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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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2
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Bunduc CM, Bitter W, Houben E. Structure and Function of the Mycobacterial Type VII Secretion Systems. Annu Rev Microbiol 2020; 74:315-335. [DOI: 10.1146/annurev-micro-012420-081657] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria have evolved intricate secretion machineries for the successful delivery of large molecules across their cell envelopes. Such specialized secretion systems allow a variety of bacteria to thrive in specific host environments. In mycobacteria, type VII secretion systems (T7SSs) are dedicated protein transport machineries that fulfill diverse and crucial roles, ranging from metabolite uptake to immune evasion and subversion to conjugation. Since the discovery of mycobacterial T7SSs about 15 y ago, genetic, structural, and functional studies have provided insight into the roles and functioning of these secretion machineries. Here, we focus on recent advances in the elucidation of the structure and mechanism of mycobacterial T7SSs in protein secretion. As many of these systems are essential for mycobacterial growth or virulence, they provide opportunities for the development of novel therapies to combat a number of relevant mycobacterial diseases.
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Affiliation(s)
- Catalin M. Bunduc
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - W. Bitter
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, 1007 MB Amsterdam, The Netherlands
| | - E.N.G. Houben
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
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3
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van Winden VJC, Houben ENG, Braunstein M. Protein Export into and across the Atypical Diderm Cell Envelope of Mycobacteria. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0043-2018. [PMID: 31400094 PMCID: PMC10957183 DOI: 10.1128/microbiolspec.gpp3-0043-2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 02/07/2023] Open
Abstract
Mycobacteria, including the infamous pathogen Mycobacterium tuberculosis, are high-GC Gram-positive bacteria with a distinctive cell envelope. Although there is a typical inner membrane, the mycobacterial cell envelope is unusual in having its peptidoglycan layer connected to a polymer of arabinogalactan, which in turn is covalently attached to long-chain mycolic acids that help form a highly impermeable mycobacterial outer membrane. This complex double-membrane, or diderm, cell envelope imparts mycobacteria with unique requirements for protein export into and across the cell envelope for secretion into the extracellular environment. In this article, we review the four protein export pathways known to exist in mycobacteria: two conserved systems that exist in all types of bacteria (the Sec and Tat pathways) and two specialized systems that exist in mycobacteria, corynebacteria, and a subset of low-GC Gram-positive bacteria (the SecA2 and type VII secretion pathways). We describe the progress made over the past 15 years in understanding each of these mycobacterial export pathways, and we highlight the need for research to understand the specific steps of protein export across the mycobacterial outer membrane.
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Affiliation(s)
- Vincent J C van Winden
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Edith N G Houben
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines, and Systems, Vrije Universiteit, Amsterdam, The Netherlands
| | - Miriam Braunstein
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599
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4
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van Winden VJC, Damen MPM, Ummels R, Bitter W, Houben ENG. Protease domain and transmembrane domain of the type VII secretion mycosin protease determine system-specific functioning in mycobacteria. J Biol Chem 2019; 294:4806-4814. [PMID: 30692196 DOI: 10.1074/jbc.ra118.007090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/17/2019] [Indexed: 11/06/2022] Open
Abstract
Mycobacteria use type VII secretion systems to secrete proteins across their highly hydrophobic diderm cell envelope. Pathogenic mycobacteria, such as Mycobacterium tuberculosis and Mycobacterium marinum, have up to five of these systems, named ESX-1 to ESX-5. Most of these systems contain a set of five conserved membrane components, of which the four Ecc proteins form the core membrane-embedded secretion complex. The fifth conserved membrane protein, mycosin protease (MycP), is not part of the core complex but is essential for secretion, as it stabilizes this membrane complex. Here we investigated which MycP domains are required for this stabilization by producing hybrid constructs between MycP1 and MycP5 in M. marinum and analyzed their effect on ESX-1 and ESX-5 secretion. We found that both the protease and transmembrane domain are required for the ESX system-specific function of mycosins. In addition, we observed that the transmembrane domain strongly affects MycP protein levels. We also show that the extended loops 1 and 2 in the protease domain are probably primarily involved in MycP stability, whereas loop 3 and the MycP5-specific loop 5 are dispensable. The atypical propeptide, or N-terminal extension, is required only for MycP stability. Finally, we show that the protease domain of MycPP1, encoded by the esx-P1 locus on the pRAW plasmid, is functionally redundant to the protease domain of MycP5 These results provide the first insight into the regions of mycosins involved in interaction with and stabilization of their respective ESX complexes.
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Affiliation(s)
- Vincent J C van Winden
- From the Department of Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands and
| | - Merel P M Damen
- the Section of Molecular Microbiology, Amsterdam Institute of Molecules, Medicines, and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Roy Ummels
- From the Department of Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands and
| | - Wilbert Bitter
- From the Department of Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands and.,the Section of Molecular Microbiology, Amsterdam Institute of Molecules, Medicines, and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Edith N G Houben
- the Section of Molecular Microbiology, Amsterdam Institute of Molecules, Medicines, and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
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Liu H, Zhang R, Li L, Zhou L, Xu Y. The high expression of Aspergillus pseudoglaucus protease in Escherichia coli for hydrolysis of soy protein and milk protein. Prep Biochem Biotechnol 2018; 48:725-733. [PMID: 30303449 DOI: 10.1080/10826068.2018.1508035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The hydrolysates of soy protein and milk protein are nutritional and functional food ingredients. Aspergillus pseudoglaucus aspergillopepsin I (App) is an acidic protease, including signal peptide, propeptide, and catalytic domain. Here, we cloned the catalytic domain App with or without propeptide in Escherichia coli. The results showed that the App without propeptide was not expressed or did not exhibit activity and App with propeptide (proApp) was highly expressed with a specific activity of 903 U/mg. Moreover, the denaturation temperature of proApp was 4.1 °C higher than App's. The proApp showed 104 U/mg and 252 U/mg hydrolysis activities towards soy protein and milk protein under acidic conditions. By RP-HPLC analysis, the peptides obtained from the hydrolysates of soy protein and milk protein were hydrophilic peptides. This work first demonstrates efficient proteolysis of soy protein and milk protein through the functional expression of full-length proApp, which will likely have valuable industrial applications.
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Affiliation(s)
- Haiyan Liu
- a Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology , Jiangnan University , Wuxi , P. R. China
| | - Rongzhen Zhang
- a Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology , Jiangnan University , Wuxi , P. R. China
| | - Lihong Li
- a Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology , Jiangnan University , Wuxi , P. R. China
| | - Lixian Zhou
- a Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology , Jiangnan University , Wuxi , P. R. China
| | - Yan Xu
- a Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology , Jiangnan University , Wuxi , P. R. China
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6
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Expression and production of soluble Mycobacterium tuberculosis H37Rv mycosin-3. Biochem Biophys Rep 2016; 5:448-452. [PMID: 28955852 PMCID: PMC5600315 DOI: 10.1016/j.bbrep.2016.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 11/29/2022] Open
Abstract
Mycobacteria encode five type VII secretion system (T7SS) or ESX for nutrient acquisition and virulence. Mycosins are membrane-anchored components of ESX with serine protease activity but an unidentified substrate range. Establishing the substrate specificity of individual mycosins will help to elucidate individual ESX functions. Mycosin-1 and -3 orthologues from two environmental mycobacterial species, Mycobacterium smegmatis and Mycobacterium thermoresistibile, have been heterologously produced, but mycosins from Mycobacterium tuberculosis (Mtb) remain to be studied. Here we describe the successful production of Mtb mycosin-3 as a first step in investigating its structure and function. Production of soluble mycosin-3 from Mtb H37Rv. Soluble mycosin-3 was produced in E. coli strain Arctic Express. Soluble mycosin-3 without its N-terminal extension region was produced.
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Hamza A, Wagner JM, Wei NN, Kwiatkowski S, Zhan CG, Watt DS, Korotkov KV. Application of the 4D fingerprint method with a robust scoring function for scaffold-hopping and drug repurposing strategies. J Chem Inf Model 2014; 54:2834-45. [PMID: 25229183 PMCID: PMC4210175 DOI: 10.1021/ci5003872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Two
factors contribute to the inefficiency associated with screening
pharmaceutical library collections as a means of identifying new drugs:
[1] the limited success of virtual screening (VS) methods in identifying
new scaffolds; [2] the limited accuracy of computational methods in
predicting off-target effects. We recently introduced a 3D shape-based
similarity algorithm of the SABRE program, which encodes a consensus
molecular shape pattern of a set of active ligands into a 4D fingerprint
descriptor. Here, we report a mathematical model for shape similarity
comparisons and ligand database filtering using this 4D fingerprint
method and benchmarked the scoring function HWK (Hamza–Wei–Korotkov),
using the 81 targets of the DEKOIS database. Subsequently, we applied
our combined 4D fingerprint and HWK scoring function
VS approach in scaffold-hopping and drug repurposing using the National
Cancer Institute (NCI) and Food and Drug Administration (FDA) databases,
and we identified new inhibitors with different scaffolds of MycP1 protease from the mycobacterial ESX-1 secretion system. Experimental
evaluation of nine compounds from the NCI database and three from
the FDA database displayed IC50 values ranging from 70
to 100 μM against MycP1 and possessed high structural
diversity, which provides departure points for further structure–activity
relationship (SAR) optimization. In addition, this study demonstrates
that the combination of our 4D fingerprint algorithm and the HWK scoring function may provide a means for identifying
repurposed drugs for the treatment of infectious diseases and may
be used in the drug-target profile strategy.
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Affiliation(s)
- Adel Hamza
- Department of Molecular and Cellular Biochemistry, ‡Center for Structural Biology, §Center for Pharmaceutical Research and Innovation, College of Pharmacy, ∥Molecular Modeling and Biopharmaceutical Center, and ⊥Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, United States
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Hamza A, Wagner JM, Evans T, Frasinyuk MS, Kwiatkowski S, Zhan CG, Watt DS, Korotkov KV. Novel mycosin protease MycP₁ inhibitors identified by virtual screening and 4D fingerprints. J Chem Inf Model 2014; 54:1166-73. [PMID: 24628123 PMCID: PMC4010288 DOI: 10.1021/ci500025r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Indexed: 01/17/2023]
Abstract
The rise of drug-resistant Mycobacterium tuberculosis lends urgency to the need for new drugs for the treatment of tuberculosis (TB). The identification of a serine protease, mycosin protease-1 (MycP₁), as the crucial agent in hydrolyzing the virulence factor, ESX-secretion-associated protein B (EspB), potentially opens the door to new tuberculosis treatment options. Using the crystal structure of mycobacterial MycP₁ in the apo form, we performed an iterative ligand- and structure-based virtual screening (VS) strategy to identify novel, nonpeptide, small-molecule inhibitors against MycP₁ protease. Screening of ∼485,000 ligands from databases at the Genomics Research Institute (GRI) at the University of Cincinnati and the National Cancer Institute (NCI) using our VS approach, which integrated a pharmacophore model and consensus molecular shape patterns of active ligands (4D fingerprints), identified 81 putative inhibitors, and in vitro testing subsequently confirmed two of them as active inhibitors. Thereafter, the lead structures of each VS round were used to generate a new 4D fingerprint that enabled virtual rescreening of the chemical libraries. Finally, the iterative process identified a number of diverse scaffolds as lead compounds that were tested and found to have micromolar IC₅₀ values against the MycP₁ target. This study validated the efficiency of the SABRE 4D fingerprints as a means of identifying novel lead compounds in each screening round of the databases. Together, these results underscored the value of using a combination of in silico iterative ligand- and structure-based virtual screening of chemical libraries with experimental validation for the identification of promising structural scaffolds, such as the MycP₁ inhibitors.
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Affiliation(s)
- Adel Hamza
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M. Wagner
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Timothy
J. Evans
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mykhaylo S. Frasinyuk
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Institute
of Bioorganic Chemistry and Petrochemistry, Kyiv-94, 02660, Ukraine
| | - Stefan Kwiatkowski
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - David S. Watt
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Konstantin V. Korotkov
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
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