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Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 2023; 12:e80218. [PMID: 37642294 PMCID: PMC10501769 DOI: 10.7554/elife.80218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species (ROS) but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.
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Affiliation(s)
- Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | | | - Hussain Beig
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shalini Birua
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sathya Narayanan Nagarajan
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Vikrant Kumar Sinha
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Areejit Samal
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
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Andongma BT, Huang Y, Chen F, Tang Q, Yang M, Chou SH, Li X, He J. In silico design of a promiscuous chimeric multi-epitope vaccine against Mycobacterium tuberculosis. Comput Struct Biotechnol J 2023; 21:991-1004. [PMID: 36733703 PMCID: PMC9883148 DOI: 10.1016/j.csbj.2023.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Tuberculosis (TB) is a global health threat, killing approximately 1.5 million people each year. The eradication of Mycobacterium tuberculosis, the main causative agent of TB, is increasingly challenging due to the emergence of extensive drug-resistant strains. Vaccination is considered an effective way to protect the host from pathogens, but the only clinically approved TB vaccine, Bacillus Calmette-Guérin (BCG), has limited protection in adults. Multi-epitope vaccines have been found to enhance immunity to diseases by selectively combining epitopes from several candidate proteins. This study aimed to design a multi-epitope vaccine against TB using an immuno-informatics approach. Through functional enrichment, we identified eight proteins secreted by M. tuberculosis that are either required for pathogenesis, secreted into extracellular space, or both. We then analyzed the epitopes of these proteins and selected 16 helper T lymphocyte epitopes with interferon-γ inducing activity, 15 cytotoxic T lymphocyte epitopes, and 10 linear B-cell epitopes, and conjugated them with adjuvant and Pan HLA DR-binding epitope (PADRE) using appropriate linkers. Moreover, we predicted the tertiary structure of this vaccine, its potential interaction with Toll-Like Receptor-4 (TLR4), and the immune response it might elicit. The results showed that this vaccine had a strong affinity for TLR4, which could significantly stimulate CD4+ and CD8+ cells to secrete immune factors and B lymphocytes to secrete immunoglobulins, so as to obtain good humoral and cellular immunity. Overall, this multi-epitope protein was predicted to be stable, safe, highly antigenic, and highly immunogenic, which has the potential to serve as a global vaccine against TB.
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Affiliation(s)
- Binda T. Andongma
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yazheng Huang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Fang Chen
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
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Secretome of Paenibacillus sp. S-12 provides an insight about its survival and possible pathogenicity. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01032-4. [PMID: 36642775 DOI: 10.1007/s12223-023-01032-4] [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: 09/11/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Our aim in this study was to characterize and investigate the secretome of Paenibacillus sp. S-12 by nanoLC-MS/MS tool-based analysis of trypsin digested culture supernatant proteins. Using a bioinformatics and combined approach of mass spectrometry, we identified 657 proteins in the secretome. Bioinformatic tools such as PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb were used for the subcellular localization and categorization of secretome on basis of signal peptides. Among the identified proteins, more than 25% of the secretome proteins were associated with virulence proteins including flagellar, adherence, and immune modulators. Gene ontology analysis using Blast2GO tools categorized 60 proteins of the secretome into biological processes, cellular components, and molecular functions. KEGG pathway analysis identified the enzymes or proteins involved in various biosynthesis and degradation pathways. Functional analysis of secretomes reveals a large number of proteins involved in the uptake and exchange of nutrients, colonization, and chemotaxis. A good number of proteins were involved in survival and defense mechanism against oxidative stress, the production of toxins and antimicrobial compounds. The present study is the first report of the in-depth protein profiling of Paenibacillus bacterium. In summary, the current findings of Paenibacillus sp. S-12 secretome provide basic information to understand its survival and the possible pathogenic mechanism.
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Shantal CJN, Juan CC, Lizbeth BUS, Carlos HGJ, Estela GPB. Candida glabrata is a successful pathogen: an artist manipulating the immune response. Microbiol Res 2022; 260:127038. [DOI: 10.1016/j.micres.2022.127038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
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Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
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6
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Bonilla-Muro MG, Hernández de la Cruz ON, Gonzalez-Barrios JA, Alcaráz-Estrada SL, Castañón-Arreola M. EsxA mainly contributes to the miR-155 overexpression in human monocyte-derived macrophages and potentially affect the immune mechanism of macrophages through miRNA dysregulation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 54:185-192. [PMID: 31561988 DOI: 10.1016/j.jmii.2019.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 03/24/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND/PURPOSE Mycobacterium tuberculosis is a successful intracellular pathogen that uses multiple proteins to survive within macrophages, one of the most remarkable is the virulence factor EsxA. In this study, we evaluate the participation of EsxA in the miRNAs expression profile of human monocyte-derived macrophages (hMDM), to mapping out the contribution of this virulence factor in the miRNA profile and how these changes can influence and alter immune-related processes and pathways. METHODS The cytotoxic effect of rEsxA on hMDM was evaluated by the neutral red assay. The evaluation of miRNA expression profile in infected and rEsxA-stimulated hMDM was done using TaqMan Low Density Assays, and in silico analyses was carried on to construct Protein-Protein Interaction network of miRNAs targets. RESULTS miR-155 was the only miRNA upregulated consistently in hMDM infected with M. tuberculosis H37Rv or stimulated with rEsxA. In hMDM stimulated with rEsxA, we found 25 miRNA's dysregulated (8 up-regulated and 17 down-regulated). The most significant were the miR-155 and miR-622 that has been observed in the analysis carried out with two different endogenous controls (U6 snRNA and RNU44) for the normalization of expression analysis. This result suggests that rEsxA induces the deregulation of miRNAs that potentially target genes in key pathways for the infection control, like the MAPK signaling pathway, cytokines, and chemokine signaling pathways, and several connected pathways involved in mycobacterial uptake, vesicular traffic, and endosome maturation. CONCLUSION Higher expression levels of miR-155 suggest potential roles of these miRNA in EsxA-dependent immune subversion.
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Affiliation(s)
| | | | - Juan Antonio Gonzalez-Barrios
- Coordinación de Capacitación, Desarrollo e Investigación, Hospital Regional 1º de Octubre, ISSSTE, Mexico City, Mexico
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Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL. Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response. Cell Rep 2019; 26:3574-3585.e3. [PMID: 30917313 PMCID: PMC6508871 DOI: 10.1016/j.celrep.2019.02.109] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 02/27/2019] [Indexed: 01/20/2023] Open
Abstract
To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type I IFNs and antibody production. Dual RNA-seq on patient lesions identifies two independent molecular measures of M. leprae, each of which correlates with distinct aspects of the host immune response. The fraction of bacterial transcripts, reflecting bacterial burden, correlates with a host type I IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial mRNA:rRNA ratio, reflecting bacterial viability, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for the interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease.
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Affiliation(s)
- Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Priscila Andrade
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Bruno J A Silva
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Rosane M B Teles
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan Bryson
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | | | - Teia Noel
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jing Lu
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Euzenir Sarno
- Department of Mycobacteriosis, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Douglas Young
- National Institute for Medical Research, Mycobacterial Research Division, London NW7 1AA, UK; The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Ramanuj Lahiri
- Health Resources and Services Administration (HRSA), National Hansen's Disease Program (NHDP), Baton Rouge, LA, USA
| | - Diana L Williams
- Health Resources and Services Administration (HRSA), National Hansen's Disease Program (NHDP), Baton Rouge, LA, USA; Department of Pathobiological Sciences, Louisiana State University (LSU), Baton Rouge, LA, USA
| | - Sarah Fortune
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | - Barry R Bloom
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert L Modlin
- Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA.
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Agarwal S, Ghosh S, Sharma S, Kaur K, Verma I. Mycobacterium tuberculosis H37Rv expresses differential proteome during intracellular survival within alveolar epithelial cells compared with macrophages. Pathog Dis 2018; 76:5052203. [DOI: 10.1093/femspd/fty058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/28/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- S Agarwal
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - S Ghosh
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - S Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - K Kaur
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - I Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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9
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Comprehensive profiling of functional attributes, virulence potential and evolutionary dynamics in mycobacterial secretomes. World J Microbiol Biotechnol 2017; 34:5. [DOI: 10.1007/s11274-017-2388-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/30/2017] [Indexed: 11/25/2022]
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10
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Joseph S, Yuen A, Singh V, Hmama Z. Mycobacterium tuberculosis Cpn60.2 (GroEL2) blocks macrophage apoptosis via interaction with mitochondrial mortalin. Biol Open 2017; 6:481-488. [PMID: 28288970 PMCID: PMC5399554 DOI: 10.1242/bio.023119] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Earlier studies suggested that Mycobacterium tuberculosis (Mtb) proteins exported within the host macrophage play an essential role in tuberculosis pathogenesis. In fact, Mtb proteins interact with and deactivate key regulators of many macrophage functions such as phago-lysosome fusion and antigen presentation, resulting in the intracellular persistence of pathogenic mycobacteria. Cpn60.2 is an abundant Mtb chaperone protein, restricted to cell cytoplasm and surface, that was reported to be essential for bacterial growth. Here, we provide evidence that once Mtb is ingested by the macrophage, Cpn60.2 is able to detach from the bacterial surface and crosses the phagosomal membrane towards mitochondria organelles. Once there, Cpn60.2 interacts with host mortalin, a member of the HSP 70 gene family that contributes to apoptosis modulation. In this regard, we showed that Cpn60.2 blocks macrophage apoptosis, a phenotype that is reversed when cells are pretreated with a specific mortalin inhibitor. Our findings have extended the current knowledge of the Mtb Cpn60.2 functions to add a strong anti-apoptotic activity dependent on its interaction with mitochondrial mortalin, which otherwise promotes Mtb survival in the hostile macrophage environment.
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Affiliation(s)
- Sunil Joseph
- Division of Infectious Diseases, Department of Medicine, Vancouver Costal Health Research Institute, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Alex Yuen
- Division of Infectious Diseases, Department of Medicine, Vancouver Costal Health Research Institute, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Vijender Singh
- Division of Infectious Diseases, Department of Medicine, Vancouver Costal Health Research Institute, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Zakaria Hmama
- Division of Infectious Diseases, Department of Medicine, Vancouver Costal Health Research Institute, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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Elizabeth MC, Hernández de la Cruz ON, Mauricio CA. Infection of J774A.1 with different Mycobacterium species induces differential immune and miRNA-related responses. Microbiol Immunol 2017; 60:356-63. [PMID: 27041510 DOI: 10.1111/1348-0421.12380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/01/2016] [Accepted: 03/21/2016] [Indexed: 11/30/2022]
Abstract
Macrophages act as a reservoir for Mycobacterium tuberculosis, producing latent infection in approximately 90% of infected people. In this study, J774A.1 mouse macrophage cell line response and microRNA (miRNA) expression during infection with the most relevant mycobacterial strains for humans (M. tuberculosis, M. bovis and M. bovis BCG) was explored. No significant differences in bacillary loads were observed between activate and naive macrophages infected with M. tuberculosis and M. bovis. Nitrite production inhibition and infection control were in accordance with the virulence of the strain. Expression of let-7e, miR-21, miR-155, miR-210 and miR-223 was opposite in the two species and miR-146b* and miR-1224 expression seemed to be part of the general response to infection.
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Affiliation(s)
- Mendoza-Coronel Elizabeth
- Genomic Sciences Program, Autonomous University of Mexico City, 290 San Lorenzo, Benito Juárez, Col del Valle Sur, 03100 Ciudad de México, México
| | - Olga Nohemí Hernández de la Cruz
- Genomic Sciences Program, Autonomous University of Mexico City, 290 San Lorenzo, Benito Juárez, Col del Valle Sur, 03100 Ciudad de México, México
| | - Castañón-Arreola Mauricio
- Genomic Sciences Program, Autonomous University of Mexico City, 290 San Lorenzo, Benito Juárez, Col del Valle Sur, 03100 Ciudad de México, México
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12
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Xu L, Shahid S, Shen J, Emanuelsson EAC, Patterson DA. A wide range and high resolution one-filtration molecular weight cut-off method for aqueous based nanofiltration and ultrafiltration membranes. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
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Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Cornejo-Granados F, Zatarain-Barrón ZL, Cantu-Robles VA, Mendoza-Vargas A, Molina-Romero C, Sánchez F, Del Pozo-Yauner L, Hernández-Pando R, Ochoa-Leyva A. Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets. Front Microbiol 2017; 8:128. [PMID: 28223967 PMCID: PMC5293778 DOI: 10.3389/fmicb.2017.00128] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a druggability analysis of the secretomes, we found potential drug targets such as cytochrome P450, thiol peroxidase, the Ag85C, and Ribonucleoside Reductase in the secreted proteins that could be used as drug targets for novel treatments against Tuberculosis.
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Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Zyanya L Zatarain-Barrón
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Vito A Cantu-Robles
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | | | | | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Luis Del Pozo-Yauner
- Laboratorio de Estructura de Proteínas, National Institute of Genomic Medicine Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Laboratory, Department of Pathology, National Institute of Medical Science and Nutrition "Salvador Zubirán" Mexico City, Mexico
| | - Adrián Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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15
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Sharma D, Lata M, Singh R, Deo N, Venkatesan K, Bisht D. Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS. Front Microbiol 2016; 7:1816. [PMID: 27895634 PMCID: PMC5108770 DOI: 10.3389/fmicb.2016.01816] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/25/2022] Open
Abstract
Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved. As proteins are involved in most of the biological processes, these act as a potential diagnostic markers and drug targets. In the present study we analyzed the purely cytosolic proteome of amikacin (AK) and kanamycin (KM) resistant Mycobacterium tuberculosis isolates by proteomic and bioinformatic approaches. Twenty protein spots were found to have over expressed in resistant isolates and were identified. Among these Rv3208A, Rv2623, Rv1360, Rv2140c, Rv1636, and Rv2185c are six proteins with unknown functions or undefined role. Docking results showed that AK and KM binds to the conserved domain (DUF, USP-A, Luciferase, PEBP and Polyketidecyclase/dehydrase domain) of these hypothetical proteins and over expression of these proteins might neutralize/modulate the effect of drug molecules. TBPred and GPS-PUP predicted cytoplasmic nature and potential pupylation sites within these identified proteins, respectively. String analysis also suggested that over expressed proteins along with their interactive partners might be involved in aminoglycosides resistance. Cumulative effect of these over expressed proteins could be involved in AK and KM resistance by mitigating the toxicity, repression of drug target and neutralizing affect. These findings need further exploitation for the expansion of newer therapeutics or diagnostic markers against AK and KM resistance so that an extreme condition like XDR-TB can be prevented.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Nirmala Deo
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases Agra, India
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