conclude that the unfolding of the protein substrate is required during transport.
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44
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Abstract
Escherichia coli bacterial cells produce multiple types of adhesion pili that mediate cell-cell and cell-host attachments. These pili (also called 'fimbriae') are large biopolymers that are comprised of subunits assembled via a sophisticated micro-machinery into helix-like structures that are anchored in the bacterial outer membrane. They are commonly essential for initiation of disease and thus provide a potential target for antibacterial prevention and treatment. To develop new therapeutics for disease prevention and treatment we need to understand the molecular mechanisms and the direct role of adhesion pili during pathogenesis. These helix-like pilus structures possess fascinating and unique biomechanical properties that have been thoroughly investigated using high-resolution imaging techniques, force spectroscopy and fluid flow chambers. In this chapter, we first discuss the structure of pili and the micro-machinery responsible for the assembly process. Thereafter, we present methods for measurement of the biomechanics of adhesion pili, including optical tweezers. Data demonstrate unique biomechanical properties of pili that allow bacteria to sustain binding during in vivo fluid shear forces. We thereafter summarize the current biomechanical findings related to adhesion pili and show that pili biomechanical properties are niche-specific. That is, the data suggest that there is an organ-specific adaptation of pili that facilitates infection of the bacteria's target tissue. Thus, pilus biophysical properties are an important part of Escherichia coli pathogenesis, allowing bacteria to overcome hydrodynamic challenges in diverse environments.
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Affiliation(s)
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA.
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45
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Schiffrin B, Brockwell DJ, Radford SE. Outer membrane protein folding from an energy landscape perspective. BMC Biol 2017; 15:123. [PMID: 29268734 PMCID: PMC5740924 DOI: 10.1186/s12915-017-0464-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cell envelope is essential for the survival of Gram-negative bacteria. This specialised membrane is densely packed with outer membrane proteins (OMPs), which perform a variety of functions. How OMPs fold into this crowded environment remains an open question. Here, we review current knowledge about OMP folding mechanisms in vitro and discuss how the need to fold to a stable native state has shaped their folding energy landscapes. We also highlight the role of chaperones and the β-barrel assembly machinery (BAM) in assisting OMP folding in vivo and discuss proposed mechanisms by which this fascinating machinery may catalyse OMP folding.
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Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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46
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The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod. Structure 2017; 25:1829-1838.e4. [PMID: 29129382 PMCID: PMC5719983 DOI: 10.1016/j.str.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 12/19/2022]
Abstract
Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro.
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47
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Bamert RS, Lundquist K, Hwang H, Webb CT, Shiota T, Stubenrauch CJ, Belousoff MJ, Goode RJA, Schittenhelm RB, Zimmerman R, Jung M, Gumbart JC, Lithgow T. Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery. Mol Microbiol 2017; 106:142-156. [PMID: 28752534 DOI: 10.1111/mmi.13757] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
The assembly of proteins into bacterial outer membranes is a key cellular process that we are only beginning to understand, mediated by the β-barrel assembly machinery (BAM). Two crucial elements of that machinery are the core BAM complex and the translocation and assembly module (TAM), with each containing a member of the Omp85 superfamily of proteins: BamA in the BAM complex, TamA in the TAM. Here, we used the substrate protein FimD as a model to assess the selectivity of substrate interactions for the TAM relative to those of the BAM complex. A peptide scan revealed that TamA and BamA bind the β-strands of FimD, and do so selectively. Chemical cross-linking and molecular dynamics are consistent with this interaction taking place between the first and last strand of the TamA barrel domain, providing the first experimental evidence of a lateral gate in TamA: a structural element implicated in membrane protein assembly. We suggest that the lateral gates in TamA and BamA provide different environments for substrates to engage, with the differences observed here beginning to address how the TAM can be more effective than the BAM complex in the folding of some substrate proteins.
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Affiliation(s)
- Rebecca S Bamert
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chaille T Webb
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Takoya Shiota
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Christopher J Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Mathew J Belousoff
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Robert J A Goode
- Monash Biomedical Proteomics Facility, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Richard Zimmerman
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg 66421, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg 66421, Germany
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
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48
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Pakharukova N, Tuittila M, Paavilainen S, Zavialov A. Methylation, crystallization and SAD phasing of the Csu pilus CsuC-CsuE chaperone-adhesin subunit pre-assembly complex from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2017; 73:450-454. [PMID: 28777087 PMCID: PMC5544001 DOI: 10.1107/s2053230x17009566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/27/2017] [Indexed: 11/10/2022] Open
Abstract
Acinetobacter baumannii is one of the most difficult Gram-negative bacteria to control and treat. This pathogen forms biofilms on hospital surfaces and medical devices using Csu pili assembled via the archaic chaperone-usher pathway. To uncover the mechanism of bacterial attachment to abiotic surfaces, it was aimed to determine the crystal structure of the pilus tip adhesin CsuE. The CsuC-CsuE chaperone-subunit pre-assembly complex was purified from the periplasm of Escherichia coli overexpressing CsuC and CsuE. Despite the high purity of the complex, no crystals could be obtained. This challenge was solved by the methylation of lysine residues. The complex was crystallized in 0.1 M bis-tris pH 5.5, 17% PEG 3350 using the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.31 Å and belonged to the triclinic space group P1, with unit-cell parameters a = 53.84, b = 63.85, c = 89.25 Å, α = 74.65, β = 79.65, γ = 69.07°. Initial phases were derived from a single anomalous diffraction experiment using a selenomethionine derivative.
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Affiliation(s)
- Natalia Pakharukova
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Minna Tuittila
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Sari Paavilainen
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Anton Zavialov
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
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49
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Innovative Solutions to Sticky Situations: Antiadhesive Strategies for Treating Bacterial Infections. Microbiol Spectr 2017; 4. [PMID: 27227305 DOI: 10.1128/microbiolspec.vmbf-0023-2015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial adherence to host tissue is an essential process in pathogenesis, necessary for invasion and colonization and often required for the efficient delivery of toxins and other bacterial effectors. As existing treatment options for common bacterial infections dwindle, we find ourselves rapidly approaching a tipping point in our confrontation with antibiotic-resistant strains and in desperate need of new treatment options. Bacterial strains defective in adherence are typically avirulent and unable to cause infection in animal models. The importance of this initial binding event in the pathogenic cascade highlights its potential as a novel therapeutic target. This article seeks to highlight a variety of strategies being employed to treat and prevent infection by targeting the mechanisms of bacterial adhesion. Advancements in this area include the development of novel antivirulence therapies using small molecules, vaccines, and peptides to target a variety of bacterial infections. These therapies target bacterial adhesion through a number of mechanisms, including inhibition of pathogen receptor biogenesis, competition-based strategies with receptor and adhesin analogs, and the inhibition of binding through neutralizing antibodies. While this article is not an exhaustive description of every advancement in the field, we hope it will highlight several promising examples of the therapeutic potential of antiadhesive strategies.
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50
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Manteca A, Alonso-Caballero Á, Fertin M, Poly S, De Sancho D, Perez-Jimenez R. The influence of disulfide bonds on the mechanical stability of proteins is context dependent. J Biol Chem 2017. [PMID: 28642368 DOI: 10.1074/jbc.m117.784934] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces. For this purpose, we chose the pilus protein FimG from Gram-negative bacteria and a disulfide-bonded variant of the I91 human cardiac titin polyprotein. Our results show that disulfide bonds can alter the mechanical stability of proteins in different ways depending on the properties of the system. Specifically, disulfide-bonded FimG undergoes a 30% increase in its mechanical stability compared with its reduced counterpart, whereas the unfolding force of I91 domains experiences a decrease of 15% relative to the WT form. Using a coarse-grained simulation model, we rationalized that the increase in mechanical stability of FimG is due to a shift in the mechanical unfolding pathway. The simple topology-based explanation suggests a neutral effect in the case of titin. In summary, our results indicate that disulfide bonds in proteins act in a context-dependent manner rather than simply as mechanical lockers, underscoring the importance of considering disulfide bonds both computationally and experimentally when studying the mechanical properties of proteins.
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Affiliation(s)
- Aitor Manteca
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
| | | | - Marie Fertin
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
| | - Simon Poly
- the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany, and
| | - David De Sancho
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain, .,the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Raul Perez-Jimenez
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain, .,the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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