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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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Dhindwal P, Boniecki MT, Moore SA. Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone. Protein Sci 2024; 33:e4882. [PMID: 38151822 PMCID: PMC10804663 DOI: 10.1002/pro.4882] [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: 07/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
In bacterial flagellum biogenesis, secretion of the hook-filament junction proteins FlgK and FlgL and completion of the flagellum requires the FlgN chaperone. Similarly, the related FliT chaperone is necessary for the secretion of the filament cap protein FliD and binds the flagellar export gate protein FlhA and the flagellum ATPase FliI. FlgN and FliT require FliJ for effective substrate secretion. In Helicobacter pylori, neither FlgN, FliT, nor FliJ have been annotated. We demonstrate that the genome location of HP1120 is identical to that of flgN in other flagellated bacteria and that HP1120 is the homolog of Campylobacter jejuni FlgN. A modeled HP1120 structure contains three α-helices and resembles the FliT chaperone, sharing a similar substrate-binding pocket. Using pulldowns and thermophoresis, we show that both HP1120 and a HP1120Δ126-144 deletion mutant bind to FlgK with nanomolar affinity, but not to the filament cap protein FliD, confirming that HP1120 is FlgN. Based on size-exclusion chromatography and multi-angle light scattering, H. pylori FlgN binds to FlgK with 1:1 stoichiometry. Overall structural similarities between FlgN and FliT suggest that substrate recognition on FlgN primarily involves an antiparallel coiled-coil interface between the third helix of FlgN and the C-terminal helix of the substrate. A FlgNΔ126-144 N100A, Y103A, S111I triple mutant targeting this interface significantly impairs the binding of FlgK. Finally, we demonstrate that FlgNΔ126-144 , like FliT, binds with sub-micromolar affinity to the flagellum ATPase FliI or its N-terminal domain. Hence FlgN and FliT likely couple delivery of low-abundance export substrates to the flagellum ATPase FliI.
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Affiliation(s)
- Poonam Dhindwal
- Department of Biochemistry, Microbiology and ImmunologyCollege of Medicine, University of SaskatchewanSaskatoonCanada
| | - Michal T. Boniecki
- Department of Biochemistry, Microbiology and ImmunologyCollege of Medicine, University of SaskatchewanSaskatoonCanada
| | - Stanley A. Moore
- Department of Biochemistry, Microbiology and ImmunologyCollege of Medicine, University of SaskatchewanSaskatoonCanada
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3
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Zilkenat S, Kim E, Dietsche T, Monjarás Feria JV, Torres-Vargas CE, Mebrhatu MT, Wagner S. Blue Native PAGE Analysis of Bacterial Secretion Complexes. Methods Mol Biol 2024; 2715:331-362. [PMID: 37930539 DOI: 10.1007/978-1-0716-3445-5_22] [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 protein secretion systems serve to translocate substrate proteins across up to three biological membranes, a task accomplished by hydrophobic, membrane-spanning macromolecular complexes. The overexpression, purification, and biochemical characterization of these complexes is often difficult, thus impeding progress in understading structure and function of these systems. Blue native (BN) polyacrylamide gel electrophoresis (PAGE) allows for the investigation of these transmembrane complexes right from their originating membranes, without the need of long preparative steps, and is amenable to the parallel characterization of a number of samples under near-native conditions. Here, we present protocols for sample preparation, one-dimensional BN PAGE and two-dimensional BN/SDS PAGE, as well as for downstream analysis by staining, immunoblotting, and mass spectrometry on the example of the type III secretion system encoded on Salmonella pathogenicity island 1.
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Affiliation(s)
- Susann Zilkenat
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Eunjin Kim
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Tobias Dietsche
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Julia V Monjarás Feria
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Claudia E Torres-Vargas
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Mehari Tesfazgi Mebrhatu
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), Partner-site Tübingen, Tübingen, Germany.
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany.
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4
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Minamino T, Kinoshita M. Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. EcoSal Plus 2023; 11:eesp00112023. [PMID: 37260402 PMCID: PMC10729930 DOI: 10.1128/ecosalplus.esp-0011-2023] [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: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 01/28/2024]
Abstract
Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of Salmonella enterica serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of Salmonella flagella.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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5
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Worrall LJ, Majewski DD, Strynadka NCJ. Structural Insights into Type III Secretion Systems of the Bacterial Flagellum and Injectisome. Annu Rev Microbiol 2023; 77:669-698. [PMID: 37713458 DOI: 10.1146/annurev-micro-032521-025503] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Two of the most fascinating bacterial nanomachines-the broadly disseminated rotary flagellum at the heart of cellular motility and the eukaryotic cell-puncturing injectisome essential to specific pathogenic species-utilize at their core a conserved export machinery called the type III secretion system (T3SS). The T3SS not only secretes the components that self-assemble into their extracellular appendages but also, in the case of the injectisome, subsequently directly translocates modulating effector proteins from the bacterial cell into the infected host. The injectisome is thought to have evolved from the flagellum as a minimal secretory system lacking motility, with the subsequent acquisition of additional components tailored to its specialized role in manipulating eukaryotic hosts for pathogenic advantage. Both nanomachines have long been the focus of intense interest, but advances in structural and functional understanding have taken a significant step forward since 2015, facilitated by the revolutionary advances in cryo-electron microscopy technologies. With several seminal structures of each nanomachine now captured, we review here the molecular similarities and differences that underlie their diverse functions.
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Affiliation(s)
- Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
| | - Dorothy D Majewski
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
- Current affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
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6
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Meir A, Macé K, Vegunta Y, Williams SM, Waksman G. Substrate recruitment mechanism by gram-negative type III, IV, and VI bacterial injectisomes. Trends Microbiol 2023; 31:916-932. [PMID: 37085348 DOI: 10.1016/j.tim.2023.03.005] [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: 10/28/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/23/2023]
Abstract
Bacteria use a wide arsenal of macromolecular substrates (DNA and proteins) to interact with or infect prokaryotic and eukaryotic cells. To do so, they utilize substrate-injecting secretion systems or injectisomes. However, prior to secretion, substrates must be recruited to specialized recruitment platforms and then handed over to the secretion apparatus for secretion. In this review, we provide an update on recent advances in substrate recruitment and delivery by gram-negative bacterial recruitment platforms associated with Type III, IV, and VI secretion systems.
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Affiliation(s)
- Amit Meir
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Current address: MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK.
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Yogesh Vegunta
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Sunanda M Williams
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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7
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Hu G, Wang Y, Blake C, Nordgaard M, Liu X, Wang B, Kovács ÁT. Parallel genetic adaptation of Bacillus subtilis to different plant species. Microb Genom 2023; 9:mgen001064. [PMID: 37466402 PMCID: PMC10438812 DOI: 10.1099/mgen.0.001064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Plant growth-promoting rhizobacteria benefit plants by stimulating their growth or protecting them against phytopathogens. Rhizobacteria must colonize and persist on plant roots to exert their benefits. However, little is known regarding the processes by which rhizobacteria adapt to different plant species, or behave under alternating host plant regimes. Here, we used experimental evolution and whole-population whole-genome sequencing to analyse how Bacillus subtilis evolves on Arabidopsis thaliana and tomato seedlings, and under an alternating host plant regime, in a static hydroponic setup. We observed parallel evolution across multiple levels of biological organization in all conditions, which was greatest for the two heterogeneous, multi-resource, spatially structured environments at the genetic level. Species-specific adaptation at the genetic level was also observed, possibly caused by the selection stress imposed by different host plants. Furthermore, a trade-off between motility and biofilm development was supported by mutational changes in motility- and biofilm-related genes. Finally, we identified several condition-specific and common targeted genes in different environments by comparing three different B. subtilis biofilm adaptation settings. The results demonstrate a common evolutionary pattern when B. subtilis is adapting to the plant rhizosphere in similar conditions, and reveal differences in genetic mechanisms between different host plants. These findings will likely support strain improvements for sustainable agriculture.
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Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Xin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Bo Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Shenzhen, 518083 Shenzhen, PR China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333BE Leiden, Netherlands
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8
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Flacht L, Lunelli M, Kaszuba K, Chen ZA, Reilly FJO, Rappsilber J, Kosinski J, Kolbe M. Integrative structural analysis of the type III secretion system needle complex from Shigella flexneri. Protein Sci 2023; 32:e4595. [PMID: 36790757 PMCID: PMC10019453 DOI: 10.1002/pro.4595] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
The type III secretion system (T3SS) is a large, transmembrane protein machinery used by various pathogenic gram-negative bacteria to transport virulence factors into the host cell during infection. Understanding the structure of T3SSs is crucial for future developments of therapeutics that could target this system. However, much of the knowledge about the structure of T3SS is available only for Salmonella, and it is unclear how this large assembly is conserved across species. Here, we combined cryo-electron microscopy, cross-linking mass spectrometry, and integrative modeling to determine the structure of the T3SS needle complex from Shigella flexneri. We show that the Shigella T3SS exhibits unique features distinguishing it from other structurally characterized T3SSs. The secretin pore complex adopts a new fold of its C-terminal S domain and the pilotin MxiM[SctG] locates around the outer surface of the pore. The export apparatus structure exhibits a conserved pseudohelical arrangement but includes the N-terminal domain of the SpaS[SctU] subunit, which was not present in any of the previously published virulence-related T3SS structures. Similar to other T3SSs, however, the apparatus is anchored within the needle complex by a network of flexible linkers that either adjust conformation to connect to equivalent patches on the secretin oligomer or bind distinct surface patches at the same height of the export apparatus. The conserved and unique features delineated by our analysis highlight the necessity to analyze T3SS in a species-specific manner, in order to fully understand the underlying molecular mechanisms of these systems. The structure of the type III secretion system from Shigella flexneri delineates conserved and unique features, which could be used for the development of broad-range therapeutics.
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Affiliation(s)
- Lara Flacht
- Department for Structural Infection BiologyCenter for Structural Systems Biology (CSSB) & Helmholtz Centre for Infection Research (HZI)HamburgGermany
- Dynamics of Viral Structures, Leibniz Institute for Virology (LIV)HamburgGermany
| | - Michele Lunelli
- Department for Structural Infection BiologyCenter for Structural Systems Biology (CSSB) & Helmholtz Centre for Infection Research (HZI)HamburgGermany
| | - Karol Kaszuba
- Department for Structural Infection BiologyCenter for Structural Systems Biology (CSSB) & Helmholtz Centre for Infection Research (HZI)HamburgGermany
- Centre for Structural Systems Biology (CSSB) & European Molecular Biology Laboratory (EMBL)HamburgGermany
| | - Zhuo Angel Chen
- Technische Universität Berlin, Institute of Biotechnology, Chair of BioanalyticsBerlinGermany
| | - Francis J. O'. Reilly
- Technische Universität Berlin, Institute of Biotechnology, Chair of BioanalyticsBerlinGermany
| | - Juri Rappsilber
- Technische Universität Berlin, Institute of Biotechnology, Chair of BioanalyticsBerlinGermany
- University of Edinburgh, Wellcome Centre for Cell BiologyEdinburghUK
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB) & European Molecular Biology Laboratory (EMBL)HamburgGermany
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Michael Kolbe
- Department for Structural Infection BiologyCenter for Structural Systems Biology (CSSB) & Helmholtz Centre for Infection Research (HZI)HamburgGermany
- MIN‐FacultyUniversity HamburgHamburgGermany
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9
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Kinoshita M, Namba K, Minamino T. Purification of the Transmembrane Polypeptide Channel Complex of the Salmonella Flagellar Type III Secretion System. Methods Mol Biol 2023; 2646:3-15. [PMID: 36842101 DOI: 10.1007/978-1-0716-3060-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Many motile bacteria employ the flagellar type III secretion system (fT3SS) to build the flagellum on the cell surface. The fT3SS consists of a transmembrane export gate complex, which acts as a proton/protein antiporter that couples proton flow with flagellar protein export, and a cytoplasmic ATPase ring complex, which works as an activator of the export gate complex. Three transmembrane proteins, FliP, FliQ, and FliR, form a core structure of the export gate complex, and this core complex serves as a polypeptide channel that allows flagellar structural subunits to be translocated across the cytoplasmic membrane. Here, we describe the methods for overproduction, solubilization, and purification of the Salmonella FliP/FliQ/FliR complex.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.
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10
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Lloyd CJ, Klose KE. The Vibrio Polar Flagellum: Structure and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:77-97. [PMID: 36792872 DOI: 10.1007/978-3-031-22997-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Here we discuss the structure and regulation of the Vibrio flagellum and its role in the virulence of pathogenic species. We will cover some of the novel insights into the structure of this nanomachine that have recently been enabled by cryoelectron tomography. We will also highlight the recent genetic studies that have increased our understanding in flagellar synthesis specifically at the bacterial cell pole, temporal regulation of flagellar genes, and how the flagellum enables directional motility through Run-Reverse-Flick cycles.
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Affiliation(s)
- Cameron J Lloyd
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA.,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA
| | - Karl E Klose
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA. .,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA.
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11
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Chen P, Goldberg MB. Recent insights into type-3 secretion system injectisome structure and mechanism of human enteric pathogens. Curr Opin Microbiol 2023; 71:102232. [PMID: 36368294 PMCID: PMC10510281 DOI: 10.1016/j.mib.2022.102232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
Type-3 secretion system injectisomes are multiprotein complexes that translocate bacterial effector proteins from the cytoplasm of gram-negative bacteria directly into the cytosol of eukaryotic host cells. These systems are present in more than 30 bacterial species, including numerous human, animal, and plant pathogens. We review recent discoveries of structural and molecular mechanisms of effector protein translocation through the injectisomes and recent advances in the understanding of mechanisms of activation of effector protein secretion.
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Affiliation(s)
- Poyin Chen
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Marcia B Goldberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Broad Institute, Cambridge, MA, USA.
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12
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Minamino T, Kinoshita M, Morimoto YV, Namba K. Activation mechanism of the bacterial flagellar dual-fuel protein export engine. Biophys Physicobiol 2022; 19:e190046. [PMID: 36567733 PMCID: PMC9751260 DOI: 10.2142/biophysico.bppb-v19.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022] Open
Abstract
Bacteria employ the flagellar type III secretion system (fT3SS) to construct flagellum, which acts as a supramolecular motility machine. The fT3SS of Salmonella enterica serovar Typhimurium is composed of a transmembrane export gate complex and a cytoplasmic ATPase ring complex. The transmembrane export gate complex is fueled by proton motive force across the cytoplasmic membrane and is divided into four distinct functional parts: a dual-fuel export engine; a polypeptide channel; a membrane voltage sensor; and a docking platform. ATP hydrolysis by the cytoplasmic ATPase complex converts the export gate complex into a highly efficient proton (H+)/protein antiporter that couples inward-directed H+ flow with outward-directed protein export. When the ATPase ring complex does not work well in a given environment, the export gate complex will remain inactive. However, when the electric potential difference, which is defined as membrane voltage, rises above a certain threshold value, the export gate complex becomes an active H+/protein antiporter to a considerable degree, suggesting that the export gate complex has a voltage-gated activation mechanism. Furthermore, the export gate complex also has a sodium ion (Na+) channel to couple Na+ influx with flagellar protein export. In this article, we review our current understanding of the activation mechanism of the dual-fuel protein export engine of the fT3SS. This review article is an extended version of a Japanese article, Membrane voltage-dependent activation of the transmembrane export gate complex in the bacterial flagellar type III secretion system, published in SEIBUTSU BUTSURI Vol. 62, p165-169 (2022).
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Affiliation(s)
- Tohru Minamino
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miki Kinoshita
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yusuke V. Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Namba
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan,RIKEN SPring-8 Center, Suita, Osaka 565-0871, Japan,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka 565-0871, Japan
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13
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Hotinger JA, Gallagher AH, May AE. Phage-Related Ribosomal Proteases (Prps): Discovery, Bioinformatics, and Structural Analysis. Antibiotics (Basel) 2022; 11:antibiotics11081109. [PMID: 36009978 PMCID: PMC9405229 DOI: 10.3390/antibiotics11081109] [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: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Many new antimicrobials are analogs of existing drugs, sharing the same targets and mechanisms of action. New antibiotic targets are critically needed to combat the growing threat of antimicrobial-resistant bacteria. Phage-related ribosomal proteases (Prps) are a recently structurally characterized antibiotic target found in pathogens such as Staphylococcus aureus, Clostridioides difficile, and Streptococcus pneumoniae. These bacteria encode an N-terminal extension on their ribosomal protein L27 that is not present in other bacteria. The cleavage of this N-terminal extension from L27 by Prp is necessary to create a functional ribosome. Thus, Prp inhibition may serve as an alternative to direct binding and inhibition of the ribosome. This bioinformatic and structural analysis covers the discovery, function, and structural characteristics of known Prps. This information will be helpful in future endeavors to design selective therapeutics targeting the Prps of important pathogens.
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14
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Qu D, Jiang M, Duffin C, Hughes KT, Chevance FFV. Targeting early proximal-rod component substrate FlgB to FlhB for flagellar-type III secretion in Salmonella. PLoS Genet 2022; 18:e1010313. [PMID: 35819991 PMCID: PMC9307174 DOI: 10.1371/journal.pgen.1010313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/22/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
The Salmonella flagellar secretion apparatus is a member of the type III secretion (T3S) family of export systems in bacteria. After completion of the flagellar motor structure, the hook-basal body (HBB), the flagellar T3S system undergoes a switch from early to late substrate secretion, which results in the expression and assembly of the external, filament propeller-like structure. In order to characterize early substrate secretion-signals in the flagellar T3S system, the FlgB, and FlgC components of the flagellar rod, which acts as the drive-shaft within the HBB, were subject to deletion mutagenesis to identify regions of these proteins that were important for secretion. The β-lactamase protein lacking its Sec-dependent secretion signal (Bla) was fused to the C-terminus of FlgB and FlgC and used as a reporter to select for and quantify the secretion of FlgB and FlgC into the periplasm. Secretion of Bla into the periplasm confers resistance to ampicillin. In-frame deletions of amino acids 9 through 18 and amino acids 39 through 58 of FlgB decreased FlgB secretion levels while deleting amino acid 6 through 14 diminished FlgC secretion levels. Further PCR-directed mutagenesis indicated that amino acid F45 of FlgB was critical for secretion. Single amino acid mutagenesis revealed that all amino acid substitutions at F45 of FlgB position impaired rod assembly, which was due to a defect of FlgB secretion. An equivalent F49 position in FlgC was essential for assembly but not for secretion. This study also revealed that a hydrophobic patch in the cleaved C-terminal domain of FlhB is critical for recognition of FlgB at F45. Type III secretion (T3S) is the means by which proteins are secreted from the bacterial cytoplasm to build flagella for motility and injectisome structures that facilitate pathogenesis. T3S is the only secretion system known to date that undergoes a secretion-specificity switch. For the assembly of the bacterial flagellum, the T3S system initially secretes early substrates to build the hook-basal body (HBB), which is the main component that makes up the flagellar motor. Upon HBB completion, the flagellar T3S system becomes specific for late substrates, which make up the long external filament that acts as the propeller of the motility organelle. This work identifies important sites of interaction between an early substrate, FlgB and a target site at the cytoplasmic base of T3S apparatus. A second early substrate, FlgC, lacks the targeting interaction found for FlgB suggesting a mechanism that distinguishes early substrates, and may indicate an order to early substrate secretion to facilitate the order of protein subunit assembly for the flagellum.
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Affiliation(s)
- Daofeng Qu
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Mengxue Jiang
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Calder Duffin
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Kelly T. Hughes
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Fabienne F. V. Chevance
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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15
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Minamino T, Kinoshita M, Namba K. Insight Into Distinct Functional Roles of the Flagellar ATPase Complex for Flagellar Assembly in Salmonella. Front Microbiol 2022; 13:864178. [PMID: 35602071 PMCID: PMC9114704 DOI: 10.3389/fmicb.2022.864178] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Most motile bacteria utilize the flagellar type III secretion system (fT3SS) to construct the flagellum, which is a supramolecular motility machine consisting of basal body rings and an axial structure. Each axial protein is translocated via the fT3SS across the cytoplasmic membrane, diffuses down the central channel of the growing flagellar structure and assembles at the distal end. The fT3SS consists of a transmembrane export complex and a cytoplasmic ATPase ring complex with a stoichiometry of 12 FliH, 6 FliI and 1 FliJ. This complex is structurally similar to the cytoplasmic part of the FOF1 ATP synthase. The export complex requires the FliH12-FliI6-FliJ1 ring complex to serve as an active protein transporter. The FliI6 ring has six catalytic sites and hydrolyzes ATP at an interface between FliI subunits. FliJ binds to the center of the FliI6 ring and acts as the central stalk to activate the export complex. The FliH dimer binds to the N-terminal domain of each of the six FliI subunits and anchors the FliI6-FliJ1 ring to the base of the flagellum. In addition, FliI exists as a hetero-trimer with the FliH dimer in the cytoplasm. The rapid association-dissociation cycle of this hetero-trimer with the docking platform of the export complex promotes sequential transfer of export substrates from the cytoplasm to the export gate for high-speed protein transport. In this article, we review our current understanding of multiple roles played by the flagellar cytoplasmic ATPase complex during efficient flagellar assembly.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,RIKEN SPring-8 Center and Center for Biosystems Dynamics Research, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Osaka, Japan
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16
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Jenkins J, Worrall L, Strynadka N. Recent structural advances towards understanding of the bacterial type III secretion injectisome. Trends Biochem Sci 2022; 47:795-809. [DOI: 10.1016/j.tibs.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022]
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17
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Bryant OJ, Dhillon P, Hughes C, Fraser GM. Recognition of discrete export signals in early flagellar subunits during bacterial Type III secretion. eLife 2022; 11:66264. [PMID: 35238774 PMCID: PMC8983047 DOI: 10.7554/elife.66264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Type III Secretion Systems (T3SS) deliver subunits from the bacterial cytosol to nascent cell surface flagella. Early flagellar subunits that form the rod and hook substructures are unchaperoned and contain their own export signals. A gate recognition motif (GRM) docks them at the FlhBc component of the FlhAB-FliPQR export gate, but the gate must then be opened and subunits must be unfolded to pass through the flagellar channel. This induced us to seek further signals on the subunits. Here, we identify a second signal at the extreme N-terminus of flagellar rod and hook subunits and determine that key to the signal is its hydrophobicity. We show that the two export signal elements are recognised separately and sequentially, as the N-terminal signal is recognised by the flagellar export machinery only after subunits have docked at FlhBC via the GRM. The position of the N-terminal hydrophobic signal in the subunit sequence relative to the GRM appeared to be important, as a FlgD deletion variant (FlgDshort), in which the distance between the N-terminal signal and the GRM was shortened, 'stalled' at the export machinery and was not exported. The attenuation of motility caused by FlgDshort was suppressed by mutations that destabilised the closed conformation of the FlhAB-FliPQR export gate, suggesting that the hydrophobic N-terminal signal might trigger opening of the flagellar export gate.
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Affiliation(s)
- Owain J Bryant
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Paraminder Dhillon
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Colin Hughes
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Gillian M Fraser
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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18
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Abstract
The bacterial flagellum is a large macromolecular assembly that acts as propeller, providing motility through the rotation of a long extracellular filament. It is composed of over 20 different proteins, many of them highly oligomeric. Accordingly, it has attracted a huge amount of interest amongst researchers and the wider public alike. Nonetheless, most of its molecular details had long remained elusive.This however has changed recently, with the emergence of cryo-EM to determine the structure of protein assemblies at near-atomic resolution. Within a few years, the atomic details of most of the flagellar components have been elucidated, revealing not only its overall architecture but also the molecular details of its rotation mechanism. However, many questions remained unaddressed, notably on the complexity of the assembly of such an intricate machinery.In this chapter, we review the current state of our understanding of the bacterial flagellum structure, focusing on the recent development from cryo-EM. We also highlight the various elements that still remain to be fully characterized. Finally, we summarize the existing model for flagellum assembly and discuss some of the outstanding questions that are still pending in our understanding of the diversity of assembly pathways.
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Affiliation(s)
- Natalie S Al-Otaibi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
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19
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Homma M, Nishikino T, Kojima S. Achievements in bacterial flagellar research with focus on Vibrio species. Microbiol Immunol 2021; 66:75-95. [PMID: 34842307 DOI: 10.1111/1348-0421.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022]
Abstract
In 1980's, the most genes involved in the bacterial flagellar function and formation had been isolated though many of their functions or roles were not clarified. Bacterial flagella are the primary locomotive organ and are not necessary for growing in vitro but are probably essential for living in natural condition and are involved in the pathogenicity. In vitro, the flagella-deficient strains can grow at rates similar to wild-type strains. More than 50 genes are responsible for flagellar function, and the flagellum is constructed by more than 20 structural proteins. The maintenance cost of flagellum is high as several genes are required for its development. The fact that it evolved as a motor organ even with such the high cost shows that the motility is indispensable to survive under the harsh environment of Earth. In this review, we focus on flagella-related research conducted by the authors for about 40 years and flagellar research focused on Vibrio spp. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
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20
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Bryant OJ, Fraser GM. Regulation of bacterial Type III Secretion System export gate opening by substrates and the FliJ stalk of the flagellar ATPase. FEBS J 2021; 289:2628-2641. [PMID: 34812581 DOI: 10.1111/febs.16294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/13/2021] [Accepted: 11/22/2021] [Indexed: 01/12/2023]
Abstract
Type III Secretion Systems (T3SS) transport proteins from the bacterial cytosol for assembly into cell surface nanomachines or direct delivery into target eukaryotic cells. At the core of the flagellar T3SS, the FlhAB-FliPQR export gate regulates protein entry into the export channel whilst maintaining the integrity of the cell membrane. Here, we identify critical residues in the export gate FliR plug that stabilise the closed conformation, preserving the membrane permeability barrier, and we show that the gate opens and closes in response to export substrate availability. Our data indicate that FlhAB-FliPQR gate opening, which is triggered by substrate export signals, is energised by FlhA in a proton motive force-dependent manner. We present evidence that the export substrate and the FliJ stalk of the flagellar ATPase provide mechanistically distinct, non-redundant gate-activating signals that are critical for efficient export.
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21
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Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate. J Mol Biol 2021; 433:167188. [PMID: 34454944 DOI: 10.1016/j.jmb.2021.167188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022]
Abstract
Type III protein secretion is widespread in Gram-negative pathogens. It comprises the injectisome with a surface-exposed needle and an inner membrane translocase. The translocase contains the SctRSTU export channel enveloped by the export gate subunit SctV that binds chaperone/exported clients and forms a putative ante-chamber. We probed the assembly, function, structure and dynamics of SctV from enteropathogenic E. coli (EPEC). In both EPEC and E. coli lab strains, SctV forms peripheral oligomeric clusters that are detergent-extracted as homo-nonamers. Membrane-embedded SctV9 is necessary and sufficient to act as a receptor for different chaperone/exported protein pairs with distinct C-domain binding sites that are essential for secretion. Negative staining electron microscopy revealed that peptidisc-reconstituted His-SctV9 forms a tripartite particle of ∼22 nm with a N-terminal domain connected by a short linker to a C-domain ring structure with a ∼5 nm-wide inner opening. The isolated C-domain ring was resolved with cryo-EM at 3.1 Å and structurally compared to other SctV homologues. Its four sub-domains undergo a three-stage "pinching" motion. Hydrogen-deuterium exchange mass spectrometry revealed this to involve dynamic and rigid hinges and a hyper-flexible sub-domain that flips out of the ring periphery and binds chaperones on and between adjacent protomers. These motions are coincident with local conformational changes at the pore surface and ring entry mouth that may also be modulated by the ATPase inner stalk. We propose that the intrinsic dynamics of the SctV protomer are modulated by chaperones and the ATPase and could affect allosterically the other subunits of the nonameric ring during secretion.
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22
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Guse A, Halte M, Hüsing S, Erhardt M. Hook-basal-body assembly state dictates substrate specificity of the flagellar type-III secretion system. Mol Microbiol 2021; 116:1189-1200. [PMID: 34467587 DOI: 10.1111/mmi.14805] [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: 05/18/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/01/2022]
Abstract
The assembly of the bacterial flagellum is orchestrated by the secretion of distinct early and late secretion substrates via the flagellar-specific type-III secretion system (fT3SS). However, how the fT3SS is able to distinguish between the different (early and late) substrate classes during flagellar assembly remains poorly understood. In this study, we investigated the substrate selectivity and specificity of the fT3SS of Salmonella enterica at different assembly stages. For this, we developed an experimental setup that allowed us to synchronize hook-basal-body assembly and to monitor early and late substrate secretion of fT3SSs operating in either early or late secretion mode, respectively. Our results demonstrate that the fT3SS features a remarkable specificity for only the substrates required at the respective assembly stage. No crosstalk of substrates was observed for fT3SSs operating in the opposing secretion mode. We further found that a substantial fraction of fT3SS surprisingly remained in early secretion mode. Our results thus suggest that the secretion substrate specificity switch of the fT3SS is unidirectional and irreversible. The developed secretion substrate reporter system further provides a platform for future investigations of the underlying molecular mechanisms of the elusive substrate recognition of the T3SS.
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Affiliation(s)
- Alina Guse
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Halte
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Svenja Hüsing
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marc Erhardt
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
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23
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Smallets S, Kendall MM. Post-transcriptional regulation in attaching and effacing pathogens: integration of environmental cues and the impact on gene expression and host interactions. Curr Opin Microbiol 2021; 63:238-243. [PMID: 34450388 DOI: 10.1016/j.mib.2021.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022]
Abstract
To establish infection, enteric pathogens integrate environmental cues to navigate the gastrointestinal tract and precisely control expression of virulence determinants. Emerging data indicate that post-transcriptional and post-translational gene regulation plays a key role in virulence regulation and pathogen adaptation to the host environment. Here, we highlight recent studies that reveal how physiologically relevant signals initiate post-transcriptional and post-translational regulatory circuits and the impact on virulence gene expression in the attaching and effacing pathogens, enteropathogenic Escherichia coli, enterohemorrhagic E. coli O157:H7, and Citrobacter rodentium.
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Affiliation(s)
- Sarah Smallets
- Department of Biology, University of Virginia, 485 McCormick Rd., Charlottesville, VA, 22904, USA
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, 1340 Jefferson Park Ave., Charlottesville, VA, 22908, USA.
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24
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Singh N, Kronenberger T, Eipper A, Weichel F, Franz-Wachtel M, Macek B, Wagner S. Conserved Salt Bridges Facilitate Assembly of the Helical Core Export Apparatus of a Salmonella enterica Type III Secretion System. J Mol Biol 2021; 433:167175. [PMID: 34303721 DOI: 10.1016/j.jmb.2021.167175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022]
Abstract
Virulence-associated type III secretion systems (T3SS) are utilized by Gram negative bacterial pathogens for injection of effector proteins into eukaryotic host cells. The transmembrane export apparatus at the core of T3SS is composed of a unique helical complex of the hydrophobic proteins SctR, SctS, SctT, and SctU. These components comprise a number of highly conserved charged residues within their hydrophobic domains. The structure of the closed state of the core complex SctR5S4T1 revealed that several of these residues form inter- and intramolecular salt bridges, some of which have to be broken for pore opening. Mutagenesis of individual residues was shown to compromise assembly or secretion of both, the virulence-associated and the related flagellar T3SS. However, the exact role of these conserved charged residues in the assembly and function of T3SS remains elusive. Here we performed an in-depth mutagenesis analysis of these residues in the T3SS of Salmonella Typhimurium, coupled to blue native PAGE, in vivo photocrosslinking and luciferase-based secretion assays. Our data show that these conserved salt bridges are not critical for assembly of the respective protein but rather facilitate the incorporation of the following subunit into the assembling complex. Our data also indicate that these conserved charged residues are critical for type III-dependent secretion and reveal a functional link between SctSE44 and SctTR204 and the cytoplasmic domain of SctU in gating the T3SS injectisome. Overall, our analysis provides an unprecedented insight into the delicate requirements for the assembly and function of the machinery at the core of T3SS.
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Affiliation(s)
- Nidhi Singh
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Thales Kronenberger
- University Hospital Tübingen, Department of Internal Medicine VIII, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Andrea Eipper
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Felix Weichel
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany; Partner-site Tübingen, German Center for Infection Research (DZIF), Tübingen, Germany
| | | | - Boris Macek
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; Partner-site Tübingen, German Center for Infection Research (DZIF), Tübingen, Germany.
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25
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Hu H, Santiveri M, Wadhwa N, Berg HC, Erhardt M, Taylor NMI. Structural basis of torque generation in the bi-directional bacterial flagellar motor. Trends Biochem Sci 2021; 47:160-172. [PMID: 34294545 DOI: 10.1016/j.tibs.2021.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022]
Abstract
The flagellar stator unit is an oligomeric complex of two membrane proteins (MotA5B2) that powers bi-directional rotation of the bacterial flagellum. Harnessing the ion motive force across the cytoplasmic membrane, the stator unit operates as a miniature rotary motor itself to provide torque for rotation of the flagellum. Recent cryo-electron microscopic (cryo-EM) structures of the stator unit provided novel insights into its assembly, function, and subunit stoichiometry, revealing the ion flux pathway and the torque generation mechanism. Furthermore, in situ cryo-electron tomography (cryo-ET) studies revealed unprecedented details of the interactions between stator unit and rotor. In this review, we summarize recent advances in our understanding of the structure and function of the flagellar stator unit, torque generation, and directional switching of the motor.
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Affiliation(s)
- Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Navish Wadhwa
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Marc Erhardt
- Institut für Biologie/Bakterienphysiologie, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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26
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Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries. Nat Commun 2021; 12:4223. [PMID: 34244518 PMCID: PMC8270960 DOI: 10.1038/s41467-021-24507-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/22/2021] [Indexed: 01/25/2023] Open
Abstract
The bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque generation and rotation switch, and a large symmetry mismatch between these two rings has been a long puzzle, especially with respect to their role in motor function. Here, using cryoEM structural analysis of the flagellar basal body and the MS ring formed by full-length FliF from Salmonella enterica, we show that the native MS ring is formed by 34 FliF subunits with no symmetry variation. Symmetry analysis of the C ring shows a variation with a peak at 34-fold, suggesting flexibility in C ring assembly. Finally, our data also indicate that FliF subunits assume two different conformations, contributing differentially to the inner and middle parts of the M ring and thus resulting in 23- and 11-fold subsymmetries in the inner and middle M ring, respectively. The internal core of the M ring, formed by 23 subunits, forms a hole of the right size to accommodate the protein export gate. The bacterial flagellar MS ring is a core transmembrane complex within the flagellar basal body. Here, cryoEM analysis suggests that the MS ring is formed by 34 full-length FliF subunits, with 23- and 11-fold subsymmetries in the inner and middle M ring, respectively.
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27
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Hüsing S, Halte M, van Look U, Guse A, Gálvez EJC, Charpentier E, Blair DF, Erhardt M, Renault TT. Control of membrane barrier during bacterial type-III protein secretion. Nat Commun 2021; 12:3999. [PMID: 34183670 PMCID: PMC8239009 DOI: 10.1038/s41467-021-24226-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/02/2021] [Indexed: 11/09/2022] Open
Abstract
Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigate how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs. Type-III secretion systems (T3SSs) are capable of translocating proteins with high speed while maintaining the membrane barrier for small molecules. Here, a structure-function analysis of the T3SS pore complex elucidates the precise mechanisms enabling the gating and the conformational changes required for protein substrate secretion.
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Affiliation(s)
- Svenja Hüsing
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Manuel Halte
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulf van Look
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Alina Guse
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J C Gálvez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - David F Blair
- School of Biology, University of Utah, Salt Lake City, UT, USA
| | - Marc Erhardt
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany. .,Max Planck Unit for the Science of Pathogens, Berlin, Germany.
| | - Thibaud T Renault
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany. .,Max Planck Unit for the Science of Pathogens, Berlin, Germany. .,CNRS, UMR 5234, Université de Bordeaux, Bordeaux, France. .,Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.
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28
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Kuhlen L, Johnson S, Cao J, Deme JC, Lea SM. Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein. PLoS One 2021; 16:e0252800. [PMID: 34143799 PMCID: PMC8213127 DOI: 10.1371/journal.pone.0252800] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomer’s cytoplasmic domain, which stabilises the nonameric ring assembly.
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Affiliation(s)
- Lucas Kuhlen
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Steven Johnson
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
| | - Jerry Cao
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Justin C. Deme
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
| | - Susan M. Lea
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
- * E-mail:
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29
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Johnson S, Furlong EJ, Deme JC, Nord AL, Caesar JJE, Chevance FFV, Berry RM, Hughes KT, Lea SM. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol 2021; 6:712-721. [PMID: 33931760 PMCID: PMC7610862 DOI: 10.1038/s41564-021-00895-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023]
Abstract
The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids1-3. Here, we present structures of the intact Salmonella flagellar basal body4, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.
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Affiliation(s)
- Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Ashley L Nord
- Department of Physics, University of Oxford, Oxford, UK
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | | | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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30
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CesL Regulates Type III Secretion Substrate Specificity of the Enteropathogenic E. coli Injectisome. Microorganisms 2021; 9:microorganisms9051047. [PMID: 34067942 PMCID: PMC8152094 DOI: 10.3390/microorganisms9051047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
The type III secretion system (T3SS) is a complex molecular device used by several pathogenic bacteria to translocate effector proteins directly into eukaryotic host cells. One remarkable feature of the T3SS is its ability to secrete different categories of proteins in a hierarchical manner, to ensure proper assembly and timely delivery of effectors into target cells. In enteropathogenic Escherichia coli, the substrate specificity switch from translocator to effector secretion is regulated by a gatekeeper complex composed of SepL, SepD, and CesL proteins. Here, we report a characterization of the CesL protein using biochemical and genetic approaches. We investigated discrepancies in the phenotype among different cesL deletion mutants and showed that CesL is indeed essential for translocator secretion and to prevent premature effector secretion. We also demonstrated that CesL engages in pairwise interactions with both SepL and SepD. Furthermore, while association of SepL to the membrane does not depended on CesL, the absence of any of the proteins forming the heterotrimeric complex compromised the intracellular stability of each component. In addition, we found that CesL interacts with the cytoplasmic domains of the export gate components EscU and EscV. We propose a mechanism for substrate secretion regulation governed by the SepL/SepD/CesL complex.
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31
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Kinoshita M, Namba K, Minamino T. A positive charge region of Salmonella FliI is required for ATPase formation and efficient flagellar protein export. Commun Biol 2021; 4:464. [PMID: 33846530 PMCID: PMC8041783 DOI: 10.1038/s42003-021-01980-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 03/12/2021] [Indexed: 01/28/2023] Open
Abstract
The FliH2FliI complex is thought to pilot flagellar subunit proteins from the cytoplasm to the transmembrane export gate complex for flagellar assembly in Salmonella enterica. FliI also forms a homo-hexamer to hydrolyze ATP, thereby activating the export gate complex to become an active protein transporter. However, it remains unknown how this activation occurs. Here we report the role of a positively charged cluster formed by Arg-26, Arg-27, Arg-33, Arg-76 and Arg-93 of FliI in flagellar protein export. We show that Arg-33 and Arg-76 are involved in FliI ring formation and that the fliI(R26A/R27A/R33A/R76A/R93A) mutant requires the presence of FliH to fully exert its export function. We observed that gain-of-function mutations in FlhB increased the probability of substrate entry into the export gate complex, thereby restoring the export function of the ∆fliH fliI(R26A/R27A/R33A/R76A/R93A) mutant. We suggest that the positive charge cluster of FliI is responsible not only for well-regulated hexamer assembly but also for substrate entry into the gate complex. Kinoshita, Namba and Minamino show that a cluster of positively-charged arginines in the Salmonella FliI is necessary for formation of the FliI homo-hexamer ATPase. Through loss- and gain-of-function experiments, they demonstrate that hexamer assembly is also responsible for efficient export of flagellar proteins during flagellar assembly.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.,RIKEN SPring-8 Center and Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.
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32
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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33
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The FlgN chaperone activates the Na +-driven engine of the Salmonella flagellar protein export apparatus. Commun Biol 2021; 4:335. [PMID: 33712678 PMCID: PMC7955116 DOI: 10.1038/s42003-021-01865-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/17/2021] [Indexed: 01/13/2023] Open
Abstract
The bacterial flagellar protein export machinery consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. The gate complex has two intrinsic and distinct H+-driven and Na+-driven engines to drive the export of flagellar structural proteins. Salmonella wild-type cells preferentially use the H+-driven engine under a variety of environmental conditions. To address how the Na+-driven engine is activated, we analyzed the fliJ(Δ13–24) fliH(Δ96–97) mutant and found that the interaction of the FlgN chaperone with FlhA activates the Na+-driven engine when the ATPase complex becomes non-functional. A similar activation can be observed with either of two single-residue substitutions in FlhA. Thus, it is likely that the FlgN-FlhA interaction generates a conformational change in FlhA that allows it to function as a Na+ channel. We propose that this type of activation would be useful for flagellar construction under conditions in which the proton motive force is severely restricted. Minamino et al. report that the bacterial FlgN chaperone acts as a switch to activate a backup mechanism for H+-coupled flagellar protein export by interacting with FlhAC to activate the Na+-driven export engine. The proposed mechanism helps to explain how bacteria can maintain flagellar protein export when the ATPase complex export machinery becomes non-functional.
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34
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A Novel Small RNA Promotes Motility and Virulence of Enterohemorrhagic Escherichia coli O157:H7 in Response to Ammonium. mBio 2021; 12:mBio.03605-20. [PMID: 33688013 PMCID: PMC8092317 DOI: 10.1128/mbio.03605-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The process by which bacteria sense environmental cues to regulate their virulence is complex. Several studies have focused on regulating the expression of the locus of enterocyte effacement pathogenicity island in the typical gut pathogenic bacterium, O157. Enterohemorrhagic Escherichia coli serotype O157:H7 (O157) is a critical, foodborne, human intestinal pathogen that causes severe acute hemorrhagic diarrhea, abdominal cramping, and even death. Small RNAs (sRNAs) are noncoding regulatory molecules that sense environmental changes and trigger various virulence-related signaling pathways; however, few such sRNAs have been identified in O157. Here, we report a novel sRNA, EsrF that senses high ammonium concentrations in the colon and enhances O157 pathogenicity by promoting bacterial motility and adhesion to host cells. Specifically, EsrF was found to directly interact with the 5′ untranslated regions of the flagellar biosynthetic gene, flhB, mRNA and increase its abundance, thereby upregulating expression of essential flagellar genes, including flhD, flhC, fliA, and fliC, leading to elevated O157 motility and virulence. Meanwhile, an infant rabbit model of O157 infection showed that deletion of esrF and flhB significantly attenuates O157 pathogenicity. Furthermore, NtrC—the response regulator of the NtrC/B two-component system—was found to exert direct, negative regulation of esrF expression. Meanwhile, high ammonium concentrations in the colon release the inhibitory effect of NtrC on esrF, thereby enhancing its expression and subsequently promoting bacterial colonization in the host colon. Our work reveals a novel, sRNA-centered, virulence-related signaling pathway in O157 that senses high ammonium concentrations. These findings provide novel insights for future research on O157 pathogenesis and targeted treatment strategies.
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35
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Miletic S, Fahrenkamp D, Goessweiner-Mohr N, Wald J, Pantel M, Vesper O, Kotov V, Marlovits TC. Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation. Nat Commun 2021; 12:1546. [PMID: 33750771 PMCID: PMC7943601 DOI: 10.1038/s41467-021-21143-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
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Affiliation(s)
- Sean Miletic
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Fahrenkamp
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Nikolaus Goessweiner-Mohr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Maurice Pantel
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Oliver Vesper
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Vadim Kotov
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany.,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany. .,Centre for Structural Systems Biology (CSSB), Hamburg, Germany. .,Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany. .,Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria. .,Research Institute of Molecular Pathology (IMP), Vienna, Austria.
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36
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Protein Export via the Type III Secretion System of the Bacterial Flagellum. Biomolecules 2021; 11:biom11020186. [PMID: 33572887 PMCID: PMC7911332 DOI: 10.3390/biom11020186] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022] Open
Abstract
The bacterial flagellum and the related virulence-associated injectisome system of pathogenic bacteria utilize a type III secretion system (T3SS) to export substrate proteins across the inner membrane in a proton motive force-dependent manner. The T3SS is composed of an export gate (FliPQR/FlhA/FlhB) located in the flagellar basal body and an associated soluble ATPase complex in the cytoplasm (FliHIJ). Here, we summarise recent insights into the structure, assembly and protein secretion mechanisms of the T3SS with a focus on energy transduction and protein transport across the cytoplasmic membrane.
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37
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Nishikino T, Kojima S, Homma M. [Flagellar related genes and functions in Vibrio]. Nihon Saikingaku Zasshi 2021; 75:195-214. [PMID: 33390367 DOI: 10.3412/jsb.75.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteria can move or swim by flagella. On the other hand, the motile ability is not necessary to live at all. In laboratory, the flagella-deficient strains can grow just like the wild-type strains. The flagellum is assembled from more than 20 structural proteins and there are more than 50 genes including the structural genes to regulate or support the flagellar formation. The cost to construct the flagellum is so expensive. The fact that it evolved as a motor organ means even at such the large cost shows that the flagellum is essential for survival in natural condition. In this review, we would like to focus on the flagella-related researches conducted by the authors and the flagellar research on Vibrio spp.
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Affiliation(s)
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
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38
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Milne-Davies B, Wimmi S, Diepold A. Adaptivity and dynamics in type III secretion systems. Mol Microbiol 2020; 115:395-411. [PMID: 33251695 DOI: 10.1111/mmi.14658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 01/07/2023]
Abstract
The type III secretion system is the common core of two bacterial molecular machines: the flagellum and the injectisome. The flagellum is the most widely distributed prokaryotic locomotion device, whereas the injectisome is a syringe-like apparatus for inter-kingdom protein translocation, which is essential for virulence in important human pathogens. The successful concept of the type III secretion system has been modified for different bacterial needs. It can be adapted to changing conditions, and was found to be a dynamic complex constantly exchanging components. In this review, we highlight the flexibility, adaptivity, and dynamic nature of the type III secretion system.
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Affiliation(s)
- Bailey Milne-Davies
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stephan Wimmi
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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39
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Hook JC, Blagotinsek V, Pané-Farré J, Mrusek D, Altegoer F, Dornes A, Schwan M, Schier L, Thormann KM, Bange G. A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria. Front Microbiol 2020; 11:564161. [PMID: 33384667 PMCID: PMC7771051 DOI: 10.3389/fmicb.2020.564161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.
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Affiliation(s)
- John C Hook
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Vitan Blagotinsek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Devid Mrusek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Lukas Schier
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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40
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Umrekar TR, Cohen E, Drobnič T, Gonzalez-Rodriguez N, Beeby M. CryoEM of bacterial secretion systems: A primer for microbiologists. Mol Microbiol 2020; 115:366-382. [PMID: 33140482 DOI: 10.1111/mmi.14637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
"CryoEM" has come of age, enabling considerable structural insights into many facets of molecular biology. Here, we present a primer for microbiologists to understand the capabilities and limitations of two complementary cryoEM techniques for studying bacterial secretion systems. The first, single particle analysis, determines the structures of purified protein complexes to resolutions sufficient for molecular modeling, while the second, electron cryotomography and subtomogram averaging, tends to determine more modest resolution structures of protein complexes in intact cells. We illustrate these abilities with examples of insights provided into how secretion systems work by cryoEM, with a focus on type III secretion systems.
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Affiliation(s)
| | - Eli Cohen
- Department of Life Sciences, Imperial College London, London, UK
| | - Tina Drobnič
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, UK
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41
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Bajunaid W, Haidar-Ahmad N, Kottarampatel AH, Ourida Manigat F, Silué N, F. Tchagang C, Tomaro K, Campbell-Valois FX. The T3SS of Shigella: Expression, Structure, Function, and Role in Vacuole Escape. Microorganisms 2020; 8:microorganisms8121933. [PMID: 33291504 PMCID: PMC7762205 DOI: 10.3390/microorganisms8121933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Shigella spp. are one of the leading causes of infectious diarrheal diseases. They are Escherichia coli pathovars that are characterized by the harboring of a large plasmid that encodes most virulence genes, including a type III secretion system (T3SS). The archetypal element of the T3SS is the injectisome, a syringe-like nanomachine composed of approximately 20 proteins, spanning both bacterial membranes and the cell wall, and topped with a needle. Upon contact of the tip of the needle with the plasma membrane, the injectisome secretes its protein substrates into host cells. Some of these substrates act as translocators or effectors whose functions are key to the invasion of the cytosol and the cell-to-cell spread characterizing the lifestyle of Shigella spp. Here, we review the structure, assembly, function, and methods to measure the activity of the injectisome with a focus on Shigella, but complemented with data from other T3SS if required. We also present the regulatory cascade that controls the expression of T3SS genes in Shigella. Finally, we describe the function of translocators and effectors during cell-to-cell spread, particularly during escape from the vacuole, a key element of Shigella’s pathogenesis that has yet to reveal all of its secrets.
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Affiliation(s)
- Waad Bajunaid
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nathaline Haidar-Ahmad
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anwer Hasil Kottarampatel
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caetanie F. Tchagang
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kyle Tomaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - François-Xavier Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Correspondence:
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Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
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Abstract
The independent naming of components of injectisome-type type III secretion systems in different bacterial species has resulted in considerable confusion, impeding accessibility of the literature and hindering communication between scientists of the same field. A unified nomenclature had been proposed by Hueck more than 20 years ago. It found little attention for many years, but usage was sparked again by recent reviews and an international type III secretion meeting in 2016. Here, we propose that the field consistently switches to an extended version of this nomenclature to be no longer lost in translation.
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