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Delerue T, Chareyre S, Anantharaman V, Gilmore MC, Popham DL, Cava F, Aravind L, Ramamurthi KS. Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561273. [PMID: 37986874 PMCID: PMC10659427 DOI: 10.1101/2023.10.06.561273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Bacillus subtilis spores are produced inside the cytosol of a mother cell. Spore surface assembly requires the SpoVK protein in the mother cell, but its function is unknown. Here, we report that SpoVK is a dedicated chaperone from a distinct higher-order clade of AAA+ ATPases that activates the peptidoglycan glycosyltransferase MurG during sporulation, even though MurG does not normally require activation by a chaperone during vegetative growth. MurG redeploys to the spore surface during sporulation, where we show that the local pH is reduced and propose that this change in cytosolic nanoenvironment necessitates a specific chaperone for proper MurG function. Further, we show that SpoVK participates in a developmental checkpoint in which improper spore surface assembly inactivates SpoVK, which leads to sporulation arrest. The AAA+ ATPase clade containing SpoVK includes other dedicated chaperones involved in secretion, cell-envelope biosynthesis, and carbohydrate metabolism, suggesting that such fine-tuning might be a widespread feature of different subcellular nanoenvironments.
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Affiliation(s)
- Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael C. Gilmore
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Gracy J, Vallejos-Sanchez K, Cohen-Gonsaud M. SecretoMyc, a web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools. Tuberculosis (Edinb) 2023; 141:102375. [PMID: 37429152 DOI: 10.1016/j.tube.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
To better understand the interaction between the host and the Mycobacterium tuberculosis pathogen, it is critical to identify its potential secreted proteins. While various experimental methods have been successful in identifying proteins under specific culture conditions, they have not provided a comprehensive characterisation of the secreted proteome. We utilized a combination of bioinformatics servers and in-house software to identify all potentially secreted proteins from six mycobacterial genomes through the three secretion systems: SEC, TAT, and T7SS. The results are presented in a database that can be crossed referenced to selected proteomics and transcriptomics studies (https://secretomyc.cbs.cnrs.fr). In addition, thanks to the recent availability of Alphafold models, we developed a tool in order to identify the structural homologues among the mycobacterial genomes.
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Affiliation(s)
- Jérôme Gracy
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France
| | - Katherine Vallejos-Sanchez
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France; Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Martin Cohen-Gonsaud
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France.
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Famelis N, Geibel S, van Tol D. Mycobacterial type VII secretion systems. Biol Chem 2023; 0:hsz-2022-0350. [PMID: 37276364 DOI: 10.1515/hsz-2022-0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
Mycobacteria, such as the pathogen M. tuberculosis, utilize up to five paralogous type VII secretion systems to transport proteins across their cell envelope. Since these proteins associate in pairs that depend on each other for transport to a different extent, the secretion pathway to the bacterial surface remained challenging to address. Structural characterization of the inner-membrane embedded secretion machineries along with recent advances on the substrates' co-dependencies for transport allow for the first time more detailed and testable models for secretion.
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Affiliation(s)
- Nikolaos Famelis
- Institute for Molecular Infection Biology, Julius Maximilian University of Würzburg, D-97080 Würzburg, Germany
| | - Sebastian Geibel
- Leiden Institute of Chemistry, Leiden University, NL-2333 CC Leiden, Netherlands
| | - Daan van Tol
- Leiden Institute of Chemistry, Leiden University, NL-2333 CC Leiden, Netherlands
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Dwivedi M, Bajpai K. The chamber of secretome in Mycobacterium tuberculosis as a potential therapeutic target. Biotechnol Genet Eng Rev 2022; 39:1-44. [PMID: 35613080 DOI: 10.1080/02648725.2022.2076031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mycobacterium tuberculosis (MTB) causes one of the ancient diseases, Tuberculosis, affects people around the globe and its severity can be understood by its classification as a second infectious disease after COVID-19 and the 13th leading cause of death according to a WHO report. Despite having advanced diagnostic approaches and therapeutic strategies, unfortunately, TB is still spreading across the population due to the emergence of drug-resistance MTB and Latent TB infection (LTBI). We are seeking for effective approaches to overcome these hindrances and efficient treatment for this perilous disease. Therefore, there is an urgent need to develop drugs based on operative targeting of the bacterial system that could result in both efficient treatment and lesser emergence of MDR-TB. One such promising target could be the secretory systems and especially the Type 7 secretory system (T7SS-ESX) of Mycobacterium tuberculosis, which is crucial for the secretion of effector proteins as well as in establishing host-pathogen interactions of the tubercle bacilli. The five paralogous ESX systems (ESX-1 to EXS-5) have been observed by in silico genome analysis of MTB, among which ESX-1 and ESX-5 are substantial for virulence and mediating host cellular inflammasome. The bacterium growth and virulence can be modulated by targeting the T7SS. In the present review, we demonstrate the current status of therapeutics against MTB and focus on the function and cruciality of T7SS along with other secretory systems as a promising therapeutic target against Tuberculosis.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Kriti Bajpai
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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Vaughn B, Abu Kwaik Y. Idiosyncratic Biogenesis of Intracellular Pathogens-Containing Vacuoles. Front Cell Infect Microbiol 2021; 11:722433. [PMID: 34858868 PMCID: PMC8632064 DOI: 10.3389/fcimb.2021.722433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
While most bacterial species taken up by macrophages are degraded through processing of the bacteria-containing vacuole through the endosomal-lysosomal degradation pathway, intravacuolar pathogens have evolved to evade degradation through the endosomal-lysosomal pathway. All intra-vacuolar pathogens possess specialized secretion systems (T3SS-T7SS) that inject effector proteins into the host cell cytosol to modulate myriad of host cell processes and remodel their vacuoles into proliferative niches. Although intravacuolar pathogens utilize similar secretion systems to interfere with their vacuole biogenesis, each pathogen has evolved a unique toolbox of protein effectors injected into the host cell to interact with, and modulate, distinct host cell targets. Thus, intravacuolar pathogens have evolved clear idiosyncrasies in their interference with their vacuole biogenesis to generate a unique intravacuolar niche suitable for their own proliferation. While there has been a quantum leap in our knowledge of modulation of phagosome biogenesis by intravacuolar pathogens, the detailed biochemical and cellular processes affected remain to be deciphered. Here we discuss how the intravacuolar bacterial pathogens Salmonella, Chlamydia, Mycobacteria, Legionella, Brucella, Coxiella, and Anaplasma utilize their unique set of effectors injected into the host cell to interfere with endocytic, exocytic, and ER-to-Golgi vesicle traffic. However, Coxiella is the main exception for a bacterial pathogen that proliferates within the hydrolytic lysosomal compartment, but its T4SS is essential for adaptation and proliferation within the lysosomal-like vacuole.
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Affiliation(s)
- Bethany Vaughn
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States.,Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY, United States
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Rivera-Calzada A, Famelis N, Llorca O, Geibel S. Type VII secretion systems: structure, functions and transport models. Nat Rev Microbiol 2021; 19:567-584. [PMID: 34040228 DOI: 10.1038/s41579-021-00560-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Type VII secretion systems (T7SSs) have a key role in the secretion of effector proteins in non-pathogenic mycobacteria and pathogenic mycobacteria such as Mycobacterium tuberculosis, the main causative agent of tuberculosis. Tuberculosis-causing mycobacteria, still accounting for 1.4 million deaths annually, rely on paralogous T7SSs to survive in the host and efficiently evade its immune response. Although it is still unknown how effector proteins of T7SSs cross the outer membrane of the diderm mycobacterial cell envelope, recent advances in the structural characterization of these secretion systems have revealed the intricate network of interactions of conserved components in the plasma membrane. This structural information, added to recent advances in the molecular biology and regulation of mycobacterial T7SSs as well as progress in our understanding of their secreted effector proteins, is shedding light on the inner working of the T7SS machinery. In this Review, we highlight the implications of these studies and the derived transport models, which provide new scenarios for targeting the deathly human pathogen M. tuberculosis.
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Affiliation(s)
- Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
| | - Nikolaos Famelis
- Institute for Molecular Infection Biology, Julius-Maximilian University of Würzburg, Würzburg, Germany.,Rudolf Virchow Center for Integrative and Translational Biomedicine, Julius-Maximilian University of Würzburg, Würzburg, Germany
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sebastian Geibel
- Institute for Molecular Infection Biology, Julius-Maximilian University of Würzburg, Würzburg, Germany. .,Rudolf Virchow Center for Integrative and Translational Biomedicine, Julius-Maximilian University of Würzburg, Würzburg, Germany.
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Lagune M, Petit C, Sotomayor FV, Johansen MD, Beckham KSH, Ritter C, Girard-Misguich F, Wilmanns M, Kremer L, Maurer FP, Herrmann JL. Conserved and specialized functions of Type VII secretion systems in non-tuberculous mycobacteria. MICROBIOLOGY-SGM 2021; 167. [PMID: 34224347 DOI: 10.1099/mic.0.001054] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Non-tuberculous mycobacteria (NTM) are a large group of micro-organisms comprising more than 200 individual species. Most NTM are saprophytic organisms and are found mainly in terrestrial and aquatic environments. In recent years, NTM have been increasingly associated with infections in both immunocompetent and immunocompromised individuals, prompting significant efforts to understand the diverse pathogenic and signalling traits of these emerging pathogens. Since the discovery of Type VII secretion systems (T7SS), there have been significant developments regarding the role of these complex systems in mycobacteria. These specialised systems, also known as Early Antigenic Secretion (ESX) systems, are employed to secrete proteins across the inner membrane. They also play an essential role in virulence, nutrient uptake and conjugation. Our understanding of T7SS in mycobacteria has significantly benefited over the last few years, from the resolution of ESX-3 structure in Mycobacterium smegmatis, to ESX-5 structures in Mycobacterium xenopi and Mycobacterium tuberculosis. In addition, ESX-4, considered until recently as a non-functional system in both pathogenic and non-pathogenic mycobacteria, has been proposed to play an important role in the virulence of Mycobacterium abscessus; an increasingly recognized opportunistic NTM causing severe lung diseases. These major findings have led to important new insights into the functional mechanisms of these biological systems, their implication in virulence, nutrient acquisitions and cell wall shaping, and will be discussed in this review.
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Affiliation(s)
- Marion Lagune
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180, Montigny-Le-Bretonneux, France
| | - Cecile Petit
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Flor Vásquez Sotomayor
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Matt D Johansen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France.,Present address: Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, NSW, Australia
| | - Kathrine S H Beckham
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Christina Ritter
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Fabienne Girard-Misguich
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180, Montigny-Le-Bretonneux, France
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France.,INSERM, IRIM, 34293 Montpellier, France
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180, Montigny-Le-Bretonneux, France.,APHP, GHU Paris-Saclay, Hôpital Raymond Poincaré, Service de Microbiologie, Garches, France
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