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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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2
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Meng R, Jiang M, Cui Z, Chang JY, Yang K, Jakana J, Yu X, Wang Z, Hu B, Zhang J. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat Commun 2019; 10:3130. [PMID: 31311931 PMCID: PMC6635492 DOI: 10.1038/s41467-019-11126-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
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Affiliation(s)
- Ran Meng
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
- Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xinzhe Yu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.
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3
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Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G, Li H. Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Cell 2008; 133:640-52. [PMID: 18485872 PMCID: PMC3036173 DOI: 10.1016/j.cell.2008.03.033] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/22/2008] [Accepted: 03/28/2008] [Indexed: 11/19/2022]
Abstract
Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the structural basis for pilus fiber assembly and secretion performed by the outer membrane assembly platform--the usher--is revealed by the crystal structure of the translocation domain of the P pilus usher PapC and single particle cryo-electron microscopy imaging of the FimD usher bound to a translocating type 1 pilus assembly intermediate. These structures provide molecular snapshots of a twinned-pore translocation machinery in action. Unexpectedly, only one pore is used for secretion, while both usher protomers are used for chaperone-subunit complex recruitment. The translocating pore itself comprises 24 beta strands and is occluded by a folded plug domain, likely gated by a conformationally constrained beta-hairpin. These structures capture the secretion of a virulence factor across the outer membrane of gram-negative bacteria.
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Affiliation(s)
- Han Remaut
- Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom
- These authors contributed equally to this work
| | - Chunyan Tang
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- These authors contributed equally to this work
| | - Nadine S. Henderson
- Center for Infectious Diseases, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794-5120, USA
| | - Jerome S. Pinkner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tao Wang
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Scott J. Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David G. Thanassi
- Center for Infectious Diseases, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794-5120, USA
| | - Gabriel Waksman
- Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom
| | - Huilin Li
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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Collins RF, Saleem M, Derrick JP. Purification and three-dimensional electron microscopy structure of the Neisseria meningitidis type IV pilus biogenesis protein PilG. J Bacteriol 2007; 189:6389-96. [PMID: 17616599 PMCID: PMC1951934 DOI: 10.1128/jb.00648-07] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 06/26/2007] [Indexed: 11/20/2022] Open
Abstract
Type IV pili are surface-exposed retractable fibers which play a key role in the pathogenesis of Neisseria meningitidis and other gram-negative pathogens. PilG is an integral inner membrane protein and a component of the type IV pilus biogenesis system. It is related by sequence to the extensive GspF family of secretory proteins, which are involved in type II secretion processes. PilG was overexpressed and purified from Escherichia coli membranes by detergent extraction and metal ion affinity chromatography. Analysis of the purified protein by perfluoro-octanoic acid polyacrylamide gel electrophoresis showed that PilG formed dimers and tetramers. A three-dimensional (3-D) electron microscopy structure of the PilG multimer was determined using single-particle averaging applied to samples visualized by negative staining. Symmetry analysis of the unsymmetrized 3-D volume provided further evidence that the PilG multimer is a tetramer. The reconstruction also revealed an asymmetric bilobed structure approximately 125 A in length and 80 A in width. The larger lobe within the structure was identified as the N terminus by location of Ni-nitrilotriacetic acid nanogold particles to the N-terminal polyhistidine tag. We propose that the smaller lobe corresponds to the periplasmic domain of the protein, with the narrower "waist" region being the transmembrane section. This constitutes the first report of a 3-D structure of a member of the GspF family and suggests a physical basis for the role of the protein in linking cytoplasmic and periplasmic protein components of the type II secretion and type IV pilus biogenesis systems.
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Affiliation(s)
- Richard F Collins
- Faculties of Life Sciences and Engineering/Physical Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, United Kingdom
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Kim K, Oh J, Han D, Kim EE, Lee B, Kim Y. Crystal structure of PilF: functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa. Biochem Biophys Res Commun 2005; 340:1028-38. [PMID: 16403447 DOI: 10.1016/j.bbrc.2005.12.108] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 12/15/2005] [Indexed: 11/23/2022]
Abstract
PilF is a requisite protein involved in the type 4 pilus biogenesis system from the Gram-negative human pathogenic bacteria, Pseudomonas aeruginosa. We determined the PilF structure at a 2.2A resolution; this includes six tandem tetratrico peptide repeat (TPR) units forming right-handed superhelix. PilF structure was similar to the heat shock protein organizing protein, which interacts with the C-terminal peptide of Hsp90 and Hsp70 via a concave Asn ladder in the inner groove of TPR superhelix. After simulated screening, the C-terminal pentapeptides of PilG, PilU, PilY, and PilZ proved to be a likely candidate binding to PilF, which are ones of 25 necessary components involved in the type 4 pilus biogenesis system. We proposed that PilF would be critical as a bridgehead in protein-protein interaction and thereby, PilF may bind a necessary molecule in type 4 pilus biogenesis system such as PilG, PilU, PilY, and PilZ.
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Affiliation(s)
- Kyunggon Kim
- Division of Molecular Genomic Medicine, College of Medicine, Seoul National University, Yongon-Dong, Seoul 110-799, Republic of Korea
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Collins RF, Frye SA, Kitmitto A, Ford RC, Tønjum T, Derrick JP. Structure of the Neisseria meningitidis Outer Membrane PilQ Secretin Complex at 12 Å Resolution. J Biol Chem 2004; 279:39750-6. [PMID: 15254043 DOI: 10.1074/jbc.m405971200] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial pathogen Neisseria meningitidis expresses long, thin, retractile fibers (called type IV pili) from its cell surface and uses these adhesive structures to mediate primary attachment to epithelial cells during host colonization and invasion. PilQ is an outer membrane protein complex that is essential for the translocation of these pili across the outer membrane. Here, we present the structure of the PilQ complex determined by cryoelectron microscopy to 12 A resolution. The dominant feature of the structure is a large central cavity, formed by four arm features that spiral upwards from a squared ring base and meet to form a prominent cap region. The cavity, running through the center of the complex, is continuous and is effectively sealed at both the top and bottom. Analysis of the complex using self-orientation and by examination of two-dimensional crystals indicates a strong C4 rotational symmetry, with a much weaker C12 rotational symmetry, consistent with PilQ possessing true C4 symmetry with C12 quasi-symmetry. We therefore suggest that the complex is a homododecamer, formed by association of 12 PilQ polypeptide chains into a tetramer of trimers. The structure of the PilQ complex, with its large and well defined central chamber, suggests that it may not function solely as a passive portal in the outer membrane, but could be actively involved in mediating pilus assembly or modification.
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Affiliation(s)
- Richard F Collins
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, United Kingdom
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Craig L, Taylor RK, Pique ME, Adair BD, Arvai AS, Singh M, Lloyd SJ, Shin DS, Getzoff ED, Yeager M, Forest KT, Tainer JA. Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell 2003; 11:1139-50. [PMID: 12769840 DOI: 10.1016/s1097-2765(03)00170-9] [Citation(s) in RCA: 238] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pilin assembly into type IV pili is required for virulence by bacterial pathogens that cause diseases such as cholera, pneumonia, gonorrhea, and meningitis. Crystal structures of soluble, N-terminally truncated pilin from Vibrio cholera toxin-coregulated pilus (TCP) and full-length PAK pilin from Pseudomonas aeruginosa reveal a novel TCP fold, yet a shared architecture for the type IV pilins. In each pilin subunit a conserved, extended, N-terminal alpha helix wrapped by beta strands anchors the structurally variable globular head. Inside the assembled pilus, characterized by cryo-electron microscopy and crystallography, the extended hydrophobic alpha helices make multisubunit contacts to provide mechanical strength and flexibility. Outside, distinct interactions of adaptable heads contribute surface variation for specificity of pilus function in antigenicity, motility, adhesion, and colony formation.
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Affiliation(s)
- Lisa Craig
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Collins RF, Ford RC, Kitmitto A, Olsen RO, Tønjum T, Derrick JP. Three-dimensional structure of the Neisseria meningitidis secretin PilQ determined from negative-stain transmission electron microscopy. J Bacteriol 2003; 185:2611-7. [PMID: 12670986 PMCID: PMC152620 DOI: 10.1128/jb.185.8.2611-2617.2003] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PilQ secretin from the pathogenic bacterium Neisseria meningitidis is an integral outer membrane protein complex which plays a crucial role in the biogenesis of type IV pili. We present here the first three-dimensional structure of this type of secretin at 2.5-nm resolution, obtained by single-particle averaging methods applied to the purified protein complex visualized in a negative stain. In projection, the PilQ complex is circular, with a donut-like appearance. When viewed from the side it has a rounded, conical profile. The complex was demonstrated to have 12-fold rotational symmetry, and this property was used to improve the quality of the density map by symmetry averaging. The dominant feature of the structure is a cavity, 10 nm deep, within the center of the molecule. The cavity is funnel-shaped in cross section, measures 6.5 nm in diameter at the top of the complex, and tapers to a closed point, effectively blocking formation of a continuous pore through the PilQ complex. These results suggest that the complex would have to undergo a conformational change in order to accommodate an assembled pilus fiber of diameter 6.5 nm running through the outer membrane.
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Affiliation(s)
- Richard F Collins
- Department of Biomolecular Sciences, UMIST, Manchester M60 1QD, United Kingdom
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Hahn E, Wild P, Hermanns U, Sebbel P, Glockshuber R, Häner M, Taschner N, Burkhard P, Aebi U, Müller SA. Exploring the 3D molecular architecture of Escherichia coli type 1 pili. J Mol Biol 2002; 323:845-57. [PMID: 12417198 DOI: 10.1016/s0022-2836(02)01005-7] [Citation(s) in RCA: 188] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An integrated approach combining information gained by Fourier transformation, linear Markham superposition (real space) and mass-per-length measurement by scanning transmission electron microscopy was used to analyze the helical structure of the rod-like type 1 pili expressed by uropathogenic Escherichia coli strain W3110. The 3D reconstruction calculated from the experimental data showed the pili to be 6.9nm wide, right-handed helical tubes with a 19.31(+/-0.34)nm long helical repeat comprising 27 FimA monomers associated head-to-tail in eight turns of the genetic one-start helix. Adjacent turns of the genetic helix are connected via three binding sites making the pilus rod rather stiff. In situ immuno-electron microscopy experiments showed the minor subunit (FimH) mediating pilus adhesion to bladder epithelial cells to be the distal protein of the pilus tip, which had a spring-like appearance at higher magnification. The subunits FimG and FimF connect FimH to the FimA rod, the sequential orientation being FimA-FimF-FimG-FimH. The electron density map calculated at 18A resolution from an atomic model of the pilus rod (built using the pilin domain FimH together with the G1 strand of FimC as a template for FimA and applying the optimal helical parameters determined to the head-to-tail interaction model for pilus assembly) was practically identical with that of the actual 3D reconstruction.
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MESH Headings
- Adhesins, Escherichia coli/chemistry
- Adhesins, Escherichia coli/ultrastructure
- Bacterial Adhesion
- Bacterial Proteins/chemistry
- Bacterial Proteins/ultrastructure
- Endopeptidases
- Escherichia coli/chemistry
- Escherichia coli/pathogenicity
- Escherichia coli/physiology
- Escherichia coli/ultrastructure
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/ultrastructure
- Fimbriae Proteins/chemistry
- Fimbriae Proteins/ultrastructure
- Fimbriae, Bacterial/chemistry
- Fimbriae, Bacterial/classification
- Fimbriae, Bacterial/ultrastructure
- Humans
- Image Processing, Computer-Assisted
- Macromolecular Substances
- Microscopy, Electron, Scanning Transmission
- Microscopy, Immunoelectron
- Models, Molecular
- Protein Subunits
- Virulence
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Affiliation(s)
- Erik Hahn
- Institute of Veterinary Anatomy, University of Zürich, Switzerland
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