1
|
Tzfadia O, Gijsbers A, Vujkovic A, Snobre J, Vargas R, Dewaele K, Meehan CJ, Farhat M, Hakke S, Peters PJ, de Jong BC, Siroy A, Ravelli RBG. Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiol Spectr 2024:e0381623. [PMID: 38874407 DOI: 10.1128/spectrum.03816-23] [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: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/15/2024] Open
Abstract
Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens. IMPORTANCE We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.
Collapse
Affiliation(s)
- Oren Tzfadia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Abril Gijsbers
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alexandra Vujkovic
- Clinical Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- ADReM Data Lab, University of Antwerp, Antwerp, Belgium
| | - Jihad Snobre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaas Dewaele
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Axel Siroy
- Unité de soutien à l'Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM, IECB, US1, Université de Bordeaux, Pessac, France
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| |
Collapse
|
2
|
Robbins L, Balaram A, Dejneka S, McMahon M, Najibi Z, Pawlowicz P, Conrad WH. Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model. Sci Rep 2023; 13:8551. [PMID: 37237156 DOI: 10.1038/s41598-023-35632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC-MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
Collapse
Affiliation(s)
- Laurel Robbins
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Ariane Balaram
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Stefanie Dejneka
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Matthew McMahon
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Zarina Najibi
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Peter Pawlowicz
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - William H Conrad
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA.
| |
Collapse
|
3
|
Sreelatha S, Nagarajan U, Natarajan S. Protein targets in Mycobacterium tuberculosis and their inhibitors for therapeutic implications: A narrative review. Int J Biol Macromol 2023:125022. [PMID: 37244342 DOI: 10.1016/j.ijbiomac.2023.125022] [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: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancement in the area of anti-tubercular drug development has been full-fledged, yet, a very less number of drug molecules have reached phase II clinical trials, and therefore "End-TB" is still a global challenge. Inhibitors to specific metabolic pathways of Mycobacterium tuberculosis (Mtb) gain importance in strategizing anti-tuberculosis drug discovery. The lead compounds that target DNA replication, protein synthesis, cell wall biosynthesis, bacterial virulence and energy metabolism are emerging as potential chemotherapeutic options against Mtb growth and survival within the host. In recent times, the in silico approaches have become most promising tools in the identification of suitable inhibitors for specific protein targets of Mtb. An update in the fundamental understanding of these inhibitors and the mechanism of interaction may bring hope to future perspectives in novel drug development and delivery approaches. This review provides a collective impression of the small molecules with potential antimycobacterial activities and their target pathways in Mtb such as cell wall biosynthesis, DNA replication, transcription and translation, efflux pumps, antivirulence pathways and general metabolism. The mechanism of interaction of specific inhibitor with their respective protein targets has been discussed. The comprehensive knowledge of such an impactful area of research would essentially reflect in the discovery of novel drug molecules and effective delivery approaches. This narrative review encompasses the knowledge of emerging targets and promising n that could potentially translate in to the anti-TB-drug discovery.
Collapse
Affiliation(s)
- Souparnika Sreelatha
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Usharani Nagarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Saravanan Natarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India.
| |
Collapse
|
4
|
Horetski M, Gorlova A, Płocińska R, Brzostek A, Faletrov Y, Dziadek J, Shkumatov V. Synthesis, Optical Properties, Preliminary Antimycobacterial Evaluation and Docking Studies of Trifluoroacetylated 3‐Pyrrolyl Boron‐Dipyrromethene. ChemistrySelect 2022. [DOI: 10.1002/slct.202200506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Matvey Horetski
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
| | - Anna Gorlova
- Department of Natural Sciences Novosibirsk State University 1 Pirogova Street. Novosibirsk 630090 Russia
| | - Renata Płocińska
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Anna Brzostek
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Yaroslav Faletrov
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
| | - Jarosław Dziadek
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Vladimir Shkumatov
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Kriti Bajpai
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Abstract
The type VII protein secretion system (T7SS) of Staphylococcus aureus is encoded at the ess locus. T7 substrate recognition and protein transport are mediated by EssC, a membrane-bound multidomain ATPase. Four EssC sequence variants have been identified across S. aureus strains, each accompanied by a specific suite of substrate proteins. The ess genes are upregulated during persistent infection, and the secretion system contributes to virulence in disease models. It also plays a key role in intraspecies competition, secreting nuclease and membrane-depolarizing toxins that inhibit the growth of strains lacking neutralizing immunity proteins. A genomic survey indicates that the T7SS is widely conserved across staphylococci and is encoded in clusters that contain diverse arrays of toxin and immunity genes. The presence of genomic islands encoding multiple immunity proteins in species such as Staphylococcus warneri that lack the T7SS points to a major role for the secretion system in bacterial antagonism. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Lisa Bowman
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom; ,
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom; ,
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
Collapse
Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
| |
Collapse
|
10
|
Bunduc CM, Fahrenkamp D, Wald J, Ummels R, Bitter W, Houben ENG, Marlovits TC. Structure and dynamics of a mycobacterial type VII secretion system. Nature 2021; 593:445-448. [PMID: 33981042 PMCID: PMC8131196 DOI: 10.1038/s41586-021-03517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/06/2021] [Indexed: 11/20/2022]
Abstract
Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year1. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope2,3. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP5 protease. A trimer of MycP5 caps a central periplasmic dome-like chamber that is formed by three EccB5 dimers, with the proteolytic sites of MycP5 facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP5 show disruption of the EccB5 periplasmic assembly and increased flexibility, which highlights the importance of MycP5 for complex integrity. Beneath the EccB5-MycP5 chamber, dimers of the EccC5 ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC5 domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.
Collapse
Affiliation(s)
- Catalin M Bunduc
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dirk Fahrenkamp
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology, Hamburg, Germany
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Edith N G Houben
- Molecular Microbiology Section, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Hamburg, Germany.
- Institute of Structural and Systems Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Deutsches Elektron Synchrotron DESY, Hamburg, Germany.
| |
Collapse
|
11
|
Modeling Tubercular ESX-1 Secretion Using Mycobacterium marinum. Microbiol Mol Biol Rev 2020; 84:84/4/e00082-19. [DOI: 10.1128/mmbr.00082-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pathogenic mycobacteria cause chronic and acute diseases ranging from human tuberculosis (TB) to nontubercular infections.
Mycobacterium tuberculosis
causes both acute and chronic human tuberculosis. Environmentally acquired nontubercular mycobacteria (NTM) cause chronic disease in humans and animals. Not surprisingly, NTM and
M. tuberculosis
often use shared molecular mechanisms to survive within the host. The ESX-1 system is a specialized secretion system that is essential for virulence and is functionally conserved between
M. tuberculosis
and
Mycobacterium marinum
.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
A Chimeric EccB-MycP Fusion Protein is Functional and a Stable Component of the ESX-5 Type VII Secretion System Membrane Complex. J Mol Biol 2020; 432:1265-1278. [DOI: 10.1016/j.jmb.2019.12.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 11/24/2022]
|
14
|
Poweleit N, Czudnochowski N, Nakagawa R, Trinidad DD, Murphy KC, Sassetti CM, Rosenberg OS. The structure of the endogenous ESX-3 secretion system. eLife 2019; 8:52983. [PMID: 31886769 PMCID: PMC6986878 DOI: 10.7554/elife.52983] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/30/2019] [Indexed: 12/15/2022] Open
Abstract
The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism Mycobacterium smegmatis. The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB3, EccC3, and EccE3 and two copies of the EccD3 protein. In the structure, the protomers form a stable dimer that is consistent with assembly into a larger oligomer. The ESX-3 structure provides a framework for further study of these important bacterial transporters.
Collapse
Affiliation(s)
- Nicole Poweleit
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, University of California, San Francisco, San Francisco, United States
| | - Nadine Czudnochowski
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, University of California, San Francisco, San Francisco, United States
| | - Rachel Nakagawa
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, United States
| | - Donovan D Trinidad
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, University of California, San Francisco, San Francisco, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Oren S Rosenberg
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
15
|
Famelis N, Rivera-Calzada A, Degliesposti G, Wingender M, Mietrach N, Skehel JM, Fernandez-Leiro R, Böttcher B, Schlosser A, Llorca O, Geibel S. Architecture of the mycobacterial type VII secretion system. Nature 2019; 576:321-325. [PMID: 31597161 DOI: 10.1038/s41586-019-1633-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 09/06/2019] [Indexed: 11/09/2022]
Abstract
Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems1. A molecular understanding of the type VII secretion mechanism has been hampered owing to a lack of three-dimensional structures of the fully assembled secretion apparatus. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis. The core of the ESX-3 secretion machine consists of four protein components-EccB3, EccC3, EccD3 and EccE3, in a 1:1:2:1 stoichiometry-which form two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The domain of unknown function (DUF) adjacent to the stalk is identified as an ATPase domain that is essential for secretion. EccB3 is predominantly periplasmatic, but a small segment crosses the membrane and contacts the stalk domain. This suggests that conformational changes in the stalk domain-triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF-could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from that of other known secretion machines2, and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence.
Collapse
Affiliation(s)
- Nikolaos Famelis
- Institute for Molecular Infection Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Maria Wingender
- Institute for Molecular Infection Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Nicole Mietrach
- Institute for Molecular Infection Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | | | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bettina Böttcher
- Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, Electron Microscopy Facility, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
| | - Sebastian Geibel
- Institute for Molecular Infection Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany. .,Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Exploration of some new secretory proteins to be employed for companion diagnosis of Mycobacterium tuberculosis. Immunol Lett 2019; 209:67-74. [PMID: 30898660 DOI: 10.1016/j.imlet.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 01/09/2023]
Abstract
Tuberculosis (TB) is a highly infectious disease and its early and precise diagnosis is essential to reduce morbidity and mortality of patients. Since the routine diagnostic tests (like Monteux, AFB smear microscopy, chest X-Ray) do not give infallible results, additional tests are always recommended. Therefore to address the concerns about non-specificity of the present battery of diagnostic tests, we have attempted to analyze some unique secretory antigens which could be able to identify the stage specific infection of MTB. In this study, we have used recombinant proteins CFP-10, ESAT-6, Ag85 A, Ag85B, Ag85C, PE3, PE4 and Mycp1 to eliminate heterogeneity and cross reactivity in clinical diagnosis. Amplified genes were cloned and over-expressed in Escherichia coli BL21 (DE3). The recombinantly purified proteins were used as antigens against 158 sera samples of TB patients. Secretory proteins showed better response than the PPD control. Among all the used antigens PE3 and PE4 proteins showed better reactivity levels among all the groups of TB patients. The secretions of CFP-10 and ESAT-6 were also higher as compared to other secretory proteins like Ag85 A, Ag85B, Ag85C and MycP1.The clinical use of these newly identified secretory antigens could be of significant value for the confirmatory, rapid, simple and low-cost diagnosis of TB patients.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Bainomugisa A, Lavu E, Hiashiri S, Majumdar S, Honjepari A, Moke R, Dakulala P, Hill-Cawthorne GA, Pandey S, Marais BJ, Coulter C, Coin L. Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades. Microb Genom 2018; 4. [PMID: 29310751 PMCID: PMC5857374 DOI: 10.1099/mgen.0.000147] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012–2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation. The Beijing sub-lineage strain demonstrated a high degree of co-resistance between isoniazid and ethionamide (80/95; 84.2 %) attributed to an inhA promoter mutation combined with inhA and ndh coding mutations. Multi-drug resistance, observed in 78/95 samples, emerged with the acquisition of a typical rpoB mutation together with a compensatory rpoC mutation in the 1980s. There was independent acquisition of fluoroquinolone and aminoglycoside resistance, and evidence of local transmission of extensively drug resistant (XDR) strains from 2009. These findings underline the importance of whole genome sequencing in informing an effective public health response to MDR/XDR TB.
Collapse
Affiliation(s)
- Arnold Bainomugisa
- 1Faculty of Medicine, University of Queensland, Brisbane, Australia.,2Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Evelyn Lavu
- 3Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Stenard Hiashiri
- 4Western Province Health Office, Western Province, Papua New Guinea
| | | | - Alice Honjepari
- 4Western Province Health Office, Western Province, Papua New Guinea
| | - Rendi Moke
- 6National Department of Health, Port Moresby, Papua New Guinea
| | - Paison Dakulala
- 6National Department of Health, Port Moresby, Papua New Guinea
| | | | - Sushil Pandey
- 8Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | - Ben J Marais
- 7School of Public Health, University of Sydney, Sydney, Australia
| | - Chris Coulter
- 8Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | - Lachlan Coin
- 2Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| |
Collapse
|
20
|
Abstract
Mycobacterial 6-kDa early secreted antigenic target (ESAT-6) system (ESX) exporters transport proteins across the cytoplasmic membrane. Many proteins transported by ESX systems are then translocated across the mycobacterial cell envelope and secreted from the cell. Although the mechanism underlying protein transport across the mycolate outer membrane remains elusive, the ESX systems are closely connected with and localize to the cell envelope. Links between ESX-associated proteins, cell wall synthesis, and the maintenance of cell envelope integrity have been reported. Genes encoding the ESX systems and those required for biosynthesis of the mycobacterial envelope are coregulated. Here, we review the interplay between ESX systems and the mycobacterial cell envelope.
Collapse
|
21
|
Abstract
The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serine protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity.
Collapse
|
22
|
Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol 2017; 1561:139-169. [PMID: 28236237 DOI: 10.1007/978-1-4939-6798-8_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding. Rosetta FlexPepDock was built to generate precise models of protein-peptide complex structures, by effectively addressing the challenge of the considerable conformational flexibility of the peptide. Rosetta FlexPepBind is an extension of this protocol that allows characterizing peptide-binding affinities and specificities of various biological systems, based on the structural models generated by Rosetta FlexPepDock. We provide detailed descriptions and guidelines for the usage of these protocols, and on a specific example, we highlight the variety of different challenges that can be met and the questions that can be answered with Rosetta FlexPepDock.
Collapse
|
23
|
Abstract
Type VII secretion (T7S) systems of mycobacteria secrete substrates over the unusual diderm cell envelope. Furthermore, T7S gene clusters are present throughout the phylum Actinobacteria, and functional T7S-like systems have been identified in Firmicutes. Most of the T7S substrates can be divided into two families: the Esx proteins, which are found in both Firmicutes and Actinobacteria, and the PE and PPE proteins, which are more mycobacterium-specific. Members of both families have been shown to be secreted as folded heterodimers, suggesting that this is a conserved feature of T7S substrates. Most knowledge of the mechanism of T7S and the roles of T7S systems in virulence comes from studies of pathogenic mycobacteria. These bacteria can contain up to five T7S systems, called ESX-1 to ESX-5, each having its own role in bacterial physiology and virulence. In this article, we discuss the general composition of T7S systems and the role of the individual components in secretion. These conserved components include two membrane proteins with (predicted) enzymatic activities: a predicted ATPase (EccC), likely to be required for energy provision of T7S, and a subtilisin-like protease (MycP) involved in processing of specific substrates. Additionally, we describe the role of a conserved intracellular chaperone in T7S substrate recognition, based on recently published crystal structures and molecular analysis. Finally, we discuss system-specific features of the different T7S systems in mycobacteria and their role in pathogenesis and provide an overview of the role of T7S in virulence of other pathogenic bacteria.
Collapse
|
24
|
Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes. mBio 2016; 7:mBio.01471-16. [PMID: 27795391 PMCID: PMC5082899 DOI: 10.1128/mbio.01471-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Pathogenic mycobacteria contain up to five type VII secretion (T7S) systems, ESX-1 to ESX-5. One of the conserved T7S components is the serine protease mycosin (MycP). Strikingly, whereas MycP is essential for secretion, the protease activity of MycP1 in Mycobacterium tuberculosis has been shown to be dispensable for secretion. The essential role of MycP therefore remains unclear. Here we show that MycP1 and MycP5 of M. marinum have similar phenotypes, confirming that MycP has a second unknown function that is essential for its T7S system. To investigate whether this role is related to proper functioning of the T7S membrane complex, we first analyzed the composition of the ESX-1 membrane complex and showed that this complex consists of EccBCDE1, similarly to what was previously shown for ESX-5. Surprisingly, while mycosins are not an integral part of these purified core complexes, we noticed that the stability of both the ESX-1 complex and the ESX-5 complex is compromised in the absence of their MycP subunit. Additional interaction studies showed that, although mycosins are not part of the central ESX membrane complex, they loosely associate with this complex. We hypothesize that this MycP association with the core membrane complex is crucial for the integrity and functioning of the T7S machinery. Among the major virulence factors of pathogenic mycobacteria are the type VII secretion (T7S) systems. Three of these systems, ESX-1, ESX-3, and ESX-5, have been shown to be crucial for virulence or viability. Here we describe the function of mycosin proteases, which are conserved components within these systems. We show that MycP1 and MycP5 have a second, proteolytic-independent function which is essential for the T7S system. We additionally found that this second essential role is related to the stabilization and proper functioning of their respective ESX membrane core complexes. Finally, we found that this is mediated by a loose association of MycP with the complex. Understanding the essential role of mycosins in type VII secretion systems, which play central roles in the virulence and viability of pathogenic mycobacteria, may provide new intervention strategies to treat tuberculosis.
Collapse
|
25
|
Abstract
Mycobacterium tuberculosis uses sophisticated secretion systems, named 6 kDa early secretory antigenic target (ESAT6) protein family secretion (ESX) systems (also known as type VII secretion systems), to export a set of effector proteins that helps the pathogen to resist or evade the host immune response. Since the discovery of the esx loci during the M. tuberculosis H37Rv genome project, structural biology, cell biology and evolutionary analyses have advanced our knowledge of the function of these systems. In this Review, we highlight the intriguing roles that these studies have revealed for ESX systems in bacterial survival and pathogenicity during infection with M. tuberculosis. Furthermore, we discuss the diversity of ESX systems that has been described among mycobacteria and selected non-mycobacterial species. Finally, we consider how our knowledge of ESX systems might be applied to the development of novel strategies for the treatment and prevention of disease.
Collapse
|
26
|
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.
Collapse
|
27
|
Zhang XL, Li DF, Fleming J, Wang LW, Zhou Y, Wang DC, Zhang XE, Bi LJ. Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase. FASEB J 2015; 29:4804-14. [PMID: 26396239 DOI: 10.1096/fj.15-270843] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/27/2015] [Indexed: 11/11/2022]
Abstract
Pathogenic mycobacteria transport virulence factors across their complex cell wall via a type VII secretion system (T7SS)/early secreted antigenic target-6 of kDa secretion system (ESX). ESX conserved component (Ecc) B, a core component of the T7SS architecture, is predicted to be a membrane bound protein, but little is known about its structure and function. Here, we characterize EccB1, showing that it is an ATPase with no sequence or structural homology to other ATPases located in the cell envelope of Mycobacterium tuberculosis H37Rv. We obtained the crystal structure of an EccB1-ΔN72 truncated transmembrane helix and performed modeling and ATP docking studies, showing that EccB1 likely exists as a hexamer. Sequence alignment and ATPase activity determination of EccB1 homologues indicated the presence of 3 conserved motifs in the N- and C-terminals of EccB1-ΔN72 that assemble together between 2 membrane proximal domains of the EccB1-ΔN72 monomer. Models of the EccB1 hexamer show that 2 of the conserved motifs are involved in ATPase activity and form an ATP binding pocket located on the surface of 2 adjacent molecules. Our results suggest that EccB may act as the energy provider in the transport of T7SS virulence factors and may be involved in the formation of a channel across the mycomembrane.
Collapse
Affiliation(s)
- Xiao-Li Zhang
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - De-Feng Li
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Li-Wei Wang
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Da-Cheng Wang
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Xian-En Zhang
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| | - Li-Jun Bi
- *State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; National Laboratory of Biomacromolecules and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Graduate School, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
28
|
Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis. J Struct Biol 2015; 191:236-44. [PMID: 26051906 DOI: 10.1016/j.jsb.2015.06.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/16/2015] [Accepted: 06/02/2015] [Indexed: 02/03/2023]
Abstract
Mycobacterium tuberculosis secretes multiple virulence factors during infection via the general Sec and Tat pathways, and via specialized ESX secretion systems, also referred to as type VII secretion systems. The ESX-1 secretion system is an important virulence determinant because deletion of ESX-1 leads to attenuation of M. tuberculosis. ESX-1 secreted protein B (EspB) contains putative PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains, and a C-terminal domain, which is processed by MycP1 protease during secretion. We determined the crystal structure of PE-PPE domains of EspB, which represents an all-helical, elongated molecule closely resembling the structure of the PE25-PPE41 heterodimer despite limited sequence similarity. Also, we determined the structure of full-length EspB, which does not have interpretable electron density for the C-terminal domain confirming that it is largely disordered. Comparative analysis of EspB in cell lysate and culture filtrates of M. tuberculosis revealed that mature secreted EspB forms oligomers. Electron microscopy analysis showed that the N-terminal fragment of EspB forms donut-shaped particles. These data provide a rationale for the future investigation of EspB's role in M. tuberculosis pathogenesis.
Collapse
|
29
|
Costa TRD, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M, Waksman G. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat Rev Microbiol 2015; 13:343-59. [DOI: 10.1038/nrmicro3456] [Citation(s) in RCA: 655] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
30
|
Assessing the progress of Mycobacterium tuberculosis H37Rv structural genomics. Tuberculosis (Edinb) 2015; 95:131-6. [DOI: 10.1016/j.tube.2014.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/05/2014] [Accepted: 12/17/2014] [Indexed: 11/19/2022]
|
31
|
Structure of EspB from the ESX-1 Type VII Secretion System and Insights into its Export Mechanism. Structure 2015; 23:571-583. [DOI: 10.1016/j.str.2015.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/17/2014] [Accepted: 12/23/2014] [Indexed: 12/29/2022]
|
32
|
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
![]()
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.
Collapse
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
| | | | | | | | | | | | | |
Collapse
|
33
|
Frasinyuk MS, Kwiatkowski S, Wagner JM, Evans TJ, Reed RW, Korotkov KV, Watt DS. Pentapeptide boronic acid inhibitors of Mycobacterium tuberculosis MycP1 protease. Bioorg Med Chem Lett 2014; 24:3546-8. [PMID: 24915878 DOI: 10.1016/j.bmcl.2014.05.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 01/16/2023]
Abstract
Mycosin protease-1 (MycP1) cleaves ESX secretion-associated protein B (EspB) that is a virulence factor of Mycobacterium tuberculosis, and accommodates an octapeptide, AVKAASLG, as a short peptide substrate. Because peptidoboronic acids are known inhibitors of serine proteases, the synthesis and binding of a boronic acid analog of the pentapeptide cleavage product, AVKAA, was studied using MycP1 variants from Mycobacterium thermoresistible (MycP1mth), Mycobacterium smegmatis (MycP1msm) and M. tuberculosis (MycP1mtu). We synthesized the boropentapeptide, HAlaValLysAlaAlaB(OH)2 (1) and the analogous pinanediol PD-protected HAlaValLysAlaAlaBO2(PD) (2) using an Fmoc/Boc peptide strategy. The pinanediol boropentapeptide 2 displayed IC50 values 121.6±25.3 μM for MycP1mth, 93.2±37.3 μM for MycP1msm and 37.9±5.2 μM for MycP1mtu. Such relatively strong binding creates a chance for crystalizing the complex with 2 and finding the structure of the unknown MycP1 catalytic site that would potentially facilitate the development of new anti-tuberculosis drugs.
Collapse
Affiliation(s)
- Mykhaylo S Frasinyuk
- Institute of Bioorganic Chemistry and Petrochemistry, Kyiv-94 02660, Ukraine; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Stefan Kwiatkowski
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA; Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Jonathan M Wagner
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Timothy J Evans
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Robert W Reed
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - David S Watt
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA; Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA; Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA.
| |
Collapse
|
34
|
Siegrist MS, Steigedal M, Ahmad R, Mehra A, Dragset MS, Schuster BM, Philips JA, Carr SA, Rubin EJ. Mycobacterial Esx-3 requires multiple components for iron acquisition. mBio 2014; 5:e01073-14. [PMID: 24803520 PMCID: PMC4010830 DOI: 10.1128/mbio.01073-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 03/28/2014] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT The type VII secretion systems are conserved across mycobacterial species and in many Gram-positive bacteria. While the well-characterized Esx-1 pathway is required for the virulence of pathogenic mycobacteria and conjugation in the model organism Mycobacterium smegmatis, Esx-3 contributes to mycobactin-mediated iron acquisition in these bacteria. Here we show that several Esx-3 components are individually required for function under low-iron conditions but that at least one, the membrane-bound protease MycP3 of M. smegmatis, is partially expendable. All of the esx-3 mutants tested, including the ΔmycP3ms mutant, failed to export the native Esx-3 substrates EsxHms and EsxGms to quantifiable levels, as determined by targeted mass spectrometry. Although we were able to restore low-iron growth to the esx-3 mutants by genetic complementation, we found a wide range of complementation levels for protein export. Indeed, minute quantities of extracellular EsxHms and EsxGms were sufficient for iron acquisition under our experimental conditions. The apparent separation of Esx-3 function in iron acquisition from robust EsxGms and EsxHms secretion in the ΔmycP3ms mutant and in some of the complemented esx-3 mutants compels reexamination of the structure-function relationships for type VII secretion systems. IMPORTANCE Mycobacteria have several paralogous type VII secretion systems, Esx-1 through Esx-5. Whereas Esx-1 is required for pathogenic mycobacteria to grow within an infected host, Esx-3 is essential for growth in vitro. We and others have shown that Esx-3 is required for siderophore-mediated iron acquisition. In this work, we identify individual Esx-3 components that contribute to this process. As in the Esx-1 system, most mutations that abolish Esx-3 protein export also disrupt its function. Unexpectedly, however, ultrasensitive quantitation of Esx-3 secretion by multiple-reaction-monitoring mass spectrometry (MRM-MS) revealed that very low levels of export were sufficient for iron acquisition under similar conditions. Although protein export clearly contributes to type VII function, the relationship is not absolute.
Collapse
Affiliation(s)
- M. Sloan Siegrist
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | - Rushdy Ahmad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alka Mehra
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, New York, USA
| | | | - Brian M. Schuster
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jennifer A. Philips
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Chang JH, Desveaux D, Creason AL. The ABCs and 123s of bacterial secretion systems in plant pathogenesis. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:317-45. [PMID: 24906130 DOI: 10.1146/annurev-phyto-011014-015624] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacteria have many export and secretion systems that translocate cargo into and across biological membranes. Seven secretion systems contribute to pathogenicity by translocating proteinaceous cargos that can be released into the extracellular milieu or directly into recipient cells. In this review, we describe these secretion systems and how their complexities and functions reflect differences in the destinations, states, functions, and sizes of the translocated cargos as well as the architecture of the bacterial cell envelope. We examine the secretion systems from the perspective of pathogenic bacteria that proliferate within plant tissues and highlight examples of translocated proteins that contribute to the infection and disease of plant hosts.
Collapse
Affiliation(s)
- Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331; ,
| | | | | |
Collapse
|
37
|
Houben ENG, Korotkov KV, Bitter W. Take five - Type VII secretion systems of Mycobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1707-16. [PMID: 24263244 DOI: 10.1016/j.bbamcr.2013.11.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 11/18/2022]
Abstract
Mycobacteria use type VII secretion (T7S) systems to secrete proteins across their complex cell envelope. Pathogenic mycobacteria, such as the notorious pathogen Mycobacterium tuberculosis, have up to five of these secretion systems, named ESX-1 to ESX-5. At least three of these secretion systems are essential for mycobacterial virulence and/or viability. Elucidating T7S is therefore essential to understand the success of M. tuberculosis and other pathogenic mycobacteria as pathogens, and could be instrumental to identify novel targets for drug- and vaccine-development. Recently, significant progress has been achieved in the identification of T7S substrates and a general secretion motif. In addition, a start has been made with unraveling the mechanism of secretion and the structural analysis of the different subunits. This review summarizes these recent findings, which are incorporated in a working model of this complex machinery. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
Collapse
Affiliation(s)
- Edith N G Houben
- VU University, Amsterdam, The Netherlands; VU University Medical Center, Amsterdam, The Netherlands.
| | | | - Wilbert Bitter
- VU University, Amsterdam, The Netherlands; VU University Medical Center, Amsterdam, The Netherlands
| |
Collapse
|
38
|
The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability. Protein Cell 2013; 4:921-31. [PMID: 24248472 DOI: 10.1007/s13238-013-3089-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
Mycosin-1 protease (MycP1) is a serine protease anchored to the inner membrane of Mycobacterium tuberculosis, and is essential in virulence factor secretion through the ESX-1 type VII secretion system (T7SS). Bacterial physiology studies demonstrated that MycP1 plays a dual role in the regulation of ESX-1 secretion and virulence, primarily through cleavage of its secretion substrate EspB. MycP1 contains a putative N-terminal inhibitory propeptide and a catalytic triad of Asp-His-Ser, classic hallmarks of a subtilase family serine protease. The MycP1 propeptide was previously reported to be initially inactive and activated after prolonged incubation. In this study, we have determined crystal structures of MycP1 with (MycP1²⁴⁻⁴²²) and without (MycP1⁶³⁻⁴²²) the propeptide, and conducted EspB cleavage assays using the two proteins. Very high structural similarity was observed in the two crystal structures. Interestingly, protease assays demonstrated positive EspB cleavage for both proteins, indicating that the putative propeptide does not inhibit protease activity. Molecular dynamic simulations showed higher rigidity in regions guarding the entrance to the catalytic site in MycP1²⁴⁻⁴²² than in MycP1⁶³⁻⁴²², suggesting that the putative propeptide might contribute to the conformational stability of the active site cleft and surrounding regions.
Collapse
|
39
|
Wagner JM, Evans TJ, Chen J, Zhu H, Houben ENG, Bitter W, Korotkov KV. Understanding specificity of the mycosin proteases in ESX/type VII secretion by structural and functional analysis. J Struct Biol 2013; 184:115-28. [PMID: 24113528 DOI: 10.1016/j.jsb.2013.09.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/28/2022]
Abstract
Mycobacteria use specialized ESX secretion systems to transport proteins across their cell membranes in order to manipulate their environment. In pathogenic Mycobacterium tuberculosis there are five paralogous ESX secretion systems, named ESX-1 through ESX-5. Each system includes a subtilisin-like protease (mycosin or MycP) as a core component essential for secretion. Here we report crystal structures of MycP1 and MycP3, the mycosins expressed by the ESX-1 and ESX-3 systems, respectively. In both mycosins the putative propeptide wraps around the catalytic domain and does not occlude the active site. The extensive contacts between the putative propeptide and catalytic domain, which include a disulfide bond, suggest that the N-terminal extension is an integral part of the active mycosin. The catalytic residues of MycP1 and MycP3 are located in a deep active site groove in contrast with an exposed active site in majority of subtilisins. We show that MycP1 specifically cleaves ESX-1 secretion-associated protein B (EspB) in vitro at residues Ala358 and Ala386. We also systematically characterize the specificity of MycP1 using peptide libraries, and show that it has evolved a narrow specificity relative to other subtilisins. Finally, comparison of the MycP1 and MycP3 structures suggest that both enzymes have stringent and different specificity profiles that result from the structurally distinct active site pockets, which could explain the system specific functioning of these proteases.
Collapse
Affiliation(s)
- Jonathan M Wagner
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
| | | | | | | | | | | | | |
Collapse
|