1
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Farci D, Milenkovic S, Iesu L, Tanas M, Ceccarelli M, Piano D. Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans. J Biol Chem 2024; 300:105537. [PMID: 38072042 PMCID: PMC10828601 DOI: 10.1016/j.jbc.2023.105537] [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: 10/05/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024] Open
Abstract
The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
| | - Stefan Milenkovic
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Luca Iesu
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Marta Tanas
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
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2
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Hoff SE, Zinke M, Izadi-Pruneyre N, Bonomi M. Bonds and bytes: The odyssey of structural biology. Curr Opin Struct Biol 2024; 84:102746. [PMID: 38101027 DOI: 10.1016/j.sbi.2023.102746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of structural biology, no single method comprehensively reveals the behavior of biological systems across various spatiotemporal scales. Instead, we have a versatile toolkit of techniques, each contributing a piece to the overall puzzle. Integrative structural biology combines different techniques to create accurate and precise multi-scale models that expand our understanding of complex biological systems. This review outlines recent advancements in computational and experimental methods in structural biology, with special focus on recent Artificial Intelligence techniques, emphasizes integrative approaches that combine different types of data for precise spatiotemporal modeling, and provides an outlook into future directions of this field.
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Affiliation(s)
- S E Hoff
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
| | - M Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France. https://twitter.com/ZinkeMaximilian
| | - N Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
| | - M Bonomi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France.
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3
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Mom J, Chouikha I, Valette O, Pieulle L, Pelicic V. Systematic functional analysis of the Com pilus in Streptococcus sanguinis: a minimalistic type 4 filament dedicated to DNA uptake in monoderm bacteria. mBio 2024; 15:e0266723. [PMID: 38095871 PMCID: PMC10790768 DOI: 10.1128/mbio.02667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type 4 filaments (T4F) are nanomachines ubiquitous in prokaryotes, centered on filamentous polymers of type 4 pilins. T4F are exceptionally versatile and widespread virulence factors in bacterial pathogens. The mechanisms of filament assembly and the many functions they facilitate remain poorly understood because of the complexity of T4F machineries. This hinders the development of anti-T4F drugs. The significance of our research lies in characterizing the simplest known T4F-the Com pilus that mediates DNA uptake in competent monoderm bacteria-and showing that four protein components universally conserved in T4F are sufficient for filament assembly. The Com pilus becomes a model for elucidating the mechanisms of T4F assembly.
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Affiliation(s)
- Jeremy Mom
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Iman Chouikha
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laetitia Pieulle
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
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4
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de Amorim GC, Bardiaux B, Izadi-Pruneyre N. Structural Analysis of Proteins from Bacterial Secretion Systems and Their Assemblies by NMR Spectroscopy. Methods Mol Biol 2024; 2715:503-517. [PMID: 37930547 DOI: 10.1007/978-1-0716-3445-5_30] [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] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are built up from proteins with different physicochemical characteristics, such as highly hydrophobic transmembrane polypeptides, and soluble periplasmic or intracellular domains. A single complex can be composed of more than ten proteins with distinct features, spreading through different cellular compartments. The membrane and multicompartment nature of the proteins, and their large molecular weight make their study challenging. However, information on their structure and assemblies is required to understand their mechanisms and interfere with them. An alternative strategy is to work with soluble domains and peptides corresponding to the regions of interest of the proteins.Here, we describe a simple and fast protocol to evaluate the stability, folding, and interaction of protein sub-complexes by using solution-state Nuclear Magnetic Resonance (NMR) spectroscopy. This technique is widely used for protein structure and protein-ligand interaction analysis in solution.
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Affiliation(s)
- Gisele Cardoso de Amorim
- Núcleo Multidisciplinar de Pesquisa em Biologia, Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
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5
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Izadi-Pruneyre N, Karami Y, Nilges M. Structure and Dynamics of Type 4a Pili and Type 2 Secretion System Endopili. Subcell Biochem 2024; 104:549-563. [PMID: 38963500 DOI: 10.1007/978-3-031-58843-3_21] [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] [Indexed: 07/05/2024]
Abstract
Within the highly diverse type four filament (TFF or T4F) superfamily, the machineries of type IVa pili (T4aP) and the type 2 secretion system (T2SS) in diderm bacteria exhibit a substantial sequence similarity despite divergent functions and distinct appearances: T4aP can extend micrometers beyond the outer membrane, whereas the endopili in the T2SS are restricted to the periplasm. The determination of the structure of individual components and entire filaments is crucial to understand how their structure enables them to serve different functions. However, the dynamics of these filaments poses a challenge for their high-resolution structure determination. This review presents different approaches that have been used to study the structure and dynamics of T4aP and T2SS endopili by means of integrative structural biology, cryo-electron microscopy (cryo-EM), and molecular dynamics simulations. Their conserved features and differences are presented. The non-helical stretch in the long-conserved N-terminal helix which is characteristic of all members of the TFF and the impact of calcium on structure, function, and dynamics of these filaments are discussed in detail.
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Affiliation(s)
- Nadia Izadi-Pruneyre
- Bacterial Transmembrane Systems Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France
| | - Yasaman Karami
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France.
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6
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Anger R, Pieulle L, Shahin M, Valette O, Le Guenno H, Kosta A, Pelicic V, Fronzes R. Structure of a heteropolymeric type 4 pilus from a monoderm bacterium. Nat Commun 2023; 14:7143. [PMID: 37932265 PMCID: PMC10628169 DOI: 10.1038/s41467-023-42872-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
Type 4 pili (T4P) are important virulence factors, which belong to a superfamily of nanomachines ubiquitous in prokaryotes, called type 4 filaments (T4F). T4F are defined as helical polymers of type 4 pilins. Recent advances in cryo-electron microscopy (cryo-EM) led to structures of several T4F, revealing that the long N-terminal α-helix (α1) - the trademark of pilins - packs in the centre of the filaments to form a hydrophobic core. In diderm bacteria - all available bacterial T4F structures are from diderm species - a portion of α1 is melted (unfolded). Here we report that this architecture is conserved in phylogenetically distant monoderm species by determining the structure of Streptococcus sanguinis T4P. Our 3.7 Å resolution cryo-EM structure of S. sanguinis heteropolymeric T4P and the resulting full atomic model including all minor pilins highlight universal features of bacterial T4F and have widespread implications in understanding T4F biology.
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Affiliation(s)
- Robin Anger
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS (UMR 5234), Pessac, France
| | - Laetitia Pieulle
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS (UMR 7283), Marseille, France
| | - Meriam Shahin
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS (UMR 7283), Marseille, France
| | - Hugo Le Guenno
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, Marseille, France
| | - Artemis Kosta
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, Marseille, France
| | - Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS (UMR 7283), Marseille, France.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
| | - Rémi Fronzes
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS (UMR 5234), Pessac, France.
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7
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Barbat B, Douzi B, Ball G, Tribout M, El Karkouri K, Kellenberger C, Voulhoux R. Insights into dynamics and gating properties of T2SS secretins. SCIENCE ADVANCES 2023; 9:eadg6996. [PMID: 37792935 PMCID: PMC10550240 DOI: 10.1126/sciadv.adg6996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023]
Abstract
Secretins are outer membrane (OM) channels found in various bacterial nanomachines that secrete or assemble large extracellular structures. High-resolution 3D structures of type 2 secretion system (T2SS) secretins revealed bimodular channels with a C-module, holding a conserved central gate and an optional top gate, followed by an N-module for which multiple structural organizations have been proposed. Here, we perform a structure-driven in vivo study of the XcpD secretin, which validates one of the organizations of the N-module whose flexibility enables alternative conformations. We also show the existence of the central gate in vivo and its required flexibility, which is key for substrate passage and watertightness control. Last, functional, genomic, and phylogenetic analyses indicate that the optional top gate provides a gain of watertightness. Our data illustrate how the gating properties of T2SS secretins allow these large channels to overcome the duality between the necessity of preserving the OM impermeability while simultaneously promoting the secretion of large, folded effectors.
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Affiliation(s)
- Brice Barbat
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | - Badreddine Douzi
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
- Université de Lorraine, INRAE, DynAMic, Nancy, F-54000 France
| | - Geneviève Ball
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | - Mathilde Tribout
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | | | | | - Romé Voulhoux
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
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8
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Li Y, Santos-Moreno J, Francetic O. The periplasmic coiled coil formed by the assembly platform proteins PulL and PulM is critical for function of the Klebsiella type II secretion system. Res Microbiol 2023; 174:104075. [PMID: 37141929 DOI: 10.1016/j.resmic.2023.104075] [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: 09/28/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
Bacteria use type II secretion systems (T2SS) to secrete to their surface folded proteins that confer diverse functions, from nutrient acquisition to virulence. In the Klebsiella species, T2SS-mediated secretion of pullulanase (PulA) requires assembly of a dynamic filament called the endopilus. The inner membrane assembly platform (AP) subcomplex is essential for endopilus assembly and PulA secretion. AP components PulL and PulM interact with each other through their C-terminal globular domains and transmembrane segments. Here, we investigated the roles of their periplasmic helices, predicted to form a coiled coil, in assembly and function of the PulL-PulM complex. PulL and PulM variants lacking these periplasmic helices were defective for interaction in the bacterial two-hybrid (BACTH) assay. Their functions in PulA secretion and assembly of PulG subunits into endopilus filaments were strongly reduced. Interestingly, deleting the cytoplasmic peptide of PulM nearly abolished the function of variant PulMΔN and its interaction with PulG, but not with PulL, in the BACTH assay. Nevertheless, PulL was specifically proteolyzed in the presence of the PulMΔN variant, suggesting that PulM N-terminal peptide stabilizes PulL in the cytoplasm. We discuss the implications of these results for the T2S endopilus and type IV pilus assembly mechanisms.
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Affiliation(s)
- Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Javier Santos-Moreno
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
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9
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Treuner-Lange A, Zheng W, Viljoen A, Lindow S, Herfurth M, Dufrêne YF, Søgaard-Andersen L, Egelman EH. Large pilin subunits provide distinct structural and mechanical properties for the Myxococcus xanthus type IV pilus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550172. [PMID: 37503255 PMCID: PMC10370171 DOI: 10.1101/2023.07.22.550172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA of Myxococcus xanthus is unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in the M. xanthus PilA are due to a larger C-terminal domain. We solved the structure of the M. xanthus T4P (T4P Mx ) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4P Mx follows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4P Mx is significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4P Mx variants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions.
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10
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Wang F, Craig L, Liu X, Rensing C, Egelman EH. Microbial nanowires: type IV pili or cytochrome filaments? Trends Microbiol 2023; 31:384-392. [PMID: 36446702 PMCID: PMC10033339 DOI: 10.1016/j.tim.2022.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
A dynamic field of study has emerged involving long-range electron transport by extracellular filaments in anaerobic bacteria, with Geobacter sulfurreducens being used as a model system. The interest in this topic stems from the potential uses of such systems in bioremediation, energy generation, and new bio-based nanotechnology for electronic devices. These conductive extracellular filaments were originally thought, based upon low-resolution observations of dried samples, to be type IV pili (T4P). However, the recently published atomic structure for the T4P from G. sulfurreducens, obtained by cryo-electron microscopy (cryo-EM), is incompatible with the numerous models that have been put forward for electron conduction. As with all high-resolution structures of T4P, the G. sulfurreducens T4P structure shows a partial melting of the α-helix that substantially impacts the aromatic residue positions such that they are incompatible with conductivity. Furthermore, new work using high-resolution cryo-EM shows that conductive filaments thought to be T4P are actually polymerized cytochromes, with stacked heme groups forming a continuous conductive wire, or extracellular DNA. Recent atomic structures of three different cytochrome filaments from G. sulfurreducens suggest that such polymers evolved independently on multiple occasions. The expectation is that such polymerized cytochromes may be found emanating from other anaerobic organisms.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
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11
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Shaliutina-Loginova A, Francetic O, Doležal P. Bacterial Type II Secretion System and Its Mitochondrial Counterpart. mBio 2023; 14:e0314522. [PMID: 36971557 PMCID: PMC10128026 DOI: 10.1128/mbio.03145-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Over the billions of years that bacteria have been around, they have evolved several sophisticated protein secretion nanomachines to deliver toxins, hydrolytic enzymes, and effector proteins into their environments. Of these, the type II secretion system (T2SS) is used by Gram-negative bacteria to export a wide range of folded proteins from the periplasm across the outer membrane.
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12
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Pelicic V. Mechanism of assembly of type 4 filaments: everything you always wanted to know (but were afraid to ask). MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36947586 DOI: 10.1099/mic.0.001311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Type 4 filaments (T4F) are a superfamily of filamentous nanomachines - virtually ubiquitous in prokaryotes and functionally versatile - of which type 4 pili (T4P) are the defining member. T4F are polymers of type 4 pilins, assembled by conserved multi-protein machineries. They have long been an important topic for research because they are key virulence factors in numerous bacterial pathogens. Our poor understanding of the molecular mechanisms of T4F assembly is a serious hindrance to the design of anti-T4F therapeutics. This review attempts to shed light on the fundamental mechanistic principles at play in T4F assembly by focusing on similarities rather than differences between several (mostly bacterial) T4F. This holistic approach, complemented by the revolutionary ability of artificial intelligence to predict protein structures, led to an intriguing mechanistic model of T4F assembly.
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Affiliation(s)
- Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
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13
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Garnett JA. I shall be released: Assembly platform dynamics during type II secretion. Structure 2023; 31:123-125. [PMID: 36736296 DOI: 10.1016/j.str.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this issue of Structure, Dazzoni et al. solve the high-resolution homo- and hetero-dimeric structures of the Klebsiella oxytoca PulL and PulM C-terminal domains and unravel an uncharacterized dynamic interaction interface that is required for correct function of the type II secretion system.
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Affiliation(s)
- James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.
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14
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Dazzoni R, Li Y, López-Castilla A, Brier S, Mechaly A, Cordier F, Haouz A, Nilges M, Francetic O, Bardiaux B, Izadi-Pruneyre N. Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system. Structure 2023; 31:152-165.e7. [PMID: 36586404 DOI: 10.1016/j.str.2022.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022]
Abstract
Type II secretion systems (T2SSs) allow diderm bacteria to secrete hydrolytic enzymes, adhesins, or toxins important for growth and virulence. To promote secretion of folded proteins, T2SSs assemble periplasmic filaments called pseudopili or endopili at an inner membrane subcomplex, the assembly platform (AP). Here, we combined biophysical approaches, nuclear magnetic resonance (NMR) and X-ray crystallography, to study the Klebsiella AP components PulL and PulM. We determined the structure and associations of their periplasmic domains and describe the structure of the heterodimer formed by their ferredoxin-like domains. We show how structural complementarity and plasticity favor their association during the secretion process. Cysteine scanning and crosslinking data provided additional constraints to build a structural model of the PulL-PulM assembly in the cellular context. Our structural and functional insights, together with the relative cellular abundance of its components, support the role of AP as a dynamic hub that orchestrates pilus polymerization.
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Affiliation(s)
- Régine Dazzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Aracelys López-Castilla
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Sébastien Brier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Florence Cordier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Michael Nilges
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
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15
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Characterization of a glycan-binding complex of minor pilins completes the analysis of Streptococcus sanguinis type 4 pili subunits. Proc Natl Acad Sci U S A 2023; 120:e2216237120. [PMID: 36626560 PMCID: PMC9934059 DOI: 10.1073/pnas.2216237120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Type 4 filaments (T4F)-of which type 4 pili (T4P) are the archetype-are a superfamily of nanomachines nearly ubiquitous in prokaryotes. T4F are polymers of one major pilin, which also contain minor pilins whose roles are often poorly understood. Here, we complete the structure/function analysis of the full set of T4P pilins in the opportunistic bacterial pathogen Streptococcus sanguinis. We determined the structure of the minor pilin PilA, which is unexpectedly similar to one of the subunits of a tip-located complex of four minor pilins, widely conserved in T4F. We found that PilA interacts and dramatically stabilizes the minor pilin PilC. We determined the structure of PilC, showing that it is a modular pilin with a lectin module binding a subset of glycans prevalent in the human glycome, the host of S. sanguinis. Altogether, our findings support a model whereby the minor pilins in S. sanguinis T4P form a tip-located complex promoting adhesion to various host receptors. This has general implications for T4F.
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16
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Hughes-Games A, Davis SA, Hill DJ. Direct visualization of sequence-specific DNA binding by gonococcal type IV pili. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35920810 DOI: 10.1099/mic.0.001224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria gonorrhoeae, the causative agent of gonorrhoea, is a major burden on global healthcare systems, with an estimated ~80-90 million new global cases annually. This burden is exacerbated by increasing levels of antimicrobial resistance, which has greatly limited viable antimicrobial therapies. Decreasing gonococcal drug susceptibility has been driven largely by accumulation of chromosomal resistance determinants, which can be acquired through natural transformation, whereby DNA in the extracellular milieu is imported into cells and incorporated into the genome by homologous recombination. N. gonorrhoeae possesses a specialized system for DNA uptake, which strongly biases transformation in favour of DNA from closely related bacteria by recognizing a 10-12 bp DNA uptake sequence (DUS) motif, which is highly overrepresented in their chromosomal DNA. This process relies on numerous proteins, including the DUS-specific receptor ComP, which assemble retractile protein filaments termed type IV pili (T4P) extending from the cell surface, and one model for neisserial DNA uptake proposes that these filaments bind DNA in a DUS-dependent manner before retracting to transport DNA into the periplasm. However, conflicting evidence indicates that elongated pilus filaments may not have such a direct role in DNA binding uptake as this model suggests. Here, we quantitatively measured DNA binding to gonococcal T4P fibres by directly visualizing binding complexes with confocal fluorescence microscopy in order to confirm the sequence-specific, comP-dependent DNA binding capacity of elongated T4P fibres. This supports the idea that pilus filaments could be responsible for initially capturing DNA in the first step of sequence-specific DNA uptake.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK.,School of Chemistry, University of Bristol, Bristol, UK
| | - Sean A Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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17
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Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
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18
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Zareh MM, Mohamed SF, Elsheikh AM. Polymeric Electrochemical Sensor for Calcium Based on DNA. Polymers (Basel) 2022; 14:polym14091896. [PMID: 35567065 PMCID: PMC9104553 DOI: 10.3390/polym14091896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Plastic membranes containing deoxyribonucleic acid (DNA) as an electroactive material were acting as Ca2+ selective sensors. Diethyl phthalate (DEP), dioctyl Phthalate (DOP), or nitrophenyl octyl ether (NPOE) were used as plasticizers and polyvinyl chloride (PVC) was the membrane matrix. A sensor with a membrane composition of 120 mg PVC, 60 mg DOP plasticizer, and 2 mg DNA ionophore (DNA: DOP: PVC, 1.0:29.2:0.1 mole) was found to have the best performance. The slope of the calibration graph was 30 mV decade−1. The optimum pH range was 5.7–9.5 for 0.01 M Ca2+. The sensor response time was fast (2–3 s) with a long working period (up to 3 weeks). Excellent selectivity for Ca2+ was indicated by the values of selectivity coefficients for different selected interference. The sensor was used effectively for the estimation of calcium in real samples (fruits, calcium syrup, milk, and dairy products).
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19
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A noncanonical cytochrome c stimulates calcium binding by PilY1 for type IVa pili formation. Proc Natl Acad Sci U S A 2022; 119:2115061119. [PMID: 35121662 PMCID: PMC8833165 DOI: 10.1073/pnas.2115061119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 12/23/2022] Open
Abstract
Type IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many several other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets that are incompletely understood. Here, we report that minor pilins and PilY1 (PilY1.1) of cluster_1 form priming and tip complexes contingent on calcium and a noncanonical cytochrome c (TfcP) with an unusual His/Cys heme ligation. We provide evidence that TfcP is unlikely to participate in electron transport and instead stimulates calcium binding by PilY1.1 at low-calcium concentrations, thereby stabilizing PilY1.1 and enabling T4aP function in a broader range of calcium concentrations. These results not only identify a previously undescribed function of cytochromes c but also illustrate how incorporation of an accessory factor expands the environmental range under which the T4aP system functions.
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20
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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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21
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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22
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Major tail proteins of bacteriophages of the order Caudovirales. J Biol Chem 2021; 298:101472. [PMID: 34890646 PMCID: PMC8718954 DOI: 10.1016/j.jbc.2021.101472] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/18/2022] Open
Abstract
Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.
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23
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Karami Y, López-Castilla A, Ori A, Thomassin JL, Bardiaux B, Malliavin T, Izadi-Pruneyre N, Francetic O, Nilges M. Computational and biochemical analysis of type IV pilus dynamics and stability. Structure 2021; 29:1397-1409.e6. [PMID: 34520738 DOI: 10.1016/j.str.2021.07.008] [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: 04/13/2021] [Revised: 06/14/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022]
Abstract
Type IV pili (T4P) are distinctive dynamic filaments at the surface of many bacteria that can rapidly extend and retract and withstand strong forces. T4P are important virulence factors in many human pathogens, including Enterohemorrhagic Escherichia coli (EHEC). The structure of the EHEC T4P has been determined by integrating nuclear magnetic resonance (NMR) and cryo-electron microscopy data. To better understand pilus assembly, stability, and function, we performed a total of 108 ms all-atom molecular dynamics simulations of wild-type and mutant T4P. Extensive characterization of the conformational landscape of T4P in different conditions of temperature, pH, and ionic strength is complemented with targeted mutagenesis and biochemical analyses. Our simulations and NMR experiments reveal a conserved set of residues defining a calcium-binding site at the interface between three pilin subunits. Calcium binding enhances T4P stability ex vivo and in vitro, supporting the role of this binding site as a potential pocket for drug design.
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Affiliation(s)
- Yasaman Karami
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Aracelys López-Castilla
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Andrea Ori
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Jenny-Lee Thomassin
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Therese Malliavin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
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24
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Budowa i znaczenie II systemu sekrecji białek w ekologii i patogenezie Legionella pneumophila. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pałeczki Legionella pneumophila pasożytują w komórkach odległych filogenetycznie gospodarzy, w środowisku wodnym w pierwotniakach, a w organizmie człowieka w makrofagach alweolarnych. Zdolność tych bakterii do wewnątrzkomórkowego namnażania się w komórkach fagocytujących, wyspecjalizowanych do niszczenia mikroorganizmów, ma podstawowe znaczenie dla rozwoju nietypowego zapalenia płuc zwanego chorobą legionistów. Umiejscowione na kilku różnych loci chromosomu bakteryjnego geny II systemu sekrecji L. pneumophila kodują co najmniej 25 białek, w tym enzymy o aktywności lipolitycznej, proteolitycznej, rybonukleazy oraz białka unikalne bakterii Legionella. W środowisku naturalnym T2SS L. pneumophila odgrywa decydującą rolę w ekologii tych drobnoustrojów determinując ich zdolność do przeżycia zarówno w postaci planktonicznej, jak i w strukturach biofilmu w słodkowodnych zbiornikach o niskiej temperaturze. Białka T2SS umożliwiają L. pneumophila zakażenie różnych gatunków pierwotniaków, a substraty tego systemu określają zakres pierwotniaczego gospodarza. Namnażanie się bakterii w różnorodnych pierwotniakach przyczynia się do ich rozsiewania oraz transmisji do antropogenicznych źródeł. Białka wydzielane za pomocą II systemu sekrecji determinują również zdolność L. pneumophila do zakażania mysich makrofagów alweolarnych i szpiku kostnego, ludzkich makrofagów linii U937 i THP-1 oraz komórek nabłonkowych pęcherzyków płucnych. Enzymy wydzielane za pomocą tego systemu, takie jak: proteazy, aminopeptydazy czy fosfolipazy umożliwiają pozyskanie substancji pokarmowych oraz powodują destrukcję tkanki płucnej myszy. W organizmie człowieka białka T2SS przyczyniają się do osłabienia wrodzonej odpowiedzi immunologicznej na zakażenie L. pneumophila przez hamowanie indukcji prozapalnych cytokin (IL-6, TNF-α, IL-1 oraz IL-8).
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25
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Dazzoni R, López-Castilla A, Cordier F, Bardiaux B, Nilges M, Francetic O, Izadi-Pruneyre N. 1H, 15 N and 13C resonance assignments of the C-terminal domain of PulL, a component of the Klebsiella oxytoca type II secretion system. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:455-459. [PMID: 34410621 DOI: 10.1007/s12104-021-10045-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Type II secretion systems (T2SS) allow Gram-negative bacteria to transport toxins and enzymes from the periplasm to the external milieu, and are thus important for the pathogenicity of bacteria. To drive secretion, T2SS assemble filaments called pseudopili closely related to bacterial type IV pili. These filaments are non-covalent polymers of proteins that are assembled by an inner membrane complex called the assembly platform connected to a cytoplasmic ATPase motor. In the Klebsiella oxytoca T2SS, the PulL protein from the assembly platform is essential for pseudopilus assembly and protein secretion. However, its role in these processes is not well understood. To decipher the molecular basis of PulL function, we used solution NMR to study its structure and interactions with other components of the machinery. Here as a first step, we report the 1H, 15 N and 13C backbone and side-chain chemical shift assignments of the C-terminal periplasmic domain of PulL and its secondary structure based on NMR data.
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Affiliation(s)
- Régine Dazzoni
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France
| | - Aracelys López-Castilla
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France
| | - Florence Cordier
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France
- Biological NMR Technological Platform, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, 75724, Paris, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, 75724, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France.
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26
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Structure of Geobacter pili reveals secretory rather than nanowire behaviour. Nature 2021; 597:430-434. [PMID: 34471289 PMCID: PMC9127704 DOI: 10.1038/s41586-021-03857-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires1 is important in a range of globally important environmental phenomena2, as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein1. However, previous structural analyses have demonstrated that, during extracellular electron transfer, cells do not produce pili but rather nanowires made up of the cytochromes OmcS2,3 and OmcZ4. Here we show that Geobacter sulfurreducens binds PilA-N to PilA-C to assemble heterodimeric pili, which remain periplasmic under nanowire-producing conditions that require extracellular electron transfer5. Cryo-electron microscopy revealed that C-terminal residues of PilA-N stabilize its copolymerization with PilA-C (to form PilA-N-C) through electrostatic and hydrophobic interactions that position PilA-C along the outer surface of the filament. PilA-N-C filaments lack π-stacking of aromatic side chains and show a conductivity that is 20,000-fold lower than that of OmcZ nanowires. In contrast with surface-displayed type 4 pili, PilA-N-C filaments show structure, function and localization akin to those of type 2 secretion pseudopili6. The secretion of OmcS and OmcZ nanowires is lost when pilA-N is deleted and restored when PilA-N-C filaments are reconstituted. The substitution of pilA-N with the type 4 pili of other microorganisms also causes a loss of secretion of OmcZ nanowires. As all major phyla of prokaryotes use systems similar to type 4 pili, this nanowire translocation machinery may have a widespread effect in identifying the evolution and prevalence of diverse electron-transferring microorganisms and in determining nanowire assembly architecture for designing synthetic protein nanowires.
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27
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van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D. Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens. Diagnostics (Basel) 2021; 11:diagnostics11071259. [PMID: 34359341 PMCID: PMC8305138 DOI: 10.3390/diagnostics11071259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
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Affiliation(s)
- Alex van Belkum
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
- Correspondence: (A.v.B.); (D.L.)
| | | | - Benjamin Bardiaux
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Sarah V. Barrass
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Sarah J. Butcher
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Tuğçe Çaykara
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Rucha Datar
- BioMérieux, Microbiology R&D, 38390 La Balme Les Grottes, France;
| | | | - Adrian Goldman
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Manisha Goyal
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Theis Jacobsen
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Pirjo H. Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Andreas Kiessling
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Juan Leva Bueno
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Anchal Malik
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Paul A. Milner
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Michael Nilges
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Nicole Pamme
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Sally A. Peyman
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Pablo Rodriguez-Mateos
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Maria G. Sande
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Carla Joana Silva
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Aleksandra Cecylia Stasiak
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
- Correspondence: (A.v.B.); (D.L.)
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Structural interactions define assembly adapter function of a type II secretion system pseudopilin. Structure 2021; 29:1116-1127.e8. [PMID: 34139172 DOI: 10.1016/j.str.2021.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/15/2021] [Accepted: 05/28/2021] [Indexed: 01/13/2023]
Abstract
The type IV filament superfamily comprises widespread membrane-associated polymers in prokaryotes. The type II secretion system (T2SS), a virulence pathway in many pathogens, belongs to this superfamily. A knowledge gap in understanding of the T2SS is the molecular role of a small "pseudopilin" protein. Using multiple biophysical techniques, we have deciphered how this missing component of the Xcp T2SS architecture is structurally integrated, and thereby unlocked its function. We demonstrate that low-abundance XcpH is the adapter that bridges a trimeric initiating tip complex, XcpIJK, with a periplasmic filament of XcpG subunits. Each pseudopilin protein caps an XcpG protofilament in an overall pseudopilus compatible with dimensions of the periplasm and the outer membrane-spanning secretin through which substrates pass. Unexpectedly, to fulfill its adapter function, the XcpH N-terminal helix must be unwound, a property shared with XcpG subunits. We provide an experimentally validated three-dimensional structural model of a complete type IV filament.
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29
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Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun 2021; 12:2947. [PMID: 34011950 PMCID: PMC8134430 DOI: 10.1038/s41467-021-23046-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion. Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.
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Affiliation(s)
- Lenka Horváthová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tomáš Pánek
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Jan Pyrih
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alžběta Motyčková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Veronika Klápšťová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martina Vinopalová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lenka Marková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Luboš Voleman
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Markéta Petrů
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zuzana Vaitová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Čepička
- Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Klára Hryzáková
- Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague 2, Czech Republic
| | - Karel Harant
- Faculty of Science, Proteomic core facility, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Basel, Switzerland
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague 4, Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.
| | - Pavel Doležal
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic.
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30
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Lakshmi BA, Sangubotla R, Kim J, Ha HT, Kim S. Lanthanum mediated rutin yellow-fluorescent carbon dots as multifaceted sensing probes for the detection of calcium ions in melanoma and plant cells. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 120:111644. [DOI: 10.1016/j.msec.2020.111644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/08/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022]
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31
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Naskar S, Hohl M, Tassinari M, Low HH. The structure and mechanism of the bacterial type II secretion system. Mol Microbiol 2020; 115:412-424. [PMID: 33283907 DOI: 10.1111/mmi.14664] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Indexed: 12/17/2022]
Abstract
The type II secretion system (T2SS) is a multi-protein complex used by many bacteria to move substrates across their cell membrane. Substrates released into the environment serve as local and long-range effectors that promote nutrient acquisition, biofilm formation, and pathogenicity. In both animals and plants, the T2SS is increasingly recognized as a key driver of virulence. The T2SS spans the bacterial cell envelope and extrudes substrates through an outer membrane secretin channel using a pseudopilus. An inner membrane assembly platform and a cytoplasmic motor controls pseudopilus assembly. This microreview focuses on the structure and mechanism of the T2SS. Advances in cryo-electron microscopy are enabling increasingly elaborate sub-complexes to be resolved. However, key questions remain regarding the mechanism of pseudopilus extension and retraction, and how this is coupled with the choreography of the substrate moving through the secretion system. The T2SS is part of an ancient type IV filament superfamily that may have been present within the last universal common ancestor (LUCA). Overall, mechanistic principles that underlie T2SS function have implication for other closely related systems such as the type IV and tight adherence pilus systems.
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Affiliation(s)
- Souvik Naskar
- Department of Infectious Disease, Imperial College, London, UK
| | - Michael Hohl
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK
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32
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Secrete or perish: The role of secretion systems in Xanthomonas biology. Comput Struct Biotechnol J 2020; 19:279-302. [PMID: 33425257 PMCID: PMC7777525 DOI: 10.1016/j.csbj.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria of the Xanthomonas genus are mainly phytopathogens of a large variety of crops of economic importance worldwide. Xanthomonas spp. rely on an arsenal of protein effectors, toxins and adhesins to adapt to the environment, compete with other microorganisms and colonize plant hosts, often causing disease. These protein effectors are mainly delivered to their targets by the action of bacterial secretion systems, dedicated multiprotein complexes that translocate proteins to the extracellular environment or directly into eukaryotic and prokaryotic cells. Type I to type VI secretion systems have been identified in Xanthomonas genomes. Recent studies have unravelled the diverse roles played by the distinct types of secretion systems in adaptation and virulence in xanthomonads, unveiling new aspects of their biology. In addition, genome sequence information from a wide range of Xanthomonas species and pathovars have become available recently, uncovering a heterogeneous distribution of the distinct families of secretion systems within the genus. In this review, we describe the architecture and mode of action of bacterial type I to type VI secretion systems and the distribution and functions associated with these important nanoweapons within the Xanthomonas genus.
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33
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Sheppard D, Berry JL, Denise R, Rocha EPC, Matthews S, Pelicic V. The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold. J Biol Chem 2020; 295:6594-6604. [PMID: 32273343 PMCID: PMC7212644 DOI: 10.1074/jbc.ra120.013316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, Streptococcus sanguinis (ComGCSS) and Streptococcus pneumoniae (ComGCSP), revealing that this pilin displays extensive structural conservation. Strikingly, ComGCSS and ComGCSP exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.
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Affiliation(s)
- Devon Sheppard
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jamie-Lee Berry
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rémi Denise
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
- Sorbonne Université, Collège doctoral, Paris 75005, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
| | - Steve Matthews
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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34
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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries. Trends Microbiol 2020; 28:372-386. [DOI: 10.1016/j.tim.2020.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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35
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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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36
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Ghosal D, Kim KW, Zheng H, Kaplan M, Truchan HK, Lopez AE, McIntire IE, Vogel JP, Cianciotto NP, Jensen GJ. In vivo structure of the Legionella type II secretion system by electron cryotomography. Nat Microbiol 2019; 4:2101-2108. [PMID: 31754273 PMCID: PMC6879910 DOI: 10.1038/s41564-019-0603-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
Abstract
The type II secretion system (T2SS) is a multiprotein envelope-spanning assembly that translocates a wide range of virulence factors, enzymes and effectors through the outer membrane of many Gram-negative bacteria1-3. Here, using electron cryotomography and subtomogram averaging methods, we reveal the in vivo structure of an intact T2SS imaged within the human pathogen Legionella pneumophila. Although the T2SS has only limited sequence and component homology with the evolutionarily related type IV pilus (T4P) system4,5, we show that their overall architectures are remarkably similar. Despite similarities, there are also differences, including, for example, that the T2SS-ATPase complex is usually present but disengaged from the inner membrane, the T2SS has a much longer periplasmic vestibule and it has a short-lived flexible pseudopilus. Placing atomic models of the components into our electron cryotomography map produced a complete architectural model of the intact T2SS that provides insights into the structure and function of its components, its position within the cell envelope and the interactions between its different subcomplexes.
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Affiliation(s)
- Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ki Woo Kim
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- School of Ecology and Environmental System, Kyungpook National University, Sangju, Korea
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou City, Henan Province, China
| | - Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hilary K Truchan
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alberto E Lopez
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ian E McIntire
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, Pasadena, CA, USA.
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37
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Jacobsen T, Bardiaux B, Francetic O, Izadi-Pruneyre N, Nilges M. Structure and function of minor pilins of type IV pili. Med Microbiol Immunol 2019; 209:301-308. [PMID: 31784891 PMCID: PMC7248040 DOI: 10.1007/s00430-019-00642-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023]
Abstract
Type IV pili are versatile and highly flexible fibers formed on the surface of many Gram-negative and Gram-positive bacteria. Virulence and infection rate of several pathogenic bacteria, such as Neisseria meningitidis and Pseudomonas aeruginosa, are strongly dependent on the presence of pili as they facilitate the adhesion of the bacteria to the host cell. Disruption of the interactions between the pili and the host cells by targeting proteins involved in this interaction could, therefore, be a treatment strategy. A type IV pilus is primarily composed of multiple copies of protein subunits called major pilins. Additional proteins, called minor pilins, are present in lower abundance, but are essential for the assembly of the pilus or for its specific functions. One class of minor pilins is required to initiate the formation of pili, and may form a complex similar to that identified in the related type II secretion system. Other, species-specific minor pilins in the type IV pilus system have been shown to promote additional functions such as DNA binding, aggregation and adherence. Here, we will review the structure and the function of the minor pilins from type IV pili.
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Affiliation(s)
- Theis Jacobsen
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France.,Sorbonne Université, Complexité du Vivant, 75005, Paris, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France.
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38
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Chernyatina AA, Low HH. Core architecture of a bacterial type II secretion system. Nat Commun 2019; 10:5437. [PMID: 31780649 PMCID: PMC6882859 DOI: 10.1038/s41467-019-13301-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae. We show that 7 proteins form a ~2.4 MDa complex that spans the cell envelope. The outer membrane complex includes the secretin PulD, with all domains modelled, and the pilotin PulS. The inner membrane assembly platform components PulC, PulE, PulL, PulM and PulN have a relative stoichiometric ratio of 2:1:1:1:1. The PulE ATPase, PulL and PulM combine to form a flexible hexameric hub. Symmetry mismatch between the outer membrane complex and assembly platform is overcome by PulC linkers spanning the periplasm, with PulC HR domains binding independently at the secretin base. Our results show that the T2SS has a highly dynamic modular architecture, with implication for pseudo-pilus assembly and substrate loading.
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Affiliation(s)
| | - Harry H Low
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK.
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39
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Yue J, Li L, Cao L, Zan M, Yang D, Wang Z, Chang Z, Mei Q, Miao P, Dong WF. Two-Step Hydrothermal Preparation of Carbon Dots for Calcium Ion Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:44566-44572. [PMID: 31682396 DOI: 10.1021/acsami.9b13737] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
It is well known that the calcium ion is essential for maintaining life activities in living organisms, and it is of great significance to detect the intracellular calcium concentration. For the detection of calcium ions, we developed a new type of fluorescent carbon dots (CDs), whose surface was modified by ethylenebis(oxyethylenenitrilo)tetraacetic acid (EGTA) through a secondary hydrothermal method. This is a simple and convenient chemical preparation method because all reactions are carried out in the same autoclave, and the final product is directly the EGTA-modified CDs. The CDs exhibit bright blue fluorescence, and as the calcium concentration increases, the fluorescence intensity drops sharply. The fluorescence quenching correlates with the concentration of calcium ions and has a good linearity in the range of 15-300 μM with a detection limit of 0.38 μM. The experimental results confirmed that the detection of calcium ions by CDs is a static fluorescence quenching process. Also, cytotoxicity test and cellular imaging experiments have shown that the CDs are nontoxic and biocompatible.
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Affiliation(s)
- Juan Yue
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Li Li
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Lei Cao
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Minghui Zan
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Dian Yang
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Zheng Wang
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Zhimin Chang
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Qian Mei
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Peng Miao
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
| | - Wen-Fei Dong
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Science (CAS) , 88 Keling Road , Suzhou 215163 , Jiangsu , People's Republic of China
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Abstract
The type II secretion system (T2SS) delivers toxins and a range of hydrolytic enzymes, including proteases, lipases, and carbohydrate-active enzymes, to the cell surface or extracellular space of Gram-negative bacteria. Its contribution to survival of both extracellular and intracellular pathogens as well as environmental species of proteobacteria is evident. This dynamic, multicomponent machinery spans the entire cell envelope and consists of a cytoplasmic ATPase, several inner membrane proteins, a periplasmic pseudopilus, and a secretin pore embedded in the outer membrane. Despite the trans-envelope configuration of the T2S nanomachine, proteins to be secreted engage with the system first once they enter the periplasmic compartment via the Sec or TAT export system. Thus, the T2SS is specifically dedicated to their outer membrane translocation. The many sequence and structural similarities between the T2SS and type IV pili suggest a common origin and argue for a pilus-mediated mechanism of secretion. This minireview describes the structures, functions, and interactions of the individual T2SS components and the general architecture of the assembled T2SS machinery and briefly summarizes the transport and function of a growing list of T2SS exoproteins. Recent advances in cryo-electron microscopy, which have led to an increased understanding of the structure-function relationship of the secretin channel and the pseudopilus, are emphasized.
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41
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Bardiaux B, de Amorim GC, Luna Rico A, Zheng W, Guilvout I, Jollivet C, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O. Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus. Structure 2019; 27:1082-1093.e5. [PMID: 31056419 PMCID: PMC7003672 DOI: 10.1016/j.str.2019.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/18/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022]
Abstract
Bacterial type 4a pili are dynamic surface filaments that promote bacterial adherence, motility, and macromolecular transport. Their genes are highly conserved among enterobacteria and their expression in enterohemorrhagic Escherichia coli (EHEC) promotes adhesion to intestinal epithelia and pro-inflammatory signaling. To define the molecular basis of EHEC pilus assembly, we determined the structure of the periplasmic domain of its major subunit PpdD (PpdDp), a prototype of an enterobacterial pilin subfamily containing two disulfide bonds. The structure of PpdDp, determined by NMR, was then docked into the density envelope of purified EHEC pili obtained by cryoelectron microscopy (cryo-EM). Cryo-EM reconstruction of EHEC pili at ∼8 Å resolution revealed extremely high pilus flexibility correlating with a large extended region of the pilin stem. Systematic mutagenesis combined with functional and interaction analyses identified charged residues essential for pilus assembly. Structural information on exposed regions and interfaces between EHEC pilins is relevant for vaccine and drug discovery.
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Affiliation(s)
- Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Gisele Cardoso de Amorim
- NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Areli Luna Rico
- NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Camille Jollivet
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
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42
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Bardiaux B, Cordier F, Brier S, López-Castilla A, Izadi-Pruneyre N, Nilges M. Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches. JOURNAL OF BIOMOLECULAR NMR 2019; 73:293-303. [PMID: 31124002 PMCID: PMC6692295 DOI: 10.1007/s10858-019-00246-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Secretion pili, bacterial fibers responsible for transporting proteins to the extracellular milieu in some secretion systems, are very strong structures but at the same time highly flexible. Their flexibility and helical symmetry make structure determination at atomic resolution a challenging task. We have previously used an integrative structural biology approach including liquid-state NMR, cryo-electron microscopy (cryo-EM), and modeling to determine the pseudo-atomic resolution structure of the type 2 secretion system pseudopilus in a mutant form, where we employed NMR to determine the high resolution structure of the pilin (the monomer building block of the pilus). In this work, we determine the pseudo-atomic structure of the wild type pilus, and compare the dynamics of wild type and mutant pili by normal mode analysis. We present a detailed NMR analysis of the dynamics of the pilin in isolation, and compare dynamics and solvent accessibility of isolated and assembled pilins by Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS). These complementary approaches provide a comprehensive view of internal and overall dynamics of pili, crucial for their function.
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Affiliation(s)
- Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France
| | - Florence Cordier
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France
- Biological NMR Technological Platform, Center for Technological Resources and Research, Department of Structural Biology and Chemistry, Institut Pasteur; CNRS UMR3528, Paris, France
| | - Sébastien Brier
- Biological NMR Technological Platform, Center for Technological Resources and Research, Department of Structural Biology and Chemistry, Institut Pasteur; CNRS UMR3528, Paris, France
| | - Aracelys López-Castilla
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France.
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur; CNRS UMR3528; CNRS USR3756, Paris, France.
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43
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Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. An extensively glycosylated archaeal pilus survives extreme conditions. Nat Microbiol 2019; 4:1401-1410. [PMID: 31110358 PMCID: PMC6656605 DOI: 10.1038/s41564-019-0458-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/15/2019] [Indexed: 11/09/2022]
Abstract
Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 Å resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence-an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | | | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | | | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Nicholas Sherman
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - David Prangishvili
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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44
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Abstract
Microtubules are polymers of αβ-tubulin that play important roles in the cell. Regulation of their dynamics is critical for function and includes the posttranslational modification of tubulin. While most of tubulin modifications reside in the flexible C-terminal tail of tubulin, acetylation of α-tubulin on K40 is localized to the inside of the microtubule, within the so-called αK40 loop. Using high-resolution cryo-EM maps of acetylated and deacetylated microtubules, in conjunction with molecular-dynamics methods, we found that acetylation restricts the range of motion of the αK40 loop. In the deacetylated state, the loop extends deeper into the microtubule lumen and samples a greater number of conformations that we propose increase its accessibility to the acetylase and likely influence lateral contacts. Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.
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45
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Meshcheryakov VA, Shibata S, Schreiber MT, Villar-Briones A, Jarrell KF, Aizawa SI, Wolf M. High-resolution archaellum structure reveals a conserved metal-binding site. EMBO Rep 2019; 20:embr.201846340. [PMID: 30898768 PMCID: PMC6500986 DOI: 10.15252/embr.201846340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 02/16/2019] [Accepted: 02/27/2019] [Indexed: 01/09/2023] Open
Abstract
Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of Methanococcus archaella by X‐ray crystallography and cryo‐EM. The crystal structure of Methanocaldococcus jannaschii FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo‐EM reconstruction from Methanococcus maripaludis archaella at 4 Å resolution created with helical single‐particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N‐linked glycosylation by cryo‐EM and mass spectrometry. The crystal structure reveals a highly conserved metal‐binding site, which is validated by mass spectrometry and electron energy‐loss spectroscopy. We show in vitro that the metal‐binding site, which appears to be a widespread property of archaellin, is required for filament integrity.
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Affiliation(s)
- Vladimir A Meshcheryakov
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Makoto Tokoro Schreiber
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Kenneth F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
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46
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Berry JL, Gurung I, Anonsen JH, Spielman I, Harper E, Hall AMJ, Goosens VJ, Raynaud C, Koomey M, Biais N, Matthews S, Pelicic V. Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis. J Biol Chem 2019; 294:6796-6808. [PMID: 30837269 PMCID: PMC6497953 DOI: 10.1074/jbc.ra118.006917] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/27/2019] [Indexed: 11/06/2022] Open
Abstract
Type IV pili (Tfp) are functionally versatile filaments, widespread in prokaryotes, that belong to a large class of filamentous nanomachines known as type IV filaments (Tff). Although Tfp have been extensively studied in several Gram-negative pathogens where they function as key virulence factors, many aspects of their biology remain poorly understood. Here, we performed a global biochemical and structural analysis of Tfp in a recently emerged Gram-positive model, Streptococcus sanguinis In particular, we focused on the five pilins and pilin-like proteins involved in Tfp biology in S. sanguinis We found that the two major pilins, PilE1 and PilE2, (i) follow widely conserved principles for processing by the prepilin peptidase PilD and for assembly into filaments; (ii) display only one of the post-translational modifications frequently found in pilins, i.e. a methylated N terminus; (iii) are found in the same heteropolymeric filaments; and (iv) are not functionally equivalent. The 3D structure of PilE1, solved by NMR, revealed a classical pilin-fold with a highly unusual flexible C terminus. Intriguingly, PilE1 more closely resembles pseudopilins forming shorter Tff than bona fide Tfp-forming major pilins, underlining the evolutionary relatedness among different Tff. Finally, we show that S. sanguinis Tfp contain a low abundance of three additional proteins processed by PilD, the minor pilins PilA, PilB, and PilC. These findings provide the first global biochemical and structural picture of a Gram-positive Tfp and have fundamental implications for our understanding of a widespread class of filamentous nanomachines.
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Affiliation(s)
- Jamie-Lee Berry
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ishwori Gurung
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jan Haug Anonsen
- the Department of Biological Sciences, Proteomics and Mass Spectrometry Unit, University of Oslo, 0371 Oslo, Norway.,the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Ingrid Spielman
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Elliot Harper
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alexander M J Hall
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vivianne J Goosens
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire Raynaud
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael Koomey
- the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Nicolas Biais
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Steve Matthews
- the Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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47
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Luna Rico A, Zheng W, Petiot N, Egelman EH, Francetic O. Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli. Mol Microbiol 2019; 111:732-749. [PMID: 30561149 DOI: 10.1111/mmi.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 12/17/2022]
Abstract
Type 4a pili (T4aP) are long, thin and dynamic fibres displayed on the surface of diverse bacteria promoting adherence, motility and transport functions. Genomes of many Enterobacteriaceae contain conserved gene clusters encoding putative T4aP assembly systems. However, their expression has been observed only in few strains including Enterohaemorrhagic Escherichia coli (EHEC) and their inducers remain unknown. Here we used EHEC genomic DNA as a template to amplify and assemble an artificial operon composed of four gene clusters encoding 13 pilus assembly proteins. Controlled expressions of this operon in nonpathogenic E. coli strains led to efficient assembly of T4aP composed of the major pilin PpdD, as shown by shearing assays and immunofluorescence microscopy. When compared with PpdD pili assembled in a heterologous Klebsiella T2SS type 2 secretion system (T2SS) by using cryo-electron microscopy (cryoEM), these pili showed indistinguishable helical parameters, emphasizing that major pilins are the principal determinants of the fibre structure. Bacterial two-hybrid analysis identified several interactions of PpdD with T4aP assembly proteins, and with components of the T2SS that allow for heterologous fibre assembly. These studies lay ground for further characterization of the T4aP structure, function and biogenesis in enterobacteria.
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Affiliation(s)
- Areli Luna Rico
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France.,Structural Bioinformatics Unit and NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nathalie Petiot
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
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48
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Zhang Y, Faucher F, Zhang W, Wang S, Neville N, Poole K, Zheng J, Jia Z. Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa. PLoS Pathog 2018; 14:e1007343. [PMID: 30346996 PMCID: PMC6211770 DOI: 10.1371/journal.ppat.1007343] [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: 05/23/2018] [Revised: 11/01/2018] [Accepted: 09/19/2018] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa utilizes the Type II secretion system (T2SS) to translocate a wide range of large, structured protein virulence factors through the periplasm to the extracellular environment for infection. In the T2SS, five pseudopilins assemble into the pseudopilus that acts as a piston to extrude exoproteins out of cells. Through structure determination of the pseudopilin complexes of XcpVWX and XcpVW and function analysis, we have confirmed that two minor pseudopilins, XcpV and XcpW, constitute a core complex indispensable to the pseudopilus tip. The absence of either XcpV or -W resulted in the non-functional T2SS. Our small-angle X-ray scattering experiment for the first time revealed the architecture of the entire pseudopilus tip and established the working model. Based on the interaction interface of complexes, we have developed inhibitory peptides. The structure-based peptides not only disrupted of the XcpVW core complex and the entire pseudopilus tip in vitro but also inhibited the T2SS in vivo. More importantly, these peptides effectively reduced the virulence of P. aeruginosa towards Caenorhabditis elegans. The Type II secretion system has been characterized as an important virulence factor translocation machine that secrets various toxic proteins from the periplasm into the extracellular milieu used by a wide spectrum of Gram-negative bacteria. Through the characterization of the structure of the pseudopilus tip complex by protein crystallography and small-angle X-ray scattering, we have identified a critical interaction interface in the core binary complex formed by two minor pseudopilins, XcpV and–W, in Pseudomonas aeruginosa. Based on the interaction interface, two inhibitory peptides were developed, which showed potency of disrupting the entire pseudopilus tip complex and further inhibited the Type II secretion system. When applied to Caenorhabditis elegans, these peptides prevent the killing of worms by the P. aeruginosa. Our work has represented the first successful research on the inhibition of the Type II secretion system based on the structure of the pseudopilus tip complex.
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Affiliation(s)
- Yichen Zhang
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Frédérick Faucher
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Wenwen Zhang
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Shu Wang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Keith Poole
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
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49
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Rapisarda C, Tassinari M, Gubellini F, Fronzes R. Using Cryo-EM to Investigate Bacterial Secretion Systems. Annu Rev Microbiol 2018; 72:231-254. [PMID: 30004822 DOI: 10.1146/annurev-micro-090817-062702] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial secretion systems are responsible for releasing macromolecules to the extracellular milieu or directly into other cells. These membrane complexes are associated with pathogenicity and bacterial fitness. Understanding of these large assemblies has exponentially increased in the last few years thanks to electron microscopy. In fact, a revolution in this field has led to breakthroughs in characterizing the structures of secretion systems and other macromolecular machineries so as to obtain high-resolution images of complexes that could not be crystallized. In this review, we give a brief overview of structural advancements in the understanding of secretion systems, focusing in particular on cryo-electron microscopy, whether tomography or single-particle analysis. We describe how such techniques have contributed to knowledge of the mechanism of macromolecule secretion in bacteria and the impact they will have in the future.
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Affiliation(s)
- Chiara Rapisarda
- Structure et Fonction des Nanomachines Bactériennes, Institut Européen de Chimie et Biologie, 33607 Pessac, France; , .,CNRS UMR5234, Université de Bordeaux, 33076 Bordeaux, France
| | - Matteo Tassinari
- Institut Pasteur, Unité de Microbiologie Structurale, 75724 Paris, France; .,CNRS UMR3528, Institut Pasteur, 75015 Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Unité de Microbiologie Structurale, 75724 Paris, France; .,CNRS UMR3528, Institut Pasteur, 75015 Paris, France
| | - Rémi Fronzes
- Structure et Fonction des Nanomachines Bactériennes, Institut Européen de Chimie et Biologie, 33607 Pessac, France; , .,CNRS UMR5234, Université de Bordeaux, 33076 Bordeaux, France
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Li L, Ma X, Dong W, Miao P, Tang Y. Electrochemical Determination of Ca 2+ Based On Recycling Formation of Highly Selective DNAzyme and Gold Nanoparticle-Mediated Amplification. Bioconjug Chem 2018. [PMID: 29528621 DOI: 10.1021/acs.bioconjchem.8b00096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Calcium ion (Ca2+) plays a critical and indispensable role in many physiological and biochemical processes in the human body. In this report, we demonstrate a novel electrochemical method for the determination of the Ca2+ level aided by three functional DNA probes and gold nanoparticles (AuNPs). It affords high selectivity in sensing Ca2+ over other metal cations, which is due to the adoption of the DNAzyme at the electrode interface with exceptionally high binding ability. This method also integrates recycling formation of DNAzyme and AuNPs-mediated amplification; thus, high sensitivity is promised. Therefore, this work provides a favorable way to probe Ca2+ for biomedical applications.
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Affiliation(s)
- Li Li
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Xiaoyi Ma
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Wenfei Dong
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
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