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Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC. Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nat Microbiol 2024; 9:1089-1102. [PMID: 38538833 PMCID: PMC10994853 DOI: 10.1038/s41564-024-01644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024]
Abstract
Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
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Affiliation(s)
- Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Xiaolong Liu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Kjær
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- Newcastle University Biosciences Institute, Newcastle University, Newcastle, UK
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
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2
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Feldmüller M, Ericson CF, Afanasyev P, Lien YW, Weiss GL, Wollweber F, Schoof M, Hurst M, Pilhofer M. Stepwise assembly and release of Tc toxins from Yersinia entomophaga. Nat Microbiol 2024; 9:405-420. [PMID: 38316932 PMCID: PMC10847046 DOI: 10.1038/s41564-024-01611-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Tc toxins are virulence factors of bacterial pathogens. Although their structure and intoxication mechanism are well understood, it remains elusive where this large macromolecular complex is assembled and how it is released. Here we show by an integrative multiscale imaging approach that Yersinia entomophaga Tc (YenTc) toxin components are expressed only in a subpopulation of cells that are 'primed' with several other potential virulence factors, including filaments of the protease M66/StcE. A phage-like lysis cassette is required for YenTc release; however, before resulting in complete cell lysis, the lysis cassette generates intermediate 'ghost' cells, which may serve as assembly compartments and become packed with assembled YenTc holotoxins. We hypothesize that this stepwise mechanism evolved to minimize the number of cells that need to be killed. The occurrence of similar lysis cassettes in diverse organisms indicates a conserved mechanism for Tc toxin release that may apply to other extracellular macromolecular machines.
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Affiliation(s)
- Miki Feldmüller
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Charles F Ericson
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | | | - Yun-Wei Lien
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Gregor L Weiss
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Florian Wollweber
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Marion Schoof
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
| | - Mark Hurst
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.
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3
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Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E. Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota. Nat Commun 2024; 15:429. [PMID: 38200008 PMCID: PMC10781749 DOI: 10.1038/s41467-023-44426-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
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Affiliation(s)
- Thibault R Bongiovanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Casey J Latario
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Youn Le Cras
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Danica Schmidtke
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA
| | - Maxence Vincent
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Artemis Kosta
- Microscopy Core Facility, Institut de Microbiologie de la Méditerranée (IMM), FR3479, CNRS, Aix-Marseille University, Marseille, France
| | - Jan Orth
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA.
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
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4
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Garrett SR, Mietrach N, Deme J, Bitzer A, Yang Y, Ulhuq FR, Kretschmer D, Heilbronner S, Smith TK, Lea SM, Palmer T. A type VII-secreted lipase toxin with reverse domain arrangement. Nat Commun 2023; 14:8438. [PMID: 38114483 PMCID: PMC10730906 DOI: 10.1038/s41467-023-44221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.
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Affiliation(s)
- Stephen R Garrett
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicole Mietrach
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Justin Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Alina Bitzer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Yaping Yang
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Fatima R Ulhuq
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Terry K Smith
- School of Biology, Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Tracy Palmer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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5
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Wu S, Coureuil M, Nassif X, Tautz L. Enzyme mechanistic studies of NMA1982, a protein tyrosine phosphatase and potential virulence factor in Neisseria meningitidis. Sci Rep 2023; 13:22015. [PMID: 38086986 PMCID: PMC10716126 DOI: 10.1038/s41598-023-49561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/09/2023] [Indexed: 12/18/2023] Open
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine PTP. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
- Shuangding Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Mathieu Coureuil
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Xavier Nassif
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
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6
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Kunze M, Alder NN, Hwang I, Roussel G, Karamyshev AL. Editorial: Targeting signals in protein trafficking and transport. Front Physiol 2023; 14:1338852. [PMID: 38143916 PMCID: PMC10748493 DOI: 10.3389/fphys.2023.1338852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Guillaume Roussel
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology, and Transplantation, Rega Institute, Katholieke Universiteit-Leuven, Leuven, Belgium
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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7
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Sun Y, Nie Q, Zhang S, He H, Zuo S, Chen C, Yang J, Chen H, Hu J, Li S, Cheng J, Zhang B, Zheng Z, Pan S, Huang P, Lian L, Nie S. Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a. Nat Commun 2023; 14:7740. [PMID: 38007572 PMCID: PMC10676405 DOI: 10.1038/s41467-023-43622-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023] Open
Abstract
Gut microbiota plays a key role in insulin resistance (IR). Here we perform a case-control study of Chinese adults (ChiCTR2200065715) and identify that Parabacteroides distasonis is inversely correlated with IR. Treatment with P. distasonis improves IR, strengthens intestinal integrity, and reduces systemic inflammation in mice. We further demonstrate that P. distasonis-derived nicotinic acid (NA) is a vital bioactive molecule that fortifies intestinal barrier function via activating intestinal G-protein-coupled receptor 109a (GPR109a), leading to ameliorating IR. We also conduct a bioactive dietary fiber screening to induce P. distasonis growth. Dendrobium officinale polysaccharide (DOP) shows favorable growth-promoting effects on P. distasonis and protects against IR in mice simultaneously. Finally, the reduced P. distasonis and NA levels were also validated in another human type 2 diabetes mellitus cohort. These findings reveal the unique mechanisms of P. distasonis on IR and provide viable strategies for the treatment and prevention of IR by bioactive dietary fiber.
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Affiliation(s)
- Yonggan Sun
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Qixing Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Shanshan Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Huijun He
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Sheng Zuo
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Chunhua Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Jingrui Yang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Haihong Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Jielun Hu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Song Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Jiaobo Cheng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Baojie Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Zhitian Zheng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Shijie Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Ping Huang
- Department of Nutrition, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lu Lian
- Department of Nutrition, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China.
- China-Canada Joint Lab of Food Science and Technology, Nanchang University, Nanchang, China.
- Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China.
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8
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Wang C, Chen M, Shao Y, Jiang M, Li Q, Chen L, Wu Y, Cen S, Waterfield NR, Yang J, Yang G. Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system. Commun Biol 2023; 6:1195. [PMID: 38001377 PMCID: PMC10673891 DOI: 10.1038/s42003-023-05580-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Type VI secretion systems (T6SSs) deliver effectors into target cells. Besides structural and effector proteins, many other proteins, such as adaptors, co-effectors and accessory proteins, are involved in this process. MIX domains can assist in the delivery of T6SS effectors when encoded as a stand-alone gene or fused at the N-terminal of the effector. However, whether there are other conserved domains exhibiting similar encoding forms to MIX in T6SS remains obscure. Here, we scanned publicly available bacterial genomes and established a database which include 130,825 T6SS vgrG loci from 45,041 bacterial genomes. Based on this database, we revealed six domain families encoded within vgrG loci, which are either fused at the C-terminus of VgrG/N-terminus of T6SS toxin or encoded by an independent gene. Among them, DUF2345 was further validated and shown to be indispensable for the T6SS effector delivery and LysM was confirmed to assist the interaction between VgrG and the corresponding effector. Together, our results implied that these widely distributed domain families with similar genetic configurations may be required for the T6SS effector recruitment process.
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Affiliation(s)
- Caihong Wang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mingxing Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yuhan Shao
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mengyuan Jiang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yun Wu
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- CAMS Key Laboratory of Antiviral Drug Research, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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9
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Cheng Y, Han J, Song M, Zhang S, Cao Q. Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM. Nat Commun 2023; 14:7503. [PMID: 37980359 PMCID: PMC10657474 DOI: 10.1038/s41467-023-43359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
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Affiliation(s)
- Yijia Cheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jianting Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meinai Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shuqin Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China.
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10
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Pherribo GJ, Taga ME. Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs. ISME J 2023; 17:1785-1788. [PMID: 37322284 PMCID: PMC10504361 DOI: 10.1038/s41396-023-01452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Microbial communities host many auxotrophs-organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by "producers" remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in the release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis of Escherichia coli and Bacteroides thetaiotaomicron amino acid producers can support the growth of engineered Escherichia coli amino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.
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Affiliation(s)
- Gordon J Pherribo
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
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11
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Helliwell E, Choi D, Merritt J, Kreth J. Environmental influences on Streptococcus sanguinis membrane vesicle biogenesis. ISME J 2023; 17:1430-1444. [PMID: 37355741 PMCID: PMC10432417 DOI: 10.1038/s41396-023-01456-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Membrane vesicles are produced by Gram-negative and Gram-positive bacteria. While membrane vesicles are potent elicitors of eukaryotic cells and involved in cell-cell communication, information is scarce about their general biology in the context of community members and the environment. Streptococcus sanguinis, a Gram-positive oral commensal, is prevalent in the oral cavity and well-characterized for its ability to antagonize oral pathobionts. We have found that production and dissemination of membrane vesicles by S. sanguinis is dependent on environmental and community factors. Co-culture with interacting commensal Corynebacterium durum, as well as with the periodontal pathobiont Filifactor alocis had no effect on S. sanguinis vesicle number and size, whereas the periodontal pathobiont Porphyromonas gingivalis abolished S. sanguinis vesicle production. Using both correlation and differential expression analyses to examine the transcriptomic changes underlying vesicle production, we found that differential expression of genes encoding proteins related to the cytoplasmic membrane and peptidoglycan correlate with the abundance of membrane vesicles. Proteomic characterizations of the vesicle cargo identified a variety of proteins, including those predicted to influence host interactions or host immune responses. Cell culture studies of gingival epithelial cells demonstrated that both crude and highly purified membrane vesicles could induce the expression of IL-8, TNF-α, IL-1β, and Gro-α within 6 hours of inoculation at levels comparable to whole cells. Our findings suggest that production of membrane vesicles by S. sanguinis is heavily influenced by community and environmental factors and plays an important role in communication with host cells.
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Affiliation(s)
- Emily Helliwell
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA.
| | - Dongseok Choi
- Department of Community Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- School of Public Health, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, USA.
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR, USA.
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12
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Kanarek K, Fridman CM, Bosis E, Salomon D. The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors. Nat Commun 2023; 14:4983. [PMID: 37591831 PMCID: PMC10435454 DOI: 10.1038/s41467-023-40659-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Bacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells during interbacterial competition, host colonization, or when resisting predation. Identifying effectors is a challenging task, as they lack canonical secretion signals or universally conserved domains. Here, we identify a protein domain, RIX, that defines a class of polymorphic T6SS cargo effectors. RIX is widespread in the Vibrionaceae family and is located at N-termini of proteins containing diverse antibacterial and anti-eukaryotic toxic domains. We demonstrate that RIX-containing proteins are delivered via T6SS into neighboring cells and that RIX is necessary and sufficient for T6SS-mediated secretion. In addition, RIX-containing proteins can enable the T6SS-mediated delivery of other cargo effectors by a previously undescribed mechanism. The identification of RIX-containing proteins significantly enlarges the repertoire of known T6SS effectors, especially those with anti-eukaryotic activities. Furthermore, our findings also suggest that T6SSs may play an underappreciated role in the interactions between vibrios and eukaryotes.
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Affiliation(s)
- Katarzyna Kanarek
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chaya Mushka Fridman
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel.
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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13
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Yu Z, Wu Y, Chen M, Huo T, Zheng W, Ludtke SJ, Shi X, Wang Z. Author Correction: Membrane translocation process revealed by in situ structures of type II secretion system secretins. Nat Commun 2023; 14:4833. [PMID: 37563200 PMCID: PMC10415358 DOI: 10.1038/s41467-023-40656-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Affiliation(s)
- Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaoming Wu
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Tong Huo
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wei Zheng
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cryo Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaodong Shi
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Cryo Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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14
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Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
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Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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15
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Emani SS, Kan A, Storms T, Bonanno S, Law J, Ray S, Joshi NS. Periplasmic stress contributes to a trade-off between protein secretion and cell growth in Escherichia coli Nissle 1917. Synth Biol (Oxf) 2023; 8:ysad013. [PMID: 37601821 PMCID: PMC10439730 DOI: 10.1093/synbio/ysad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/29/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
Maximizing protein secretion is an important target in the design of engineered living systems. In this paper, we characterize a trade-off between cell growth and per-cell protein secretion in the curli biofilm secretion system of Escherichia coli Nissle 1917. Initial characterization using 24-h continuous growth and protein production monitoring confirms decreased growth rates at high induction, leading to a local maximum in total protein production at intermediate induction. Propidium iodide (PI) staining at the endpoint indicates that cellular death is a dominant cause of growth reduction. Assaying variants with combinatorial constructs of inner and outer membrane secretion tags, we find that diminished growth at high production is specific to secretory variants associated with periplasmic stress mediated by outer membrane secretion and periplasmic accumulation of protein containing the outer membrane transport tag. RNA sequencing experiments indicate upregulation of known periplasmic stress response genes in the highly secreting variant, further implicating periplasmic stress in the growth-secretion trade-off. Overall, these results motivate additional strategies for optimizing total protein production and longevity of secretory engineered living systems Graphical Abstract.
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Affiliation(s)
| | - Anton Kan
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Timothy Storms
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Shanna Bonanno
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Jade Law
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sanhita Ray
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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16
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Yu Z, Wu Y, Chen M, Huo T, Zheng W, Ludtke SJ, Shi X, Wang Z. Membrane translocation process revealed by in situ structures of type II secretion system secretins. Nat Commun 2023; 14:4025. [PMID: 37419909 PMCID: PMC10329019 DOI: 10.1038/s41467-023-39583-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
The GspD secretin is the outer membrane channel of the bacterial type II secretion system (T2SS) which secrets diverse toxins that cause severe diseases such as diarrhea and cholera. GspD needs to translocate from the inner to the outer membrane to exert its function, and this process is an essential step for T2SS to assemble. Here, we investigate two types of secretins discovered so far in Escherichia coli, GspDα, and GspDβ. By electron cryotomography subtomogram averaging, we determine in situ structures of key intermediate states of GspDα and GspDβ in the translocation process, with resolution ranging from 9 Å to 19 Å. In our results, GspDα and GspDβ present entirely different membrane interaction patterns and ways of transitioning the peptidoglycan layer. From this, we hypothesize two distinct models for the membrane translocation of GspDα and GspDβ, providing a comprehensive perspective on the inner to outer membrane biogenesis of T2SS secretins.
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Affiliation(s)
- Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaoming Wu
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Tong Huo
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wei Zheng
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cryo Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaodong Shi
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Cryo Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Sá-Pessoa J, López-Montesino S, Przybyszewska K, Rodríguez-Escudero I, Marshall H, Ova A, Schroeder GN, Barabas P, Molina M, Curtis T, Cid VJ, Bengoechea JA. A trans-kingdom T6SS effector induces the fragmentation of the mitochondrial network and activates innate immune receptor NLRX1 to promote infection. Nat Commun 2023; 14:871. [PMID: 36797302 DOI: 10.1038/s41467-023-36629-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Bacteria can inhibit the growth of other bacteria by injecting effectors using a type VI secretion system (T6SS). T6SS effectors can also be injected into eukaryotic cells to facilitate bacterial survival, often by targeting the cytoskeleton. Here, we show that the trans-kingdom antimicrobial T6SS effector VgrG4 from Klebsiella pneumoniae triggers the fragmentation of the mitochondrial network. VgrG4 colocalizes with the endoplasmic reticulum (ER) protein mitofusin 2. VgrG4 induces the transfer of Ca2+ from the ER to the mitochondria, activating Drp1 (a regulator of mitochondrial fission) thus leading to mitochondrial network fragmentation. Ca2+ elevation also induces the activation of the innate immunity receptor NLRX1 to produce reactive oxygen species (ROS). NLRX1-induced ROS limits NF-κB activation by modulating the degradation of the NF-κB inhibitor IκBα. The degradation of IκBα is triggered by the ubiquitin ligase SCFβ-TrCP, which requires the modification of the cullin-1 subunit by NEDD8. VgrG4 abrogates the NEDDylation of cullin-1 by inactivation of Ubc12, the NEDD8-conjugating enzyme. Our work provides an example of T6SS manipulation of eukaryotic cells via alteration of the mitochondria.
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18
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Louche A, Blanco A, Lacerda TLS, Cancade-Veyre L, Lionnet C, Bergé C, Rolando M, Lembo F, Borg JP, Buchrieser C, Nagahama M, Gérard FCA, Gorvel JP, Gueguen-Chaignon V, Terradot L, Salcedo SP. Brucella effectors NyxA and NyxB target SENP3 to modulate the subcellular localisation of nucleolar proteins. Nat Commun 2023; 14:102. [PMID: 36609656 DOI: 10.1038/s41467-022-35763-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
The cell nucleus is a primary target for intracellular bacterial pathogens to counteract immune responses and hijack host signalling pathways to cause disease. Here we identify two Brucella abortus effectors, NyxA and NyxB, that interfere with host protease SENP3, and this facilitates intracellular replication of the pathogen. The translocated Nyx effectors directly interact with SENP3 via a defined acidic patch (identified from the crystal structure of NyxB), preventing nucleolar localisation of SENP3 at late stages of infection. By sequestering SENP3, the effectors promote cytoplasmic accumulation of nucleolar AAA-ATPase NVL and ribosomal protein L5 (RPL5) in effector-enriched structures in the vicinity of replicating bacteria. The shuttling of ribosomal biogenesis-associated nucleolar proteins is inhibited by SENP3 and requires the autophagy-initiation protein Beclin1 and the SUMO-E3 ligase PIAS3. Our results highlight a nucleomodulatory function of two Brucella effectors and reveal that SENP3 is a crucial regulator of the subcellular localisation of nucleolar proteins during Brucella infection, promoting intracellular replication of the pathogen.
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19
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Wang D, Zhu L, Zhen X, Yang D, Li C, Chen Y, Wang H, Qu Y, Liu X, Yin Y, Gu H, Xu L, Wan C, Wang Y, Ouyang S, Shen X. A secreted effector with a dual role as a toxin and as a transcriptional factor. Nat Commun 2022; 13:7779. [PMID: 36522324 DOI: 10.1038/s41467-022-35522-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria have evolved multiple secretion systems for delivering effector proteins into the cytosol of neighboring cells, but the roles of many of these effectors remain unknown. Here, we show that Yersinia pseudotuberculosis secretes an effector, CccR, that can act both as a toxin and as a transcriptional factor. The effector is secreted by a type VI secretion system (T6SS) and can enter nearby cells of the same species and other species (such as Escherichia coli) via cell-cell contact and in a contact-independent manner. CccR contains an N-terminal FIC domain and a C-terminal DNA-binding domain. In Y. pseudotuberculosis cells, CccR inhibits its own expression by binding through its DNA-binding domain to the cccR promoter, and affects the expression of other genes through unclear mechanisms. In E. coli cells, the FIC domain of CccR AMPylates the cell division protein FtsZ, inducing cell filamentation and growth arrest. Thus, our results indicate that CccR has a dual role, modulating gene expression in neighboring cells of the same species, and inhibiting the growth of competitors.
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20
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Diez-Gutiérrez L, Vicente LS, Sáenz J, Esquivel A, Barron LJR, Chávarri M. Biosynthesis of gamma-aminobutyric acid by Lactiplantibacillus plantarum K16 as an alternative to revalue agri-food by-products. Sci Rep 2022; 12:18904. [PMID: 36344571 DOI: 10.1038/s41598-022-22875-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Probiotic metabolites, known as postbiotics, have received attention due to their wide variety of promoting health effects. One of the most exciting postbiotic is gamma-aminobutyric acid (GABA), widely produced by lactic acid bacteria, due to its benefits in health. In addition, the performance of the biosynthesis of GABA by Lactiplantibacillus plantarum could be modulated through the modification of fermentation parameters. Due to their high nutritional value, agri-food by-products could be considered a useful fermentation source for microorganisms. Therefore, these by-products were proposed as fermentation substrates to produce GABA in this study. Previously, several experiments in Man Rogosa Sharpe (MRS) broth were performed to identify the most critical parameters to produce GABA using the strain Lactiplantibacillus plantarum K16. The percentage of inoculum, the initial pH, and the concentration of nutrients, such as monosodium glutamate or glucose, significantly affected the biosynthetic pathway of GABA. The highest GABA yield was obtained with 500 mM of monosodium glutamate and 25 g/L of glucose, and an initial pH of 5.5 and 1.2% inoculum. Furthermore, these investigated parameters were used to evaluate the possibility of using tomato, green pepper, apple, or orange by-products to get GABA-enriched fermented media, which is an excellent way to revalorise them.
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21
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Li Y, Chen M, Ma Y, Yang Y, Cheng Y, Ma H, Ren D, Chen P. Regulation of viable/inactivated/lysed probiotic Lactobacillus plantarum H6 on intestinal microbiota and metabolites in hypercholesterolemic mice. NPJ Sci Food 2022; 6:50. [PMID: 36316361 PMCID: PMC9622822 DOI: 10.1038/s41538-022-00167-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
Evidence suggests that probiotic interventions reduce non-communicable diseases (NCDs) risk. However, its therapeutic effect and mechanism are still unclear. To evaluate the hypocholesterolemic effect of Lactobacillus plantarum H6 (L.p H6), a new commercial patent strain capable of preventing hypercholesterolemia, and its mechanism in depth, three states of the strain were prepared, namely, viable (vH6), heat-inactivated (iH6), and ultrasonically-lysed (uH6) bacteria cells. The results showed that v/i/uH6 cells could lower serum and liver blood lipid levels, alleviate liver damage and improve glucose tolerance test (GTT) and insulin tolerance test (ITT) indexes. v/i/uH6 cells improved the gut microbial composition and significantly reduced the Firmicutes to Bacteroidetes ratio (F/B ratio) in feces. In particular, Muribaculaceae may be a potential biomarker for effective cholesterol reduction. Also, the recovery of these biochemical indices and gut microbiome was found following fecal microbiota transplantation (FMT) using stool from vH6 treated mice. The v/i/uH6 cells increased the intestinal flora metabolism of vitamins-cofactors, as well as amino acids, while decreasing the relative content of primary bile acids. The Pearson correlation analysis showed that norank_f__Muribaculaceae and Lactobacillus had a negative correlation with blood lipid levels. Overall, v/i/uH6 cells were effective in improving hypercholesterolemia in mice, and this effect was attributed partly to the regulation of intestinal microbiota and metabolites related to lipid metabolism. Our findings provided a theoretical basis for the industrial development of probiotics and postbiotics and the treatment of cholesterol diseases.
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Affiliation(s)
- Yue Li
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Mengling Chen
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Yuxuan Ma
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Yue Yang
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Ying Cheng
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Huijing Ma
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Dayong Ren
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
| | - Ping Chen
- grid.464353.30000 0000 9888 756XCollege of Food Science and Engineering, Jilin Agricultural University, 130118 Changchun, China
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22
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Watkins DW, Williams SL, Collinson I. A bacterial secretosome for regulated envelope biogenesis and quality control? Microbiology (Reading) 2022; 168. [PMID: 36260397 DOI: 10.1099/mic.0.001255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Gram-negative bacterial envelope is the first line of defence against environmental stress and antibiotics. Therefore, its biogenesis is of considerable fundamental interest, as well as a challenge to address the growing problem of antimicrobial resistance. All bacterial proteins are synthesised in the cytosol, so inner- and outer-membrane proteins, and periplasmic residents have to be transported to their final destinations via specialised protein machinery. The Sec translocon, a ubiquitous integral inner-membrane (IM) complex, is key to this process as the major gateway for protein transit from the cytosol to the cell envelope; this can be achieved during their translation, or afterwards. Proteins need to be directed into the inner-membrane (usually co-translational), otherwise SecA utilises ATP and the proton-motive-force (PMF) to drive proteins across the membrane post-translationally. These proteins are then picked up by chaperones for folding in the periplasm, or delivered to the β-barrel assembly machinery (BAM) for incorporation into the outer-membrane. The core hetero-trimeric SecYEG-complex forms the hub for an extensive network of interactions that regulate protein delivery and quality control. Here, we conduct a biochemical exploration of this 'secretosome' -a very large, versatile and inter-changeable assembly with the Sec-translocon at its core; featuring interactions that facilitate secretion (SecDF), inner- and outer-membrane protein insertion (respectively, YidC and BAM), protein folding and quality control (e.g. PpiD, YfgM and FtsH). We propose the dynamic interplay amongst these, and other factors, act to ensure efficient envelope biogenesis, regulated to accommodate the requirements of cell elongation and division. We believe this organisation is critical for cell wall biogenesis and remodelling and thus its perturbation could be a means for the development of anti-microbials.
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Affiliation(s)
- Daniel W Watkins
- School of Biochemistry, University of Bristol, BS8 1TD, UK.,Present address: CytoSeek, Science Creates Old Market, Midland Road, Bristol, BS20JZ, UK
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, BS8 1TD, UK
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23
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Pakharukova N, Malmi H, Tuittila M, Dahlberg T, Ghosal D, Chang YW, Myint SL, Paavilainen S, Knight SD, Lamminmäki U, Uhlin BE, Andersson M, Jensen G, Zavialov AV. Archaic chaperone-usher pili self-secrete into superelastic zigzag springs. Nature 2022; 609:335-340. [PMID: 35853476 PMCID: PMC9452303 DOI: 10.1038/s41586-022-05095-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria1-3. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Henri Malmi
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Minna Tuittila
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Tobias Dahlberg
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Si Lhyam Myint
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sari Paavilainen
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Stefan David Knight
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Bernt Eric Uhlin
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Magnus Andersson
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anton V Zavialov
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland.
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24
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Liu X, Khara P, Baker ML, Christie PJ, Hu B. Author Correction: Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids. Nat Commun 2022; 13:2837. [PMID: 35577897 PMCID: PMC9110712 DOI: 10.1038/s41467-022-30584-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xiangan Liu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA.
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA.
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25
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Zhang L, Kent JE, Whitaker M, Young DC, Herrmann D, Aleshin AE, Ko YH, Cingolani G, Saad JS, Moody DB, Marassi FM, Ehrt S, Niederweis M. A periplasmic cinched protein is required for siderophore secretion and virulence of Mycobacterium tuberculosis. Nat Commun 2022; 13:2255. [PMID: 35474308 PMCID: PMC9042941 DOI: 10.1038/s41467-022-29873-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Iron is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis. To acquire iron from the host, M. tuberculosis uses the siderophores called mycobactins and carboxymycobactins. Here, we show that the rv0455c gene is essential for M. tuberculosis to grow in low-iron medium and that secretion of both mycobactins and carboxymycobactins is drastically reduced in the rv0455c deletion mutant. Both water-soluble and membrane-anchored Rv0455c are functional in siderophore secretion, supporting an intracellular role. Lack of Rv0455c results in siderophore toxicity, a phenotype observed for other siderophore secretion mutants, and severely impairs replication of M. tuberculosis in mice, demonstrating the importance of Rv0455c and siderophore secretion during disease. The crystal structure of a Rv0455c homolog reveals a novel protein fold consisting of a helical bundle with a 'cinch' formed by an essential intramolecular disulfide bond. These findings advance our understanding of the distinct M. tuberculosis siderophore secretion system.
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Affiliation(s)
- Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - James E Kent
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Meredith Whitaker
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - David C Young
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dominik Herrmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Alexander E Aleshin
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Francesca M Marassi
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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26
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Amin H, Ilangovan A, Costa TRD. Architecture of the outer-membrane core complex from a conjugative type IV secretion system. Nat Commun 2021; 12:6834. [PMID: 34824240 PMCID: PMC8617172 DOI: 10.1038/s41467-021-27178-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation.
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Affiliation(s)
- Himani Amin
- grid.7445.20000 0001 2113 8111MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ UK
| | - Aravindan Ilangovan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Tiago R. D. Costa
- grid.7445.20000 0001 2113 8111MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ UK
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27
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Zheng X, Marsman G, Lacey KA, Chapman JR, Goosmann C, Ueberheide BM, Torres VJ. The cell envelope of Staphylococcus aureus selectively controls the sorting of virulence factors. Nat Commun 2021; 12:6193. [PMID: 34702812 DOI: 10.1038/s41467-021-26517-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus bi-component pore-forming leukocidins are secreted toxins that directly target and lyse immune cells. Intriguingly, one of the leukocidins, Leukocidin AB (LukAB), is found associated with the bacterial cell envelope in addition to secreted into the extracellular milieu. Here, we report that retention of LukAB on the bacterial cells provides S. aureus with a pre-synthesized active toxin that kills immune cells. On the bacteria, LukAB is distributed as discrete foci in two distinct compartments: membrane-proximal and surface-exposed. Through genetic screens, we show that a membrane lipid, lysyl-phosphatidylglycerol (LPG), and lipoteichoic acid (LTA) contribute to LukAB deposition and release. Furthermore, by studying non-covalently surface-bound proteins we discovered that the sorting of additional exoproteins, such as IsaB, Hel, ScaH, and Geh, are also controlled by LPG and LTA. Collectively, our study reveals a multistep secretion system that controls exoprotein storage and protein translocation across the S. aureus cell wall.
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28
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Bunduc CM, Fahrenkamp D, Wald J, Ummels R, Bitter W, Houben ENG, Marlovits TC. Structure and dynamics of a mycobacterial type VII secretion system. Nature 2021; 593:445-448. [PMID: 33981042 PMCID: PMC8131196 DOI: 10.1038/s41586-021-03517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/06/2021] [Indexed: 11/20/2022]
Abstract
Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year1. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope2,3. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP5 protease. A trimer of MycP5 caps a central periplasmic dome-like chamber that is formed by three EccB5 dimers, with the proteolytic sites of MycP5 facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP5 show disruption of the EccB5 periplasmic assembly and increased flexibility, which highlights the importance of MycP5 for complex integrity. Beneath the EccB5-MycP5 chamber, dimers of the EccC5 ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC5 domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.
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Affiliation(s)
- Catalin M Bunduc
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dirk Fahrenkamp
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Edith N G Houben
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Hamburg, Germany.
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany.
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29
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Long CM, Beare PA, Cockrell DC, Fintzi J, Tesfamariam M, Shaia CI, Heinzen RA. Contributions of lipopolysaccharide and the type IVB secretion system to Coxiella burnetii vaccine efficacy and reactogenicity. NPJ Vaccines 2021; 6:38. [PMID: 33741986 PMCID: PMC7979919 DOI: 10.1038/s41541-021-00296-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Coxiella burnetii is the bacterial causative agent of the zoonosis Q fever. The current human Q fever vaccine, Q-VAX®, is a fixed, whole cell vaccine (WCV) licensed solely for use in Australia. C. burnetii WCV administration is associated with a dermal hypersensitivity reaction in people with pre-existing immunity to C. burnetii, limiting wider use. Consequently, a less reactogenic vaccine is needed. Here, we investigated contributions of the C. burnetii Dot/Icm type IVB secretion system (T4BSS) and lipopolysaccharide (LPS) in protection and reactogenicity of fixed WCVs. A 32.5 kb region containing 23 dot/icm genes was deleted in the virulent Nine Mile phase I (NMI) strain and the resulting mutant was evaluated in guinea pig models of C. burnetii infection, vaccination-challenge, and post-vaccination hypersensitivity. The NMI ∆dot/icm strain was avirulent, protective as a WCV against a robust C. burnetii challenge, and displayed potentially altered reactogenicity compared to NMI. Nine Mile phase II (NMII) strains of C. burnetii that produce rough LPS, were similarly tested. NMI was significantly more protective than NMII as a WCV; however, both vaccines exhibited similar reactogenicity. Collectively, our results indicate that, like phase I LPS, the T4BSS is required for full virulence by C. burnetii. Conversely, unlike phase I LPS, the T4BSS is not required for vaccine-induced protection. LPS length does not appear to contribute to reactogenicity while the T4BSS may contribute to this response. NMI ∆dot/icm represents an avirulent phase I strain with full vaccine efficacy, illustrating the potential of genetically modified C. burnetii as improved WCVs.
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Affiliation(s)
- Carrie M Long
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
| | - Paul A Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Diane C Cockrell
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan Fintzi
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mahelat Tesfamariam
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl I Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Robert A Heinzen
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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30
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Wimmi S, Balinovic A, Jeckel H, Selinger L, Lampaki D, Eisemann E, Meuskens I, Linke D, Drescher K, Endesfelder U, Diepold A. Dynamic relocalization of cytosolic type III secretion system components prevents premature protein secretion at low external pH. Nat Commun 2021; 12:1625. [PMID: 33712575 PMCID: PMC7954860 DOI: 10.1038/s41467-021-21863-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
Many bacterial pathogens use a type III secretion system (T3SS) to manipulate host cells. Protein secretion by the T3SS injectisome is activated upon contact to any host cell, and it has been unclear how premature secretion is prevented during infection. Here we report that in the gastrointestinal pathogens Yersinia enterocolitica and Shigella flexneri, cytosolic injectisome components are temporarily released from the proximal interface of the injectisome at low external pH, preventing protein secretion in acidic environments, such as the stomach. We show that in Yersinia enterocolitica, low external pH is detected in the periplasm and leads to a partial dissociation of the inner membrane injectisome component SctD, which in turn causes the dissociation of the cytosolic T3SS components. This effect is reversed upon restoration of neutral pH, allowing a fast activation of the T3SS at the native target regions within the host. These findings indicate that the cytosolic components form an adaptive regulatory interface, which regulates T3SS activity in response to environmental conditions.
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Affiliation(s)
- Stephan Wimmi
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Alexander Balinovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Lisa Selinger
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dimitrios Lampaki
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg, Germany
| | - Emma Eisemann
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- James Madison University, Harrisonburg, VA, USA
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Ulrike Endesfelder
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.
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31
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Tak U, Dokland T, Niederweis M. Pore-forming Esx proteins mediate toxin secretion by Mycobacterium tuberculosis. Nat Commun 2021; 12:394. [PMID: 33452244 DOI: 10.1038/s41467-020-20533-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium tuberculosis secretes the tuberculosis necrotizing toxin (TNT) to kill host cells. Here, we show that the WXG100 proteins EsxE and EsxF are essential for TNT secretion. EsxE and EsxF form a water-soluble heterodimer (EsxEF) that assembles into oligomers and long filaments, binds to membranes, and forms stable membrane-spanning channels. Electron microscopy of EsxEF reveals mainly pentameric structures with a central pore. Mutations of both WXG motifs and of a GXW motif do not affect dimerization, but abolish pore formation, membrane deformation and TNT secretion. The WXG/GXW mutants are locked in conformations with altered thermostability and solvent exposure, indicating that the WXG/GXW motifs are molecular switches controlling membrane interaction and pore formation. EsxF is accessible on the bacterial cell surface, suggesting that EsxEF form an outer membrane channel for toxin export. Thus, our study reveals a protein secretion mechanism in bacteria that relies on pore formation by small WXG proteins.
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32
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Smith WPJ, Brodmann M, Unterweger D, Davit Y, Comstock LE, Basler M, Foster KR. The evolution of tit-for-tat in bacteria via the type VI secretion system. Nat Commun 2020; 11:5395. [PMID: 33106492 PMCID: PMC7589516 DOI: 10.1038/s41467-020-19017-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals with poisoned needles (the type VI secretion system) after being stabbed themselves. Our modelling shows tit-for-tat retaliation is a surprisingly poor evolutionary strategy, because tit-for-tat cells lack the first-strike advantage of preemptive attackers. However, if cells retaliate strongly and fire back multiple times, we find that reciprocation is highly effective. We test our predictions by competing Pseudomonas aeruginosa (a tit-for-tat species) with Vibrio cholerae (random-firing), revealing that P. aeruginosa does indeed fire multiple times per incoming attack. Our work suggests bacterial competition has led to a particular form of reciprocation, where the principle is that of strong retaliation, or 'tits-for-tat'.
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Affiliation(s)
- William P J Smith
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Maj Brodmann
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Yohan Davit
- Institut de Mécanique des Fluides de Toulouse, CNRS and Université de Toulouse, 31400, Toulouse, France
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Marek Basler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Bleves S, Galán JE, Llosa M. Bacterial injection machines: Evolutionary diverse but functionally convergent. Cell Microbiol 2020; 22:e13157. [PMID: 31891220 DOI: 10.1111/cmi.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/19/2019] [Indexed: 12/23/2022]
Abstract
Many human pathogens use Type III, Type IV, and Type VI secretion systems to deliver effectors into their target cells. The contribution of these secretion systems to microbial virulence was the main focus of a workshop organised by the International University of Andalusia in Spain. The meeting addressed structure-function, substrate recruitment, and translocation processes, which differ widely on the different secretion machineries, as well as the nature of the translocated effectors and their roles in subverting the host cell. An excellent panel of worldwide speakers presented the state of the art of the field, highlighting the involvement of bacterial secretion in human disease and discussing mechanistic aspects of bacterial pathogenicity, which can provide the bases for the development of novel antivirulence strategies.
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Affiliation(s)
- Sophie Bleves
- LISM (Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255), IMM (Institut de Microbiologie de la Méditerranée), Aix-Marseille Univ and CNRS, Marseille, France
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut
| | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
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34
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Allsopp LP, Bernal P, Nolan LM, Filloux A. Causalities of war: The connection between type VI secretion system and microbiota. Cell Microbiol 2020; 22:e13153. [PMID: 31872954 PMCID: PMC7540082 DOI: 10.1111/cmi.13153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/23/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Microbiota niches have space and/or nutrient restrictions, which has led to the coevolution of cooperation, specialisation, and competition within the population. Different animal and environmental niches contain defined resident microbiota that tend to be stable over time and offer protection against undesired intruders. Yet fluxes can occur, which alter the composition of a bacterial population. In humans, the microbiota are now considered a key contributor to maintenance of health and homeostasis, and its alteration leads to dysbiosis. The bacterial type VI secretion system (T6SS) transports proteins into the environment, directly into host cells or can function as an antibacterial weapon by killing surrounding competitors. Upon contact with neighbouring cells, the T6SS fires, delivering a payload of effector proteins. In the absence of an immunity protein, this results in growth inhibition or death of prey leading to a competitive advantage for the attacker. It is becoming apparent that the T6SS has a role in modulating and shaping the microbiota at multiple levels, which is the focus of this review. Discussed here is the T6SS, its role in competition, key examples of its effect upon the microbiota, and future avenues of research.
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Affiliation(s)
- Luke P Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura M Nolan
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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McCallum M, Benlekbir S, Nguyen S, Tammam S, Rubinstein JL, Burrows LL, Howell PL. Multiple conformations facilitate PilT function in the type IV pilus. Nat Commun 2019; 10:5198. [PMID: 31729381 PMCID: PMC6858323 DOI: 10.1038/s41467-019-13070-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C2 symmetry; however, most of these ATPases crystallize with either C3 or C6 symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C2, C3, and C6 conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C2 conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Samir Benlekbir
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Sheryl Nguyen
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Stephanie Tammam
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1l7, Canada.
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - P Lynne Howell
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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Tukenmez U, Aktas B, Aslim B, Yavuz S. The relationship between the structural characteristics of lactobacilli-EPS and its ability to induce apoptosis in colon cancer cells in vitro. Sci Rep 2019; 9:8268. [PMID: 31164685 PMCID: PMC6547643 DOI: 10.1038/s41598-019-44753-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/28/2019] [Indexed: 12/24/2022] Open
Abstract
Colon cancer is one of the most common cancer around the world. Exopolysaccharides (EPSs) produced by lactobacilli as potential prebiotics have been found to have an anti-tumor effect. In this study, lyophilized EPSs of four Lactobacillus spp. for their impact on apoptosis in colon cancer cells (HT-29) was evaluated using flow cytometry. The relationship between capability of a lactobacilli-EPS to induce apoptosis and their monosaccharide composition, molecular weight (MW), and linkage type was investigated by HPLC, SEC, and NMR, respectively. Changes in apoptotic-markers were examined by qPCR and Western Blotting. EPSs were capable of inhibiting proliferation in a time-dependent manner and induced apoptosis via increasing the expression of Bax, Caspase 3 and 9 while decreasing Bcl-2 and Survivin. All EPSs contained mannose, glucose, and N-acetylglucosamine with different relative proportions. Some contained arabinose or fructose. MW ranged from 102-104Da with two or three fractions. EPS of L. delbrueckii ssp. bulgaricus B3 having the highest amount of mannose and the lowest amount of glucose, showed the highest apoptosis induction. In conclusion, lactobacilli-EPSs inhibit cell proliferation in HT-29 via apoptosis. Results suggest that a relationship exists between the ability of EPS to induce apoptosis and its mannose and glucose composition.
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Affiliation(s)
| | - Busra Aktas
- Faculty of Arts and Science, Department of Molecular Biology and Genetics, Burdur Mehmet Akif Ersoy University, Burdur, Turkey.
| | - Belma Aslim
- Faculty of Science, Department of Biology, Gazi University, Ankara, Turkey
| | - Serkan Yavuz
- Faculty of Science, Department of Chemistry, Gazi University, Ankara, Turkey
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De Lise F, Mensitieri F, Rusciano G, Dal Piaz F, Forte G, Di Lorenzo F, Molinaro A, Zarrelli A, Romanucci V, Cafaro V, Sasso A, Filippelli A, Di Donato A, Izzo V. Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles. J Microbiol 2019; 57:498-508. [PMID: 31054137 DOI: 10.1007/s12275-019-8483-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/12/2018] [Accepted: 12/24/2018] [Indexed: 02/06/2023]
Abstract
Outer membrane vesicles (OMVs) are nanostructures of 20-200 nm diameter deriving from the surface of several Gram-negative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical "fingerprint", suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.
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Bracken HA, Woolhead CA. Increased freedom of movement in the nascent chain results in dynamic changes in the structure of the SecM arrest motif. Biosci Rep 2019; 39:BSR20181246. [PMID: 30563926 DOI: 10.1042/BSR20181246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
Ribosomes are responsible for the synthesis of all cellular proteins. Due to the diversity of sequence and properties, it was initially believed that translating nascent chains would travel unhindered through the ribosome exit tunnel, however a small but increasing number of proteins have been identified that interact with the exit tunnel to induce translational arrest, Escherichia coli (E. coli) secretion monitor (SecM) is one such stalling peptide. How and why these peptides interact with the exit tunnel is not fully understood, however key features required for stalling appear to be an essential peptide arrest motif at the C-terminus and compaction of the nascent chain within the exit tunnel upon stalling. Mutagenesis of the SecM arrest sequence has identified three conservative point mutations that can retain a degree of stalling in this highly conserved sequence. This level of stalling is further increased when coupled with mutation of a non-essential arrest motif residue P153A. Further analysis of these mutants by pegylation assays indicates that this increase in stalling activity during translation is due to the ability of the P153A mutation to reintroduce compaction of the nascent chain within the exit tunnel possibly due to the improved flexibility of the nascent chain provided by the removal of a restrictive proline residue. The data presented here suggest that arrest sequences may be more prevalent and less highly conserved than previously thought, and highlight the significance of the interactions between the nascent chain and the exit tunnel to affecting translation arrest.
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39
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Oliver D. Substrate Proteins Take Shape at an Improved Bacterial Translocon. J Bacteriol 2019; 201:e00618-18. [PMID: 30322856 DOI: 10.1128/JB.00618-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
Characterization of Sec-dependent bacterial protein transport has often relied on an in vitro protein translocation system comprised in part of Escherichia coli inverted inner membrane vesicles or, more recently, purified SecYEG translocons reconstituted into liposomes using mostly a single substrate (proOmpA). A paper published in this issue (P. Bariya and L. Randall, J Bacteriol 201:e00493-18, 2019, https://doi.org/10.1128/JB.00493-18) finds that inclusion of SecA protein during SecYEG proteoliposome reconstitution dramatically improves the number of active translocons. This experimentally useful and intriguing result that may arise from SecA membrane integration properties is discussed here. Furthermore, determination of the rate-limiting transport step for nine different substrates implicates the mature region distal to the signal peptide in the observed rate constant differences, indicating that more nuanced transport models that respond to differences in protein sequence and structure are needed.
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Abstract
Secretion of proteins into the extracellular environment is crucial for the normal physiology and virulence of pathogenic bacteria. Type I signal peptidase (SPase I) mediates the final step of bacterial secretion, by cleaving proteins at their signal peptide once they are translocated by the Sec or twin-arginine (Tat) translocon. SPase I has long been thought to be essential for viability in multiple bacterial pathogens. Challenging this view, we and others have recently created Staphylococcus aureus bacteria lacking the SPase I SpsB that are viable and able to grow in vitro when over-expressing a native gene cassette encoding for a putative ABC transporter. This transporter apparently compensates for SpsB's essential function by mediating alternative cleavage of a subset of proteins at a site distinct from the SpsB-cleavage site, leading to SpsB-independent secretion. This alternative secretion system also drives the main mechanism of resistance to an arylomycin-derived SpsB inhibitor, by means of mutations in a putative transcriptional repressor (cro/cI) causing over-expression of the ABC transporter. These findings raise multiple interesting biological questions. Unraveling the mechanism of SpsB-independent secretion may provide an interesting twist to the paradigm of bacterial secretion.
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Affiliation(s)
- Wouter L Hazenbos
- Department of Infectious Diseases, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Elizabeth Skippington
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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41
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Abstract
A paper published in this issue of the Journal of Bacteriology (D. Huber, M. Jamshad, R. Hanmer, D. Schibich, K. Döring, I. Marcomini, G. Kramer, and B. Bukau, J Bacteriol 199:e0622-16, 2017, https://doi.org/10.1128/JB.00622-16) provides us with a timely reminder that all is not as clear as we had previously thought in the general bacterial secretion system. The paper describes a new mode of secretion through the Sec system—“uncoupled cotranslocation”—for the passage of proteins across the bacterial inner membrane and suggests that we might rethink the nature and mechanism of the targeting and transport steps toward protein export.
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42
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Weber BS, Ly PM, Irwin JN, Pukatzki S, Feldman MF. A multidrug resistance plasmid contains the molecular switch for type VI secretion in Acinetobacter baumannii. Proc Natl Acad Sci U S A 2015; 112:9442-7. [PMID: 26170289 DOI: 10.1073/pnas.1502966112] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infections with Acinetobacter baumannii, one of the most troublesome and least studied multidrug-resistant superbugs, are increasing at alarming rates. A. baumannii encodes a type VI secretion system (T6SS), an antibacterial apparatus of Gram-negative bacteria used to kill competitors. Expression of the T6SS varies among different strains of A. baumannii, for which the regulatory mechanisms are unknown. Here, we show that several multidrug-resistant strains of A. baumannii harbor a large, self-transmissible resistance plasmid that carries the negative regulators for T6SS. T6SS activity is silenced in plasmid-containing, antibiotic-resistant cells, while part of the population undergoes frequent plasmid loss and activation of the T6SS. This activation results in T6SS-mediated killing of competing bacteria but renders A. baumannii susceptible to antibiotics. Our data show that a plasmid that has evolved to harbor antibiotic resistance genes plays a role in the differentiation of cells specialized in the elimination of competing bacteria.
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Abstract
Proteins of the secretin family form large macromolecular complexes, which assemble in the outer membrane of Gram-negative bacteria. Secretins are major components of type II and III secretion systems and are linked to extrusion of type IV pili (T4P) and to DNA uptake. By electron cryo-tomography of whole Thermus thermophilus cells, we determined the in situ structure of a T4P molecular machine in the open and the closed state. Comparison reveals a major conformational change whereby the N-terminal domains of the central secretin PilQ shift by ∼30 Å, and two periplasmic gates open to make way for pilus extrusion. Furthermore, we determine the structure of the assembled pilus. DOI:http://dx.doi.org/10.7554/eLife.07380.001 Gram-negative bacteria can cause serious diseases in humans, such as cholera and bacterial meningitis. These bacteria are surrounded by two membranes: an inner membrane and an outer membrane. Proteins called secretins are components of several large molecular complexes that are embedded within the outer membrane. Some secretin-containing complexes form pores in the bacterial membranes and allow molecules to pass in or out of the cell. Some secretins also form part of the machinery that allow Gram-negative bacteria to grow fibre-like structures called type IV pili. These pili help bacteria that cause infections to move and stick to host cells, where they can also trigger massive changes in the host cells' architecture. Multiple copies of a secretin protein called PilQ form a channel in the outer membrane of the bacteria that allows a type IV pilus to grow out of the surface of the cell. The pilus can then hook the bacteria onto surfaces and other cells. There is evidence to suggest the type IV pilus machinery is involved in the uptake of DNA from other bacteria, an important but poorly understood process that has contributed to the spread of multi-drug resistance. Now, Gold et al. have used a cutting-edge technique called ‘electron cryo-tomography’ to analyse the three-dimensional structure of the machinery that builds the type IV pili in the membranes of a bacterium called Thermus thermophilus. This analysis revealed that, similar to many other channel complexes, the PilQ channel can be ‘open’ or ‘closed’. When pili are absent, the channel is closed, but the channel opens when pili are present. Further analysis also revealed the structure of an assembled pilus. Next, Gold et al. studied the open state of the type IV pilus in more detail and observed that a region of each of the PilQ proteins moves a considerable distance to make way for the pilus to enter the central pore. These results will pave the way for future studies of type IV pili and other secretin-containing complexes and underpin efforts to investigate new drug targets to combat bacterial infections. DOI:http://dx.doi.org/10.7554/eLife.07380.002
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Affiliation(s)
- Vicki A M Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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VieBrock L, Evans SM, Beyer AR, Larson CL, Beare PA, Ge H, Singh S, Rodino KG, Heinzen RA, Richards AL, Carlyon JA. Orientia tsutsugamushi ankyrin repeat-containing protein family members are Type 1 secretion system substrates that traffic to the host cell endoplasmic reticulum. Front Cell Infect Microbiol 2015; 4:186. [PMID: 25692099 PMCID: PMC4315096 DOI: 10.3389/fcimb.2014.00186] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/11/2014] [Indexed: 11/18/2022] Open
Abstract
Scrub typhus is an understudied, potentially fatal infection that threatens one billion persons in the Asia-Pacific region. How the causative obligate intracellular bacterium, Orientia tsutsugamushi, facilitates its intracellular survival and pathogenesis is poorly understood. Many intracellular bacterial pathogens utilize the Type 1 (T1SS) or Type 4 secretion system (T4SS) to translocate ankyrin repeat-containing proteins (Anks) that traffic to distinct subcellular locations and modulate host cell processes. The O. tsutsugamushi genome encodes one of the largest known bacterial Ank repertoires plus T1SS and T4SS components. Whether these potential virulence factors are expressed during infection, how the Anks are potentially secreted, and to where they localize in the host cell are not known. We determined that O. tsutsugamushi transcriptionally expresses 20 unique ank genes as well as genes for both T1SS and T4SS during infection of mammalian host cells. Examination of the Anks' C-termini revealed that the majority of them resemble T1SS substrates. Escherichia coli expressing a functional T1SS was able to secrete chimeric hemolysin proteins bearing the C-termini of 19 of 20 O. tsutsugamushi Anks in an HlyBD-dependent manner. Thus, O. tsutsugamushi Anks C-termini are T1SS-compatible. Conversely, Coxiella burnetii could not secrete heterologously expressed Anks in a T4SS-dependent manner. Analysis of the subcellular distribution patterns of 20 ectopically expressed Anks revealed that, while 6 remained cytosolic or trafficked to the nucleus, 14 localized to, and in some cases, altered the morphology of the endoplasmic reticulum. This study identifies O. tsutsugamushi Anks as T1SS substrates and indicates that many display a tropism for the host cell secretory pathway.
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Affiliation(s)
- Lauren VieBrock
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
| | - Sean M Evans
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
| | - Andrea R Beyer
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
| | - Charles L Larson
- Coxiella Pathogenesis Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health Hamilton, MT, USA
| | - Paul A Beare
- Coxiella Pathogenesis Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health Hamilton, MT, USA
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Naval Medical Research Center Silver Spring, MD, USA
| | - Smita Singh
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
| | - Kyle G Rodino
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
| | - Robert A Heinzen
- Coxiella Pathogenesis Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health Hamilton, MT, USA
| | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center Silver Spring, MD, USA
| | - Jason A Carlyon
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine Richmond, VA, USA
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