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Yan L, Lai HY, Leung TCN, Cheng HF, Chen X, Tsui SKW, Ngai SM, Au SWN. PE/PPE Proteome and ESX-5 Substrate Spectrum in Mycobacterium marinum. Int J Mol Sci 2024; 25:9550. [PMID: 39273496 PMCID: PMC11395111 DOI: 10.3390/ijms25179550] [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: 07/13/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/15/2024] Open
Abstract
PE/PPE proteins secreted by the ESX-5 type VII secretion system constitute a major protein repertoire in pathogenic mycobacteria and are essential for bacterial survival, pathogenicity, and host-pathogen interaction; however, little is known about their expression and secretion. The scarcity of arginine and lysine residues in PE/PPE protein sequences and the high homology of their N-terminal domains limit protein identification using classical trypsin-based proteomic methods. This study used endoproteinase AspN and trypsin to characterize the proteome of Mycobacterium marinum. Twenty-seven PE/PPE proteins were uniquely identified in AspN digests, especially PE_PGRS proteins. These treatments allowed the identification of approximately 50% of the PE/PPE pool encoded in the genome. Moreover, EspG5 pulldown assays retrieved 44 ESX-5-associated PPE proteins, covering 85% of the PPE pool in the identified proteome. The identification of PE/PE_PGRS proteins in the EspG5 interactome suggested the presence of PE-PPE pairs. The correlation analysis between protein abundance and phylogenetic relationships found potential PE/PPE pairs, indicating the presence of multiple PE/PE_PGRS partners in one PPE. We validated that EspG5 interacted with PPE31 and PPE32 and mapped critical residues for complex formation. The modified proteomic platform increases the coverage of PE/PPE proteins and elucidates the expression and localization of these proteins.
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Affiliation(s)
- Lili Yan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Hiu Ying Lai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Thomas Chun Ning Leung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Hiu Fu Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Xin Chen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Sai Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Shannon Wing Ngor Au
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
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Granados-Tristán AL, Hernández-Luna CE, González-Escalante LA, Camacho-Moll ME, Silva-Ramírez B, Bermúdez de León M, Peñuelas-Urquides K. ESX-3 secretion system in Mycobacterium: An overview. Biochimie 2024; 216:46-55. [PMID: 37879428 DOI: 10.1016/j.biochi.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Mycobacteria are microorganisms distributed in the environment worldwide, and some of them, such as Mycobacterium tuberculosis or M. leprae, are pathogenic. The hydrophobic mycobacterial cell envelope has low permeation and bacteria need to export products across their structure. Mycobacteria possess specialized protein secretion systems, such as the Early Secretory Antigenic Target 6 secretion (ESX) system. Five ESX loci have been described in M. tuberculosis, called ESX-1 to ESX-5. The ESX-3 secretion system has been associated with mycobacterial metabolism and growth. The locus of this system is highly conserved across mycobacterial species. Metallo-proteins regulate negative ESX-3 transcription in high conditions of iron and zinc. Moreover, this secretion system is part of an antioxidant regulatory pathway linked to Zinc. EccA3, EccB3, EccC3, EccD3, and EccE3 are components of the ESX-3 secretion machinery, whereas EsxG-EsxH, PE5-PPE4, and PE15-PPE20 are proteins secreted by this system. In addition, EspG3 and MycP3 are complementary proteins involved in transport and proteolysis respectively. This system is associated to mycobacterial virulence by releasing the bacteria from the phagosome and inhibiting endomembrane damage response. Furthermore, components of this system inhibit the host immune response by reducing the recognition of M. tuberculosis-infected cells. The components of the ESX-3 secretion system play a role in drug resistance and cell wall integrity. Moreover, the expression data of this system indicated that external and internal factors affect ESX-3 locus expression. This review provides an overview of new findings on the ESX-3 secretion system, its regulation, expression, and functions.
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Affiliation(s)
- Ana Laura Granados-Tristán
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico; Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Carlos Eduardo Hernández-Luna
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Laura Adiene González-Escalante
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
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3
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Yari S, Afrough P, Yari F, Ghazanfari Jajin M, Fateh A, Hadizadeh Tasbiti A. A potent subset of Mycobacterium tuberculosis glycoproteins as relevant candidates for vaccine and therapeutic target. Sci Rep 2023; 13:22194. [PMID: 38092899 PMCID: PMC10719292 DOI: 10.1038/s41598-023-49665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Tuberculosis (TB) remains one of the most afflictive bacterial infections globally. In high burden TB countries, surveillance, diagnosis and treatment of drug resistant TB (RR and X/MDRTB) display a crucial public health challenge. Therefore, we need new TB vaccines; diagnostic and therapeutic strategies to briskly prevent disease promotion; reduce drug-resistant TB and protect everyone from disease. The study identified various potent membrane and cell wall M. tuberculosis glycolipoproteins that are relevant for diagnostics, drug and vaccine discovery. A M. tuberculosis Proskauer and Beck broth culture was extracted for total proteins by ammonium sulfate method. After ConA-Affinity Chromatography reputed glycoproteins were collected followed by 2DE gel electrophoresis and LC Mass spectrometry. A total of 293 glycoproteins were identified using GlycoPP and IEDB database. Probable conserved trans-membrane protein (Rv0954), LpqN (Rv0583), PPE68 (Rv3873), Phosphate-binding protein (Rv0932c), PPE61 (Rv3532) and LprA (Rv1270c), had the highest glycosylation percentage value with 13.86%, 11.84%, 11.68%, 11.1%, 10.59% and10.2%, respectively. Our study discloses several dominant glycoproteins that play roles in M. tuberculosis survival, and immunogenicity. These include glycoproteins involved in antigenicity, transport and biosynthesis of M. tuberculosis cell envelope, pathogen-host interaction and drug efflux pumps, which are considered as a feasible drug targets or TB new vaccine candidates.
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Affiliation(s)
- Shamsi Yari
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Parviz Afrough
- Hepatitis Research Center, Shahid Rahimi Hospital, Aligoudarz School of Nursing, Lorestan University of Medical Science, Khorramabad, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion, Tehran, Iran
| | - Morteza Ghazanfari Jajin
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Abolfazl Fateh
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Alireza Hadizadeh Tasbiti
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran.
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Boardman ER, Palmer T, Alcock F. Interbacterial competition mediated by the type VIIb secretion system. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001420. [PMID: 38116759 PMCID: PMC10765036 DOI: 10.1099/mic.0.001420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Successful occupancy of a given niche requires the colonising bacteria to interact extensively with the biotic and abiotic environment, including other resident microbes. Bacteria have evolved a range of protein secretion machines for this purpose with eleven such systems identified to date. The type VIIb secretion system (T7SSb) is utilised by Bacillota to secrete a range of protein substrates, including antibacterial toxins targeting closely related strains, and the system as a whole has been implicated in a range of activities such as iron acquisition, intercellular signalling, host colonisation and virulence. This review covers the components and secretion mechanism of the T7SSb, the substrates of these systems and their roles in Gram-positive bacteria, with a focus on interbacterial competition.
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Affiliation(s)
- Eleanor R. Boardman
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Felicity Alcock
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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5
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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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6
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Sankey N, Merrick H, Singh P, Rogers J, Reddi A, Hartson SD, Mitra A. Role of the Mycobacterium tuberculosis ESX-4 Secretion System in Heme Iron Utilization and Pore Formation by PPE Proteins. mSphere 2023; 8:e0057322. [PMID: 36749044 PMCID: PMC10117145 DOI: 10.1128/msphere.00573-22] [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: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is transmitted through aerosols and primarily colonizes within the lung. The World Health Organization estimates that Mtb kills ~1.4 million people every year. A key aspect that makes Mtb such a successful pathogen is its ability to overcome iron limitation mounted by the host immune response. In our previous studies, we have shown that Mtb can utilize iron from heme, the largest source of iron in the human host, and that it uses two redundant heme utilization pathways. In this study, we show that the ESX-4 type VII secretion system (T7SS) is necessary for extracellular heme uptake into the Mtb cell through both heme utilization pathways. ESX-4 influences the secretion of the culture filtrate proteins Rv0125 and Rv1085c, which are also necessary for efficient heme utilization. We also discovered that deletion of the alternative sigma factor SigM significantly reduced Mtb heme utilization through both pathways and predict that SigM is a global positive regulator of core heme utilization genes of both pathways. Finally, we present the first direct evidence that some mycobacterial PPE (proline-proline-glutamate motif) proteins of the PPE protein family are pore-forming membrane proteins. Altogether, we identified core components of both Mtb Heme utilization pathways that were previously unknown and identified a novel channel-forming membrane protein of Mtb. IMPORTANCE M. tuberculosis (Mtb) is completely dependent on iron acquisition in the host to cause disease. The largest source of iron for Mtb in the human host is heme. Here, we show that the ancestral ESX-4 type VII secretion system is required for the efficient utilization of heme as a source of iron, which is an essential nutrient. This is another biological function identified for ESX-4 in Mtb, whose contribution to Mtb physiology is poorly understood. A most exciting finding is that some mycobacterial PPE (proline-proline-glutamate motif) proteins that have been implicated in the nutrient acquisition are membrane proteins that can form channels in a lipid bilayer. These observations have far-reaching implications because they support an emerging theme that PPE proteins can function as channel proteins in the outer mycomembrane for nutrient acquisition. Mtb has evolved a heme uptake system that is drastically different from all other known bacterial heme acquisition systems.
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Affiliation(s)
- November Sankey
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Haley Merrick
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Padam Singh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Amit Reddi
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Steven D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Avishek Mitra
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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7
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D'Souza C, Kishore U, Tsolaki AG. The PE-PPE Family of Mycobacterium tuberculosis: Proteins in Disguise. Immunobiology 2023; 228:152321. [PMID: 36805109 DOI: 10.1016/j.imbio.2022.152321] [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: 06/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis has thrived in parallel with humans for millennia, and despite our efforts, M. tuberculosis continues to plague us, currently infecting a third of the world's population. The success of M. tuberculosis has recently been attributed, in part, to the PE-PPE family; a unique collection of 168 proteins fundamentally involved in the pathogenesis of M. tuberculosis. The PE-PPE family proteins have been at the forefront of intense research efforts since their discovery in 1998 and whilst our knowledge and understanding has significantly advanced over the last two decades, many important questions remain to be elucidated. This review consolidates and examines the vast body of existing literature regarding the PE-PPE family proteins, with respect to the latest developments in elucidating their evolution, structure, subcellular localisation, function, and immunogenicity. This review also highlights significant inconsistencies and contradictions within the field. Additionally, possible explanations for these knowledge gaps are explored. Lastly, this review poses many important questions, which need to be addressed to complete our understanding of the PE-PPE family, as well as highlighting the challenges associated with studying this enigmatic family of proteins. Further research into the PE-PPE family, together with technological advancements in genomics and proteomics, will undoubtedly improve our understanding of the pathogenesis of M. tuberculosis, as well as identify key targets/candidates for the development of novel drugs, diagnostics, and vaccines.
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Affiliation(s)
- Christopher D'Souza
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom
| | - Uday Kishore
- Department of Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anthony G Tsolaki
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom.
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8
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The ESX-1 Substrate PPE68 Has a Key Function in ESX-1-Mediated Secretion in Mycobacterium marinum. mBio 2022; 13:e0281922. [PMID: 36409073 PMCID: PMC9765416 DOI: 10.1128/mbio.02819-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mycobacteria use specialized type VII secretion systems (T7SSs) to secrete proteins across their diderm cell envelope. One of the T7SS subtypes, named ESX-1, is a major virulence determinant in pathogenic species such as Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum. ESX-1 secretes a variety of substrates, called Esx, PE, PPE, and Esp proteins, at least some of which are folded heterodimers. Investigation into the functions of these substrates is problematic, because of the intricate network of codependent secretion between several ESX-1 substrates. Here, we describe the ESX-1 substrate PPE68 as essential for secretion of the highly immunogenic substrates EsxA and EspE via the ESX-1 system in M. marinum. While secreted PPE68 is processed on the cell surface, the majority of cell-associated PPE68 of M. marinum and M. tuberculosis is present in a cytosolic complex with its PE partner and the EspG1 chaperone. Interfering with the binding of EspG1 to PPE68 blocked its export and the secretion of EsxA and EspE. In contrast, esxA was not required for the secretion of PPE68, revealing a hierarchy in codependent secretion. Remarkably, the final 10 residues of PPE68, a negatively charged domain, seem essential for EspE secretion, but not for the secretion of EsxA and of PPE68 itself. This indicates that distinctive domains of PPE68 are involved in secretion of the different ESX-1 substrates. Based on these findings, we propose a mechanistic model for the central role of PPE68 in ESX-1-mediated secretion and substrate codependence. IMPORTANCE Pathogenic mycobacteria, such Mycobacterium tuberculosis and Mycobacterium marinum, use a type VII secretion system (T7SS) subtype, called ESX-1, to mediate intracellular survival via phagosomal rupture and subsequent translocation of the mycobacterium to the host cytosol. Identifying the ESX-1 substrate that is responsible for this process is problematic because of the intricate network of codependent secretion between ESX-1 substrates. Here, we show the central role of the ESX-1 substrate PPE68 for the secretion of ESX-1 substrates in Mycobacterium marinum. Unravelling the mechanism of codependent secretion will aid the functional understanding of T7SSs and will allow the analysis of the individual roles of ESX-1 substrates in the virulence caused by the significant human pathogen Mycobacterium tuberculosis.
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9
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Gijsbers A, Eymery M, Gao Y, Menart I, Vinciauskaite V, Siliqi D, Peters PJ, McCarthy A, Ravelli RBG. The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis. J Biol Chem 2022; 299:102761. [PMID: 36463964 PMCID: PMC9811218 DOI: 10.1016/j.jbc.2022.102761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Pathogenic species from the Mycobacterium genus are responsible for a number of adverse health conditions in humans and animals that threaten health security and the economy worldwide. Mycobacteria have up to five specialized secretion systems (ESX-1 to ESX-5) that transport virulence factors across their complex cell envelope to facilitate manipulation of their environment. In pathogenic species, these virulence factors influence the immune system's response and are responsible for membrane disruption and contributing to cell death. While structural details of these secretion systems have been recently described, gaps still remain in the structural understanding of the secretion mechanisms of most substrates. Here, we describe the crystal structure of Mycobacterium tuberculosis ESX-1 secretion-associated substrate EspB bound to its chaperone EspK. We found that EspB interacts with the C-terminal domain of EspK through its helical tip. Furthermore, cryogenic electron microscopy, size exclusion chromatography analysis, and small-angle X-ray scattering experiments show that EspK keeps EspB in its secretion-competent monomeric form and prevents its oligomerization. The structure presented in this study suggests an additional secretion mechanism in ESX-1, analogous to the chaperoning of proline-glutamate (PE)-proline-proline-glutamate (PPE) proteins by EspG, where EspK facilitates the secretion of EspB in Mycobacterium species.
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Affiliation(s)
- Abril Gijsbers
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | | | - Ye Gao
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Isabella Menart
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Vanesa Vinciauskaite
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | | | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands.
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10
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Abstract
Bacterial type VIIb secretion systems (T7SSb) are multisubunit integral membrane protein complexes found in Firmicutes that play a role in both bacterial competition and virulence by secreting toxic effector proteins. The majority of characterized T7SSb effectors adopt a polymorphic domain architecture consisting of a conserved N-terminal Leu-X-Gly (LXG) domain and a variable C-terminal toxin domain. Recent work has started to reveal the diversity of toxic activities exhibited by LXG effectors; however, little is known about how these proteins are recruited to the T7SSb apparatus. In this work, we sought to characterize genes encoding domains of unknown function (DUFs) 3130 and 3958, which frequently cooccur with LXG effector-encoding genes. Using coimmunoprecipitation-mass spectrometry analyses, in vitro copurification experiments, and T7SSb secretion assays, we found that representative members of these protein families form heteromeric complexes with their cognate LXG domain and in doing so, function as targeting factors that promote effector export. Additionally, an X-ray crystal structure of a representative DUF3958 protein, combined with predictive modeling of DUF3130 using AlphaFold2, revealed structural similarity between these protein families and the ubiquitous WXG100 family of T7SS effectors. Interestingly, we identified a conserved FxxxD motif within DUF3130 that is reminiscent of the YxxxD/E “export arm” found in mycobacterial T7SSa substrates and mutation of this motif abrogates LXG effector secretion. Overall, our data experimentally link previously uncharacterized bacterial DUFs to type VIIb secretion and reveal a molecular signature required for LXG effector export.
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11
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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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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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14
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Gijsbers A, Vinciauskaite V, Siroy A, Gao Y, Tria G, Mathew A, Sánchez-Puig N, López-Iglesias C, Peters PJ, Ravelli RBG. Priming mycobacterial ESX-secreted protein B to form a channel-like structure. Curr Res Struct Biol 2021; 3:153-164. [PMID: 34337436 PMCID: PMC8313811 DOI: 10.1016/j.crstbi.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/20/2021] [Accepted: 06/17/2021] [Indexed: 01/24/2023] Open
Abstract
ESX-1 is a major virulence factor of Mycobacterium tuberculosis, a secretion machinery directly involved in the survival of the microorganism from the immune system defence. It disrupts the phagosome membrane of the host cell through a contact-dependent mechanism. Recently, the structure of the inner-membrane core complex of the homologous ESX-3 and ESX-5 was resolved; however, the elements involved in the secretion through the outer membrane or those acting on the host cell membrane are unknown. Protein substrates might form this missing element. Here, we describe the oligomerisation process of the ESX-1 substrate EspB, which occurs upon cleavage of its C-terminal region and is favoured by an acidic environment. Cryo-electron microscopy data shows that quaternary structure of EspB is conserved across slow growing species, but not in the fast growing M. smegmatis. EspB assembles into a channel with dimensions and characteristics suitable for the transit of ESX-1 substrates, as shown by the presence of another EspB trapped within. Our results provide insight into the structure and assembly of EspB, and suggests a possible function as a structural element of ESX-1.
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Affiliation(s)
- Abril Gijsbers
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Vanesa Vinciauskaite
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Axel Siroy
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Ye Gao
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Giancarlo Tria
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Anjusha Mathew
- Division of Imaging Mass Spectrometry, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Nuria Sánchez-Puig
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
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15
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Tran HKR, Grebenc DW, Klein TA, Whitney JC. Bacterial type VII secretion: An important player in host-microbe and microbe-microbe interactions. Mol Microbiol 2021; 115:478-489. [PMID: 33410158 DOI: 10.1111/mmi.14680] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/19/2022]
Abstract
Type VII secretion systems (T7SSs) are poorly understood protein export apparatuses found in mycobacteria and many species of Gram-positive bacteria. To date, this pathway has predominantly been studied in Mycobacterium tuberculosis, where it has been shown to play an essential role in virulence; however, much less studied is an evolutionarily divergent subfamily of T7SSs referred to as the T7SSb. The T7SSb is found in the major Gram-positive phylum Firmicutes where it was recently shown to target both eukaryotic and prokaryotic cells, suggesting a dual role for this pathway in host-microbe and microbe-microbe interactions. In this review, we compare the current understanding of the molecular architectures and substrate repertoires of the well-studied mycobacterial T7SSa systems to that of recently characterized T7SSb pathways and highlight how these differences may explain the observed biological functions of this understudied protein export machine.
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Affiliation(s)
- Hiu-Ki R Tran
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dirk W Grebenc
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Timothy A Klein
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
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