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De Maio F, Berisio R, Manganelli R, Delogu G. PE_PGRS proteins of Mycobacterium tuberculosis: A specialized molecular task force at the forefront of host-pathogen interaction. Virulence 2021; 11:898-915. [PMID: 32713249 PMCID: PMC7550000 DOI: 10.1080/21505594.2020.1785815] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To the PE_PGRS protein subfamily belongs a group of surface-exposed mycobacterial antigens that in Mycobacterium tuberculosis (Mtb) H37Rv accounts to more than 65 genes, 51 of which are thought to express a functional protein. PE_PGRS proteins share a conserved structural architecture with three main domains: the N-terminal PE domain; the PGRS domain, that can vary in sequence and size and is characterized by the presence of multiple GGA-GGX amino acid repeats; the highly conserved sequence containing the GRPLI motif that links the PE and PGRS domains; the unique C-terminus end that can vary in size from few to up to ≈ 300 amino acids. pe_pgrs genes emerged in slow-growing mycobacteria and expanded and diversified in MTBC and few other pathogenic mycobacteria. Interestingly, despite sequence homology and apparent redundancy, PE_PGRS proteins seem to have evolved a peculiar function. In this review, we summarize the actual knowledge on this elusive protein family in terms of evolution, structure, and function, focusing on the role of PE_PGRS in TB pathogenesis. We provide an original hypothesis on the role of the PE domain and propose a structural model for the polymorphic PGRS domain that might explain how so similar proteins can have different physiological functions.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" , Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore , Rome, Italy
| | - Rita Berisio
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB , Naples, Italy
| | | | - Giovanni Delogu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore , Rome, Italy.,Mater Olbia Hospital , Olbia, Italy
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2
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Burggraaf MJ, Speer A, Meijers AS, Ummels R, van der Sar AM, Korotkov KV, Bitter W, Kuijl C. Type VII Secretion Substrates of Pathogenic Mycobacteria Are Processed by a Surface Protease. mBio 2019; 10:e01951-19. [PMID: 31662454 PMCID: PMC6819658 DOI: 10.1128/mbio.01951-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/30/2019] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis, one of the world's most severe infectious diseases, is caused by Mycobacterium tuberculosis A major weapon of this pathogen is a unique cell wall that protects the pathogen from eradication by the immune system. Mycobacteria have specialized secretion systems, e.g., type VII secretion or ESX systems, to transport substrates across this cell wall. The largest group of proteins that are secreted by these ESX systems are the PE proteins. Previously, it was shown that the N-terminal PE domain of about 100 amino acids is required for secretion. Here, we describe the identification of an aspartic protease, designated PecA, that removes (part of) this PE domain at the cell surface. Nearly all of the observed PE_PGRS proteins are processed by PecA. Interestingly, the protease itself is also a secreted PE protein and subject to self-cleavage. Furthermore, a defect in surface processing has no effect on the activity of the PE lipase protein LipY but does seem to affect the functioning of other virulence factors, as a pecA mutant strain of Mycobacterium marinum shows moderate attenuation in zebrafish larvae. In conclusion, our results reveal the presence of a functional aspartic acid protease in M. marinum that cleaves LipY, itself as well as other members of the PE_PGRS family. Finally, mutants lacking PecA show growth attenuation in vivo, suggesting that PecA plays a role during infection.IMPORTANCE Aspartic proteases are common in eukaryotes and retroviruses but are relatively rare among bacteria (N. D. Rawlings and A. Bateman, BMC Genomics 10:437, 2009, https://doi.org/10.1186/1471-2164-10-437). In contrast to eukaryotic aspartic proteases, bacterial aspartic proteases are generally located in the cytoplasm. We have identified a surface-associated mycobacterial aspartic protease, PecA, which cleaves itself and many other type VII secretion substrates of the PE_PGRS family. PecA is present in most pathogenic mycobacterial species, including M. tuberculosis In addition, pathogenicity of M. marinum is reduced in the ΔpecA mutant, indicating that PecA contributes to virulence.
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Affiliation(s)
- Maroeska J Burggraaf
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Alexander Speer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
| | - Aniek S Meijers
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
| | - Roy Ummels
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
| | - Astrid M van der Sar
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
| | - Konstantin V Korotkov
- Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Wilbert Bitter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
- Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Coenraad Kuijl
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Microbiology and Infection Control, Amsterdam Institute of Infection & Immunity, Amsterdam, Netherlands
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Divya M B, Vemula M, Balakrishnan K, Banerjee S, Guruprasad L. Mycobacterium tuberculosis PE1 and PE2 proteins carrying conserved α/β-serine hydrolase domain are esterases hydrolyzing short to medium chain p-nitrophenyl esters. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:90-102. [DOI: 10.1016/j.pbiomolbio.2018.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/23/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
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4
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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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Sultana R, Tanneeru K, Kumar ABR, Guruprasad L. Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria. PLoS One 2016; 11:e0146786. [PMID: 26891364 PMCID: PMC4758615 DOI: 10.1371/journal.pone.0146786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022] Open
Abstract
The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
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Affiliation(s)
- Rafiya Sultana
- School of Chemistry, University of Hyderabad, Hyderabad, 500046, India
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Fishbein S, van Wyk N, Warren RM, Sampson SL. Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. Mol Microbiol 2015; 96:901-16. [PMID: 25727695 DOI: 10.1111/mmi.12981] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 01/08/2023]
Abstract
The pe/ppe genes represent one of the most intriguing aspects of the Mycobacterium tuberculosis genome. These genes are especially abundant in pathogenic mycobacteria, with more than 160 members in M. tuberculosis. Despite being discovered over 15 years ago, their function remains unclear, although various lines of evidence implicate selected family members in mycobacterial virulence. In this review, we use PE/PPE phylogeny as a framework within which we examine the diversity and putative functions of these proteins. We report on the evolution and diversity of the respective gene families, as well as the implications thereof for function and host immune recognition. We summarize recent findings on pe/ppe gene regulation, also placing this in the context of PE/PPE phylogeny. We collate data from several large proteomics datasets, providing an overview of PE/PPE localization, and discuss the implications this may have for host responses. Assessment of the current knowledge of PE/PPE diversity suggests that these proteins are not variable antigens as has been so widely speculated; however, they do clearly play important roles in virulence. Viewing the growing body of pe/ppe literature through the lens of phylogeny reveals trends in features and function that may be associated with the evolution of mycobacterial pathogenicity.
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Affiliation(s)
- S Fishbein
- Harvard School of Public Health, Boston, MA, USA.,DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - N van Wyk
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - R M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - S L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
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7
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Korotkova N, Freire D, Phan TH, Ummels R, Creekmore CC, Evans TJ, Wilmanns M, Bitter W, Parret AHA, Houben ENG, Korotkov KV. Structure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25-PPE41 dimer. Mol Microbiol 2014; 94:367-82. [PMID: 25155747 DOI: 10.1111/mmi.12770] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
Abstract
The growth or virulence of Mycobacterium tuberculosis bacilli depends on homologous type VII secretion systems, ESX-1, ESX-3 and ESX-5, which export a number of protein effectors across membranes to the bacterial surface and environment. PE and PPE proteins represent two large families of highly polymorphic proteins that are secreted by these ESX systems. Recently, it was shown that these proteins require system-specific cytoplasmic chaperones for secretion. Here, we report the crystal structure of M. tuberculosis ESX-5-secreted PE25-PPE41 heterodimer in complex with the cytoplasmic chaperone EspG(5). EspG(5) represents a novel fold that is unrelated to previously characterized secretion chaperones. Functional analysis of the EspG(5) -binding region uncovered a hydrophobic patch on PPE41 that promotes dimer aggregation, and the chaperone effectively abolishes this process. We show that PPE41 contains a characteristic chaperone-binding sequence, the hh motif, which is highly conserved among ESX-1-, ESX-3- and ESX-5-specific PPE proteins. Disrupting the interaction between EspG(5) and three different PPE target proteins by introducing different point mutations generally affected protein secretion. We further demonstrate that the EspG(5) chaperone plays an important role in the ESX secretion mechanism by keeping aggregation-prone PE-PPE proteins in their soluble state.
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Affiliation(s)
- Natalia Korotkova
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA; Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA
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