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Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
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2
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Tateishi Y, Ozeki Y, Nishiyama A, Miki M, Maekura R, Fukushima Y, Nakajima C, Suzuki Y, Matsumoto S. Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease. BMC Microbiol 2021; 21:103. [PMID: 33823816 PMCID: PMC8025370 DOI: 10.1186/s12866-021-02163-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/18/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. RESULTS In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. CONCLUSIONS Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.
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Affiliation(s)
- Yoshitaka Tateishi
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
| | - Yuriko Ozeki
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Mari Miki
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Ryoji Maekura
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Graduate School of Health Care Sciences, Jikei Institute, Osaka, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, Indonesia
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Gautam K, Negi S, Saini V. Targeting endogenous gaseous signaling molecules as novel host-directed therapies against tuberculosis infection. Free Radic Res 2021; 55:655-670. [PMID: 33641567 DOI: 10.1080/10715762.2021.1892091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Tuberculosis (TB) is a chronic pulmonary disease caused by Mycobacterium tuberculosis which is a major cause of morbidity and mortality worldwide. Due to the complexity of disease and its continuous global spread, there is an urgent need to improvise the strategies for prevention, diagnosis, and treatment. The current anti-TB regimen lasts for months and warrants strict compliance to clear infection and to minimize the risk of development of multi drug-resistant tuberculosis. This underscores the need to have new and improved therapeutics for TB treatment. Several studies have highlighted the unique ability of Mycobacterium tuberculosis to exploit host factors to support its survival inside the intracellular environment. One of the key players to mycobacterial disease susceptibility and infection are endogenous gases such as oxygen, nitric oxide, carbon monoxide and hydrogen sulfide. Nitric oxide and carbon monoxide as the physiological gaseous messengers are considered important to the outcome of Mycobacterium tuberculosis infection. The role of hydrogen sulfide in human tuberculosis is yet not fully elucidated, but this gas has been shown to play a significant role in bacterial respiration, growth and pathogenesis. This review will focus on the host factors majorly endogenous gaseous signaling molecules which contributes to Mycobacterium tuberculosis survival inside the intracellular environment and highlight the potential therapeutic targets.
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Affiliation(s)
- Kamini Gautam
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sheetal Negi
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vikram Saini
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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Rivera I, Linz B, Harvill ET. Evolution and Conservation of Bordetella Intracellular Survival in Eukaryotic Host Cells. Front Microbiol 2020; 11:557819. [PMID: 33178148 PMCID: PMC7593398 DOI: 10.3389/fmicb.2020.557819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 11/25/2022] Open
Abstract
The classical bordetellae possess several partially characterized virulence mechanisms that are studied in the context of a complete extracellular life cycle in their mammalian hosts. Yet, classical bordetellae have repeatedly been reported within dendritic cells (DCs) and alveolar macrophages in clinical samples, and in vitro experiments convincingly demonstrate that the bacteria can survive intracellularly within mammalian phagocytic cells, an ability that appears to have descended from ancestral progenitor species that lived in the environment and acquired the mechanisms to resist unicellular phagocytic predators. Many pathogens, including Mycobacterium tuberculosis, Salmonella enterica, Francisella tularensis, and Legionella pneumophila, are known to parasitize and multiply inside eukaryotic host cells. This strategy provides protection, nutrients, and the ability to disseminate systemically. While some work has been dedicated at characterizing intracellular survival of Bordetella pertussis, there is limited understanding of how this strategy has evolved within the genus Bordetella and the contributions of this ability to bacterial pathogenicity, evasion of host immunity as well as within and between-host dissemination. Here, we explore the mechanisms that control the metabolic changes accompanying intracellular survival and how these have been acquired and conserved throughout the evolutionary history of the Bordetella genus and discuss the possible implications of this strategy in the persistence and reemergence of B. pertussis in recent years.
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Affiliation(s)
- Israel Rivera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Bodo Linz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Arora SK, Naqvi N, Alam A, Ahmad J, Alsati BS, Sheikh JA, Kumar P, Mitra DK, Rahman SA, Hasnain SE, Ehtesham NZ. Mycobacterium smegmatis Bacteria Expressing Mycobacterium tuberculosis-Specific Rv1954A Induce Macrophage Activation and Modulate the Immune Response. Front Cell Infect Microbiol 2020; 10:564565. [PMID: 33163415 PMCID: PMC7583720 DOI: 10.3389/fcimb.2020.564565] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), the intracellular pathogen causing tuberculosis, has developed mechanisms that endow infectivity and allow it to modulate host immune response for its survival. Genomic and proteomic analyses of non-pathogenic and pathogenic mycobacteria showed presence of genes and proteins that are specific to M. tb. In silico studies predicted that M.tb Rv1954A is a hypothetical secretory protein that exhibits intrinsically disordered regions and possess B cell/T cell epitopes. Treatment of macrophages with Rv1954A led to TLR4-mediated activation with concomitant increase in secretion of pro-inflammatory cytokines, IL-12 and TNF-α. In vitro studies showed that rRv1954A protein or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) activates macrophages by enhancing the expression of CD80 and CD86. An upregulation in the expression of CD40 and MHC I/II was noted in the presence of Rv1954A, pointing to its role in enhancing the association of APCs with T cells and in the modulation of antigen presentation, respectively. Ms_Rv1954A showed increased infectivity, induction of ROS and RNS, and apoptosis in RAW264.7 macrophage cells. Rv1954A imparted protection against oxidative and nitrosative stress, thereby enhancing the survival of Ms_Rv1954A inside macrophages. Mice immunized with Ms_Rv1954A showed that splenomegaly and primed splenocytes restimulated with Rv1954A elicited a Th1 response. Infection of Ms_Rv1954A in mice through intratracheal instillation leads to enhanced infiltration of lymphocytes in the lungs without formation of granuloma. While Rv1954A is immunogenic, it did not cause adverse pathology. Purified Rv1954A or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) elicited a nearly two-fold higher titer of IgG response in mice, and PTB patients possess a higher IgG titer against Rv1954A, also pointing to its utility as a diagnostic marker for TB. The observed modulation of innate and adaptive immunity renders Rv1954A a vital protein in the pathophysiology of this pathogen.
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Affiliation(s)
- Simran Kaur Arora
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India.,Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Nilofer Naqvi
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Anwar Alam
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Javeed Ahmad
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Basma Saud Alsati
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | | | - Prabin Kumar
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipendra Kumar Mitra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | | | - Seyed Ehtesham Hasnain
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
| | - Nasreen Zafar Ehtesham
- Indian Council of Medical Research (ICMR)-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
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Verma T, Podder S, Mehta M, Singh S, Singh A, Umapathy S, Nandi D. Raman spectroscopy reveals distinct differences between two closely related bacterial strains, Mycobacterium indicus pranii and Mycobacterium intracellulare. Anal Bioanal Chem 2019; 411:7997-8009. [PMID: 31732785 DOI: 10.1007/s00216-019-02197-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
A common technique used to differentiate bacterial species and to determine evolutionary relationships is sequencing their 16S ribosomal RNA genes. However, this method fails when organisms exhibit high similarity in these sequences. Two such strains that have identical 16S rRNA sequences are Mycobacterium indicus pranii (MIP) and Mycobacterium intracellulare. MIP is of significance as it is used as an adjuvant for protection against tuberculosis and leprosy; in addition, it shows potent anti-cancer activity. On the other hand, M. intracellulare is an opportunistic pathogen and causes severe respiratory infections in AIDS patients. It is important to differentiate these two bacterial species as they co-exist in immuno-compromised individuals. To unambiguously distinguish these two closely related bacterial strains, we employed Raman and resonance Raman spectroscopy in conjunction with multivariate statistical tools. Phenotypic profiling for these bacterial species was performed in a kinetic manner. Differences were observed in the mycolic acid profile and carotenoid pigments to show that MIP is biochemically distinct from M. intracellulare. Resonance Raman studies confirmed that carotenoids were produced by both MIP as well as M. intracellulare, though the latter produced higher amounts. Overall, this study demonstrates the potential of Raman spectroscopy in differentiating two closely related mycobacterial strains. Graphical abstract.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Santosh Podder
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mansi Mehta
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Sarman Singh
- All India Institute of Medical Sciences, Bhopal, 462020, India
| | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India.
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India.
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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7
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Kumar P, Das G, Bhaskar S. Mycobacterium indicus pranii therapy induces tumor regression in MyD88- and TLR2-dependent manner. BMC Res Notes 2019; 12:648. [PMID: 31590685 PMCID: PMC6781299 DOI: 10.1186/s13104-019-4679-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 09/28/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Mycobacterium indicus pranii (MIP) is an atypical mycobacterium species with potent antitumor efficacy. Macrophages and dendritic cells (DCs) are antigen-presenting cells, playing key roles in the activation of antitumor immunity. We have previously shown the potent activation of macrophages and DCs by MIP, which is mediated by MyD88-TLR2 signaling axis. In the present study, we further examined the role of MyD88 and TLR2 in MIP-mediated tumor regression. RESULTS Wild-type and MyD88-/- mice were implanted with B16F10 tumor cells, treated with MIP or phosphate-buffered saline (PBS) and monitored for tumor growth. As expected, MIP therapy led to significant tumor regression in wild-type mice. However, antitumor efficacy of MIP was lost in MyD88-/- animals. Both PBS-treated (control) and MIP-treated MyD88-/- mice developed tumors with comparable volume. Since MyD88 relays TLR engagement signals, we analyzed the antitumor efficacy of MIP in TLR2-/- and TLR4-/- mice. It was observed that MIP therapy reduced tumor burden in wild-type and TLR4-/- mice but not in TLR2-/- mice. Tumor volume in MIP-treated TLR2-/- mice were comparable with those in PBS-treated wild-type animals. These results implicated the MyD88-TLR2 signaling axis in the antitumor efficacy of MIP.
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Affiliation(s)
- Pawan Kumar
- PDC-I, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Dept. of Preventive Oncology, Dr. B. R. Ambedkar Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Gobardhan Das
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sangeeta Bhaskar
- PDC-I, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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8
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Chiner-Oms Á, Comas I. Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2019; 72:10-15. [DOI: 10.1016/j.meegid.2019.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023]
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9
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Cell wall fraction of Mycobacterium indicus pranii shows potential Th1 adjuvant activity. Int Immunopharmacol 2019; 70:408-416. [PMID: 30856391 DOI: 10.1016/j.intimp.2019.02.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/16/2019] [Accepted: 02/27/2019] [Indexed: 12/29/2022]
Abstract
Very few adjuvants inducing Th1 immune response have been developed and are under clinical investigation. Hence, there is the need to find an adjuvant that elicits strong Th1 immune response which should be safe when injected in the host along with vaccines. Mycobacterium indicus pranii (MIP), a non-pathogenic vaccine candidate, has shown strong immunomodulatory activity in leprosy/tuberculosis/cancer and in genital warts patients where its administration shifted the host immune response towards Th1 type. These findings prompted us to study the components of MIP in detail for their Th1 inducing property. Since mycobacterial cell wall is very rich in immunostimulatory components and is known to play important role in immune modulation, we investigated the activity of MIP cell wall using Ovalbumin antigen (OVA) as model antigen. 'Whole cell wall' (CW) and 'aqueous soluble cell wall fractions' (ACW) induced significant Th1 immune response while 'cell wall skeleton' (CWS) induced strong Th2 type of immune response. Finally, functional activity of fractions having Th1 inducing activity was evaluated in mouse model of melanoma. CW demonstrated significant anti-tumor activity similar to whole MIP. Anti-tumor activity of CW could be correlated with enhanced tumor antigen specific Th1 immune response observed in tumor draining lymph nodes.
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van Wyk R, van Wyk M, Mashele SS, Nelson DR, Syed K. Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species. Int J Mol Sci 2019; 20:ijms20051032. [PMID: 30818787 PMCID: PMC6429209 DOI: 10.3390/ijms20051032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
In dealing with Mycobacterium tuberculosis, the causative agent of the deadliest human disease—tuberculosis (TB)—utilization of cholesterol as a carbon source indicates the possibility of using cholesterol catabolic genes/proteins as novel drug targets. However, studies on cholesterol catabolism in mycobacterial species are scarce, and the number of mycobacterial species utilizing cholesterol as a carbon source is unknown. The availability of a large number of mycobacterial species’ genomic data affords an opportunity to explore and predict mycobacterial species’ ability to utilize cholesterol employing in silico methods. In this study, comprehensive comparative analysis of cholesterol catabolic genes/proteins in 93 mycobacterial species was achieved by deducing a comprehensive cholesterol catabolic pathway, developing a software tool for extracting homologous protein data and using protein structure and functional data. Based on the presence of cholesterol catabolic homologous proteins proven or predicted to be either essential or specifically required for the growth of M. tuberculosis H37Rv on cholesterol, we predict that among 93 mycobacterial species, 51 species will be able to utilize cholesterol as a carbon source. This study’s predictions need further experimental validation and the results should be taken as a source of information on cholesterol catabolism and genes/proteins involved in this process among mycobacterial species.
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Affiliation(s)
- Rochelle van Wyk
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa.
| | - Mari van Wyk
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa.
| | - Samson Sitheni Mashele
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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Mycobacterium indicus pranii protein MIP_05962 induces Th1 cell mediated immune response in mice. Int J Med Microbiol 2018; 308:1000-1008. [PMID: 30190103 DOI: 10.1016/j.ijmm.2018.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 01/25/2023] Open
Abstract
Utility of Mycobacterium indicus pranii (MIP) as a multistage vaccine against mycobacterial infections demands identification of its protective antigens. We explored antigenicity and immunogenicity of a candidate protein MIP_05962 that depicts homology to HSP18 of M. leprae and antigen1 of Mycobacterium tuberculosis. This protein elicited substantial antibody response in immunized mice along with modulation of cellular immune response towards protective Th1 type. Both CD4+ and CD8+ subsets from immunized mice produced hallmark protective cytokines, IFN-γ, TNF-α and IL-2. This protein also enhanced the CD4+ effector memory that could act as first line of defence during infections. These results point to MIP_05962 as a protective antigen that contributes, in conjunction with others, to the protective immunity of this live vaccine candidate.
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Castejon M, Menéndez MC, Comas I, Vicente A, Garcia MJ. Whole-genome sequence analysis of the Mycobacterium avium complex and proposal of the transfer of Mycobacterium yongonense to Mycobacterium intracellulare subsp. yongonense subsp. nov. Int J Syst Evol Microbiol 2018; 68:1998-2005. [PMID: 29683417 DOI: 10.1099/ijsem.0.002767] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the Mycobacterium avium complex, as is for the cases of Mycobacterium yongonense and 'Mycobacterium indicus pranii'. These two mycobacteria, closely related to Mycobacterium intracellulare on the basis of standard phenotypic and single gene-sequences comparisons, were not considered a member of such species on the basis on some particular differences displayed by a single strain. Whole-genome sequence comparison procedures, namely the average nucleotide identity and the genome distance, showed that those two mycobacteria should be considered members of the species M. intracellulare. The results were confirmed with other whole-genome comparison supplementary methods. According to the data provided, Mycobacterium yongonense and 'Mycobacterium indicus pranii' should be considered and renamed and included as members of M. intracellulare. This study highlights the problems caused when a novel species is accepted on the basis of a single strain, as was the case for M. yongonense. Based mainly on whole-genome sequence analysis, we conclude that M. yongonense should be reclassified as a subspecies of Mycobacterium intracellulareas Mycobacterium intracellularesubsp. yongonense and 'Mycobacterium indicus pranii' classified in the same subspecies as the type strain of Mycobacterium intracellulare and classified as Mycobacterium intracellularesubsp. intracellulare.
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Affiliation(s)
- Maria Castejon
- Departamento de Medicina Preventiva y Salud Publica y Microbiologia, Universidad Autonoma de Madrid, Madrid, Spain
| | - Maria Carmen Menéndez
- Departamento de Medicina Preventiva y Salud Publica y Microbiologia, Universidad Autonoma de Madrid, Madrid, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia. Consejo Superior de Investigaciones Cientificas, Valencia, Spain.,CIBER en Epidemiologia y Salud Publica. Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Vicente
- Departamento de Medicina Preventiva y Salud Publica y Microbiologia, Universidad Autonoma de Madrid, Madrid, Spain
| | - Maria J Garcia
- Departamento de Medicina Preventiva y Salud Publica y Microbiologia, Universidad Autonoma de Madrid, Madrid, Spain
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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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14
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Schweitzer MD, Salamo O, Campos M, Schraufnagel DE, Sadikot R, Mirsaeidi M. Body habitus in patients with and without bronchiectasis and non-tuberculous mycobacteria. PLoS One 2017; 12:e0185095. [PMID: 28957340 PMCID: PMC5619759 DOI: 10.1371/journal.pone.0185095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/06/2017] [Indexed: 11/18/2022] Open
Abstract
Background Female gender, tall stature, presence of bronchiectasis are associated with pulmonary nontuberculous mycobacterial (NTM) infections. The biologic relationship between the body habitus and NTM infection is not well defined and the body habitus profile of the patients with NTM and concurrent bronchiectasis is completely unknown. Methods We conducted a case control study at the Miami VA Healthcare System and the University of Illinois Medical Center on patients with pulmonary NTM infections between 2010 and 2015. We compared pulmonary NTM subjects with and without bronchiectasis. NTM infection was confirmed by using the American Thoracic Society/ Infectious Disease Society of America criteria. Standard radiological criteria were used to define bronchiectasis in chest CT-scan. Results Two hundred twenty subjects with pulmonary NTM were enrolled in the study. Sixty six subjects (30%) had bronchiectasis on CT scan of the chest. Subjects in the bronchiectasis group included more women (p = 0.002) and were significantly older (p = 0.005). Those patients who had bronchiectasis tended to have a significantly lower weight (less than 50kg) and height ≤155 cm (p <0.0001 and p = 0.018, respectively). Kaplan–Meier analysis confirmed that subjects who had bronchiectasis were shorter and weighed less, after adjusting for gender. Conclusions This study defines a new sub-phenotype of NTM subjects with bronchiectasis who tend to be short with lower body weight. Further studies are needed to better understand and define the body habitus profiles of this new sub-phenotype and their clinical implications.
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Affiliation(s)
- Michael D. Schweitzer
- Section of Pulmonary, Department of Medicine, Miami VA Medical Center, Miami, FL, United States of America
| | - Oriana Salamo
- Section of Pulmonary, Department of Medicine, Miami VA Medical Center, Miami, FL, United States of America
| | - Michael Campos
- Section of Pulmonary, Department of Medicine, Miami VA Medical Center, Miami, FL, United States of America
- Division of Pulmonary and Critical Care, Department of Medicine, University of Miami, Miami, FL, United States of America
| | - Dean E. Schraufnagel
- Division of Pulmonary and Critical Care, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Ruxana Sadikot
- Division of Pulmonary and Critical Care, Department of Medicine, University of Emory, Atlanta, GA, United States of America
| | - Mehdi Mirsaeidi
- Section of Pulmonary, Department of Medicine, Miami VA Medical Center, Miami, FL, United States of America
- Division of Pulmonary and Critical Care, Department of Medicine, University of Miami, Miami, FL, United States of America
- * E-mail:
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Sharma SK, Katoch K, Sarin R, Balambal R, Kumar Jain N, Patel N, Murthy KJR, Singla N, Saha PK, Khanna A, Singh U, Kumar S, Sengupta A, Banavaliker JN, Chauhan DS, Sachan S, Wasim M, Tripathi S, Dutt N, Jain N, Joshi N, Penmesta SRR, Gaddam S, Gupta S, Khamar B, Dey B, Mitra DK, Arora SK, Bhaskar S, Rani R. Efficacy and Safety of Mycobacterium indicus pranii as an adjunct therapy in Category II pulmonary tuberculosis in a randomized trial. Sci Rep 2017; 7:3354. [PMID: 28611374 PMCID: PMC5469738 DOI: 10.1038/s41598-017-03514-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
Prolonged treatment of tuberculosis (TB) often leads to poor compliance, default and relapse, converting primary TB patients into category II TB (Cat IITB) cases, many of whom may convert to multi-drug resistant TB (MDR-TB). We have evaluated the immunotherapeutic potential of Mycobacterium indicus pranii (MIP) as an adjunct to Anti-Tubercular Treatment (ATT) in Cat II pulmonary TB (PTB) patients in a prospective, randomized, double blind, placebo controlled, multicentric clinical trial. 890 sputum smear positive Cat II PTB patients were randomized to receive either six intra-dermal injections (2 + 4) of heat-killed MIP at a dose of 5 × 108 bacilli or placebo once in 2 weeks for 2 months. Sputum smear and culture examinations were performed at different time points. MIP was safe with no adverse effects. While sputum smear conversion did not show any statistically significant difference, significantly higher number of patients (67.1%) in the MIP group achieved sputum culture conversion at fourth week compared to the placebo (57%) group (p = 0.0002), suggesting a role of MIP in clearance of the bacilli. Since live bacteria are the major contributors for sustained incidence of TB, the potential of MIP in clearance of the bacilli has far reaching implications in controlling the spread of the disease.
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Affiliation(s)
| | - Kiran Katoch
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases (ICMR), Agra, India
| | - Rohit Sarin
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Raman Balambal
- National Institute of Research in Tuberculosis (ICMR), Chennai, India
| | - Nirmal Kumar Jain
- SMS Medical College (Hospital for Chest Diseases and TB), Jaipur, Rajasthan, India
| | - Naresh Patel
- NHL Municipal Medical College, Ahmadabad, Gujarat, India
| | | | - Neeta Singla
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - P K Saha
- All India Institute of Medical Sciences, New Delhi, India
| | - Ashwani Khanna
- All India Institute of Medical Sciences, New Delhi, India
| | - Urvashi Singh
- All India Institute of Medical Sciences, New Delhi, India
| | - Sanjiv Kumar
- All India Institute of Medical Sciences, New Delhi, India
| | - A Sengupta
- All India Institute of Medical Sciences, New Delhi, India.,Chest Clinic and Hospital, New Delhi, India
| | - J N Banavaliker
- All India Institute of Medical Sciences, New Delhi, India.,RBTB Hospital, New Delhi, India
| | - D S Chauhan
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases (ICMR), Agra, India
| | - Shailendra Sachan
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases (ICMR), Agra, India
| | - Mohammad Wasim
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases (ICMR), Agra, India
| | | | - Nilesh Dutt
- NHL Municipal Medical College, Ahmadabad, Gujarat, India
| | - Nitin Jain
- SMS Medical College (Hospital for Chest Diseases and TB), Jaipur, Rajasthan, India
| | - Nalin Joshi
- SMS Medical College (Hospital for Chest Diseases and TB), Jaipur, Rajasthan, India
| | | | - Sumanlatha Gaddam
- Mahavir Hospital and Research Centre, Hyderabad, Andhra Pradesh, India
| | - Sanjay Gupta
- Catalyst Clinical Services Pvt. Ltd., New Delhi, India
| | | | - Bindu Dey
- Department of Biotechnology, New Delhi, India
| | | | - Sunil K Arora
- Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | | | - Rajni Rani
- National Institute of Immunology, New Delhi, India. .,Systems Biology laboratory, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.
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Sharma A, Equbal MJ, Pandey S, Sheikh JA, Ehtesham NZ, Hasnain SE, Chaudhuri TK. Immunodominant protein MIP_05962 from Mycobacterium indicus pranii displays chaperone activity. FEBS J 2017; 284:1338-1354. [PMID: 28296245 DOI: 10.1111/febs.14057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/23/2017] [Accepted: 03/07/2017] [Indexed: 12/14/2022]
Abstract
Tuberculosis, a contagious disease of infectious origin is currently a major cause of deaths worldwide. Mycobacterium indicus pranii (MIP), a saprophytic nonpathogen and a potent immunomodulator is currently being investigated as an intervention against tuberculosis along with many other diseases with positive outcome. The apparent paradox of multiple chaperones in mycobacterial species and enigma about the cellular functions of the client proteins of these chaperones need to be explored. Chaperones are the known immunomodulators; thus, there is need to exploit the proteome of MIP for identification and characterization of putative chaperones. One of the immunogenic proteins, MIP_05962 is a member of heat shock protein (HSP) 20 family due to the presence of α-crystallin domain, and has amino acid similarity with Mycobacterium lepraeHSP18 protein. The diverse functions of M. lepraeHSP18 in stress conditions implicate MIP_05962 as an important protein that needs to be explored. Biophysical and biochemical characterization of the said protein proved it to be a chaperone. The observations of aggregation prevention and refolding of substrate proteins in the presence of MIP_05962 along with interaction with non-native proteins, surface hydrophobicity, formation of large oligomers, in-vivo thermal rescue of Escherichia coli expressing MIP_05962, enhancing solubility of insoluble protein maltodextrin glucosidase (MalZ) under in-vivo conditions, and thermal stability and reversibility confirmed MIP_05962 as a molecular chaperone.
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Affiliation(s)
- Ashish Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Md Javed Equbal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Saurabh Pandey
- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Javaid A Sheikh
- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Nasreen Z Ehtesham
- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, India
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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Jenkins AO, Michel A, Rutten V. Original Mycobacterial Sin, a consequence of highly homologous antigens? Vet Microbiol 2017; 203:286-293. [PMID: 28619159 DOI: 10.1016/j.vetmic.2017.03.028] [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: 12/02/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 10/19/2022]
Abstract
The role of antigens shared between Mycobacteria in in-vivo cross-reactive immune responses in host animals, have been reported to be responsible for reduced BCG vaccination efficacy as well reduced specificity of routine immunological diagnostic tests. This presents with significant disease control challenges in humans and animals. The present review highlights the results of previous studies on the effect of pre-sensitization to environmental mycobacteria on either pathogenic mycobacteria and/or M. bovis BCG, in experimental animals. It also takes an in-depth view into assessing the genetic similarities and relationships between atypical mycobacteria and Mycobacterium tuberculosis complex (MTBC) and how they might explain the immunological imprint of environmental mycobacteria in directing the hosts' immune response upon subsequent exposure to other classes of mycobacteria. The outcome of this review suggests that genetic closeness between particular atypical mycobacteria and MTBC usually indicate a higher level of homology for certain shared protective antigens. This ultimately results in a higher level of cross reactive immune responses as compared with other atypical mycobacteria that are further away genetically. This would explain the different effects of environmental mycobacteria on MTBC that have been reported in the different studies. In other words the direction of the host immune system in response to exposure to MTBC would depend on the type of environmental mycobacteria that was encountered in the initial exposure. We also explain these mycobacterial interactions in the context of the phenomenon of "Original Mycobacterial Sin". The effects of these inevitable mycobacterial interactions on field diagnosis and control by vaccination and how to circumvent them are discussed.
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Affiliation(s)
- A O Jenkins
- Division of Immunology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa.
| | - A Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - V Rutten
- Division of Immunology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
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Mycobacterium indicus pranii as a booster vaccine enhances BCG induced immunity and confers higher protection in animal models of tuberculosis. Tuberculosis (Edinb) 2016; 101:164-173. [PMID: 27865389 DOI: 10.1016/j.tube.2016.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 11/20/2022]
Abstract
BCG, the only approved vaccine protects against severe form of childhood tuberculosis but its protective efficacy wanes in adolescence. BCG has reduced the incidence of infant TB considerably in endemic areas; therefore prime-boost strategy is the most realistic measure for control of tuberculosis in near future. Mycobacterium indicus pranii (MIP) shares significant antigenic repertoire with Mtb and BCG and has been shown to impart significant protection in animal models of tuberculosis. In this study, MIP was given as a booster to BCG vaccine which enhanced the BCG mediated immune response, resulting in higher protection. MIP booster via aerosol route was found to be more effective in protection than subcutaneous route of booster immunization. Pro-inflammatory cytokines like IFN-γ, IL-12 and IL-17 were induced at higher level in infected lungs of 'BCG-MIP' group both at mRNA expression level and in secretory form when compared with 'only BCG' group. BCG-MIP groups had increased frequency of multifunctional T cells with high MFI for IFN-γ and TNF-α in Mtb infected mice. Our data demonstrate for the first time, potential application of MIP as a booster to BCG vaccine for efficient protection against tuberculosis. This could be very cost effective strategy for efficient control of tuberculosis.
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Chakraborty C, Bandyopadhyay S, Agoramoorthy G. India's Computational Biology Growth and Challenges. Interdiscip Sci 2016; 8:263-76. [PMID: 27465042 DOI: 10.1007/s12539-016-0179-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 09/08/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, India
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20
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Khubaib M, Sheikh JA, Pandey S, Srikanth B, Bhuwan M, Khan N, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis Co-operonic PE32/PPE65 Proteins Alter Host Immune Responses by Hampering Th1 Response. Front Microbiol 2016; 7:719. [PMID: 27242739 PMCID: PMC4868851 DOI: 10.3389/fmicb.2016.00719] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 04/29/2016] [Indexed: 02/04/2023] Open
Abstract
PE/PPE genes, present in cluster with ESAT-6 like genes, are suspected to have a role in antigenic variation and virulence of Mycobacterium tuberculosis. Their roles in immune evasion and immune modulation of host are also well documented. We present evidence that PE32/PPE65 present within the RD8 region are co-operonic, co-transcribed, and co-translated, and play role in modulating host immune responses. Experiments with macrophage cell lines revealed that this protein complex suppresses pro-inflammatory cytokines such as TNF-α and IL-6 whereas also inducing high expression of anti-inflammatory IL-10. Immunization of mice with these recombinant proteins dampens an effective Th1 response as evident from reduced frequency of IFN-γ and IL-2 producing CD4+ and CD8+ T cells. IgG sub-typing from serum of immunized mice revealed high levels of IgG1 when compared with IgG2a and IgG2b. Further IgG1/IgG2a ratio clearly demonstrated that the protein complex manipulates the host immune response favorable to the pathogen. Our results demonstrate that the co-transcribed and co-translated PE32 and PPE65 antigens are involved specifically in modulating anti-mycobacterial host immune response by hampering Th1 response.
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Affiliation(s)
- Mohd Khubaib
- Inflammation Biology and Cell Signaling Laboratory, National Institute of PathologyNew Delhi, India; Dr. Reddy's Institute of Life Sciences, University of Hyderabad CampusHyderabad, India
| | - Javaid A Sheikh
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology New Delhi, India
| | - Saurabh Pandey
- Inflammation Biology and Cell Signaling Laboratory, National Institute of PathologyNew Delhi, India; Dr. Reddy's Institute of Life Sciences, University of Hyderabad CampusHyderabad, India
| | - Battu Srikanth
- Department of Biotechnology, School of Life Sciences, University of Hyderabad Hyderabad, India
| | - Manish Bhuwan
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology New Delhi, India
| | - Nooruddin Khan
- Department of Biotechnology, School of Life Sciences, University of Hyderabad Hyderabad, India
| | - Seyed E Hasnain
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad CampusHyderabad, India; Molecular Infection and Functional Biology Laboratory, Kusuma School of Biological Sciences, Indian Institute of TechnologyNew Delhi, India
| | - Nasreen Z Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology New Delhi, India
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Grover S, Gupta P, Kahlon PS, Goyal S, Grover A, Dalal K, Sabeeha, Ehtesham NZ, Hasnain SE. Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection. MOLECULAR BIOSYSTEMS 2016; 12:1615-25. [PMID: 26983646 DOI: 10.1039/c5mb00810g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis is a devastating disease, taking one human life every 20 seconds globally. We hypothesize that professional pathogens such as M.tb have acquired specific features that might assist in causing infection, persistence and transmissible pathology in their host. We have identified 121 methyltransferases (MTases) in the M.tb proteome, which use a variety of substrates - DNA, RNA, protein, intermediates of mycolic acid biosynthesis and other fatty acids - that are involved in cellular maintenance within the host. A comparative analysis of the proteome of the virulent strain H37Rv and the avirulent strain H37Ra identified 3 MTases, which displayed significant variations in terms of N-terminal extension/deletion and point mutations, possibly impacting various physicochemical properties. The cross-proteomic comparison of MTases of M.tb H37Rv with 15 different Mycobacterium species revealed the acquisition of novel MTases in a MTB complex as a function of evolution. Phylogenetic analysis revealed that these newly acquired MTases showed common roots with certain extremophiles such as halophilic and acidophilic organisms. Our results establish an evolutionary relationship of M.tb with halotolerant organisms and also the role of MTases of M.tb in withstanding the host osmotic stress, thereby pointing to their likely role in pathogenesis, virulence and niche adaptation.
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Affiliation(s)
- Sonam Grover
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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Differential roles of the hemerythrin-like proteins of Mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility. Sci Rep 2015; 5:16130. [PMID: 26607739 PMCID: PMC4660385 DOI: 10.1038/srep16130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/08/2015] [Indexed: 11/09/2022] Open
Abstract
Hemerythrin-like proteins are oxygen-carrying non-heme di-iron binding proteins and their functions have effect on oxidation-reduction regulation and antibiotic resistance. Recent studies using bioinformatic analyses suggest that multiple hemerythrin-like protein coding sequences might have been acquired by lateral gene transfer and the number of hemerythrin-like proteins varies amongst different species. Mycobacterium smegmatis contains three hemerythrin-like proteins, MSMEG_3312, MSMEG_2415 and MSMEG_6212. In this study, we have systematically analyzed all three hemerythrin-like proteins in M. smegmatis and our results identified and characterized two functional classes: MSMEG_2415 plays an important role in H2O2 susceptibility, and MSMEG_3312 and MSMEG_6212 are associated with erythromycin susceptibility. Phylogenetic analysis indicated that these three proteins have different evolutionary origins, possibly explaining their different physiological functions. Here, combined with biological and phylogenetic analyses, our results provide new insights into the evolutionary divergence of the hemerythrin-like proteins in M. smegmatis.
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Microbiological features and clinical relevance of new species of the genus Mycobacterium. Clin Microbiol Rev 2015; 27:727-52. [PMID: 25278573 DOI: 10.1128/cmr.00035-14] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are present in the environment, mainly in water, and are occasionally responsible for opportunistic infections in humans. Despite the fact that NTM are characterized by a moderate pathogenicity, the diseases caused by NTM at various body sites are increasing on a worldwide level. Among over 150 officially recognized NTM species, only two or three dozen are familiar to clinicians, and even to most microbiologists. In this paper, approximately 50 new species described in the last 8 years are reviewed, and their role in human infections is assessed on the basis of reported clinical cases. The small number of reports concerning most of the "new" mycobacterial species is responsible for the widespread conviction that they are very rare. Their role is actually largely underestimated, mainly because they often remain unrecognized and misidentified. Aiming to minimize such bias, emphasis has been placed on more common identification pitfalls. Together with new NTM, new members of the Mycobacterium tuberculosis complex described in the last few years are also an object of the present review.
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Reply to '"Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare': "M. indicus pranii" is a distinct strain, not derived from M. intracellulare, and is an organism at an evolutionary transition point between a fast grower and slow grower. mBio 2015; 6:mBio.00352-15. [PMID: 25852162 PMCID: PMC4453546 DOI: 10.1128/mbio.00352-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Li X, Tao J, Hu X, Chan J, Xiao J, Mi K. A bacterial hemerythrin-like protein MsmHr inhibits the SigF-dependent hydrogen peroxide response in mycobacteria. Front Microbiol 2015; 5:800. [PMID: 25642228 PMCID: PMC4295536 DOI: 10.3389/fmicb.2014.00800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/27/2014] [Indexed: 12/05/2022] Open
Abstract
Hydrogen peroxide (H2O2) is one of a variety of reactive oxygen species (ROS) produced by aerobic organisms. Host production of toxic H2O2 in response to pathogen infection is an important classical innate defense mechanism against invading microbes. Understanding the mechanisms by which pathogens, in response to oxidative stress, mediate defense against toxic ROS, can reveal anti-microbial targets and shed light on pathogenic mechanisms. In this study, we provide evidence that a Mycobacterium smegmatis hemerythrin-like protein MSMEG_2415, designated MsmHr, is a H2O2-modulated repressor of the SigF-mediated response to H2O2. Circular dichroism and spectrophotometric analysis of MsmHr revealed properties characteristic of a typical hemerythrin-like protein. An msmHr knockout strain of M. smegmatis mc2155 (ΔmsmHr) was more resistant to H2O2 than its parental strain, and overexpression of MsmHr increased mycobacterial susceptibility to H2O2. Mutagenesis studies revealed that the hemerythrin domain of MsmHr is required for the regulation of the H2O2 response observed in the overexpression study. We show that MsmHr inhibits the expression of SigF (MSMEG_1804), an alternative sigma factor that plays an important role in bacterial oxidative stress responses, including those elicited by H2O2, thus providing a mechanistic link between ΔmsmHr and its enhanced resistance to H2O2. Together, these results strongly suggest that MsmHr is involved in the response of mycobacteria to H2O2 by negatively regulating a sigma factor, a function not previously described for hemerythrins.
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Affiliation(s)
- Xiaojing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Jun Tao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - John Chan
- Departments of Medicine and Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY, USA
| | - Jing Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing, China ; Beijing Key Laboratory of Microbial Drug Resistance and Resistome Beijing, China
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Kumar P, John V, Marathe S, Das G, Bhaskar S. Mycobacterium indicus pranii induces dendritic cell activation, survival, and Th1/Th17 polarization potential in a TLR-dependent manner. J Leukoc Biol 2015; 97:511-20. [PMID: 25593326 DOI: 10.1189/jlb.1a0714-361r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
MIP is a nonpathogenic, soil-borne predecessor of Mycobacterium avium. It has been reported previously that MIP possesses strong immunomodulatory properties and confers protection against experimental TB and tumor. DCs, by virtue of their unmatched antigen-presentation potential, play a critical role in activation of antitumor and antimycobacterial immune response. The effect of MIP on the behavior of DCs and the underlying mechanisms, however, have not been investigated so far. In the present study, we showed that MIP induces significant secretion of IL-6, IL-12p40, IL-10, and TNF-α by DCs and up-regulates the expression of costimulatory molecules CD40, CD80, and CD86. MIP(L) induced a significantly higher response compared with MIP(K). PI and Annexin V staining showed that MIP increases DC survival by inhibiting apoptosis. Consistently, higher expression of antiapoptotic proteins Bcl-2 and Bcl-xl was observed in MIP-stimulated DCs. Cytokines, produced by naïve T cells, cocultured with MIP-stimulated DCs, showed that MIP promotes Th1/Th17 polarization potential in DCs. Response to MIP was lost in MyD88(-/-)DCs, underscoring the critical role of TLRs in MIP-induced DC activation. Further studies revealed that TLR2 and TLR9 are involved in DC activation by MIP(L), whereas MIP(K) activates the DCs through TLR2. Our findings establish the DC activation by MIP, define the behavior of MIP-stimulated DCs, and highlight the role of TLRs in MIP-induced DC activation.
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Affiliation(s)
- Pawan Kumar
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vini John
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Soumitra Marathe
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gobardhan Das
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sangeeta Bhaskar
- *National Institute of Immunology, New Delhi, India; and International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis. mBio 2014; 5:e02020. [PMID: 25370496 PMCID: PMC4222108 DOI: 10.1128/mbio.02020-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. The complete sequence analysis of Mycobacterium indicus pranii, a novel species of Mycobacterium shown earlier to have strong immunomodulatory properties and currently in use for the treatment of leprosy, places it evolutionarily at the point of transition to pathogenicity. With the purpose of establishing the importance of M. indicus pranii in providing insight into the virulence mechanism of tuberculous and nontuberculous mycobacteria, we carried out comparative genomic and proteomic analyses of 44 mycobacterial species representing nonpathogenic (NP), opportunistic (OP), and totally pathogenic (TP) mycobacteria. Our results clearly placed M. indicus pranii as an ancestor of the M. avium complex. Analyses of comparative metabolic pathways between M. indicus pranii (NP), M. tuberculosis (TP), and M. intracellulare (OP) pointed to the presence of novel alternative pathways in M. tuberculosis with implications for pathogenesis and survival in the human host and identification of new drug targets.
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Kumar P, Tyagi R, Das G, Bhaskar S. Mycobacterium indicus pranii and Mycobacterium bovis BCG lead to differential macrophage activation in Toll-like receptor-dependent manner. Immunology 2014; 143:258-68. [PMID: 24766519 DOI: 10.1111/imm.12306] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/26/2014] [Accepted: 04/22/2014] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium indicus pranii (MIP) is an atypical mycobacterial species possessing strong immunomodulatory properties. It is a potent vaccine candidate against tuberculosis, promotes Th1 immune response and protects mice from tumours. In previous studies, we demonstrated higher protective efficacy of MIP against experimental tuberculosis as compared with bacillus Calmette-Guérin (BCG). Since macrophages play an important role in the pathology of mycobacterial diseases and cancer, in the present study, we evaluated the MIP in live and killed form for macrophage activation potential, compared it with BCG and investigated the underlying mechanisms. High levels of tumour necrosis factor-α, interleukin-12p40 (IL-12p40), IL-6 and nitric oxide were produced by MIP-stimulated macrophages as compared with BCG-stimulated macrophages. Prominent up-regulation of co-stimulatory molecules CD40, CD80 and CD86 was also observed in response to MIP. Loss of response in MyD88-deficient macrophages showed that both MIP and BCG activate the macrophages in a MyD88-dependent manner. MyD88 signalling pathway culminates in nuclear factor-κB/activator protein-1 (NF-κB/AP-1) activation and higher activation of NF-κB/AP-1 was observed in response to MIP. With the help of pharmacological inhibitors and Toll-like receptor (TLR) -deficient macrophages, we observed the role of TLR2, TLR4 and intracellular TLRs in MIP-mediated macrophage activation. Stimulation of HEK293 cells expressing TLR2 in homodimeric or heterodimeric form showed that MIP has a distinctly higher level of TLR2 agonist activity compared with BCG. Further experiments suggested that TLR2 ligands are well exposed in MIP whereas they are obscured in BCG. Our findings establish the higher macrophage activation potential of MIP compared with BCG and delineate the underlying mechanism.
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Affiliation(s)
- Pawan Kumar
- National Institute of Immunology, New Delhi, India
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Lahiri A, Sanchini A, Semmler T, Schäfer H, Lewin A. Identification and comparative analysis of a genomic island in Mycobacterium avium
subsp. hominissuis. FEBS Lett 2014; 588:3906-11. [DOI: 10.1016/j.febslet.2014.08.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/26/2022]
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Gene cooption in Mycobacteria and search for virulence attributes: Comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria. Int J Med Microbiol 2014; 304:742-8. [DOI: 10.1016/j.ijmm.2014.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 02/07/2023] Open
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