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Li T, Xu B, Chen H, Shi Y, Li J, Yu M, Xia S, Wu S. Gut toxicity of polystyrene microplastics and polychlorinated biphenyls to Eisenia fetida: Single and co-exposure effects with a focus on links between gut bacteria and bacterial translocation stemming from gut barrier damage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168254. [PMID: 37923278 DOI: 10.1016/j.scitotenv.2023.168254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Microplastics' (MPs) ability to sorb and transport polychlorinated biphenyls (PCBs) in soil ecosystems warrants significant attention. Although organisms mainly encounter pollutants through the gut, the combined pollution impact of MPs and PCBs on soil fauna gut toxicity remains incompletely understood. Consequently, this study examined the gut toxicity of polystyrene MPs (PS-MPs) and PCB126 on Eisenia fetida, emphasizing the links between gut bacteria and bacterial translocation instigated by gut barrier impairment. Our findings underscored that E. fetida could ingest PS-MPs, which mitigated the PCB126 accumulation in E. fetida by 9.43 %. Exposure to PCB126 inhibited the expression of gut tight junction (TJ) protein genes. Although the presence of PS-MPs attenuated this suppression, it didn't alleviate gut barrier damage and bacterial translocation in the co-exposure group. This group demonstrated a significantly increased level of gut bacterial load (BLT, ANOVA, p = 0.005 vs control group) and lipopolysaccharide-binding protein (LBP, ANOVA, all p < 0.001 vs control, PCB, and PS groups), both of which displayed significant positive correlations with antibacterial defense. Furthermore, exposure to PS-MPs and PCB126, particularly within the co-exposure group, results in a marked decline in the dispersal ability of gut bacteria. This leads to dysbiosis (Adonis, R2 = 0.294, p = 0.001), with remarkable signature taxa such as Janthinobacterium, Microbacterium and Pseudomonas, being implicated in gut barrier dysfunction. This research illuminates the mechanism of gut toxicity induced by PS-MPs and PCB126 combined pollution in earthworms, providing novel insights for the ecological risk assessment of soil.
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Affiliation(s)
- Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Baohua Xu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hao Chen
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ying Shi
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- Jiangxi Key Laboratory of Natural Product and Functional Food, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengwei Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shaohui Xia
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shijin Wu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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2
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Granados-Tristán AL, Hernández-Luna CE, González-Escalante LA, Camacho-Moll ME, Silva-Ramírez B, Bermúdez de León M, Peñuelas-Urquides K. ESX-3 secretion system in Mycobacterium: An overview. Biochimie 2024; 216:46-55. [PMID: 37879428 DOI: 10.1016/j.biochi.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Mycobacteria are microorganisms distributed in the environment worldwide, and some of them, such as Mycobacterium tuberculosis or M. leprae, are pathogenic. The hydrophobic mycobacterial cell envelope has low permeation and bacteria need to export products across their structure. Mycobacteria possess specialized protein secretion systems, such as the Early Secretory Antigenic Target 6 secretion (ESX) system. Five ESX loci have been described in M. tuberculosis, called ESX-1 to ESX-5. The ESX-3 secretion system has been associated with mycobacterial metabolism and growth. The locus of this system is highly conserved across mycobacterial species. Metallo-proteins regulate negative ESX-3 transcription in high conditions of iron and zinc. Moreover, this secretion system is part of an antioxidant regulatory pathway linked to Zinc. EccA3, EccB3, EccC3, EccD3, and EccE3 are components of the ESX-3 secretion machinery, whereas EsxG-EsxH, PE5-PPE4, and PE15-PPE20 are proteins secreted by this system. In addition, EspG3 and MycP3 are complementary proteins involved in transport and proteolysis respectively. This system is associated to mycobacterial virulence by releasing the bacteria from the phagosome and inhibiting endomembrane damage response. Furthermore, components of this system inhibit the host immune response by reducing the recognition of M. tuberculosis-infected cells. The components of the ESX-3 secretion system play a role in drug resistance and cell wall integrity. Moreover, the expression data of this system indicated that external and internal factors affect ESX-3 locus expression. This review provides an overview of new findings on the ESX-3 secretion system, its regulation, expression, and functions.
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Affiliation(s)
- Ana Laura Granados-Tristán
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico; Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Carlos Eduardo Hernández-Luna
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Laura Adiene González-Escalante
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
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3
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Gracy J, Vallejos-Sanchez K, Cohen-Gonsaud M. SecretoMyc, a web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools. Tuberculosis (Edinb) 2023; 141:102375. [PMID: 37429152 DOI: 10.1016/j.tube.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
To better understand the interaction between the host and the Mycobacterium tuberculosis pathogen, it is critical to identify its potential secreted proteins. While various experimental methods have been successful in identifying proteins under specific culture conditions, they have not provided a comprehensive characterisation of the secreted proteome. We utilized a combination of bioinformatics servers and in-house software to identify all potentially secreted proteins from six mycobacterial genomes through the three secretion systems: SEC, TAT, and T7SS. The results are presented in a database that can be crossed referenced to selected proteomics and transcriptomics studies (https://secretomyc.cbs.cnrs.fr). In addition, thanks to the recent availability of Alphafold models, we developed a tool in order to identify the structural homologues among the mycobacterial genomes.
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Affiliation(s)
- Jérôme Gracy
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France
| | - Katherine Vallejos-Sanchez
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France; Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Martin Cohen-Gonsaud
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, France.
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4
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Martin M, deVisch A, Boudehen YM, Barthe P, Gutierrez C, Turapov O, Aydogan T, Heriaud L, Gracy J, Neyrolles O, Mukamolova GV, Letourneur F, Cohen-Gonsaud M. A Mycobacterium tuberculosis Effector Targets Mitochondrion, Controls Energy Metabolism, and Limits Cytochrome c Exit. Microbiol Spectr 2023; 11:e0106623. [PMID: 37036353 PMCID: PMC10269737 DOI: 10.1128/spectrum.01066-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 04/11/2023] Open
Abstract
Host metabolism reprogramming is a key feature of Mycobacterium tuberculosis (Mtb) infection that enables the survival of this pathogen within phagocytic cells and modulates the immune response facilitating the spread of the tuberculosis disease. Here, we demonstrate that a previously uncharacterized secreted protein from Mtb, Rv1813c, manipulates the host metabolism by targeting mitochondria. When expressed in eukaryotic cells, the protein is delivered to the mitochondrial intermembrane space and promotes the enhancement of host ATP production by boosting the oxidative phosphorylation metabolic pathway. Furthermore, the release of cytochrome c from mitochondria, an early apoptotic event in response to short-term oxidative stress, is delayed in Rv1813c-expressing cells. This study reveals a novel class of mitochondria targeting effectors from Mtb that might participate in host cell metabolic reprogramming and apoptosis control during Mtb infections. IMPORTANCE In this article, using a combination of techniques (bioinformatics, structural biology, and cell biology), we identified and characterized a new class of effectors present only in intracellular mycobacteria. These proteins specifically target host cell mitochondria when ectopically expressed in cells. We showed that one member of this family (Rv1813c) affects mitochondria metabolism in a way that might twist the immune response. This effector also inhibits the cytochrome c exit from mitochondria, suggesting that it might alter normal host cell apoptotic capacities, one of the first defenses of immune cells against Mtb infection.
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Affiliation(s)
- Marianne Martin
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Angelique deVisch
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Yves-Marie Boudehen
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse CNRS, UPS, Toulouse, France
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse CNRS, UPS, Toulouse, France
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Talip Aydogan
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Laurène Heriaud
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Jerome Gracy
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse CNRS, UPS, Toulouse, France
| | - Galina V. Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - François Letourneur
- Laboratory of Pathogen Host Interactions, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
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5
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Gupta S, Bhagavathula M, Sharma V, Sharma N, Sharma N, Biswas A, Palacios A, Salgueiro V, Lavín JL, Dogra N, Salgame P, Prados‐Rosales R, Rodríguez GM. Dynamin-like proteins mediate extracellular vesicle secretion in Mycobacterium tuberculosis. EMBO Rep 2023; 24:e55593. [PMID: 37079766 PMCID: PMC10240201 DOI: 10.15252/embr.202255593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/14/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) secretes extracellular vesicles (EVs) containing a variety of proteins, lipoproteins, and lipoglycans. While emerging evidence suggests that EVs contribute to tuberculosis pathogenesis, the factors and molecular mechanisms involved in mycobacterial EV production have not been identified. In this study, we use a genetic approach to identify Mtb proteins that mediate vesicle release in response to iron limitation and antibiotic exposure. We uncover a critical role for the isoniazid-induced, dynamin-like proteins, IniA and IniC, in mycobacterial EV biogenesis. Further characterization of a Mtb iniA mutant shows that the production of EVs enables intracellular Mtb to export bacterial components into the extracellular environment to communicate with host cells and potentially modulate the immune response. The findings advance our understanding of the biogenesis and functions of mycobacterial EVs and provide an avenue for targeting vesicle production in vivo.
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Affiliation(s)
- Shamba Gupta
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Madhuri Bhagavathula
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Vartika Sharma
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Nishant Sharma
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Nevadita Sharma
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Ashis Biswas
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Ainhoa Palacios
- Inflammation and Macrophage Plasticity LabCIC bioGUNEDerioSpain
| | - Vivian Salgueiro
- Department of Preventive Medicine and Public Health and MicrobiologyAutonoma University of MadridMadridSpain
| | | | - Navneet Dogra
- Genetics and Genomic Sciences Icahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Padmini Salgame
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
| | - Rafael Prados‐Rosales
- Department of Preventive Medicine and Public Health and MicrobiologyAutonoma University of MadridMadridSpain
| | - G Marcela Rodríguez
- Department of Medicine, New Jersey Medical School, Public Health Research InstituteRutgers UniversityNewarkNJUSA
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6
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Ho VQT, Rong MK, Habjan E, Bommer SD, Pham TV, Piersma SR, Bitter W, Ruijter E, Speer A. Dysregulation of Mycobacterium marinum ESX-5 Secretion by Novel 1,2,4-oxadiazoles. Biomolecules 2023; 13:biom13020211. [PMID: 36830581 PMCID: PMC9953084 DOI: 10.3390/biom13020211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The ESX-5 secretion system is essential for the viability and virulence of slow-growing pathogenic mycobacterial species. In this study, we identified a 1,2,4-oxadiazole derivative as a putative effector of the ESX-5 secretion system. We confirmed that this 1,2,4-oxadiazole and several newly synthesized derivatives inhibited the ESX-5-dependent secretion of active lipase LipY by Mycobacterium marinum (M. marinum). Despite reduced lipase activity, we did not observe a defect in LipY secretion itself. Moreover, we found that several other ESX-5 substrates, especially the high molecular-weight PE_PGRS MMAR_5294, were even more abundantly secreted by M. marinum treated with several 1,2,4-oxadiazoles. Analysis of M. marinum grown in the presence of different oxadiazole derivatives revealed that the secretion of LipY and the induction of PE_PGRS secretion were, in fact, two independent phenotypes, as we were able to identify structural features in the compounds that specifically induced only one of these phenotypes. Whereas the three most potent 1,2,4-oxadiazoles displayed only a mild effect on the growth of M. marinum or M. tuberculosis in culture, these compounds significantly reduced bacterial burden in M. marinum-infected zebrafish models. In conclusion, we report a 1,2,4-oxadiazole scaffold that dysregulates ESX-5 protein secretion.
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Affiliation(s)
- Vien Q. T. Ho
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Mark K. Rong
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Samantha D. Bommer
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, OncoProteomics Laboratory, AmsterdamUMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, AmsterdamUMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Eelco Ruijter
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Vrije Universiteit Medical Center, 1081 HV Amsterdam, The Netherlands
- Correspondence:
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7
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VapC toxin switches M. smegmatis cells into dormancy through 23S rRNA cleavage. Arch Microbiol 2023; 205:28. [DOI: 10.1007/s00203-022-03363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
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8
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Bythrow GV, Farhat MF, Levendosky K, Mohandas P, Germain GA, Yoo B, Quadri LEN. Mycobacterium abscessus Mutants with a Compromised Functional Link between the Type VII ESX-3 System and an Iron Uptake Mechanism Reliant on an Unusual Mycobactin Siderophore. Pathogens 2022; 11:pathogens11090953. [PMID: 36145386 PMCID: PMC9505556 DOI: 10.3390/pathogens11090953] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022] Open
Abstract
The opportunistic pathogen Mycobacterium abscessus subsp. abscessus (Mab) has become an emerging public health threat due to the increasing number of Mab-associated chronic pulmonary disease cases. Treatment requires multiple drug courses and is often combined with surgical resection. Cure rates are only ~50% due to treatment failure and comorbidities. Deeper understanding of the biology of Mab is required to illuminate potential avenues for the development of better therapeutics against Mab infections. The ESX-3 type VII protein secretion system of Mab has an important role in host inflammatory and pathological responses during infection. In this work, we demonstrate a functional link between ESX-3 and an iron uptake system based on an unusual mycobactin-type siderophore (designated MBT Ab) and exploit this link to implement a large screen for transposon mutants with an impaired ESX-3. Most mutants we identified carry insertions in genes encoding predicted ESX-3 secretion machinery components or potential ESX-3 substrates. The mutants overproduce MBT Ab, a trait consistent with an iron uptake defect. Our characterization of MBT Ab revealed structural features reminiscent of nocardial mycobactin-like compounds with cytotoxicity. This finding raises the possibility that MBT Ab may play roles in pathogenesis unlinked to iron homeostasis. The mutants generated herein will facilitate research to better understand the role of ESX-3 and its interplay with the siderophore system.
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Affiliation(s)
- Glennon V. Bythrow
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Manal F. Farhat
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Poornima Mohandas
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Gabrielle A. Germain
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Biochemistry Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Correspondence:
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9
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Characterization of the Protective Immune Responses Conferred by Recombinant BCG Overexpressing Components of Mycobacterium tuberculosis Sec Protein Export System. Vaccines (Basel) 2022; 10:vaccines10060945. [PMID: 35746553 PMCID: PMC9229301 DOI: 10.3390/vaccines10060945] [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: 05/09/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the only approved vaccine against tuberculosis (TB). However, its efficacy in preventing pulmonary TB in adults is limited. Despite its variable efficacy, BCG offers a number of unique and beneficial characteristics, which make it suitable as a vaccine vehicle to express recombinant molecules. In Mycobacterium tuberculosis, the general Sec pathway is an essential cellular process, and it is responsible for exporting the majority of proteins across the cytoplasmic membrane, including potent immune-protective antigens, such as members of the antigen 85 (Ag85) complex. We engineered BCG to overexpress the M. tuberculosis SecDFG proteins in order to improve the efficiency of the Sec-dependent export system and, thus, enhance the secretion of immunogenic proteins. BCGSecDFG displayed increased intracellular survival within macrophages in vitro and greater persistence in the lymphoid organs of vaccinated mice than parental BCG. In addition, vaccination with BCGSecDFG generated higher numbers of IFN-γ-secreting T cells in response to secreted mycobacterial antigens compared to BCG, particularly members of the Ag85 complex. Furthermore, vaccination with BCGSecDFG significantly reduced the bacterial load in the lungs and spleens of M. tuberculosis-infected mice, which was comparable to the protection afforded by parental BCG. Therefore, the modification of protein secretion in BCG can improve antigen-specific immunogenicity.
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10
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Dwivedi M, Bajpai K. The chamber of secretome in Mycobacterium tuberculosis as a potential therapeutic target. Biotechnol Genet Eng Rev 2022; 39:1-44. [PMID: 35613080 DOI: 10.1080/02648725.2022.2076031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mycobacterium tuberculosis (MTB) causes one of the ancient diseases, Tuberculosis, affects people around the globe and its severity can be understood by its classification as a second infectious disease after COVID-19 and the 13th leading cause of death according to a WHO report. Despite having advanced diagnostic approaches and therapeutic strategies, unfortunately, TB is still spreading across the population due to the emergence of drug-resistance MTB and Latent TB infection (LTBI). We are seeking for effective approaches to overcome these hindrances and efficient treatment for this perilous disease. Therefore, there is an urgent need to develop drugs based on operative targeting of the bacterial system that could result in both efficient treatment and lesser emergence of MDR-TB. One such promising target could be the secretory systems and especially the Type 7 secretory system (T7SS-ESX) of Mycobacterium tuberculosis, which is crucial for the secretion of effector proteins as well as in establishing host-pathogen interactions of the tubercle bacilli. The five paralogous ESX systems (ESX-1 to EXS-5) have been observed by in silico genome analysis of MTB, among which ESX-1 and ESX-5 are substantial for virulence and mediating host cellular inflammasome. The bacterium growth and virulence can be modulated by targeting the T7SS. In the present review, we demonstrate the current status of therapeutics against MTB and focus on the function and cruciality of T7SS along with other secretory systems as a promising therapeutic target against Tuberculosis.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Kriti Bajpai
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
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11
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Chiner-Oms Á, López MG, Moreno-Molina M, Furió V, Comas I. Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection. Proc Natl Acad Sci U S A 2022; 119:e2113600119. [PMID: 35452305 PMCID: PMC9173582 DOI: 10.1073/pnas.2113600119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug resistance profiles. Said differences usually emerge through de novo mutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ∼5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host–pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.
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Affiliation(s)
- Álvaro Chiner-Oms
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | - Mariana G. López
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | | | - Victoria Furió
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
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12
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Mouhoub E, Domenech P, Ndao M, Reed MB. The Diverse Applications of Recombinant BCG-Based Vaccines to Target Infectious Diseases Other Than Tuberculosis: An Overview. Front Microbiol 2021; 12:757858. [PMID: 34745066 PMCID: PMC8566895 DOI: 10.3389/fmicb.2021.757858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Live attenuated Bacillus Calmette-Guérin (BCG) is the world's most widely used vaccine which is mainly administered for its protection against tuberculosis (TB), particularly in young children. However, since its initial use over 100years ago, it has also proven to offer a level of protection against various other pathogens, as a consequence of its non-specific immune enhancing effects. Thus, over the past few decades, recombinant BCG (rBCG) technology has been used as a vector to create rBCG vaccines expressing heterologous antigens that elicit immunity against a range of bacterial, viral, and parasitic diseases. Our goal with this mini-review is to provide an up-to-date survey of the various techniques, approaches, and applications of rBCG-based vaccines for targeting infectious diseases other than TB.
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Affiliation(s)
- Esma Mouhoub
- The Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- The McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Pilar Domenech
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- The McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Momar Ndao
- The Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- The McGill International TB Centre, McGill University, Montreal, QC, Canada
- The Department of Medicine, McGill University, Montreal, QC, Canada
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Michael B. Reed
- The Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- The McGill International TB Centre, McGill University, Montreal, QC, Canada
- The Department of Medicine, McGill University, Montreal, QC, Canada
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13
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Jia P, Zhang Y, Xu J, Zhu M, Peng S, Zhang Y, Zhao J, Li X, Mi K, Yan D, Wang Y, Yu L, Lu Y, Shi H, Cen S. IMB-BZ as an Inhibitor Targeting ESX-1 Secretion System to Control Mycobacterial Infection. J Infect Dis 2021; 225:608-616. [PMID: 34558604 DOI: 10.1093/infdis/jiab486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/23/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Resistance to anti-tuberculosis (TB) drug is a major issue in TB control, and demands the discovery of new drugs targeting virulence factor ESX-1. METHODS We first established a high-throughput screen (HTS) assay for the discovery of ESX-1 secretion inhibitors. The positive hits were then evaluated for the potency of diminishing the survival of virulent mycobacterium and reducing bacterial virulence. We further investigated the probability of inducing drug-resistance and the underlying mechanism using M-PFC. RESULTS A robust HTS assay was developed to identify small molecules that inhibit ESX-1 secretion without impairing bacterial growth in vitro. A hit named IMB-BZ specifically inhibits the secretion of CFP-10 and reduces virulence in an ESX-1-dependent manner, therefore resulting in significant reduction in intracellular and in vivo survival of mycobacteria. Blocking the CFP-10-EccCb1 interaction directly or indirectly underlies the inhibitory effect of IMB-BZ on the secretion of CFP-10. Importantly, our finding shows that the ESX-1 inhibitors pose low risk of drug resistance development by mycobacteria in vitro as compared with traditional anti-TB drug, and exhibit high potency against chronic mycobacterial infection. CONCLUSION Targeting ESX-1 may lead to the development of novel therapeutics for tuberculosis. IMB-BZ holds the potential for future development into a new anti-TB drug.
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Affiliation(s)
- Pingping Jia
- Department of Clinical Nutrition, Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China; Department of Oncology, Capital Medical University, Beijing, 100038, China.,Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Yi Zhang
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Jian Xu
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China.,Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Shize Peng
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Kaixia Mi
- The Institute of Microbiology of the Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Yan
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Yu Lu
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Hanping Shi
- Department of Clinical Nutrition, Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China; Department of Oncology, Capital Medical University, Beijing, 100038, China
| | - Shan Cen
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, 100050, China.,Beijing Friendship Hospital, Capital Medical University, Beijing, China
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14
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Cai X, Liu L, Qiu C, Wen C, He Y, Cui Y, Li S, Zhang X, Zhang L, Tian C, Bi L, Zhou ZH, Gong W. Identification and architecture of a putative secretion tube across mycobacterial outer envelope. SCIENCE ADVANCES 2021; 7:7/34/eabg5656. [PMID: 34417177 PMCID: PMC8378821 DOI: 10.1126/sciadv.abg5656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Tuberculosis-causing mycobacteria have thick cell-wall and capsule layers that are formed from complex structures. Protein secretion across these barriers depends on a specialized protein secretion system, but none has been reported. We show that Mycobacterium tuberculosis Rv3705c and its homologous MSMEG_6251 in Mycobacterium smegmatis are tube-forming proteins in the mycobacterial envelope (TiME). Crystallographic and cryo-EM structures of these two proteins show that both proteins form rotationally symmetric rings. Two layers of TiME rings pack together in a tail-to-tail manner into a ring-shaped complex, which, in turn, stacks together to form tubes. M. smegmatis TiME was detected mainly in the cell wall and capsule. Knocking out the TiME gene markedly decreased the amount of secreted protein in the M. smegmatis culture medium, and expression of this gene in knocked-out strain partially restored the level of secreted protein. Our structure and functional data thus suggest that TiME forms a protein transport tube across the mycobacterial outer envelope.
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Affiliation(s)
- Xiaoying Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Chunhong Qiu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Chongzheng Wen
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Yao He
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Siyu Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuan Zhang
- Institute of Health Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Longhua Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Changlin Tian
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lijun Bi
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Weimin Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
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15
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Simeone R, Sayes F, Lawarée E, Brosch R. Breaching the phagosome, the case of the tuberculosis agent. Cell Microbiol 2021; 23:e13344. [PMID: 33860624 DOI: 10.1111/cmi.13344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022]
Abstract
The interactions between microbes and their hosts are among the most complex biological phenomena known today. The interaction may reach from overall beneficial interaction, as observed for most microbiome/microbiota related interactions to interaction with virulent pathogens, against which host cells have evolved sophisticated defence strategies. Among the latter, the confinement of invading pathogens in a phagosome plays a key role, which often results in the destruction of the invader, whereas some pathogens may counteract phagosomal arrest and survive by gaining access to the cytosol of the host cell. In the current review, we will discuss recent insights into this dynamic process of host-pathogen interaction, using Mycobacterium tuberculosis and related pathogenic mycobacteria as main examples.
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Affiliation(s)
- Roxane Simeone
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Fadel Sayes
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Emeline Lawarée
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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16
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Davis MM, Brock AM, DeHart TG, Boribong BP, Lee K, McClune ME, Chang Y, Cramer N, Liu J, Jones CN, Jutras BL. The peptidoglycan-associated protein NapA plays an important role in the envelope integrity and in the pathogenesis of the lyme disease spirochete. PLoS Pathog 2021; 17:e1009546. [PMID: 33984073 PMCID: PMC8118282 DOI: 10.1371/journal.ppat.1009546] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
The bacterial pathogen responsible for causing Lyme disease, Borrelia burgdorferi, is an atypical Gram-negative spirochete that is transmitted to humans via the bite of an infected Ixodes tick. In diderms, peptidoglycan (PG) is sandwiched between the inner and outer membrane of the cell envelope. In many other Gram-negative bacteria, PG is bound by protein(s), which provide both structural integrity and continuity between envelope layers. Here, we present evidence of a peptidoglycan-associated protein (PAP) in B. burgdorferi. Using an unbiased proteomics approach, we identified Neutrophil Attracting Protein A (NapA) as a PAP. Interestingly, NapA is a Dps homologue, which typically functions to bind and protect cellular DNA from damage during times of stress. While B. burgdorferi NapA is known to be involved in the oxidative stress response, it lacks the critical residues necessary for DNA binding. Biochemical and cellular studies demonstrate that NapA is localized to the B. burgdorferi periplasm and is indeed a PAP. Cryo-electron microscopy indicates that mutant bacteria, unable to produce NapA, have structural abnormalities. Defects in cell-wall integrity impact growth rate and cause the napA mutant to be more susceptible to osmotic and PG-specific stresses. NapA-linked PG is secreted in outer membrane vesicles and augments IL-17 production, relative to PG alone. Using microfluidics, we demonstrate that NapA acts as a molecular beacon-exacerbating the pathogenic properties of B. burgdorferi PG. These studies further our understanding of the B. burgdorferi cell envelope, provide critical information that underlies its pathogenesis, and highlight how a highly conserved bacterial protein can evolve mechanistically, while maintaining biological function.
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Affiliation(s)
- Marisela M. Davis
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Aaron M. Brock
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Molecular and Cellular Biology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Tanner G. DeHart
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Brittany P. Boribong
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Katherine Lee
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Mecaila E. McClune
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Nicholas Cramer
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Caroline N. Jones
- Molecular and Cellular Biology, Virginia Tech, Blacksburg, Virginia, United States of America
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Brandon L. Jutras
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Molecular and Cellular Biology, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
- Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia, United States of America
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17
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Mapping Gene-by-Gene Single-Nucleotide Variation in 8,535 Mycobacterium tuberculosis Genomes: a Resource To Support Potential Vaccine and Drug Development. mSphere 2021; 6:6/2/e01224-20. [PMID: 33692198 PMCID: PMC8546714 DOI: 10.1128/msphere.01224-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis (TB) is responsible for millions of deaths annually. More effective vaccines and new antituberculous drugs are essential to control the disease. Numerous genomic studies have advanced our knowledge about M. tuberculosis drug resistance, population structure, and transmission patterns. At the same time, reverse vaccinology and drug discovery pipelines have identified potential immunogenic vaccine candidates or drug targets. However, a better understanding of the sequence variation of all the M. tuberculosis genes on a large scale could aid in the identification of new vaccine and drug targets. Achieving this was the focus of the current study. Genome sequence data were obtained from online public sources covering seven M. tuberculosis lineages. A total of 8,535 genome sequences were mapped against M. tuberculosis H37Rv reference genome, in order to identify single nucleotide polymorphisms (SNPs). The results of the initial mapping were further processed, and a frequency distribution of nucleotide variants within genes was identified and further analyzed. The majority of genomic positions in the M. tuberculosis H37Rv genome were conserved. Genes with the highest level of conservation were often associated with stress responses and maintenance of redox balance. Conversely, genes with high levels of nucleotide variation were often associated with drug resistance. We have provided a high-resolution analysis of the single-nucleotide variation of all M. tuberculosis genes across seven lineages as a resource to support future drug and vaccine development. We have identified a number of highly conserved genes, important in M. tuberculosis biology, that could potentially be used as targets for novel vaccine candidates and antituberculous medications. IMPORTANCE Tuberculosis is an infectious disease caused by the bacterium Mycobacterium tuberculosis. In the first half of the 20th century, the discovery of the Mycobacterium bovis BCG vaccine and antituberculous drugs heralded a new era in the control of TB. However, combating TB has proven challenging, especially with the emergence of HIV and drug resistance. A major hindrance in TB control is the lack of an effective vaccine, as the efficacy of BCG is geographically variable and provides little protection against pulmonary disease in high-risk groups. Our research is significant because it provides a resource to support future drug and vaccine development. We have achieved this by developing a better understanding of the nucleotide variation of all of the M. tuberculosis genes on a large scale and by identifying highly conserved genes that could potentially be used as targets for novel vaccine candidates and antituberculous medications.
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18
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Drever K, Lim ZL, Zriba S, Chen JM. Protein Synthesis and Degradation Inhibitors Potently Block Mycobacterium tuberculosis type-7 Secretion System ESX-1 Activity. ACS Infect Dis 2021; 7:273-280. [PMID: 33534536 DOI: 10.1021/acsinfecdis.0c00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (M. tb) uses its type-7 secretion system ESX-1 to translocate key virulence effector proteins. Taking a chemical genetics approach, we demonstrate for the first time the importance of mycobacterial proteostasis to ESX-1. We show that individual treatment with inhibitors of protein synthesis (chloramphenicol and kanamycin) and protein degradation (lassomycin and bortezomib), at concentrations that only reduce M. tb growth by 50% and less, specifically block ESX-1 secretion activity in the tubercle bacillus. In contrast, the mycobacterial cell-wall synthesis inhibitor isoniazid, even at a concentration that reduces M. tb growth by 90% has no effect on ESX-1 secretion activity. We also show that chloramphenicol but not isoniazid at subinhibitory concentrations specifically attenuates ESX-1-mediated M. tb virulence in macrophages. Taken together, the results of our study identify a novel vulnerability in the ESX-1 system and offer new avenues of anti-TB drug research to neutralize this critical virulence-mediating protein secretion apparatus.
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Affiliation(s)
- Kylee Drever
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Ze Long Lim
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
| | - Slim Zriba
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
| | - Jeffrey M. Chen
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
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19
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Kinsella RL, Zhu DX, Harrison GA, Mayer Bridwell AE, Prusa J, Chavez SM, Stallings CL. Perspectives and Advances in the Understanding of Tuberculosis. ANNUAL REVIEW OF PATHOLOGY 2021; 16:377-408. [PMID: 33497258 DOI: 10.1146/annurev-pathol-042120-032916] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains a leading cause of death due to infection in humans. To more effectively combat this pandemic, many aspects of TB control must be developed, including better point of care diagnostics, shorter and safer drug regimens, and a protective vaccine. To address all these areas of need, better understanding of the pathogen, host responses, and clinical manifestations of the disease is required. Recently, the application of cutting-edge technologies to the study of Mtb pathogenesis has resulted in significant advances in basic biology, vaccine development, and antibiotic discovery. This leaves us in an exciting era of Mtb research in which our understanding of this deadly infection is improving at a faster rate than ever, and renews hope in our fight to end TB. In this review, we reflect on what is known regarding Mtb pathogenesis, highlighting recent breakthroughs that will provide leverage for the next leaps forward in the field.
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Affiliation(s)
- Rachel L Kinsella
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Gregory A Harrison
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Anne E Mayer Bridwell
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA;
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20
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Ekka MK, Meena LS. Essential biochemical, biophysical and computational inputs on efficient functioning of Mycobacterium tuberculosis H 37Rv FtsY. Int J Biol Macromol 2021; 171:59-73. [PMID: 33412199 DOI: 10.1016/j.ijbiomac.2020.12.182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis H37Rv) utilizes the signal recognition particle pathway (SRP pathway) system for secretion of various proteins from ribosomes to the extracellular surface which plays an important role in the machinery running inside the bacterium. This system comprises of three major components FtsY, FfH and 4.5S rRNA. This manuscript highlights essential factors responsible for the optimized enzymatic activity of FtsY. Kinetic parameters include Vmax and Km for the hydrolysis of GTP by ftsY which were 20.25±5.16 μM/min/mg and 39.95±7.7 μM respectively. kcat and catalytic efficiency of the reaction were 0.012±0.003 s-1 and 0.00047±0.0001 μM/s-1 respectively. These values were affected upon changing the standard conditions. Cations (Mg2+ and Mn2+) play important role in FtsY enzymatic activity as increasing Mg2+ decrease the activity. Mn2+on the other hand is required at higher concentration around 60 mM for carrying optimum GTPase activity. FtsY is hydrolyzing ATP and GDP as well and GDP acts as an inhibitor of the reaction. MD simulation shows effective binding and stabilization of the FtsY complexed structure with GTP, GDP and ATP. Mutational analysis was done at two important residues of GTP binding motif of FtsY, namely, GXXXXGK (K236) and DXXG (D367) and showed that these mutations significantly decrease FtsY GTPase activity. FtsY is comprised of α helices, but this structural pattern was shown to change with increasing concentrations of GTP and ATP which symbolize that these ligands cause significant conformational change by variating the secondary structure to transduce signals required by downstream effectors. This binding favors the functional stabilization of FtsY by destabilization of α-helix integrity. Revealing the hidden aspects of the functioning of FtsY might be an essential part for the understanding of the SRP pathway which is one of the important contributors of M. tuberculosis virulence.
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Affiliation(s)
- Mary Krishna Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India.
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21
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Quigley J, Peoples A, Sarybaeva A, Hughes D, Ghiglieri M, Achorn C, Desrosiers A, Felix C, Liang L, Malveira S, Millett W, Nitti A, Tran B, Zullo A, Anklin C, Spoering A, Ling LL, Lewis K. Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis. mBio 2020; 11:e01516-20. [PMID: 32753498 PMCID: PMC7407088 DOI: 10.1128/mbio.01516-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis, which causes tuberculosis (TB), is estimated to infect one-third of the world's population. The overall burden and the emergence of drug-resistant strains of Mycobacterium tuberculosis underscore the need for new therapeutic options against this important human pathogen. Our recent work demonstrated the success of natural product discovery in identifying novel compounds with efficacy against Mycobacterium tuberculosis Here, we improve on these methods by combining improved isolation and Mycobacterium tuberculosis selective screening to identify three new anti-TB compounds: streptomycobactin, kitamycobactin, and amycobactin. We were unable to obtain mutants resistant to streptomycobactin, and its target remains to be elucidated. We identify the target of kitamycobactin to be the mycobacterial ClpP1P2C1 protease and confirm that kitamycobactin is an analog of the previously identified compound lassomycin. Further, we identify the target of amycobactin to be the essential protein secretion pore SecY. We show further that amycobactin inhibits protein secretion via the SecY translocon. Importantly, this inhibition is bactericidal to nonreplicating Mycobacterium tuberculosis This is the first compound, to our knowledge, that targets the Sec protein secretion machinery in Mycobacterium tuberculosis This work underscores the ability of natural product discovery to deliver not only new compounds with activity against Mycobacterium tuberculosis but also compounds with novel targets.IMPORTANCE Decreasing discovery rates and increasing resistance have underscored the need for novel therapeutic options to treat Mycobacterium tuberculosis infection. Here, we screen extracts from previously uncultured soil microbes for specific activity against Mycobacterium tuberculosis, identifying three novel compounds. We further define the mechanism of action of one compound, amycobactin, and demonstrate that it inhibits protein secretion through the Sec translocation machinery.
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Affiliation(s)
- Jeffrey Quigley
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Aaron Peoples
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Asel Sarybaeva
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Dallas Hughes
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | | | - Cintia Felix
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Libang Liang
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Stephanie Malveira
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - William Millett
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Anthony Nitti
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Baldwin Tran
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Ashley Zullo
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Clemens Anklin
- Bruker Biospin Corporation, Billerica, Massachusetts, USA
| | - Amy Spoering
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Losee Lucy Ling
- NovoBiotic Pharmaceuticals, LLC, Cambridge, Massachusetts, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
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22
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Beg MA, Athar F. Molecular modeling and in silico characterization of mycobacterial Rv3101c and Rv3102c proteins: prerequisite molecular target in cell division. ACTA ACUST UNITED AC 2020. [DOI: 10.15406/ppij.2020.08.00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Ly A, Liu J. Mycobacterial Virulence Factors: Surface-Exposed Lipids and Secreted Proteins. Int J Mol Sci 2020; 21:ijms21113985. [PMID: 32498243 PMCID: PMC7312605 DOI: 10.3390/ijms21113985] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 01/15/2023] Open
Abstract
The clinically important Mycobacterium tuberculosis (M. tb) and related mycobacterial pathogens use various virulence mechanisms to survive and cause disease in their hosts. Several well-established virulence factors include the surface-exposed lipids in the mycobacterial outer membrane, as well as the Esx family proteins and the Pro-Glu (PE)/ Pro-Pro-Glu (PPE) family proteins secreted by type VII secretion systems (T7SS). Five ESX T7SS exist in M. tb and three—EsxA secretion system-1 (ESX-1), ESX-3, and ESX-5—have been implicated in virulence, yet only the structures of ESX-3 and ESX-5 have been solved to date. Here, we summarize the current research on three outer membrane lipids—phthiocerol dimycocerosates, phenolic glycolipids, and sulfolipids—as well as the secretion machinery and substrates of three mycobacterial T7SS—ESX-1, ESX-3, and ESX-5. We propose a structural model of the M. tb ESX-1 system based on the latest structural findings of the ESX-3 and ESX-5 secretion apparatuses to gain insight into the transport mechanism of ESX-associated virulence factors.
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Affiliation(s)
| | - Jun Liu
- Correspondence: ; Tel.: +1-416-946-5067
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24
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Khare SV, Choudhari SP, Phalle SP, Kumbhar SS, Choudhari PB, Masal SR, Patil AK, Dhavale RP, Bhagwat DA, Kadam AM. Optimization of Thiazolidone Scaffolds Using Pocket Modeling for Development of Potential Secretory System Inhibitors of Mycobacterium tuberculosis. Turk J Pharm Sci 2020; 16:196-205. [PMID: 32454714 DOI: 10.4274/tjps.galenos.2018.12599] [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: 02/10/2018] [Accepted: 03/22/2018] [Indexed: 12/01/2022]
Abstract
Objectives Mycobacterium tuberculosis is the causative organism of tuberculosis, which is the most lethal disease after cancer in the current decade. The development of multidrug and broadly drug-resistant strains is making the problem of tuberculosis more and more critical. In the last 40 years, only one molecule has been added to the treatment regimen. Generally, drug design and development programs target proteins whose function is known to be essential to the bacterial cell. M. tuberculosis possesses specialized protein export systems like the SecA2 export pathway and ESX pathways. Materials and Methods In the present communication, rational development of an antimycobacterial agent's targeting protein export system was carried out by integrating pocket modeling and virtual analysis. Results The 23 identified potential lead compounds were synthesized, characterized by physicochemical and spectroscopic methods like infrared and nuclear magnetic resonance spectroscopy, and further screened for antimycobacterial activity using isoniazid as standard. All the designed compounds showed profound antimycobacterial activity. Conclusion We found that Q30, M9, M26, U8, and R26 molecules had significant desirable biological activity and specific interactions with Sec of mycobacteria. Further optimization of these leads is necessary for the development of potential antimycobacterial drug candidates with fewer side effects.
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Affiliation(s)
- Shivratna V Khare
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Sujata P Choudhari
- Sarojini College of Pharmacy, Department of Pharmaceutical Analysis, Kolhapur, India
| | - Siddharth P Phalle
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Santosh S Kumbhar
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Prafulla B Choudhari
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Sambhaji R Masal
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Aakash K Patil
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutical Chemistry, Computational Chemistry Research Lab, Kolhapur, India
| | - Rakesh P Dhavale
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutics, Kolhapur, India
| | - Durgacharan A Bhagwat
- Bharati Vidyapeeth College of Pharmacy, Department of Pharmaceutics, Kolhapur, India
| | - Atul M Kadam
- Shree Santkrupa College of Pharmacy, Department of Pharmaceutics, Ghogaon, India
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25
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Lochab S, Singh Y, Sengupta S, Nandicoori VK. Mycobacterium tuberculosis exploits host ATM kinase for survival advantage through SecA2 secretome. eLife 2020; 9:51466. [PMID: 32223892 PMCID: PMC7162654 DOI: 10.7554/elife.51466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
(Mtb) produces inflections in the host signaling networks to create a favorable milieu for survival. The virulent Mtb strain, Rv caused double strand breaks (DSBs), whereas the non-virulent Ra strain triggered single-stranded DNA generation. The effectors secreted by SecA2 pathway were essential and adequate for the genesis of DSBs. Accumulation of DSBs mediated through Rv activates ATM-Chk2 pathway of DNA damage response (DDR) signaling, resulting in altered cell cycle. Instead of the classical ATM-Chk2 DDR, Mtb gains survival advantage through ATM-Akt signaling cascade. Notably, in vivo infection with Mtb led to sustained DSBs and ATM activation during chronic phase of tuberculosis. Addition of ATM inhibitor enhances isoniazid mediated Mtb clearance in macrophages as well as in murine infection model, suggesting its utility for host directed adjunct therapy. Collectively, data suggests that DSBs inflicted by SecA2 secretome of Mtb provides survival niche through activation of ATM kinase.
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Affiliation(s)
- Savita Lochab
- National Institute of Immunology, New Delhi, India.,Department of Zoology, University of Delhi, New Delhi, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, New Delhi, India
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26
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Khan HS, Nair VR, Ruhl CR, Alvarez-Arguedas S, Galvan Rendiz JL, Franco LH, Huang L, Shaul PW, Kim J, Xie Y, Mitchell RB, Shiloh MU. Identification of scavenger receptor B1 as the airway microfold cell receptor for Mycobacterium tuberculosis. eLife 2020; 9:52551. [PMID: 32134383 PMCID: PMC7065847 DOI: 10.7554/elife.52551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can enter the body through multiple routes, including via specialized transcytotic cells called microfold cells (M cell). However, the mechanistic basis for M cell entry remains undefined. Here, we show that M cell transcytosis depends on the Mtb Type VII secretion machine and its major virulence factor EsxA. We identify scavenger receptor B1 (SR-B1) as an EsxA receptor on airway M cells. SR-B1 is required for Mtb binding to and translocation across M cells in mouse and human tissue. Together, our data demonstrate a previously undescribed role for Mtb EsxA in mucosal invasion and identify SR-B1 as the airway M cell receptor for Mtb.
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Affiliation(s)
- Haaris S Khan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Vidhya R Nair
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Cody R Ruhl
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Samuel Alvarez-Arguedas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jorge L Galvan Rendiz
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Luis H Franco
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Linzhang Huang
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ron B Mitchell
- Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael U Shiloh
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
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27
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Seto S, Morimoto K, Yoshida T, Hiramatsu M, Hijikata M, Nagata T, Kikuchi F, Shiraishi Y, Kurashima A, Keicho N. Proteomic Profiling Reveals the Architecture of Granulomatous Lesions Caused by Tuberculosis and Mycobacterium avium Complex Lung Disease. Front Microbiol 2020; 10:3081. [PMID: 32010116 PMCID: PMC6978656 DOI: 10.3389/fmicb.2019.03081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/20/2019] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis (TB) and Mycobacterium avium complex lung disease (MAC-LD) are both characterized pathologically by granuloma lesions, which are typically composed of a necrotic caseum at the center surrounded by fibrotic cells and lymphocytes. Although the histological characterization of TB and MAC-LD granulomas has been well-documented, their molecular signatures have not been fully evaluated. In this research we applied mass spectrometry-based proteomics combined with laser microdissection to investigate the unique protein markers in human mycobacterial granulomatous lesions. Comparing the protein abundance between caseous and cellular sub-compartments of mycobacterial granulomas, we found distinct differences. Proteins involved in cellular metabolism in transcription and translation were abundant in cellular regions, while in caseous regions proteins related to antimicrobial response accumulated. To investigate the determinants of their heterogeneity, we compared the protein abundance in caseous regions between TB and MAC-LD granulomas. We found that several proteins were significantly abundant in the MAC-LD caseum of which proteomic profiles were different from those of the TB caseum. Immunohistochemistry demonstrated that one of these proteins, Angiogenin, specifically localized to the caseous regions of selected MAC-LD granulomas. We also detected peptides derived from mycobacterial proteins in the granulomas of both diseases. This study provides new insights into the architecture of granulomatous lesions in TB and MAC-LD.
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Affiliation(s)
- Shintaro Seto
- Department of Pathophysiology and Host Defense, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Tsutomu Yoshida
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Miyako Hiramatsu
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Minako Hijikata
- Department of Pathophysiology and Host Defense, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Toshi Nagata
- Department of Health Science, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Fumihito Kikuchi
- Department of Pathology, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yuji Shiraishi
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Atsuyuki Kurashima
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Naoto Keicho
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
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28
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Butler RE, Smith AA, Mendum TA, Chandran A, Wu H, Lefrançois L, Chambers M, Soldati T, Stewart GR. Mycobacterium bovis uses the ESX-1 Type VII secretion system to escape predation by the soil-dwelling amoeba Dictyostelium discoideum. ISME JOURNAL 2020; 14:919-930. [PMID: 31896783 PMCID: PMC7082363 DOI: 10.1038/s41396-019-0572-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/26/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium bovis is the causative agent of bovine tuberculosis and the predominant cause of zoonotic tuberculosis in people. Bovine tuberculosis occurs in farmed cattle but also in a variety of wild animals, which form a reservoir of infection. Although direct transmission of tuberculosis occurs between mammals, the low frequency of contact between different host species and abundant shedding of bacilli by infected animals suggests an infectious route via environmental contamination. Other intracellular pathogens that transmit via the environment deploy strategies to survive or exploit predation by environmental amoebae. To explore if M. bovis has this capability, we investigated its interactions with the soil and dung-dwelling amoeba, Dictyostelium discoideum. We demonstrated that M. bovis evades phagocytosis and destruction by D. discoideum and actively transits through the amoeba using the ESX-1 Type VII Secretion System as part of a programme of mechanisms, many of which have been co-opted as virulence factors in the mammalian host. This capacity of M. bovis to utilise an environmental stage between mammalian hosts may enhance its transmissibility. In addition, our data provide molecular evidence to support an evolutionary role for amoebae as training grounds for the pathogenic M. tuberculosis complex.
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Affiliation(s)
- Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Alex A Smith
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Tom A Mendum
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Aneesh Chandran
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Huihai Wu
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Louise Lefrançois
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
| | - Mark Chambers
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
| | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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29
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Veyron-Churlet R, Locht C. In Vivo Methods to Study Protein-Protein Interactions as Key Players in Mycobacterium Tuberculosis Virulence. Pathogens 2019; 8:pathogens8040173. [PMID: 31581602 PMCID: PMC6963305 DOI: 10.3390/pathogens8040173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on protein–protein interactions (PPI) can be helpful for the annotation of unknown protein functions and for the understanding of cellular processes, such as specific virulence mechanisms developed by bacterial pathogens. In that context, several methods have been extensively used in recent years for the characterization of Mycobacterium tuberculosis PPI to further decipher tuberculosis (TB) pathogenesis. This review aims at compiling the most striking results based on in vivo methods (yeast and bacterial two-hybrid systems, protein complementation assays) for the specific study of PPI in mycobacteria. Moreover, newly developed methods, such as in-cell native mass resonance and proximity-dependent biotinylation identification, will have a deep impact on future mycobacterial research, as they are able to perform dynamic (transient interactions) and integrative (multiprotein complexes) analyses.
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Affiliation(s)
- Romain Veyron-Churlet
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Camille Locht
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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30
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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.
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31
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Eoh H, Jung JU. Bacterial Protein Reshapes Host Defense toward Antiviral Responses. Mol Cell 2019; 71:483-484. [PMID: 30118676 DOI: 10.1016/j.molcel.2018.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this issue of Molecular Cell, Penn et al. (2018) report the protein interactome between Mycobacterium tuberculosis (Mtb) secreted effectors and macrophage cytosolic proteins. This Resource reveals that the interaction of Mtb effector LpqN with host CBL counteracts antibacterial defense but causes a reciprocal enhancement of antiviral defense.
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Affiliation(s)
- Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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32
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Ample glycosylation in membrane and cell envelope proteins may explain the phenotypic diversity and virulence in the Mycobacterium tuberculosis complex. Sci Rep 2019; 9:2927. [PMID: 30814666 PMCID: PMC6393673 DOI: 10.1038/s41598-019-39654-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Multiple regulatory mechanisms including post-translational modifications (PTMs) confer complexity to the simpler genomes and proteomes of Mycobacterium tuberculosis (Mtb). PTMs such as glycosylation play a significant role in Mtb adaptive processes. The glycoproteomic patterns of clinical isolates of the Mycobacterium tuberculosis complex (MTBC) representing the lineages 3, 4, 5 and 7 were characterized by mass spectrometry. A total of 2944 glycosylation events were discovered in 1325 proteins. This data set represents the highest number of glycosylated proteins identified in Mtb to date. O-glycosylation constituted 83% of the events identified, while 17% of the sites were N-glycosylated. This is the first report on N-linked protein glycosylation in Mtb and in Gram-positive bacteria. Collectively, the bulk of Mtb glycoproteins are involved in cell envelope biosynthesis, fatty acid and lipid metabolism, two-component systems, and pathogen-host interaction that are either surface exposed or located in the cell wall. Quantitative glycoproteomic analysis revealed that 101 sites on 67 proteins involved in Mtb fitness and survival were differentially glycosylated between the four lineages, among which 64% were cell envelope and membrane proteins. The differential glycosylation pattern may contribute to phenotypic variabilities across Mtb lineages. The study identified several clinically important membrane-associated glycolipoproteins that are relevant for diagnostics as well as for drug and vaccine discovery.
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33
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Regulation and overexpression studies of YidC in Mycobacterium tuberculosis. Sci Rep 2018; 8:17114. [PMID: 30459465 PMCID: PMC6244158 DOI: 10.1038/s41598-018-35475-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/02/2018] [Indexed: 11/08/2022] Open
Abstract
The preprotein translocase, YidC is an envelope protein which controls respiratory metabolism in Mycobacterium tuberculosis. Previously, we have established that depletion of yidC is deleterious for both extra- and intracellular proliferation of M. tuberculosis; however, it remains unclear how YidC expression is regulated under different growth conditions and whether its altered expression impact mycobacterial physiology. Herein, we show that yidC is expressed as an operon with upstream genes. Interestingly, expression analysis under various stress conditions reveals a distinct paradox in the profile of the yidC mRNA transcripts and the YidC protein. While YidC protein level is moderately elevated upon bacterial exposure to cell surface stresses, the corresponding mRNA transcript levels are significantly repressed under these conditions. In contrast, overexpression of M. tuberculosis yidC under a strong anhydrotetracycline-inducible promoter results in significant induction of YidC protein. Additionally, we also observe that overexpression of M. tuberculosis yidC, and not of its counterpart from fast-growing M. smegmatis, results in altered in vitro growth of bacteria, compromised integrity of bacterial cell envelope and differential expression of a small set of genes including those which are regulated under detergent stress. Overall findings of our study suggest that YidC proteins of slow- and fast-growing mycobacteria are functionally distinct despite exhibiting a great deal of identity.
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34
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Sun J, Yang LL, Chen X, Kong DX, Liu R. Integrating Multifaceted Information to Predict Mycobacterium tuberculosis-Human Protein-Protein Interactions. J Proteome Res 2018; 17:3810-3823. [PMID: 30269499 DOI: 10.1021/acs.jproteome.8b00497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB) is one of the biggest infectious disease killers caused by Mycobacterium tuberculosis (MTB). Studying the protein-protein interactions (PPIs) between MTB and human can deepen our understanding of the pathogenesis of TB and offer new clues to the treatment against MTB infection, but the experimentally validated interactions are especially scarce in this regard. Herein we proposed an integrated framework that combined template-, domain-domain interaction-, and machine learning-based methods to predict MTB-human PPIs. As a result, we established a network composed of 13 758 PPIs including 451 MTB proteins and 3167 human proteins ( http://liulab.hzau.edu.cn/MTB/ ). Compared to known human targets of various pathogens, our predicted human targets show a similar tendency in terms of the network topological properties and enrichment in important functional genes. Additionally, these human targets largely have longer sequence lengths, more protein domains, more disordered residues, lower evolutionary rates, and older protein ages. Functional analysis demonstrates that these proteins show strong preferences toward the phosphorylation, kinase activity, and signaling transduction processes and the disease and immune related pathways. Dissecting the cross-talk among top-ranked pathways suggests that the cancer pathway may serve as a bridge in MTB infection. Triplet analysis illustrates that the paired targets interacting with the same partner are adjacent to each other in the intraspecies network and tend to share similar expression patterns. Finally, we identified 36 potential anti-MTB human targets by integrating known drug target information and molecular properties of proteins.
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35
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Kumar A, Karthikeyan S. Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2018; 74:166-173. [PMID: 29497021 PMCID: PMC5947703 DOI: 10.1107/s2053230x18002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.
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Affiliation(s)
- Adarsh Kumar
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
| | - Subramanian Karthikeyan
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
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36
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Venkatesan A, Palaniyandi K, Sharma D, Bisht D, Narayanan S. Characterization of FtsY, its interaction with Ffh, and proteomic identification of their potential substrates in Mycobacterium tuberculosis. Can J Microbiol 2018; 64:243-251. [PMID: 29361248 DOI: 10.1139/cjm-2017-0385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The universally conserved signal recognition particle (SRP) pathway that mediates co-translational targeting of membrane and secretory proteins is essential for eukaryotic and prokaryotic cells. The Mycobacterium tuberculosis SRP pathway consists of 2 proteins, Ffh and FtsY, and a 4.5S RNA molecule. Although the Escherichia coli SRP pathway is well studied, understanding of the M. tuberculosis SRP pathway components is very limited. In this study, we have overexpressed and characterized the M. tuberculosis SRP receptor (SR) FtsY as a GTP binding protein. Further, we established the direct protein-protein interaction between Ffh and FtsY. The Ffh-FtsY complex formation resulted in mutual stimulation of their GTP hydrolysis activity. We also attempted to biochemically characterize the SRP components by constructing the antisense gene knockdown strains of ffh and ftsY in M. tuberculosis. Loss of ffh and ftsY resulted in a decreased in vitro growth rate of the antisense ffh strain as compared with the antisense ftsY strain. Finally, 2-D gel electrophoresis of antisense depleted ffh and ftsY strains identified differential expression of 14 proteins.
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Affiliation(s)
- Arunkumar Venkatesan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Kannan Palaniyandi
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Divakar Sharma
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Deepa Bisht
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Sujatha Narayanan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
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37
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He X, Jiang HW, Chen H, Zhang HN, Liu Y, Xu ZW, Wu FL, Guo SJ, Hou JL, Yang MK, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity. Mol Cell Proteomics 2017; 16:2243-2253. [PMID: 29018126 DOI: 10.1074/mcp.ra117.000296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.
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Affiliation(s)
- Xiang He
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- ¶Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Kun Yang
- ‖Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Yan
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao-Yu Deng
- **State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§§School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Xian-En Zhang
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; .,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,¶¶State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
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38
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Jeffrey B, Rose SJ, Gilbert K, Lewis M, Bermudez LE. Comparative analysis of the genomes of clinical isolates of Mycobacterium avium subsp. hominissuis regarding virulence-related genes. J Med Microbiol 2017; 66:1063-1075. [PMID: 28671535 DOI: 10.1099/jmm.0.000507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Mycobacterium avium subsp. hominissuis is a member of the M. avium complex, a heterogeneous group of bacteria that cause lung infection in immunocompetent patients or disseminated infection in patients with immunosuppression. The bacteria belonging to this complex have variable virulence, depending on the strain considered, and therefore a representative of the most common clinical phenotype was analysed. METHODOLOGY The genomic sequences of four M. avium subsp. hominissuis isolates obtained from clinical specimens were completed. Mav101, Mav100 and MavA5 were isolated from the blood of patients with AIDS. MavA5 was disseminated from the lung, while Mav3388 was isolated from the lungs of a patient with chronic lung disease. The sequences were annotated using the published Mav104 genome as a blueprint. Functional and virulence analyses of the sequences were carried out. Mice studies comparing the virulence of the strains were performed. RESULTS Findings showed that while Mav101 was very similar to Mav104, there were numerous differences between Mav104 and the remaining strains at nucleotide and predicted protein levels. The presence of genes associated with biofilm formation and several known virulence-related genes were sometimes differentially present among the isolates, suggesting overlapping functions by different genetic determinants. CONCLUSIONS The sequences provided important information about M. avium heterogenicity and evolution as a pathogen. The limitation is the lack of understanding on possible overlapping functions of genes/proteins.
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Affiliation(s)
- Brendan Jeffrey
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
| | - Sasha J Rose
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - Kerrigan Gilbert
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
| | - Matthew Lewis
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - Luiz E Bermudez
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA.,Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, Oregon, USA
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Gaur A, Sharma VK, Shree S, Rai N, Ramachandran R. Characterization of EccA3, a CbbX family ATPase from the ESX-3 secretion pathway of M. tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:715-724. [PMID: 28400297 DOI: 10.1016/j.bbapap.2017.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 01/08/2023]
Abstract
EccA family proteins are conserved components of ESX secretion pathways in M. tuberculosis H37Rv. Here, we report the characterization of EccA3 (Rv0282), a CbbX family AAA (ATPases Associated with diverse cellular Activities) protein from the ESX-3 pathway that is required for in vitro growth of mycobacteria, secretion of virulence factors, and acquisition of iron and zinc. EccA3 is a thermostable ATPase with a molecular weight of ~68kDa. It exists as a dodecamer in the apo form and associates as a hexamer in the presence of ATP. Its C-terminal region consists of a CbbX-like AAA-domain while the N-terminal region contains a tetratricopeptide repeat (TPR) domain with lower homology to other EccA-type proteins. Further, the C-terminal domain functions as the oligomerization domain and also exhibits ATPase activity. Mutational analysis, steady state kinetics and molecular docking studies identify R573 as the important 'sensor arginine' and R505 as an 'arginine finger' in EccA3. Dynamic fluorescence quenching experiments suggest that the N-terminal domain moves closer to the C-terminal domain upon ATP-binding. The ATP-dependent 'open-close' relative movements of the two domains might help EccA3 interaction and secretion of essential virulence factors.
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Affiliation(s)
- Amit Gaur
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, UP, India
| | - Vijay Kumar Sharma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, UP, India
| | - Sonal Shree
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, UP, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, UP, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, UP, India.
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40
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Verma R, Pinto SM, Patil AH, Advani J, Subba P, Kumar M, Sharma J, Dey G, Ravikumar R, Buggi S, Satishchandra P, Sharma K, Suar M, Tripathy SP, Chauhan DS, Gowda H, Pandey A, Gandotra S, Prasad TSK. Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis. J Proteome Res 2017; 16:1632-1645. [DOI: 10.1021/acs.jproteome.6b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Sneha Maria Pinto
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Arun Hanumana Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Pratigya Subba
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Shashidhar Buggi
- Intermediate
Reference Laboratory, State Tuberculosis Training and Demonstration Centre, Someshwaranagar, SDSTRC and RGICD Campus, Bangalore 560029, India
- Department
of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases, Someshwaranagar First Main Road, Dharmaram College
Post, Bangalore 560029, India
| | | | - Kusum Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Mrutyunjay Suar
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Srikanth Prasad Tripathy
- National Institute
for Research in Tuberculosis (Indian Council of Medical Research), Chennai 600031, India
| | - Devendra Singh Chauhan
- Department of Microbiology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (Indian Council of Medical Research), Agra 282004, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics & Integrative Biology, SukhdevVihar, New Delhi 110020, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
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41
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Walsh SI, Craney A, Romesberg FE. Not just an antibiotic target: Exploring the role of type I signal peptidase in bacterial virulence. Bioorg Med Chem 2016; 24:6370-6378. [PMID: 27769673 PMCID: PMC5279723 DOI: 10.1016/j.bmc.2016.09.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 01/23/2023]
Abstract
The looming antibiotic crisis has prompted the development of new strategies towards fighting infection. Traditional antibiotics target bacterial processes essential for viability, whereas proposed antivirulence approaches rely on the inhibition of factors that are required only for the initiation and propagation of infection within a host. Although antivirulence compounds have yet to prove their efficacy in the clinic, bacterial signal peptidase I (SPase) represents an attractive target in that SPase inhibitors exhibit broad-spectrum antibiotic activity, but even at sub-MIC doses also impair the secretion of essential virulence factors. The potential consequences of SPase inhibition on bacterial virulence have not been thoroughly examined, and are explored within this review. In addition, we review growing evidence that SPase has relevant biological functions outside of mediating secretion, and discuss how the inhibition of these functions may be clinically significant.
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Affiliation(s)
- Shawn I Walsh
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arryn Craney
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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42
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Bonnett SA, Ollinger J, Chandrasekera S, Florio S, O’Malley T, Files M, Jee JA, Ahn J, Casey A, Ovechkina Y, Roberts D, Korkegian A, Parish T. A Target-Based Whole Cell Screen Approach To Identify Potential Inhibitors of Mycobacterium tuberculosis Signal Peptidase. ACS Infect Dis 2016; 2:893-902. [PMID: 27642770 PMCID: PMC5215716 DOI: 10.1021/acsinfecdis.6b00075] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 12/31/2022]
Abstract
The general secretion (Sec) pathway is a conserved essential pathway in bacteria and is the primary route of protein export across the cytoplasmic membrane. During protein export, the signal peptidase LepB catalyzes the cleavage of the signal peptide and subsequent release of mature proteins into the extracellular space. We developed a target-based whole cell assay to screen for potential inhibitors of LepB, the sole signal peptidase in Mycobacterium tuberculosis, using a strain engineered to underexpress LepB (LepB-UE). We screened 72,000 compounds against both the Lep-UE and wild-type (wt) strains. We identified the phenylhydrazone (PHY) series as having higher activity against the LepB-UE strain. We conducted a limited structure-activity relationship determination around a representative PHY compound with differential activity (MICs of 3.0 μM against the LepB-UE strain and 18 μM against the wt); several analogues were less potent against the LepB overexpressing strain. A number of chemical modifications around the hydrazone moiety resulted in improved potency. Inhibition of LepB activity was observed for a number of compounds in a biochemical assay using cell membrane fraction derived from M. tuberculosis. Compounds did not increase cell permeability, dissipate membrane potential, or inhibit an unrelated mycobacterial enzyme, suggesting a specific mode of action related to the LepB secretory mechanism.
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Affiliation(s)
- Shilah A. Bonnett
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Susantha Chandrasekera
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Stephanie Florio
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Megan Files
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Jo-Ann Jee
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - James Ahn
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Allen Casey
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Yulia Ovechkina
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - David Roberts
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
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Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, Balasingham SV. The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics 2016; 17:791. [PMID: 27724857 PMCID: PMC5057432 DOI: 10.1186/s12864-016-3132-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. Results The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. Conclusions Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3132-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | - Line Victoria Moen
- Department of Informatics, University of Oslo, Oslo, Norway.,Current address: Department of Nutrition, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.
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44
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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.
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45
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Calder B, Albeldas C, Blackburn JM, Soares NC. Mass Spectrometry Offers Insight into the Role of Ser/Thr/Tyr Phosphorylation in the Mycobacteria. Front Microbiol 2016; 7:141. [PMID: 26904014 PMCID: PMC4751927 DOI: 10.3389/fmicb.2016.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/25/2016] [Indexed: 12/23/2022] Open
Abstract
Phosphorylation is a post translational modification which can rapidly regulate biochemical pathways by altering protein function, and has been associated with pathogenicity in bacteria. Once engulfed by host macrophages, pathogenic bacteria are exposed to harsh conditions and must respond rapidly in order to survive. The causative agent of TB, Mycobacterium tuberculosis, is unusual amongst the bacteria because it can survive within the host macrophage for decades in a latent state, demonstrating a remarkable capacity to successfully evade the host immune response. This ability may be mediated in part by regulatory mechanisms such as ser/thr/tyr phosphorylation. Mass spectrometry-based proteomics has afforded us the capacity to identify hundreds of phosphorylation sites in the bacterial proteome, allowing for comparative phosphoproteomic studies in the mycobacteria. There remains an urgent need to validate the reported phosphosites, and to elucidate their biological function in the context of pathogenicity. However, given the sheer number of putative phosphorylation events in the mycobacterial proteome, and the technical difficulty of assigning biological function to a phosphorylation event, it will not be trivial to do so. There are currently six published phosphoproteomic investigations of a member of mycobacteria. Here, we combine the datasets from these studies in order to identify commonly detected phosphopeptides and phosphosites in order to present high confidence candidates for further validation. By applying modern mass spectrometry-based techniques to improve our understanding of phosphorylation and other PTMs in pathogenic bacteria, we may identify candidates for therapeutic intervention.
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Affiliation(s)
- Bridget Calder
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Claudia Albeldas
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Jonathan M Blackburn
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
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46
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In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309. Comput Biol Chem 2015; 59 Pt A:67-80. [DOI: 10.1016/j.compbiolchem.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 01/25/2023]
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Le Chevalier F, Cascioferro A, Majlessi L, Herrmann JL, Brosch R. Mycobacterium tuberculosis evolutionary pathogenesis and its putative impact on drug development. Future Microbiol 2015; 9:969-85. [PMID: 25302954 DOI: 10.2217/fmb.14.70] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of human TB, is the most important mycobacterial pathogen in terms of global patient numbers and gravity of disease. The molecular mechanisms by which M. tuberculosis causes disease are complex and the result of host-pathogen coevolution that might have started already in the time of its Mycobacterium canettii-like progenitors. Despite research progress, M. tuberculosis still holds many secrets of its successful strategy for circumventing host defences, persisting in the host and developing resistance, which makes anti-TB treatment regimens extremely long and often inefficient. Here, we discuss what we have learned from recent studies on the evolution of the pathogen and its putative new drug targets that are essential for mycobacterial growth under in vitro or in vivo conditions.
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Affiliation(s)
- Fabien Le Chevalier
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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Rybniker J, Chen JM, Sala C, Hartkoorn RC, Vocat A, Benjak A, Boy-Röttger S, Zhang M, Székely R, Greff Z, Orfi L, Szabadkai I, Pató J, Kéri G, Cole ST. Anticytolytic screen identifies inhibitors of mycobacterial virulence protein secretion. Cell Host Microbe 2015; 16:538-48. [PMID: 25299337 DOI: 10.1016/j.chom.2014.09.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/20/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) requires protein secretion systems like ESX-1 for intracellular survival and virulence. The major virulence determinant and ESX-1 substrate, EsxA, arrests phagosome maturation and lyses cell membranes, resulting in tissue damage and necrosis that promotes pathogen spread. To identify inhibitors of Mtb protein secretion, we developed a fibroblast survival assay exploiting this phenotype and selected molecules that protect host cells from Mtb-induced lysis without being bactericidal in vitro. Hit compounds blocked EsxA secretion and promoted phagosome maturation in macrophages, thus reducing bacterial loads. Target identification studies led to the discovery of BTP15, a benzothiophene inhibitor of the histidine kinase MprB that indirectly regulates ESX-1, and BBH7, a benzyloxybenzylidene-hydrazine compound. BBH7 affects Mtb metal-ion homeostasis and revealed zinc stress as an activating signal for EsxA secretion. This screening approach extends the target spectrum of small molecule libraries and will help tackle the mounting problem of antibiotic-resistant mycobacteria.
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Affiliation(s)
- Jan Rybniker
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; 1(st) Department of Internal Medicine, University of Cologne, 50937 Cologne, Germany
| | - Jeffrey M Chen
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stefanie Boy-Röttger
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ming Zhang
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rita Székely
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Zoltán Greff
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - László Orfi
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre u. 9, 1092 Budapest, Hungary
| | - István Szabadkai
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - János Pató
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; MTA-SE Pathobiochemistry Research Group, Department of Medical Chemistry, Semmelweis University, 1094 Budapest, Hungary
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Crowther GJ, Weller SM, Jones JC, Weaver T, Fan E, Van Voorhis WC, Rosen H. The Bacterial Sec Pathway of Protein Export: Screening and Follow-Up. ACTA ACUST UNITED AC 2015; 20:921-6. [PMID: 25987586 DOI: 10.1177/1087057115587458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 04/27/2015] [Indexed: 11/16/2022]
Abstract
Most noncytoplasmic bacterial proteins are exported through the SecYEG channel in the cytoplasmic membrane. This channel and its associated proteins, collectively referred to as the Sec pathway, have strong appeal as a possible antibiotic drug target, yet progress toward new drugs targeting this pathway has been slow, perhaps due partly to many researchers' focus on a single component, the SecA ATPase. Here we report on a pathway-based screen in which beta-galactosidase (β-gal) activity is trapped in the cytoplasm of Escherichia coli cells if translocation through SecYEG is impaired. Several hit compounds passed a counterscreen distinguishing between β-gal overexpression and impaired β-gal export. However, the most extensively characterized hit gave limited E. coli growth inhibition (EC(50) ≥ 400 µM), and growth inhibition could not be unambiguously linked to the compound's effect on the Sec pathway. Our study and others underscore the challenges of finding potent druglike hits against this otherwise promising drug target.
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Affiliation(s)
| | - Sara M Weller
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jackson C Jones
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tatiana Weaver
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Henry Rosen
- Department of Medicine, University of Washington, Seattle, WA, USA
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Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z. Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics 2015; 16:100. [PMID: 25887594 PMCID: PMC4456996 DOI: 10.1186/s12859-015-0535-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/13/2015] [Indexed: 12/28/2022] Open
Abstract
Background Emergence of multiple drug resistant strains of M. tuberculosis (MDR-TB) threatens to derail global efforts aimed at reigning in the pathogen. Co-infections of M. tuberculosis with HIV are difficult to treat. To counter these new challenges, it is essential to study the interactions between M. tuberculosis and the host to learn how these bacteria cause disease. Results We report a systematic flow to predict the host pathogen interactions (HPIs) between M. tuberculosis and Homo sapiens based on sequence motifs. First, protein sequences were used as initial input for identifying the HPIs by ‘interolog’ method. HPIs were further filtered by prediction of domain-domain interactions (DDIs). Functional annotations of protein and publicly available experimental results were applied to filter the remaining HPIs. Using such a strategy, 118 pairs of HPIs were identified, which involve 43 proteins from M. tuberculosis and 48 proteins from Homo sapiens. A biological interaction network between M. tuberculosis and Homo sapiens was then constructed using the predicted inter- and intra-species interactions based on the 118 pairs of HPIs. Finally, a web accessible database named PATH (Protein interactions of M. tuberculosis and Human) was constructed to store these predicted interactions and proteins. Conclusions This interaction network will facilitate the research on host-pathogen protein-protein interactions, and may throw light on how M. tuberculosis interacts with its host. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0535-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tong Huo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Wei Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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