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Izquierdo Lafuente B, Verboom T, Coenraads S, Ummels R, Bitter W, Speer A. Vitamin B 12 uptake across the mycobacterial outer membrane is influenced by membrane permeability in Mycobacterium marinum. Microbiol Spectr 2024; 12:e0316823. [PMID: 38722177 DOI: 10.1128/spectrum.03168-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/12/2024] [Indexed: 06/06/2024] Open
Abstract
Vitamin B12 (B12) serves as a critical cofactor within mycobacterial metabolism. While some pathogenic strains can synthesize B12 de novo, others rely on host-acquired B12. In this investigation, we studied the transport of vitamin B12 in Mycobacterium marinum using B12-auxotrophic and B12-sensitive strains by deleting metH or metE, respectively. These two enzymes rely on B12 in different ways to function as methionine synthases. We used these strains to select mutants affecting B12 scavenging and confirmed their phenotypes during growth experiments in vitro. Our analysis of B12 uptake mechanisms revealed that membrane lipids and cell wall integrity play an essential role in cell envelope transport. Furthermore, we identified a potential transcription regulator that responds to B12. Our study demonstrates that M. marinum can take up exogenous B12 and that altering mycobacterial membrane integrity affects B12 uptake. Finally, during zebrafish infection using B12-auxotrophic and B12-sensitive strains, we found that B12 is available for virulent mycobacteria in vivo.IMPORTANCEOur study investigates how mycobacteria acquire essential vitamin B12. These microbes, including those causing tuberculosis, face challenges in nutrient uptake due to their strong outer layer. We focused on Mycobacterium marinum, similar to TB bacteria, to uncover its vitamin B12 absorption. We used modified strains unable to produce their own B12 and discovered that M. marinum can indeed absorb it from the environment, even during infections. Changes in the outer layer composition affect this process, and genes related to membrane integrity play key roles. These findings illuminate the interaction between mycobacteria and their environment, offering insights into combatting diseases like tuberculosis through innovative strategies. Our concise research underscores the pivotal role of vitamin B12 in microbial survival and its potential applications in disease control.
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Affiliation(s)
- Beatriz Izquierdo Lafuente
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Theo Verboom
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sita Coenraads
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
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Nicholson KR, Cronin RM, Prest RJ, Menon AR, Yang Y, Jennisch MK, Champion MM, Tobin DM, Champion PA. The antagonistic transcription factors, EspM and EspN, regulate the ESX-1 secretion system in M. marinum. mBio 2024; 15:e0335723. [PMID: 38445877 PMCID: PMC11005418 DOI: 10.1128/mbio.03357-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Bacterial pathogens use protein secretion systems to transport virulence factors and regulate gene expression. Among pathogenic mycobacteria, including Mycobacterium tuberculosis and Mycobacterium marinum, the ESAT-6 system 1 (ESX-1) secretion is crucial for host interaction. Secretion of protein substrates by the ESX-1 secretion system disrupts phagosomes, allowing mycobacteria cytoplasmic access during macrophage infections. Deletion or mutation of the ESX-1 system attenuates mycobacterial pathogens. Pathogenic mycobacteria respond to the presence or absence of the ESX-1 system in the cytoplasmic membrane by altering transcription. Under laboratory conditions, the EspM repressor and WhiB6 activator control transcription of specific ESX-1-responsive genes, including the ESX-1 substrate genes. However, deleting the espM or whiB6 gene does not phenocopy the deletion of the ESX-1 substrate genes during macrophage infection by M. marinum. In this study, we identified EspN, a critical transcription factor whose activity is masked by the EspM repressor under laboratory conditions. In the absence of EspM, EspN activates transcription of whiB6 and ESX-1 genes during both laboratory growth and macrophage infection. EspN is also independently required for M. marinum growth within and cytolysis of macrophages, similar to the ESX-1 genes, and for disease burden in a zebrafish larval model of infection. These findings suggest that EspN and EspM coordinate to counterbalance the regulation of the ESX-1 system and support mycobacterial pathogenesis.IMPORTANCEPathogenic mycobacteria, which are responsible for tuberculosis and other long-term diseases, use the ESX-1 system to transport proteins that control the host response to infection and promote bacterial survival. In this study, we identify an undescribed transcription factor that controls the expression of ESX-1 genes and is required for both macrophage and animal infection. However, this transcription factor is not the primary regulator of ESX-1 genes under standard laboratory conditions. These findings identify a critical transcription factor that likely controls expression of a major virulence pathway during infection, but whose effect is not detectable with standard laboratory strains and growth conditions.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rachel M. Cronin
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rebecca J. Prest
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Aruna R. Menon
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yuwei Yang
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Madeleine K. Jennisch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew M. Champion
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Patricia A. Champion
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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Serene LG, Webber K, Champion PA, Schorey JS. Mycobacterium tuberculosis SecA2-dependent activation of host Rig-I/MAVs signaling is not conserved in Mycobacterium marinum. PLoS One 2024; 19:e0281564. [PMID: 38394154 PMCID: PMC10889897 DOI: 10.1371/journal.pone.0281564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/02/2023] [Indexed: 02/25/2024] Open
Abstract
Retinoic acid inducible gene I (Rig-I) is a cytosolic pattern recognition receptor canonically described for its important role in sensing viral RNAs. Increasingly, bacterially-derived RNA from intracellular bacteria such as Mycobacterium tuberculosis, have been shown to activate the same host Rig-I/Mitochondrial antiviral sensing protein (MAVS) signaling pathway to drive a type-I interferon response that contributes to bacterial pathogenesis in vivo. In M. tuberculosis, this response is mediated by the protein secretion system SecA2, but little is known about whether this process is conserved in other pathogenic mycobacteria or the mechanism by which these nucleic acids gain access to the host cytoplasm. Because the M. tuberculosis and M. marinum SecA2 protein secretion systems share a high degree of genetic and functional conservation, we hypothesized that Rig-I/MAVS activation and subsequent induction of IFN-β secretion by host macrophages will also be conserved between these two mycobacterial species. To test this, we generated a ΔsecA2 M. marinum strain along with complementation strains expressing either the M. marinum or M. tuberculosis secA2 genes. Our results suggest that the ΔsecA2 strain has a growth defect in vitro but not in host macrophages. These intracellular growth curves also suggested that the calculation applied to estimate the number of bacteria added to macrophage monolayers in infection assays underestimates bacterial inputs for the ΔsecA2 strain. Therefore, to better examine secreted IFN-β levels when bacterial infection levels are equal across strains we plated bacterial CFUs at 2hpi alongside our ELISA based infections. This enabled us to normalize secreted levels of IFN-β to a standard number of bacteria. Applying this approach to both WT and MAVS-/- bone marrow derived macrophages we observed equal or higher levels of secreted IFN-β from macrophages infected with the ΔsecA2 M. marinum strain as compared to WT. Together our findings suggest that activation of host Rig-I/MAVS cytosolic sensors and subsequent induction of IFN-β response in a SecA2-dependent manner is not conserved in M. marinum under the conditions tested.
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Affiliation(s)
- Lindsay G. Serene
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Kylie Webber
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Jeffrey S. Schorey
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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4
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Lefrançois LH, Nitschke J, Wu H, Panis G, Prados J, Butler RE, Mendum TA, Hanna N, Stewart GR, Soldati T. Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals the genetic requirement for virulence and survival in amoebae and microglial cells. mSystems 2024; 9:e0132623. [PMID: 38270456 PMCID: PMC10878075 DOI: 10.1128/msystems.01326-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Tuberculosis remains the most pervasive infectious disease and the recent emergence of drug-resistant strains emphasizes the need for more efficient drug treatments. A key feature of pathogenesis, conserved between the human pathogen Mycobacterium tuberculosis and the model pathogen Mycobacterium marinum, is the metabolic switch to lipid catabolism and altered expression of virulence genes at different stages of infection. This study aims to identify genes involved in sustaining viable intracellular infection. We applied transposon sequencing (Tn-Seq) to M. marinum, an unbiased genome-wide strategy combining saturation insertional mutagenesis and high-throughput sequencing. This approach allowed us to identify the localization and relative abundance of insertions in pools of transposon mutants. Gene essentiality and fitness cost of mutations were quantitatively compared between in vitro growth and different stages of infection in two evolutionary distinct phagocytes, the amoeba Dictyostelium discoideum and the murine BV2 microglial cells. In the M. marinum genome, 57% of TA sites were disrupted and 568 genes (10.2%) were essential, which is comparable to previous Tn-Seq studies on M. tuberculosis and M. bovis. Major pathways involved in the survival of M. marinum during infection of D. discoideum are related to DNA damage repair, lipid and vitamin metabolism, the type VII secretion system (T7SS) ESX-1, and the Mce1 lipid transport system. These pathways, except Mce1 and some glycolytic enzymes, were similarly affected in BV2 cells. These differences suggest subtly distinct nutrient availability or requirement in different host cells despite the known predominant use of lipids in both amoeba and microglial cells.IMPORTANCEThe emergence of biochemically and genetically tractable host model organisms for infection studies holds the promise to accelerate the pace of discoveries related to the evolution of innate immunity and the dissection of conserved mechanisms of cell-autonomous defenses. Here, we have used the genetically and biochemically tractable infection model system Dictyostelium discoideum/Mycobacterium marinum to apply a genome-wide transposon-sequencing experimental strategy to reveal comprehensively which mutations confer a fitness advantage or disadvantage during infection and compare these to a similar experiment performed using the murine microglial BV2 cells as host for M. marinum to identify conservation of virulence pathways between hosts.
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Affiliation(s)
- Louise H. Lefrançois
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Jahn Nitschke
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Huihai Wu
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
- Bioinformatics Support Platform for data analysis, Geneva University, Medicine Faculty, Geneva, Switzerland
| | - Rachel E. Butler
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Tom A. Mendum
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Nabil Hanna
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Graham R. Stewart
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
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Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
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Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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6
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Arch M, Vidal M, Fuentes E, Abat AS, Cardona PJ. The reproductive status determines tolerance and resistance to Mycobacterium marinum in Drosophila melanogaster. Evol Med Public Health 2023; 11:332-347. [PMID: 37868078 PMCID: PMC10590161 DOI: 10.1093/emph/eoad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 07/27/2023] [Indexed: 10/24/2023] Open
Abstract
Sex and reproductive status of the host have a major impact on the immune response against infection. Our aim was to understand their impact on host tolerance or resistance in the systemic Mycobacterium marinum infection of Drosophila melanogaster. We measured host survival and bacillary load at time of death, as well as expression by quantitative real-time polymerase chain reaction of immune genes (diptericin and drosomycin). We also assessed the impact of metabolic and hormonal regulation in the protection against infection by measuring expression of upd3, impl2 and ecR. Our data showed increased resistance in actively mating flies and in mated females, while reducing their tolerance to infection. Data suggests that Toll and immune deficiency (Imd) pathways determine tolerance and resistance, respectively, while higher basal levels of ecR favours the stimulation of the Imd pathway. A dual role has been found for upd3 expression, linked to increased/decreased mycobacterial load at the beginning and later in infection, respectively. Finally, impl2 expression has been related to increased resistance in non-actively mating males. These results allow further assessment on the differences between sexes and highlights the role of the reproductive status in D. melanogaster to face infections, demonstrating their importance to determine resistance and tolerance against M. marinum infection.
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Affiliation(s)
- Marta Arch
- Tuberculosis Research Unit, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
- Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Catalonia, Spain
| | - Maria Vidal
- Tuberculosis Research Unit, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Esther Fuentes
- Tuberculosis Research Unit, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
- Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Catalonia, Spain
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, 08916 Badalona, Catalonia, Spain
| | - Anmaw Shite Abat
- Tuberculosis Research Unit, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
- Department of Veterinary Paraclinical Studies, University of Gondar, Gondar, Ethiopia
| | - Pere-Joan Cardona
- Tuberculosis Research Unit, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
- Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Catalonia, Spain
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, 08916 Badalona, Catalonia, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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The EspN transcription factor is an infection-dependent regulator of the ESX-1 system in M. marinum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528779. [PMID: 36824794 PMCID: PMC9948972 DOI: 10.1101/2023.02.15.528779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Bacterial pathogens use protein secretion systems to translocate virulence factors into the host and to control bacterial gene expression. The ESX-1 (ESAT-6 system 1) secretion system facilitates disruption of the macrophage phagosome during infection, enabling access to the cytoplasm, and regulates widespread gene expression in the mycobacterial cell. The transcription factors contributing to the ESX-1 transcriptional network during mycobacterial infection are not known. We showed that the EspM and WhiB6 transcription factors regulate the ESX-1 transcriptional network in vitro but are dispensable for macrophage infection by Mycobacterium marinum . In this study, we used our understanding of the ESX-1 system to identify EspN, a critical transcription factor that controls expression of the ESX-1 genes during infection, but whose effect is not detectable under standard laboratory growth conditions. Under laboratory conditions, EspN activity is masked by the EspM repressor. In the absence of EspM, we found that EspN is required for ESX-1 function because it activates expression of the whiB6 transcription factor gene, and specific ESX-1 substrate and secretory component genes. Unlike the other transcription factors that regulate ESX-1, EspN is required for M. marinum growth within and cytolysis of macrophages, and for disease burden in a zebrafish larval model of infection. These findings demonstrate that EspN is an infection-dependent regulator of the ESX-1 transcriptional network, which is essential for mycobacterial pathogenesis. Moreover, our findings suggest that ESX-1 expression is controlled by a genetic switch that responds to host specific signals. Importance Pathogenic mycobacteria cause acute and long-term diseases, including human tuberculosis. The ESX-1 system transports proteins that control the host response to infection and promotes bacterial survival. Although ESX-1 transports proteins, it also controls gene expression in the bacteria. In this study, we identify an undescribed transcription factor that controls the expression of ESX-1 genes, and is required for both macrophage and animal infection. However, this transcription factor is not the primary regulator of ESX-1 genes under standard laboratory conditions. These findings identify a critical transcription factor that controls expression of a major virulence pathway during infection, but whose effect is not detectable with standard laboratory strains and growth conditions.
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Ho VQT, Rong MK, Habjan E, Bommer SD, Pham TV, Piersma SR, Bitter W, Ruijter E, Speer A. Dysregulation of Mycobacterium marinum ESX-5 Secretion by Novel 1,2,4-oxadiazoles. Biomolecules 2023; 13:biom13020211. [PMID: 36830581 PMCID: PMC9953084 DOI: 10.3390/biom13020211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The ESX-5 secretion system is essential for the viability and virulence of slow-growing pathogenic mycobacterial species. In this study, we identified a 1,2,4-oxadiazole derivative as a putative effector of the ESX-5 secretion system. We confirmed that this 1,2,4-oxadiazole and several newly synthesized derivatives inhibited the ESX-5-dependent secretion of active lipase LipY by Mycobacterium marinum (M. marinum). Despite reduced lipase activity, we did not observe a defect in LipY secretion itself. Moreover, we found that several other ESX-5 substrates, especially the high molecular-weight PE_PGRS MMAR_5294, were even more abundantly secreted by M. marinum treated with several 1,2,4-oxadiazoles. Analysis of M. marinum grown in the presence of different oxadiazole derivatives revealed that the secretion of LipY and the induction of PE_PGRS secretion were, in fact, two independent phenotypes, as we were able to identify structural features in the compounds that specifically induced only one of these phenotypes. Whereas the three most potent 1,2,4-oxadiazoles displayed only a mild effect on the growth of M. marinum or M. tuberculosis in culture, these compounds significantly reduced bacterial burden in M. marinum-infected zebrafish models. In conclusion, we report a 1,2,4-oxadiazole scaffold that dysregulates ESX-5 protein secretion.
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Affiliation(s)
- Vien Q. T. Ho
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Mark K. Rong
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Samantha D. Bommer
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, OncoProteomics Laboratory, AmsterdamUMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, AmsterdamUMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Eelco Ruijter
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
- Correspondence:
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Host–Pathogen Interactions of Marine Gram-Positive Bacteria. BIOLOGY 2022; 11:biology11091316. [PMID: 36138795 PMCID: PMC9495620 DOI: 10.3390/biology11091316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Complex interactions between marine Gram-positive pathogens and fish hosts in the marine environment can result in diseases of economically important finfish, which cause economic losses in the aquaculture industry. Understanding how these pathogens interact with the fish host and generate disease will contribute to efficient prophylactic measures and treatments. To our knowledge, there are no systematic reviews on marine Gram-positive pathogens. Therefore, here we reviewed the host–pathogen interactions of marine Gram-positive pathogens from the pathogen-centric and host-centric points of view. Abstract Marine Gram-positive bacterial pathogens, including Renibacterium salmoninarum, Mycobacterium marinum, Nocardia seriolae, Lactococcus garvieae, and Streptococcus spp. cause economic losses in marine fish aquaculture worldwide. Comprehensive information on these pathogens and their dynamic interactions with their respective fish–host systems are critical to developing effective prophylactic measures and treatments. While much is known about bacterial virulence and fish immune response, it is necessary to synthesize the knowledge in terms of host–pathogen interactions as a centerpiece to establish a crucial connection between the intricate details of marine Gram-positive pathogens and their fish hosts. Therefore, this review provides a holistic view and discusses the different stages of the host–pathogen interactions of marine Gram-positive pathogens. Gram-positive pathogens can invade fish tissues, evade the fish defenses, proliferate in the host system, and modulate the fish immune response. Marine Gram-positive pathogens have a unique set of virulence factors that facilitate adhesion (e.g., adhesins, hemagglutination activity, sortase, and capsules), invasion (e.g., toxins, hemolysins/cytolysins, the type VII secretion system, and immune-suppressive proteins), evasion (e.g., free radical quenching, actin-based motility, and the inhibition of phagolysosomal fusion), and proliferation and survival (e.g., heme utilization and siderophore-mediated iron acquisition systems) in the fish host. After infection, the fish host initiates specific innate and adaptive immune responses according to the extracellular or intracellular mechanism of infection. Although efforts have continued to be made in understanding the complex interplay at the host–pathogen interface, integrated omics-based investigations targeting host–pathogen–marine environment interactions hold promise for future research.
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Habjan E, Ho VQT, Gallant J, Van Stempvoort G, Jim KK, Kuijl C, Geerke DP, Bitter W, Speer A. Anti-tuberculosis Compound Screen using a Zebrafish Infection Model identifies an Aspartyl-tRNA Synthetase Inhibitor. Dis Model Mech 2021; 14:273850. [PMID: 34643222 PMCID: PMC8713996 DOI: 10.1242/dmm.049145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/03/2021] [Indexed: 11/20/2022] Open
Abstract
Finding new anti-tuberculosis compounds with convincing in vivo activity is an ongoing global challenge to fight the emergence of multidrug-resistant Mycobacterium tuberculosis isolates. In this study, we exploited the medium-throughput capabilities of the zebrafish embryo infection model with Mycobacterium marinum as a surrogate for M. tuberculosis. Using a representative set of clinically established drugs, we demonstrate that this model could be predictive and selective for antibiotics that can be administered orally. We further used the zebrafish infection model to screen 240 compounds from an anti-tuberculosis hit library for their in vivo activity and identified 14 highly active compounds. One of the most active compounds was the tetracyclic compound TBA161, which was studied in more detail. Analysis of resistant mutants revealed point mutations in aspS (rv2572c), encoding an aspartyl-tRNA synthetase. The target was genetically confirmed, and molecular docking studies propose the possible binding of TBA161 in a pocket adjacent to the catalytic site. This study shows that the zebrafish infection model is suitable for rapidly identifying promising scaffolds with in vivo activity. Summary: Exploitation of the medium-throughput capabilities of a zebrafish embryo infection model of tuberculosis to screen compounds for their in vivo activity, one of which was characterized as an aspartyl-tRNA synthetase inhibitor.
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Affiliation(s)
- Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.,Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Vien Q T Ho
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - James Gallant
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Gunny Van Stempvoort
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Kin Ki Jim
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Coen Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Molecular Toxicology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.,Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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11
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Izquierdo Lafuente B, Ummels R, Kuijl C, Bitter W, Speer A. Mycobacterium tuberculosis Toxin CpnT Is an ESX-5 Substrate and Requires Three Type VII Secretion Systems for Intracellular Secretion. mBio 2021; 12:e02983-20. [PMID: 33653883 PMCID: PMC8092274 DOI: 10.1128/mbio.02983-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
CpnT, a NAD+ glycohydrolase, is the only known toxin that is secreted by Mycobacterium tuberculosis CpnT is composed of two domains; the C-terminal domain is the toxin, whereas the N-terminal domain is required for secretion. CpnT shows characteristics of type VII secretion (T7S) substrates, including a predicted helix-turn-helix domain followed by a secretion motif (YxxxE). Disruption of this motif indeed abolished CpnT secretion. By analyzing different mutants, we established that CpnT is specifically secreted by the ESX-5 system in Mycobacterium marinum under axenic conditions and during macrophage infection. Surprisingly, intracellular secretion of CpnT was also dependent on both ESX-1 and ESX-4. These secretion defects could be partially rescued by coinfection with wild-type bacteria, indicating that secreted effectors are involved in this process. In summary, our data reveal that three different type VII secretion systems have to be functional in order to observe intracellular secretion of the toxin CpnT.IMPORTANCE For decades, it was believed that the intracellular pathogen M. tuberculosis does not possess toxins. Only fairly recently it was discovered that CpnT is a potent secreted toxin of M. tuberculosis, causing necrotic cell death in host cells. However, until now the secretion pathway remained unknown. In our study, we were able to identify CpnT as a substrate of the mycobacterial type VII secretion system. Pathogenic mycobacteria have up to five different type VII secretion systems, called ESX-1 to ESX-5, which play distinct roles for the pathogen during growth or infection. We were able to elucidate that CpnT is exclusively secreted by the ESX-5 system in bacterial culture. However, to our surprise we discovered that, during infection studies, CpnT secretion relies on intact ESX-1, ESX-4, and ESX-5 systems. We elucidate for the first time the intertwined interplay of three different and independent secretion systems to secrete one substrate during infection.
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Affiliation(s)
- B Izquierdo Lafuente
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - R Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - C Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - W Bitter
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - A Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
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12
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Chimukuche NM, Williams MJ. Genetic Manipulation of Non-tuberculosis Mycobacteria. Front Microbiol 2021; 12:633510. [PMID: 33679662 PMCID: PMC7925387 DOI: 10.3389/fmicb.2021.633510] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Non-tuberculosis mycobacteria (NTMs) comprise a large group of organisms that are phenotypically diverse. Analysis of the growing number of completed NTM genomes has revealed both significant intra-genus genetic diversity, and a high percentage of predicted genes that appear to be unique to this group. Most NTMs have not been studied, however, the rise in NTM infections in several countries has prompted increasing interest in these organisms. Mycobacterial research has recently benefitted from the development of new genetic tools and a growing number of studies describing the genetic manipulation of NTMs have now been reported. In this review, we discuss the use of both site-specific and random mutagenesis tools in NTMs, highlighting the challenges that exist in applying these techniques to this diverse group of organisms.
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Affiliation(s)
| | - Monique J Williams
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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13
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Modeling Tubercular ESX-1 Secretion Using Mycobacterium marinum. Microbiol Mol Biol Rev 2020; 84:84/4/e00082-19. [DOI: 10.1128/mmbr.00082-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pathogenic mycobacteria cause chronic and acute diseases ranging from human tuberculosis (TB) to nontubercular infections.
Mycobacterium tuberculosis
causes both acute and chronic human tuberculosis. Environmentally acquired nontubercular mycobacteria (NTM) cause chronic disease in humans and animals. Not surprisingly, NTM and
M. tuberculosis
often use shared molecular mechanisms to survive within the host. The ESX-1 system is a specialized secretion system that is essential for virulence and is functionally conserved between
M. tuberculosis
and
Mycobacterium marinum
.
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14
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Pierson E, Wouters J. Biochemical characterization of phosphoserine phosphatase SerB2 from Mycobacterium marinum. Biochem Biophys Res Commun 2020; 530:739-744. [PMID: 32782143 DOI: 10.1016/j.bbrc.2020.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022]
Abstract
SerB2 is an essential phosphoserine phosphatase (PSP) that has been shown to be involved in Mycobacterium tuberculosis (Mtb) immune evasion mechanisms, and a drug target for the development of new antitubercular agents. A highly similar (91.0%) orthologous enzyme exists in the surrogate organism Mycobacterium marinum (Mma) and could have acquired similar properties. By homology modeling, we show that the two PSPs are expected to exhibit almost identical architectures. MmaSerB2 folds into a homodimer formed by two intertwined subunits including two ACT regulatory domains followed by a catalytic core typical of HAD (haloacid dehalogenase) phosphatases. Their in vitro catalytic properties are closely related as MmaSerB2 also depends on Mg2+ for the dephosphorylation of its substrate, O-phospho-l-serine (PS), and is most active at neutral pH and temperatures around 40 °C. Moreover, an enzyme kinetics study revealed that the enzyme is inhibited by PS as well, but at lower concentrations than MtbSerB2. Substrate inhibition could occur through the binding of PS in the second active site and/or at the ACT domains interface. Finally, previously described beta-carboline MtbSerB2 inhibitors also decrease the phosphatase activity of MmaSerB2. Altogether, these results provide useful information when M.marinum is used as a model to study immune evasion in tuberculosis.
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Affiliation(s)
- Elise Pierson
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000, Namur, Belgium.
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Medicine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), B-5000, Namur, Belgium
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15
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Mycobacteriosis and Infections with Non-tuberculous Mycobacteria in Aquatic Organisms: A Review. Microorganisms 2020; 8:microorganisms8091368. [PMID: 32906655 PMCID: PMC7564596 DOI: 10.3390/microorganisms8091368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/19/2022] Open
Abstract
The Mycobacteriaceae constitute a family of varied Gram-positive organisms that include a large number of pathogenic bacteria. Among these, non-tuberculous mycobacteria are endemic worldwide and have been associated with infections in a large number of organisms, including humans and other mammals and reptiles, as well as fish. In this review, we summarize the most recent findings regarding this group of pathogens in fish. There, four species are most commonly associated with disease outbreaks: Mycobacterium marinum, the most common of these fish mycobacterial pathogens, Mycobacterium fortuitum, Mycobacterium gordonae, and Mycobacterium chelonae. These bacteria have a broad host range: they are zoonotic, and infections have been reported in a large number of fish species. The main route of entry of the bacterium into the fish is through the gastrointestinal route, and the disease is associated with ulcerative dermatitis as well as organomegaly and the development of granulomatous lesions in the internal organs. Mycobacteriaceae are slow-growing and fastidious and isolation is difficult and time consuming and diagnostic is mostly performed using serological and molecular tools. Control of the disease is also difficult: there is currently no effective vaccine and infections react poorly to antibiotherapy. For this reason, more research is needed on the subject of these vexing pathogens.
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16
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Tateishi Y, Minato Y, Baughn AD, Ohnishi H, Nishiyama A, Ozeki Y, Matsumoto S. Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing - Implication for metabolic remodeling. Sci Rep 2020; 10:5449. [PMID: 32214196 PMCID: PMC7096427 DOI: 10.1038/s41598-020-62287-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
The global incidence of the human nontuberculous mycobacteria (NTM) disease is rapidly increasing. However, knowledge of gene essentiality under optimal growth conditions and conditions relevant to the natural ecology of NTM, such as hypoxia, is lacking. In this study, we utilized transposon sequencing to comprehensively identify genes essential for growth in Mycobacterium intracellulare. Of 5126 genes of M. intracellulare ATCC13950, 506 genes were identified as essential genes, of which 280 and 158 genes were shared with essential genes of M. tuberculosis and M. marinum, respectively. The shared genes included target genes of existing antituberculous drugs including SQ109, which targets the trehalose monomycolate transporter MmpL3. From 175 genes showing decreased fitness as conditionally essential under hypoxia, preferential carbohydrate metabolism including gluconeogenesis, glyoxylate cycle and succinate production was suggested under hypoxia. Virulence-associated genes including proteasome system and mycothiol redox system were also identified as conditionally essential under hypoxia, which was further supported by the higher effective suppression of bacterial growth under hypoxia compared to aerobic conditions in the presence of these inhibitors. This study has comprehensively identified functions essential for growth of M. intracellulare under conditions relevant to the host environment. These findings provide critical functional genomic information for drug discovery.
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Affiliation(s)
- Yoshitaka Tateishi
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan.
| | - Yusuke Minato
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Avenue S.E. Microbiology Research Facility, Minneapolis, 55455, MN, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Avenue S.E. Microbiology Research Facility, Minneapolis, 55455, MN, USA
| | - Hiroaki Ohnishi
- Department of Laboratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, 951-8510, Japan
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17
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Guan Q, Ummels R, Ben-Rached F, Alzahid Y, Amini MS, Adroub SA, van Ingen J, Bitter W, Abdallah AM, Pain A. Comparative Genomic and Transcriptomic Analyses of Mycobacterium kansasii Subtypes Provide New Insights Into Their Pathogenicity and Taxonomy. Front Cell Infect Microbiol 2020; 10:122. [PMID: 32266172 PMCID: PMC7105574 DOI: 10.3389/fcimb.2020.00122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium kansasii is an important opportunistic pathogen of humans and has a close phylogenetic relationship with Mycobacterium tuberculosis. Seven subtypes (I-VII) have been identified using molecular biology approaches, of which subtype I is the most frequent causative agent of human disease. To investigate the genotypes and pathogenic components of M. kansasii, we sequenced and compared the complete base-perfect genomes of different M. kansasii subtypes. Our findings support the proposition that M. kansasii "subtypes" I-VI, whose assemblies are currently available, should be considered as different species. Furthermore, we identified the exclusive presence of the espACD operon in M. kansasii subtype I, and we confirmed its role in the pathogenicity of M. kansasii in a cell infection model. The espACD operon is exclusively present in mycobacterial species that induce phagosomal rupture in host phagocytes and is known to be a major determinant of ESX1-mediated virulence in pathogenic mycobacteria. Comparative transcriptome analysis of the M. kansasii I-V strains identified genes potentially associated with virulence. Using a comparative genomics approach, we designed primers for PCR genotyping of M. kansasii subtypes I-V and tested their efficacy using clinically relevant strains of M. kansasii.
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Affiliation(s)
- Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Fathia Ben-Rached
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yara Alzahid
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohammad S. Amini
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sabir A. Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud UMC Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Abdallah M. Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
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18
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Genome-Wide Screens Identify Group A Streptococcus Surface Proteins Promoting Female Genital Tract Colonization and Virulence. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:862-873. [PMID: 32200972 DOI: 10.1016/j.ajpath.2019.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Group A streptococcus (GAS) is a major pathogen that impacts health and economic affairs worldwide. Although the oropharynx is the primary site of infection, GAS can colonize the female genital tract and cause severe diseases, such as puerperal sepsis, neonatal infections, and necrotizing myometritis. Our understanding of how GAS genes contribute to interaction with the primate female genital tract is limited by the lack of relevant animal models. Using two genome-wide transposon mutagenesis screens, we identified 69 GAS genes required for colonization of the primate vaginal mucosa in vivo and 96 genes required for infection of the uterine wall ex vivo. We discovered a common set of 39 genes important for GAS fitness in both environments. They include genes encoding transporters, surface proteins, transcriptional regulators, and metabolic pathways. Notably, the genes that encode the surface-exclusion protein (SpyAD) and the immunogenic secreted protein 2 (Isp2) were found to be crucial for GAS fitness in the female primate genital tract. Targeted gene deletion confirmed that isogenic mutant strains ΔspyAD and Δisp2 are significantly impaired in ability to colonize the primate genital tract and cause uterine wall pathologic findings. Our studies identified novel GAS genes that contribute to female reproductive tract interaction that warrant translational research investigation.
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19
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Butler RE, Smith AA, Mendum TA, Chandran A, Wu H, Lefrançois L, Chambers M, Soldati T, Stewart GR. Mycobacterium bovis uses the ESX-1 Type VII secretion system to escape predation by the soil-dwelling amoeba Dictyostelium discoideum. ISME JOURNAL 2020; 14:919-930. [PMID: 31896783 PMCID: PMC7082363 DOI: 10.1038/s41396-019-0572-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/26/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium bovis is the causative agent of bovine tuberculosis and the predominant cause of zoonotic tuberculosis in people. Bovine tuberculosis occurs in farmed cattle but also in a variety of wild animals, which form a reservoir of infection. Although direct transmission of tuberculosis occurs between mammals, the low frequency of contact between different host species and abundant shedding of bacilli by infected animals suggests an infectious route via environmental contamination. Other intracellular pathogens that transmit via the environment deploy strategies to survive or exploit predation by environmental amoebae. To explore if M. bovis has this capability, we investigated its interactions with the soil and dung-dwelling amoeba, Dictyostelium discoideum. We demonstrated that M. bovis evades phagocytosis and destruction by D. discoideum and actively transits through the amoeba using the ESX-1 Type VII Secretion System as part of a programme of mechanisms, many of which have been co-opted as virulence factors in the mammalian host. This capacity of M. bovis to utilise an environmental stage between mammalian hosts may enhance its transmissibility. In addition, our data provide molecular evidence to support an evolutionary role for amoebae as training grounds for the pathogenic M. tuberculosis complex.
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Affiliation(s)
- Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Alex A Smith
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Tom A Mendum
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Aneesh Chandran
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Huihai Wu
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Louise Lefrançois
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
| | - Mark Chambers
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
| | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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20
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Global Assessment of Mycobacterium avium subsp. hominissuis Genetic Requirement for Growth and Virulence. mSystems 2019; 4:4/6/e00402-19. [PMID: 31822597 PMCID: PMC6906737 DOI: 10.1128/msystems.00402-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacterial infections caused by the opportunistic pathogen Mycobacterium avium subsp. hominissuis (MAH) are currently receiving renewed attention due to increased incidence combined with difficult treatment. Insights into the disease-causing mechanisms of this species have been hampered by difficulties in genetic manipulation of the bacteria. Here, we identified and sequenced a highly transformable, virulent MAH clinical isolate susceptible to high-density transposon mutagenesis, facilitating global gene disruption and subsequent investigation of MAH gene function. By transposon insertion sequencing (TnSeq) of this strain, we defined the MAH genome-wide genetic requirement for virulence and in vitro growth and organized ∼3,500 identified transposon mutants for hypothesis-driven research. The majority (96%) of the genes we identified as essential for MAH in vitro had a mutual ortholog in the related and highly virulent Mycobacterium tuberculosis (Mtb). However, passaging our library through a mouse model of infection revealed a substantial number (54% of total hits) of novel virulence genes. More than 97% of the MAH virulence genes had a mutual ortholog in Mtb Finally, we validated novel genes required for successful MAH infection: one encoding a probable major facilitator superfamily (MFS) transporter and another encoding a hypothetical protein located in the immediate vicinity of six other identified virulence genes. In summary, we provide new, fundamental insights into the underlying genetic requirement of MAH for growth and host infection.IMPORTANCE Pulmonary disease caused by nontuberculous mycobacteria is increasing worldwide. The majority of these infections are caused by the Mycobacterium avium complex (MAC), whereof >90% are due to Mycobacterium avium subsp. hominissuis (MAH). Treatment of MAH infections is currently difficult, with a combination of antibiotics given for at least 12 months. To control MAH by improved therapy, prevention, and diagnostics, we need to understand the underlying mechanisms of infection. Here, we provide crucial insights into MAH's global genetic requirements for growth and infection. We find that the vast majority of genes required for MAH growth and virulence (96% and 97%, respectively) have mutual orthologs in the tuberculosis-causing pathogen M. tuberculosis (Mtb). However, we also find growth and virulence genes specific to MAC species. Finally, we validate novel mycobacterial virulence factors that might serve as future drug targets for MAH-specific treatment or translate to broader treatment of related mycobacterial diseases.
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21
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Raze D, Segers J, Mille C, Slupek S, Lecher S, Coutte L, Antoine R, Ducrocq L, Rouanet C, Appelmelk BJ, Locht C. Coordinate regulation of virulence and metabolic genes by the transcription factor HbhR in Mycobacterium marinum. Mol Microbiol 2019; 113:52-67. [PMID: 31587365 DOI: 10.1111/mmi.14400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 12/17/2022]
Abstract
The heparin-binding hemagglutinin (HBHA) is a multifunctional protein involved in adherence of Mycobacterium tuberculosis to non-phagocytic cells and in the formation of intracytosolic lipid inclusions. We demonstrate that the expression of hbhA is regulated by a transcriptional repressor, named HbhR, in Mycobacterium marinum. The hbhR gene, located upstream of hbhA, was identified by screening a transposon insertion library and detailed analysis of a mutant overproducing HBHA. HbhR was found to repress both hbhA and hbhR transcription by binding to the promoter regions of both genes. Complementation restored production of HBHA. RNA-seq analyses comparing the mutant and parental strains uncovered 27 genes, including hbhA, that were repressed and 20 genes activated by HbhR. Among the former, the entire locus of genes coding for a type-VII secretion system, including esxA, esxB and pe-ppe paralogs, as well as the gene coding for PspA, present in intracellular lipid vesicles, was identified, as was katG, a gene involved in the sensitivity to isoniazid. The latter category contains genes that play a role in diverse functions, such as metabolism and resistance to oxidative conditions. Thus, HbhR appears to be a master regulator, linking the transcriptional regulation of virulence, metabolic and antibiotic sensitivity genes in M. marinum.
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Affiliation(s)
- Dominique Raze
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Jérôme Segers
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Céline Mille
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Stéphanie Slupek
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Sophie Lecher
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Loïc Coutte
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Rudy Antoine
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Lucie Ducrocq
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Carine Rouanet
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Ben J Appelmelk
- Molecular Microbiology/Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Camille Locht
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
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22
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A New ESX-1 Substrate in Mycobacterium marinum That Is Required for Hemolysis but Not Host Cell Lysis. J Bacteriol 2019; 201:JB.00760-18. [PMID: 30833360 DOI: 10.1128/jb.00760-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The ESX-1 (ESAT-6 system 1) secretion system plays a conserved role in the virulence of diverse mycobacterial pathogens, including the human pathogen Mycobacterium tuberculosis and M. marinum, an environmental mycobacterial species. The ESX-1 system promotes the secretion of protein virulence factors to the extracytoplasmic environment. The secretion of these proteins triggers the host response by lysing the phagosome during macrophage infection. Using proteomic analyses of the M. marinum secretome in the presence and absence of a functional ESX-1 system, we and others have hypothesized that MMAR_2894, a PE family protein, is a potential ESX-1 substrate in M. marinum We used genetic and quantitative proteomic approaches to determine if MMAR_2894 is secreted by the ESX-1 system, and we defined the requirement of MMAR_2894 for ESX-1-mediated secretion and virulence. We show that MMAR_2894 is secreted by the ESX-1 system in M. marinum and is itself required for the optimal secretion of the known ESX-1 substrates in M. marinum Moreover, we found that MMAR_2894 was differentially required for hemolysis and cytolysis of macrophages, two lytic activities ascribed to the M. marinum ESX-1 system.IMPORTANCE Both Mycobacterium tuberculosis, the cause of human tuberculosis (TB), and Mycobacterium marinum, a pathogen of ectotherms, use the ESX-1 secretion system to cause disease. There are many established similarities between the ESX-1 systems in M. tuberculosis and in M. marinum Yet the two bacteria infect different hosts, hinting at species-specific functions of the ESX-1 system. Our findings demonstrate that MMAR_2894 is a PE protein secreted by the ESX-1 system of M. marinum We show that MMAR_2894 is required for the optimal secretion of mycobacterial proteins required for disease. Because the MMAR_2894 gene is not conserved in M. tuberculosis, our findings demonstrate that MMAR_2894 may contribute to a species-specific function of the ESX-1 system in M. marinum, providing new insight into how the M. marinum and M. tuberculosis systems differ.
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23
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Ortega Ugalde S, Boot M, Commandeur JNM, Jennings P, Bitter W, Vos JC. Function, essentiality, and expression of cytochrome P450 enzymes and their cognate redox partners in Mycobacterium tuberculosis: are they drug targets? Appl Microbiol Biotechnol 2019; 103:3597-3614. [PMID: 30810776 PMCID: PMC6469627 DOI: 10.1007/s00253-019-09697-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 11/26/2022]
Abstract
This review covers the current knowledge of the cytochrome P450 enzymes (CYPs) of the human pathogen Mycobacterium tuberculosis (Mtb) and their endogenous redox partners, focusing on their biological function, expression, regulation, involvement in antibiotic resistance, and suitability for exploitation as antitubercular targets. The Mtb genome encodes twenty CYPs and nine associated redox partners required for CYP catalytic activity. Transposon insertion mutagenesis studies have established the (conditional) essentiality of several of these enzymes for in vitro growth and host infection. Biochemical characterization of a handful of Mtb CYPs has revealed that they have specific physiological functions in bacterial virulence and persistence in the host. Analysis of the transcriptional response of Mtb CYPs and redox partners to external insults and to first-line antibiotics used to treat tuberculosis showed a diverse expression landscape, suggesting for some enzymes a potential role in drug resistance. Combining the knowledge about the physiological roles and expression profiles indicates that, at least five Mtb CYPs, CYP121A1, CYP125A1, CYP139A1, CYP142A1, and CYP143A1, as well as two ferredoxins, FdxA and FdxC, can be considered promising novel therapeutic targets.
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Affiliation(s)
- Sandra Ortega Ugalde
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Maikel Boot
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jan N M Commandeur
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Paul Jennings
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section of Molecular Microbiology, AIMMS, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - J Chris Vos
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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24
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Gislason AS, Turner K, Domaratzki M, Cardona ST. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. Microb Genom 2019; 3. [PMID: 29208119 PMCID: PMC5729917 DOI: 10.1099/mgen.0.000140] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.
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Affiliation(s)
- April S Gislason
- 1Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith Turner
- 2Monsanto Company, 700 Chesterfield Parkway W, Chesterfield, MO, 63017, USA
| | - Mike Domaratzki
- 3Department of Computer Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Silvia T Cardona
- 4Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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25
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Zhu L, Olsen RJ, Beres SB, Eraso JM, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Charbonneau ARL, Waller AS, Musser JM. Gene fitness landscape of group A streptococcus during necrotizing myositis. J Clin Invest 2019; 129:887-901. [PMID: 30667377 PMCID: PMC6355216 DOI: 10.1172/jci124994] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Abstract
Necrotizing fasciitis and myositis are devastating infections characterized by high mortality. Group A streptococcus (GAS) is a common cause of these infections, but the molecular pathogenesis is poorly understood. We report a genome-wide analysis using serotype M1 and M28 strains that identified GAS genes contributing to necrotizing myositis in nonhuman primates (NHP), a clinically relevant model. Using transposon-directed insertion-site sequencing (TraDIS), we identified 126 and 116 GAS genes required for infection by serotype M1 and M28 organisms, respectively. For both M1 and M28 strains, more than 25% of the GAS genes required for necrotizing myositis encode known or putative transporters. Thirteen GAS transporters contributed to both M1 and M28 strain fitness in NHP myositis, including putative importers for amino acids, carbohydrates, and vitamins and exporters for toxins, quorum-sensing peptides, and uncharacterized molecules. Targeted deletion of genes encoding 5 transporters confirmed that each isogenic mutant strain was significantly (P < 0.05) impaired in causing necrotizing myositis in NHPs. Quantitative reverse-transcriptase PCR (qRT-PCR) analysis showed that these 5 genes are expressed in infected NHP and human skeletal muscle. Certain substrate-binding lipoproteins of these transporters, such as Spy0271 and Spy1728, were previously documented to be surface exposed, suggesting that our findings have translational research implications.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Stephen B. Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Jesus M. Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L. Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C. Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Leslie Jenkins
- Department of Comparative Medicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Amelia R. L. Charbonneau
- Animal Health Trust, Newmarket, Suffolk, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
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26
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Abdallah AM, Weerdenburg EM, Guan Q, Ummels R, Borggreve S, Adroub SA, Malas TB, Naeem R, Zhang H, Otto TD, Bitter W, Pain A. Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator. PLoS One 2019; 14:e0211003. [PMID: 30673778 PMCID: PMC6343904 DOI: 10.1371/journal.pone.0211003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
The mycobacterial type VII secretion system ESX-1 is responsible for the secretion of a number of proteins that play important roles during host infection. The regulation of the expression of secreted proteins is often essential to establish successful infection. Using transcriptome sequencing, we found that the abrogation of ESX-1 function in Mycobacterium marinum leads to a pronounced increase in gene expression levels of the espA operon during the infection of macrophages. In addition, the disruption of ESX-1-mediated protein secretion also leads to a specific down-regulation of the ESX-1 substrates, but not of the structural components of this system, during growth in culture medium. This effect is observed in both M. marinum and M. tuberculosis. We established that down-regulation of ESX-1 substrates is the result of a regulatory process that is influenced by the putative transcriptional regulator whib6, which is located adjacent to the esx-1 locus. In addition, the overexpression of the ESX-1-associated PE35/PPE68 protein pair resulted in a significantly increased secretion of the ESX-1 substrate EsxA, demonstrating a functional link between these proteins. Taken together, these data show that WhiB6 is required for the secretion-dependent regulation of ESX-1 substrates and that ESX-1 substrates are regulated independently from the structural components, both during infection and as a result of active secretion.
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Affiliation(s)
- Abdallah M. Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
- * E-mail: (AMA); (WB); (AP)
| | - Eveline M. Weerdenburg
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Stephanie Borggreve
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Sabir A. Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Tareq B. Malas
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Raeece Naeem
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Huoming Zhang
- Bioscience Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
| | - Thomas D. Otto
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail: (AMA); (WB); (AP)
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Kingdom of Saudi Arabia
- * E-mail: (AMA); (WB); (AP)
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27
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Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ. Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes. Genome Res 2019; 29:396-406. [PMID: 30635343 PMCID: PMC6396416 DOI: 10.1101/gr.232330.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/03/2019] [Indexed: 12/22/2022]
Abstract
To understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene. These results are often ported to newly sequenced genomes by using sequence homology. However, sequence similarity does not always mean identical function or phenotype, suggesting that new methods are required to functionally annotate newly sequenced species. We have implemented comparative analysis by high-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent functions and/or different genetic interactions. Comprehensive gene dispensability comparisons with S. cerevisiae predicted diverged dispensability at 12% of conserved orthologs, and validation experiments confirmed 22 differentially essential genes. Despite their differences in essentiality, these genes were capable of cross-species complementation, demonstrating that trans-acting factors that are background-dependent contribute to differential gene essentiality. This study shows that direct experimental testing of gene disruption phenotypes across species can inform comparative genomic analyses and improve gene annotations. Our method can be widely applied in microorganisms to further our understanding of genome evolution.
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Affiliation(s)
- Monica R Sanchez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Frances Cheong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Blake T Hovde
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Sarah Bissonnette
- Department of Biological Sciences, California State University, Turlock, California 95382, USA
| | - Adam P Arkin
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Jeffrey M Skerker
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, California 94945, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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28
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Hashish E, Merwad A, Elgaml S, Amer A, Kamal H, Elsadek A, Marei A, Sitohy M. Mycobacterium marinum infection in fish and man: epidemiology, pathophysiology and management; a review. Vet Q 2018; 38:35-46. [PMID: 29493404 PMCID: PMC6831007 DOI: 10.1080/01652176.2018.1447171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/26/2018] [Indexed: 11/04/2022] Open
Abstract
Mycobacterium marinum is an opportunistic pathogen inducing infection in fresh and marine water fish. This pathogen causes necrotizing granuloma like tuberculosis, morbidity and mortality in fish. The cell wall-associated lipid phthiocerol dimycocerosates, phenolic glycolipids and ESAT-6 secretion system 1 (ESX-1) are the conserved virulence determinant of the organism. Human infections with Mycobacterium marinum hypothetically are classified into four clinical categories (type I-type IV) and have been associated with the exposure of damaged skin to polluted water from fish pools or contacting objects contaminated with infected fish. Fish mycobacteriosis is clinically manifested and characterized in man by purple painless nodules, liable to develop into superficial crusting ulceration with scar formation. Early laboratory diagnosis of M. marinum including histopathology, culture and PCR is essential and critical as the clinical response to antibiotics requires months to be attained. The pathogenicity and virulence determinants of M. marinum need to be thoroughly and comprehensively investigated and understood. In spite of accumulating information on this pathogen, the different relevant data should be compared, connected and globally compiled. This article is reviewing the epidemiology, virulence factors, diagnosis and disease management in fish while casting light on the potential associated public health hazards.
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Affiliation(s)
- Emad Hashish
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Abdallah Merwad
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Shimaa Elgaml
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Ali Amer
- Tuberculosis Unit, Animal Health Research Institute (AHRI), Giza, Egypt
| | - Huda Kamal
- Department of Meat Hygiene, National Research Center (NRC), Zagazig, Egypt
| | - Ahmed Elsadek
- Immunology Research Lab, Immunology Division, Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Egypt
| | - Ayman Marei
- Immunology Research Lab, Immunology Division, Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Egypt
| | - Mahmoud Sitohy
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Egypt
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29
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Phan TH, van Leeuwen LM, Kuijl C, Ummels R, van Stempvoort G, Rubio-Canalejas A, Piersma SR, Jiménez CR, van der Sar AM, Houben ENG, Bitter W. EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF. PLoS Pathog 2018; 14:e1007247. [PMID: 30102741 PMCID: PMC6107294 DOI: 10.1371/journal.ppat.1007247] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/23/2018] [Accepted: 07/26/2018] [Indexed: 12/31/2022] Open
Abstract
The pathogen Mycobacterium tuberculosis employs a range of ESX-1 substrates to manipulate the host and build a successful infection. Although the importance of ESX-1 secretion in virulence is well established, the characterization of its individual components and the role of individual substrates is far from complete. Here, we describe the functional characterization of the Mycobacterium marinum accessory ESX-1 proteins EccA1, EspG1 and EspH, i.e. proteins that are neither substrates nor structural components. Proteomic analysis revealed that EspG1 is crucial for ESX-1 secretion, since all detectable ESX-1 substrates were absent from the cell surface and culture supernatant in an espG1 mutant. Deletion of eccA1 resulted in minor secretion defects, but interestingly, the severity of these secretion defects was dependent on the culture conditions. Finally, espH deletion showed a partial secretion defect; whereas several ESX-1 substrates were secreted in normal amounts, secretion of EsxA and EsxB was diminished and secretion of EspE and EspF was fully blocked. Interaction studies showed that EspH binds EspE and therefore could function as a specific chaperone for this substrate. Despite the observed differences in secretion, hemolytic activity was lost in all M. marinum mutants, implying that hemolytic activity is not strictly correlated with EsxA secretion. Surprisingly, while EspH is essential for successful infection of phagocytic host cells, deletion of espH resulted in a significantly increased virulence phenotype in zebrafish larvae, linked to poor granuloma formation and extracellular outgrowth. Together, these data show that different sets of ESX-1 substrates play different roles at various steps of the infection cycle of M. marinum. M. tuberculosis is a facultative intracellular pathogen that has an intimate relationship with host macrophages. Proteins secreted by the ESX-1 secretion system play an important role in this interaction, for instance by orchestrating the escape from the phagosome into the cytosol of the macrophage. However, the exact role of the ESX-1 substrates is unknown, due to their complicated interdependency for secretion. Here, we study the function of ESX-1 accessory proteins EccA1, EspG1 and EspH in ESX-1 secretion in Mycobacterium marium, the causative agent of fish tuberculosis. We found that these proteins affect the secretion of different substrate classes, which offers an approach to study the roles of these substrate groups. An espG1 deletion broadly aborts ESX-1 secretion and thus resulted in severe attenuation in a zebrafish model for tuberculosis, whereas EccA1 is only crucial under specific growth conditions. The most surprising results were obtained for EspH. This protein seems to function as a molecular chaperone for EspE and is as such involved in the secretion of a small subset of ESX-1 substrates. Disruption of espH showed a dual character: whereas this gene is essential for the successful infection of macrophages, deletion of espH resulted in significantly increased virulence in zebrafish larvae. These data convincingly show that different subsets of ESX-1 substrates play different roles at various steps in the mycobacterial infection cycle.
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Affiliation(s)
- Trang H. Phan
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lisanne M. van Leeuwen
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Coen Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Gunny van Stempvoort
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Alba Rubio-Canalejas
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, OncoProteomics Laboratory, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Astrid M. van der Sar
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Edith N. G. Houben
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- * E-mail:
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30
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Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing. Sci Rep 2018; 8:12040. [PMID: 30104693 PMCID: PMC6089878 DOI: 10.1038/s41598-018-30152-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the "M"- and the "Aronson"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.
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Wong YC, Abd El Ghany M, Ghazzali RNM, Yap SJ, Hoh CC, Pain A, Nathan S. Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model. Front Microbiol 2018; 9:1118. [PMID: 29896180 PMCID: PMC5987112 DOI: 10.3389/fmicb.2018.01118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022] Open
Abstract
A Burkholderia cenocepacia infection usually leads to reduced survival and fatal cepacia syndrome in cystic fibrosis patients. The identification of B. cenocepacia essential genes for in vivo survival is key to designing new anti-infectives therapies. We used the Transposon-Directed Insertion Sequencing (TraDIS) approach to identify genes required for B. cenocepacia survival in the model infection host, Caenorhabditis elegans. A B. cenocepacia J2315 transposon pool of ∼500,000 mutants was used to infect C. elegans. We identified 178 genes as crucial for B. cenocepacia survival in the infected nematode. The majority of these genes code for proteins of unknown function, many of which are encoded by the genomic island BcenGI13, while other gene products are involved in nutrient acquisition, general stress responses and LPS O-antigen biosynthesis. Deletion of the glycosyltransferase gene wbxB and a histone-like nucleoid structuring (H-NS) protein-encoding gene (BCAL0154) reduced bacterial accumulation and attenuated virulence in C. elegans. Further analysis using quantitative RT-PCR indicated that BCAL0154 modulates B. cenocepacia pathogenesis via transcriptional regulation of motility-associated genes including fliC, fliG, flhD, and cheB1. This screen has successfully identified genes required for B. cenocepacia survival within the host-associated environment, many of which are potential targets for developing new antimicrobials.
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Affiliation(s)
- Yee-Chin Wong
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Moataz Abd El Ghany
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,The Westmead Institute for Medical Research and The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Raeece N M Ghazzali
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | | | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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Esx Paralogs Are Functionally Equivalent to ESX-1 Proteins but Are Dispensable for Virulence in Mycobacterium marinum. J Bacteriol 2018; 200:JB.00726-17. [PMID: 29555701 DOI: 10.1128/jb.00726-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/11/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium marinum is a nontuberculous pathogen of poikilothermic fish and an opportunistic human pathogen. Like tuberculous mycobacteria, the M. marinum M strain requires the ESX-1 (ESAT-6 system 1) secretion system for virulence in host cells. EsxB and EsxA, two major virulence factors exported by the ESX-1 system, are encoded by the esxBA genes within the ESX-1 locus. Deletion of the esxBA genes abrogates ESX-1 export and attenuates M. marinum in ex vivo and in vivo models of infection. Interestingly, there are several duplications of the esxB and esxA genes (esxB_1, esxB_2, esxA_1, esxA_2, and esxA_3) in the M. marinum M genome located outside the ESX-1 locus. We sought to understand if this region, known as ESX-6, contributes to ESX-1-mediated virulence. We found that deletion of the esxB_1 gene alone or the entire ESX-6 locus did not impact ESX-1 export or function, supporting the idea that the esxBA genes present at the ESX-1 locus are the primary contributors to ESX-1-mediated virulence. Nevertheless, overexpression of the esxB_1 locus complemented ESX-1 function in the ΔesxBA strain, signifying that the two loci are functionally equivalent. Our findings raise questions about why duplicate versions of the esxBA genes are maintained in the M. marinum M genome and how these proteins, which are functionally equivalent to virulence factors, contribute to mycobacterial biology.IMPORTANCEMycobacterium tuberculosis is the causative agent of the human disease tuberculosis (TB). There are 10.4 million cases and 1.7 million TB-associated deaths annually, making TB a leading cause of death globally. Nontuberculous mycobacteria (NTM) cause chronic human infections that are acquired from the environment. Despite differences in disease etiology, both tuberculous and NTM pathogens use the ESX-1 secretion system to cause disease. The nontubercular mycobacterial species, Mycobacterium marinum, has additional copies of specific ESX-1 genes. Our findings demonstrate that the duplicated genes do not contribute to virulence but can substitute for virulence factors in M. marinum These findings suggest that the duplicated genes may play a specific role in NTM biology.
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Brockmeier SL, Loving CL, Nicholson TL, Wang J, Peters SE, Weinert L, Chaudhuri R, Seilly DJ, Langford PR, Rycroft A, Wren BW, Maskell DJ, Tucker AW. Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs. Infect Immun 2018; 86:e00559-17. [PMID: 29203546 PMCID: PMC5820948 DOI: 10.1128/iai.00559-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis, the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.
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Affiliation(s)
| | | | | | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Roy Chaudhuri
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Andrew Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire, United Kingdom
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Structural and functional characterisation of the cytochrome P450 enzyme CYP268A2 from Mycobacterium marinum. Biochem J 2018; 475:705-722. [DOI: 10.1042/bcj20170946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 11/17/2022]
Abstract
Members of the cytochrome P450 monooxygenase family CYP268 are found across a broad range of Mycobacterium species including the pathogens Mycobacterium avium, M. colombiense, M. kansasii, and M. marinum. CYP268A2, from M. marinum, which is the first member of this family to be studied, was purified and characterised. CYP268A2 was found to bind a variety of substrates with high affinity, including branched and straight chain fatty acids (C10–C12), acetate esters, and aromatic compounds. The enzyme was also found to bind phenylimidazole inhibitors but not larger azoles, such as ketoconazole. The monooxygenase activity of CYP268A2 was efficiently reconstituted using heterologous electron transfer partner proteins. CYP268A2 hydroxylated geranyl acetate and trans-pseudoionone at a terminal methyl group to yield (2E,6E)-8-hydroxy-3,7-dimethylocta-2,6-dien-1-yl acetate and (3E,5E,9E)-11-hydroxy-6,10-dimethylundeca-3,5,9-trien-2-one, respectively. The X-ray crystal structure of CYP268A2 was solved to a resolution of 2.0 Å with trans-pseudoionone bound in the active site. The overall structure was similar to that of the related phytanic acid monooxygenase CYP124A1 enzyme from Mycobacterium tuberculosis, which shares 41% sequence identity. The active site is predominantly hydrophobic, but includes the Ser99 and Gln209 residues which form hydrogen bonds with the terminal carbonyl group of the pseudoionone. The structure provided an explanation on why CYP268A2 shows a preference for shorter substrates over the longer chain fatty acids which bind to CYP124A1 and the selective nature of the catalysed monooxygenase activity.
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Laencina L, Dubois V, Le Moigne V, Viljoen A, Majlessi L, Pritchard J, Bernut A, Piel L, Roux AL, Gaillard JL, Lombard B, Loew D, Rubin EJ, Brosch R, Kremer L, Herrmann JL, Girard-Misguich F. Identification of genes required for Mycobacterium abscessus growth in vivo with a prominent role of the ESX-4 locus. Proc Natl Acad Sci U S A 2018; 115:E1002-E1011. [PMID: 29343644 PMCID: PMC5798338 DOI: 10.1073/pnas.1713195115] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium abscessus, a rapidly growing mycobacterium (RGM) and an opportunistic human pathogen, is responsible for a wide spectrum of clinical manifestations ranging from pulmonary to skin and soft tissue infections. This intracellular organism can resist the bactericidal defense mechanisms of amoebae and macrophages, an ability that has not been observed in other RGM. M. abscessus can up-regulate several virulence factors during transient infection of amoebae, thereby becoming more virulent in subsequent respiratory infections in mice. Here, we sought to identify the M. abscessus genes required for replication within amoebae. To this end, we constructed and screened a transposon (Tn) insertion library of an M. abscessus subspecies massiliense clinical isolate for attenuated clones. This approach identified five genes within the ESX-4 locus, which in M. abscessus encodes an ESX-4 type VII secretion system that exceptionally also includes the ESX conserved EccE component. To confirm the screening results and to get further insight into the contribution of ESX-4 to M. abscessus growth and survival in amoebae and macrophages, we generated a deletion mutant of eccB4 that encodes a core structural element of ESX-4. This mutant was less efficient at blocking phagosomal acidification than its parental strain. Importantly, and in contrast to the wild-type strain, it also failed to damage phagosomes and showed reduced signs of phagosome-to-cytosol contact, as demonstrated by a combination of cellular and immunological assays. This study attributes an unexpected and genuine biological role to the underexplored mycobacterial ESX-4 system and its substrates.
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Affiliation(s)
- Laura Laencina
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Violaine Dubois
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Vincent Le Moigne
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Laleh Majlessi
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, 75015 Paris, France
| | - Justin Pritchard
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Audrey Bernut
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Laura Piel
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Anne-Laure Roux
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
| | - Jean-Louis Gaillard
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
| | - Bérengère Lombard
- Laboratoire de spectrométrie de masse protéomique, Institut Curie, Paris Science and Letters Research University, 75248 Paris, France
| | - Damarys Loew
- Laboratoire de spectrométrie de masse protéomique, Institut Curie, Paris Science and Letters Research University, 75248 Paris, France
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Roland Brosch
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, 75015 Paris, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
- INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Jean-Louis Herrmann
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France;
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
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Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments. mBio 2018; 9:mBio.02345-17. [PMID: 29382738 PMCID: PMC5790920 DOI: 10.1128/mbio.02345-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes. Only Actinobacteria and Proteobacteria were identified as steroid degraders, but we identified several alpha- and gammaproteobacterial lineages not previously known to degrade steroids. Actino- and proteobacterial steroid degraders coexisted in wastewater, while soil and rhizosphere samples contained mostly actinobacterial ones. Actinobacterial steroid degraders were found in deep ocean samples, while mostly alpha- and gammaproteobacterial ones were found in other marine samples, including sponges. Isolation of steroid-degrading bacteria from sponges confirmed their presence. Phylogenetic analysis of key steroid degradation proteins suggested their biochemical novelty in genomes from sponges and other environments. This study shows that the ecological significance as well as taxonomic and biochemical diversity of bacterial steroid degradation has so far been largely underestimated, especially in the marine environment. Microbial steroid degradation is a critical process for biomass decomposition in natural environments, for removal of important pollutants during wastewater treatment, and for pathogenesis of bacteria associated with tuberculosis and other bacteria. To date, microbial steroid degradation was mainly studied in a few model organisms, while the ecological significance of steroid degradation remained largely unexplored. This study provides the first analysis of aerobic steroid degradation in diverse natural, engineered, and host-associated environments via bioinformatic analysis of an extensive metagenome data set. We found that steroid-degrading bacteria are globally distributed and prevalent in wastewater treatment plants, soil, plant rhizospheres, and the marine environment, especially in marine sponges. We show that the ecological significance as well as the taxonomic and biochemical diversity of bacterial steroid degradation has been largely underestimated. This study greatly expands our ecological and evolutionary understanding of microbial steroid degradation.
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Cardenal-Muñoz E, Barisch C, Lefrançois LH, López-Jiménez AT, Soldati T. When Dicty Met Myco, a (Not So) Romantic Story about One Amoeba and Its Intracellular Pathogen. Front Cell Infect Microbiol 2018; 7:529. [PMID: 29376033 PMCID: PMC5767268 DOI: 10.3389/fcimb.2017.00529] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023] Open
Abstract
In recent years, Dictyostelium discoideum has become an important model organism to study the cell biology of professional phagocytes. This amoeba not only shares many molecular features with mammalian macrophages, but most of its fundamental signal transduction pathways are conserved in humans. The broad range of existing genetic and biochemical tools, together with its suitability for cell culture and live microscopy, make D. discoideum an ideal and versatile laboratory organism. In this review, we focus on the use of D. discoideum as a phagocyte model for the study of mycobacterial infections, in particular Mycobacterium marinum. We look in detail at the intracellular cycle of M. marinum, from its uptake by D. discoideum to its active or passive egress into the extracellular medium. In addition, we describe the molecular mechanisms that both the mycobacterial invader and the amoeboid host have developed to fight against each other, and compare and contrast with those developed by mammalian phagocytes. Finally, we introduce the methods and specific tools that have been used so far to monitor the D. discoideum-M. marinum interaction.
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Affiliation(s)
- Elena Cardenal-Muñoz
- Department of Biochemistry, Sciences II, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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Dunn JD, Bosmani C, Barisch C, Raykov L, Lefrançois LH, Cardenal-Muñoz E, López-Jiménez AT, Soldati T. Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses. Front Immunol 2018; 8:1906. [PMID: 29354124 PMCID: PMC5758549 DOI: 10.3389/fimmu.2017.01906] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
The soil-dwelling social amoeba Dictyostelium discoideum feeds on bacteria. Each meal is a potential infection because some bacteria have evolved mechanisms to resist predation. To survive such a hostile environment, D. discoideum has in turn evolved efficient antimicrobial responses that are intertwined with phagocytosis and autophagy, its nutrient acquisition pathways. The core machinery and antimicrobial functions of these pathways are conserved in the mononuclear phagocytes of mammals, which mediate the initial, innate-immune response to infection. In this review, we discuss the advantages and relevance of D. discoideum as a model phagocyte to study cell-autonomous defenses. We cover the antimicrobial functions of phagocytosis and autophagy and describe the processes that create a microbicidal phagosome: acidification and delivery of lytic enzymes, generation of reactive oxygen species, and the regulation of Zn2+, Cu2+, and Fe2+ availability. High concentrations of metals poison microbes while metal sequestration inhibits their metabolic activity. We also describe microbial interference with these defenses and highlight observations made first in D. discoideum. Finally, we discuss galectins, TNF receptor-associated factors, tripartite motif-containing proteins, and signal transducers and activators of transcription, microbial restriction factors initially characterized in mammalian phagocytes that have either homologs or functional analogs in D. discoideum.
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Affiliation(s)
- Joe Dan Dunn
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Cristina Bosmani
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Barisch
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Lyudmil Raykov
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Louise H Lefrançois
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Elena Cardenal-Muñoz
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Thierry Soldati
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
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Novel Genes Required for the Fitness of Streptococcus pyogenes in Human Saliva. mSphere 2017; 2:mSphere00460-17. [PMID: 29104937 PMCID: PMC5663985 DOI: 10.1128/mspheredirect.00460-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pyogenes (group A streptococcus [GAS]) causes 600 million cases of pharyngitis each year. Despite this considerable disease burden, the molecular mechanisms used by GAS to infect, cause clinical pharyngitis, and persist in the human oropharynx are poorly understood. Saliva is ubiquitous in the human oropharynx and is the first material GAS encounters in the upper respiratory tract. Thus, a fuller understanding of how GAS survives and proliferates in saliva may provide valuable insights into the molecular mechanisms at work in the human oropharynx. We generated a highly saturated transposon insertion mutant library in serotype M1 strain MGAS2221, a strain genetically representative of a pandemic clone that arose in the 1980s and spread globally. The transposon mutant library was exposed to human saliva to screen for GAS genes required for wild-type fitness in this clinically relevant fluid. Using transposon-directed insertion site sequencing (TraDIS), we identified 92 genes required for GAS fitness in saliva. The more prevalent categories represented were genes involved in carbohydrate transport/metabolism, amino acid transport/metabolism, and inorganic ion transport/metabolism. Using six isogenic mutant strains, we confirmed that each of the mutants was significantly impaired for growth or persistence in human saliva ex vivo. Mutants with an inactivated Spy0644 (sptA) or Spy0646 (sptC) gene had especially severe persistence defects. This study is the first to use of TraDIS to study bacterial fitness in human saliva. The new information we obtained will be valuable for future translational maneuvers designed to prevent or treat human GAS infections. IMPORTANCE The human bacterial pathogen Streptococcus pyogenes (group A streptococcus [GAS]) causes more than 600 million cases of pharyngitis annually worldwide, 15 million of which occur in the United States. The human oropharynx is the primary anatomic site for GAS colonization and infection, and saliva is the first material encountered. Using a genome-wide transposon mutant screen, we identified 92 GAS genes required for wild-type fitness in human saliva. Many of the identified genes are involved in carbohydrate transport/metabolism, amino acid transport/metabolism, and inorganic ion transport/metabolism. The new information is potentially valuable for developing novel GAS therapeutics and vaccine research.
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A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis. Sci Rep 2017; 7:41923. [PMID: 28165493 PMCID: PMC5292949 DOI: 10.1038/srep41923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/30/2016] [Indexed: 01/14/2023] Open
Abstract
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
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Boot M, Sparrius M, Jim KK, Commandeur S, Speer A, van de Weerd R, Bitter W. iniBAC induction Is Vitamin B12- and MutAB-dependent in Mycobacterium marinum. J Biol Chem 2016; 291:19800-19812. [PMID: 27474746 PMCID: PMC5025670 DOI: 10.1074/jbc.m116.724088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/01/2016] [Indexed: 01/29/2024] Open
Abstract
Tuberculosis can be treated with a 6-month regimen of antibiotics. Although the targets of most of the first-line antibiotics have been identified, less research has focused on the intrabacterial stress responses that follow upon treatment with antibiotics. Studying the roles of these stress genes may lead to the identification of crucial stress-coping mechanisms that can provide additional drug targets to increase treatment efficacy. A three-gene operon with unknown function that is strongly up-regulated upon treatment with isoniazid and ethambutol is the iniBAC operon. We have reproduced these findings and show that iniBAC genes are also induced in infected host cells, although with higher variability. Next, we set out to elucidate the genetic network that results in iniBAC induction in Mycobacterium marinum By transposon mutagenesis, we identified that the operon is highly induced by mutations in genes encoding enzymes of the vitamin B12 biosynthesis pathway and the vitamin B12-dependent methylmalonyl-CoA-mutase MutAB. Lipid analysis showed that a mutA::tn mutant has decreased phthiocerol dimycocerosates levels, suggesting a link between iniBAC induction and the production of methyl-branched lipids. Moreover, a similar screen in Mycobacterium bovis BCG identified that phthiocerol dimycocerosate biosynthesis mutants cause the up-regulation of iniBAC genes. Based on these data, we propose that iniBAC is induced in response to mutations that cause defects in the biosynthesis of methyl-branched lipids. The resulting metabolic stress caused by these mutations or caused by ethambutol or isoniazid treatment may be relieved by iniBAC to increase the chance of bacterial survival.
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Affiliation(s)
- Maikel Boot
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Marion Sparrius
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Kin Ki Jim
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Susanna Commandeur
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Alexander Speer
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Robert van de Weerd
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wilbert Bitter
- From the Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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42
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Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC, Pain A, Nathan S. Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS. Front Microbiol 2016; 7:1288. [PMID: 27597847 PMCID: PMC4993015 DOI: 10.3389/fmicb.2016.01288] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/04/2016] [Indexed: 12/13/2022] Open
Abstract
Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.
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Affiliation(s)
- Yee-Chin Wong
- Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia Bangi, Malaysia
| | - Moataz Abd El Ghany
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia; The Westmead Institute for Medical Research and The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, SydneyNSW, Australia
| | - Raeece Naeem
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | | | - Arnab Pain
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Sheila Nathan
- Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia Bangi, Malaysia
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43
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Guimaraes AJ, Gomes KX, Cortines JR, Peralta JM, Peralta RHS. Acanthamoeba spp. as a universal host for pathogenic microorganisms: One bridge from environment to host virulence. Microbiol Res 2016; 193:30-38. [PMID: 27825484 DOI: 10.1016/j.micres.2016.08.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Free-living amoebas (FLA) are ubiquitous environmental protists that have enormously contributed to the microbiological contamination of water sources. FLAs have displayed resistance to environmental adversities and germicides and have played important roles in the population control of microbial communities due to its predatory behavior and microbicidal activity. However, some organisms have developed resistance to the intracellular milieu of amoebas, as in the case of Acanthamoebas, which in turn, have been functioning as excellent reservoirs for amoeba-resistant microorganisms (ARMs), such as bacteria, viruses and fungi. Little is known about these relationships and interaction mechanisms, but it is speculated that the FLAs need a very broad repertoire or universal class of receptors to bind and recognize these diverse species of microorganisms. By harboring these organisms as a "Trojan Horse", the Achantamoeba has been working as an excellent vector for pathogens. Moreover, studies have demonstrated that the interaction of pathogens with Acanthamoeba results in environmental selective pressure responsible for induction and maintenance of virulence factors and increase in microbial pathogenicity. This phenomenon is correlated to the observation of higher gene number and DNA content of ARMs, when compared to their relatives which are adapted to other hosts, due to allopatric or sympatric gene transfer and acquisition, contradicting the overall genome reduction theory for intracellularly adapted pathogens. Thus, adaptation to FLAs indirectly provided a "learning" environment for pathogens to resist later to macrophages; besides the evolutionary distance, these phagocytes share similar predatory mechanisms, such as phagocytosis and phagolysossomal degradation. In this mini-review, we cover the most important aspects of Acanthamoeba biology and their interactions with endemically important human pathogens.
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Affiliation(s)
- Allan J Guimaraes
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Brazil.
| | - Kamilla Xavier Gomes
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Brazil
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - José Mauro Peralta
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil.
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44
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Ates LS, van der Woude AD, Bestebroer J, van Stempvoort G, Musters RJP, Garcia-Vallejo JJ, Picavet DI, Weerd RVD, Maletta M, Kuijl CP, van der Wel NN, Bitter W. The ESX-5 System of Pathogenic Mycobacteria Is Involved In Capsule Integrity and Virulence through Its Substrate PPE10. PLoS Pathog 2016; 12:e1005696. [PMID: 27280885 PMCID: PMC4900558 DOI: 10.1371/journal.ppat.1005696] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/20/2016] [Indexed: 11/18/2022] Open
Abstract
Mycobacteria produce a capsule layer, which consists of glycan-like polysaccharides and a number of specific proteins. In this study, we show that, in slow-growing mycobacteria, the type VII secretion system ESX-5 plays a major role in the integrity and stability of the capsule. We have identified PPE10 as the ESX-5 substrate responsible for this effect. Mutants in esx-5 and ppe10 both have impaired capsule integrity as well as reduced surface hydrophobicity. Electron microscopy, immunoblot and flow cytometry analyses demonstrated reduced amounts of surface localized proteins and glycolipids, and morphological differences in the capsular layer. Since capsular proteins secreted by the ESX-1 system are important virulence factors, we tested the effect of the mutations that cause capsular defects on virulence mechanisms. Both esx-5 and ppe10 mutants of Mycobacterium marinum were shown to be impaired in ESX-1-dependent hemolysis. In agreement with this, the ppe10 and esx5 mutants showed reduced recruitment of ubiquitin in early macrophage infection and intermediate attenuation in zebrafish embryos. These results provide a pivotal role for the ESX-5 secretion system and its substrate PPE10, in the capsular integrity of pathogenic mycobacteria. These findings open up new roads for research on the mycobacterial capsule and its role in virulence and immune modulation.
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Affiliation(s)
- Louis S Ates
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | - Aniek D van der Woude
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands.,Department of Molecular Microbiology, VU University, Amsterdam, the Netherlands
| | - Jovanka Bestebroer
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | | | - René J P Musters
- Department of Physiology and Cardiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Juan J Garcia-Vallejo
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, the Netherlands
| | - Daisy I Picavet
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Amsterdam the Netherlands
| | - Robert van de Weerd
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Coenraad P Kuijl
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands
| | - Nicole N van der Wel
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Amsterdam the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Prevention, VU University Medical Center, Amsterdam, the Netherlands.,Department of Molecular Microbiology, VU University, Amsterdam, the Netherlands
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45
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Singh VK, Berry L, Bernut A, Singh S, Carrère-Kremer S, Viljoen A, Alibaud L, Majlessi L, Brosch R, Chaturvedi V, Geurtsen J, Drancourt M, Kremer L. A unique PE_PGRS protein inhibiting host cell cytosolic defenses and sustaining full virulence of Mycobacterium marinum in multiple hosts. Cell Microbiol 2016; 18:1489-1507. [PMID: 27120981 DOI: 10.1111/cmi.12606] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/22/2016] [Accepted: 04/09/2016] [Indexed: 12/11/2022]
Abstract
Despite intense research, PE_PGRS proteins still represent an intriguing aspect of mycobacterial pathogenesis. These cell surface proteins influence virulence in several pathogenic species, but their diverse and exact functions remain unclear. Herein, we focussed on a PE_PGRS member from Mycobacterium marinum, MMAR_0242, characterized by an extended and unique C-terminal domain. We demonstrate that an M. marinum mutant carrying a transposon insertion in MMAR_0242 is highly impaired in its ability to replicate in macrophages and amoebae, because of its inability to inhibit lysosomal fusion. As a consequence, this mutant failed to survive intracellularly as evidenced by a reduced number of cytosolic actin tail-forming bacteria and by quantitative electron microscopy, which mainly localized MMAR_0242::Tn within membrane-defined vacuoles. Functional complementation studies indicated that the C-terminus, but not the N-terminal PE_PGRS domain, is required for intracellular growth/survival. In line with these findings, disruption of MMAR_0242 resulted in a highly attenuated virulence phenotype in zebrafish embryos, characterized by restricted bacterial loads and a failure to produce granulomas. Furthermore, expression of MMAR_0242 in Mycobacterium smegmatis, a non-pathogenic species naturally deficient in PE_PGRS production, resulted in increased survival in amoebae with enhanced cytotoxic cell death and increased survival in infected mice with splenomegaly. Overall, these results indicate that MMAR_0242 is required for full virulence of M. marinum and sufficient to confer pathogenic properties to M. smegmatis.
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Affiliation(s)
- Vipul K Singh
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, case 107, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France
| | - Laurence Berry
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, case 107, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France
| | - Audrey Bernut
- Centre d'étude des Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS FRE 3689, 1919 route de Mende, 34293, Montpellier, France
| | - Shubhra Singh
- Biochemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, Uttar Pradesh, India.,IFTM University, Lodhipur Rajput, Delhi Road (NH-24) Moradabad, Uttar Pradesh, 244102, India
| | - Séverine Carrère-Kremer
- INSERM U1058, Université de Montpellier and Department of Bacteriology-Virology, CHU de Montpellier, 34095, Montpellier, France
| | - Albertus Viljoen
- Centre d'étude des Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS FRE 3689, 1919 route de Mende, 34293, Montpellier, France
| | - Laeticia Alibaud
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, case 107, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France
| | - Laleh Majlessi
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, 25 rue du Dr. Roux, 75724, Paris, France
| | - Roland Brosch
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, 25 rue du Dr. Roux, 75724, Paris, France
| | - Vinita Chaturvedi
- Biochemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, Uttar Pradesh, India
| | - Jeroen Geurtsen
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 BT, Amsterdam, The Netherlands
| | - Michel Drancourt
- Université Aix-Marseille, URMITE, UMR63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Laurent Kremer
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, case 107, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France. .,Centre d'étude des Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS FRE 3689, 1919 route de Mende, 34293, Montpellier, France. .,INSERM, CPBS, 1919 route de Mende, Montpellier, France.
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46
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Shah S, Briken V. Modular Organization of the ESX-5 Secretion System in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2016; 6:49. [PMID: 27200304 PMCID: PMC4852179 DOI: 10.3389/fcimb.2016.00049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/18/2016] [Indexed: 11/30/2022] Open
Abstract
Mycobacteria utilize type VII secretion systems (T7SS) to export many of their important virulence proteins. The T7SS encompasses five homologous secretion systems (ESX-1 to ESX-5). Most pathogenic mycobacterial species, including the human pathogen Mycobacterium tuberculosis, possess all five ESX systems. The ESX-1, -3, and -5 systems are important for virulence of mycobacteria but the molecular mechanisms of their secretion apparatus and the identity and activity of secreted effector proteins are not well characterized. The different ESX systems show similarities in gene composition due to their common phylogenetic origin but recent studies demonstrate mechanistic as well as functional variations between the systems. For example, the ESX-1 system is involved in lysis of the phagosomal membrane and phagosomal escape of the bacteria while the ESX-5 system is required for mycobacterial cell wall stability and host cell lysis. Mechanistically, the ESX-1 substrates show interdependence during secretion while the ESX-5 system may use a duplicated four-gene region (ESX-5a) as an accessory system for transport of a subset of proteins of the ESX-5 secretome. In the present review we will provide an overview of the molecular components of the T7SS and their function with a particular focus on the ESX-5 system.
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Affiliation(s)
- Swati Shah
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, MD, USA
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47
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Wagner JM, Chan S, Evans TJ, Kahng S, Kim J, Arbing MA, Eisenberg D, Korotkov KV. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC STRUCTURAL BIOLOGY 2016; 16:5. [PMID: 26922638 PMCID: PMC4769845 DOI: 10.1186/s12900-016-0056-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
Background The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. Results This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB1 and EccD1. The periplasmic domain of EccB1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. The repeat domains of EccB1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD1has a ubiquitin-like fold and forms a dimer with a negatively charged groove. Conclusions These structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0056-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan M Wagner
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. .,Present address: Department of Molecular Physiology and Biological Physics and The Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA.
| | - Sum Chan
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Timothy J Evans
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. .,Present address: Division of Regulatory Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| | - Sara Kahng
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Jennifer Kim
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Mark A Arbing
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - David Eisenberg
- UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry & Biochemistry, and Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Konstantin V Korotkov
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA.
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48
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Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 2016; 32:1109-11. [PMID: 26794317 PMCID: PMC4896371 DOI: 10.1093/bioinformatics/btw022] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/13/2016] [Indexed: 12/05/2022] Open
Abstract
Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology. Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis Contact:parkhill@sanger.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Carla Cummins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Andrew J Page
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Gemma C Langridge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
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49
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Kwon YM, Ricke SC, Mandal RK. Transposon sequencing: methods and expanding applications. Appl Microbiol Biotechnol 2015; 100:31-43. [DOI: 10.1007/s00253-015-7037-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/15/2015] [Accepted: 09/20/2015] [Indexed: 12/26/2022]
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50
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Ates LS, Ummels R, Commandeur S, van der Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLoS Genet 2015; 11:e1005190. [PMID: 25938982 PMCID: PMC4418733 DOI: 10.1371/journal.pgen.1005190] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/02/2015] [Indexed: 12/03/2022] Open
Abstract
Mycobacteria possess different type VII secretion (T7S) systems to secrete proteins across their unusual cell envelope. One of these systems, ESX-5, is only present in slow-growing mycobacteria and responsible for the secretion of multiple substrates. However, the role of ESX-5 substrates in growth and/or virulence is largely unknown. In this study, we show that esx-5 is essential for growth of both Mycobacterium marinum and Mycobacterium bovis. Remarkably, this essentiality can be rescued by increasing the permeability of the outer membrane, either by altering its lipid composition or by the introduction of the heterologous porin MspA. Mutagenesis of the first nucleotide-binding domain of the membrane ATPase EccC5 prevented both ESX-5-dependent secretion and bacterial growth, but did not affect ESX-5 complex assembly. This suggests that the rescuing effect is not due to pores formed by the ESX-5 membrane complex, but caused by ESX-5 activity. Subsequent proteomic analysis to identify crucial ESX-5 substrates confirmed that all detectable PE and PPE proteins in the cell surface and cell envelope fractions were routed through ESX-5. Additionally, saturated transposon-directed insertion-site sequencing (TraDIS) was applied to both wild-type M. marinum cells and cells expressing mspA to identify genes that are not essential anymore in the presence of MspA. This analysis confirmed the importance of esx-5, but we could not identify essential ESX-5 substrates, indicating that multiple of these substrates are together responsible for the essentiality. Finally, examination of phenotypes on defined carbon sources revealed that an esx-5 mutant is strongly impaired in the uptake and utilization of hydrophobic carbon sources. Based on these data, we propose a model in which the ESX-5 system is responsible for the transport of cell envelope proteins that are required for nutrient uptake. These proteins might in this way compensate for the lack of MspA-like porins in slow-growing mycobacteria.
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Affiliation(s)
- Louis S. Ates
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Susanna Commandeur
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Robert van der Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marion Sparrius
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Eveline Weerdenburg
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Abdallah M. Abdallah
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Moataz Abd El Ghany
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Alyaa M. Abdel-Haleem
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Connie R. Jiménez
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Edith N.G. Houben
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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