1
|
Montero-Vega MT, Matilla J, Bazán E, Reimers D, De Andrés-Martín A, Gonzalo-Gobernado R, Correa C, Urbano F, Gómez-Coronado D. Fluvastatin Converts Human Macrophages into Foam Cells with Increased Inflammatory Response to Inactivated Mycobacterium tuberculosis H37Ra. Cells 2024; 13:536. [PMID: 38534380 DOI: 10.3390/cells13060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Cholesterol biosynthesis inhibitors (statins) protect hypercholesterolemic patients against developing active tuberculosis, suggesting that these drugs could help the host to control the pathogen at the initial stages of the disease. This work studies the effect of fluvastatin on the early response of healthy peripheral blood mononuclear cells (PBMCs) to inactivated Mycobacterium tuberculosis (Mtb) H37Ra. We found that in fluvastatin-treated PBMCs, most monocytes/macrophages became foamy cells that overproduced NLRP3 inflammasome components in the absence of immune stimulation, evidencing important cholesterol metabolism/immunity connections. When both fluvastatin-treated and untreated PBMCs were exposed to Mtb H37Ra, a small subset of macrophages captured large amounts of bacilli and died, concentrating the bacteria in necrotic areas. In fluvastatin-untreated cultures, most of the remaining macrophages became epithelioid cells that isolated these areas of cell death in granulomatous structures that barely produced IFNγ. By contrast, in fluvastatin-treated cultures, foamy macrophages surrounded the accumulated bacteria, degraded them, markedly activated caspase-1 and elicited a potent IFNγ/cytotoxic response. In rabbits immunized with the same bacteria, fluvastatin increased the tuberculin test response. We conclude that statins may enhance macrophage efficacy to control Mtb, with the help of adaptive immunity, offering a promising tool in the design of alternative therapies to fight tuberculosis.
Collapse
Affiliation(s)
- María Teresa Montero-Vega
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Joaquín Matilla
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Eulalia Bazán
- Servicio de Neurobiología-Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Diana Reimers
- Servicio de Neurobiología-Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Ana De Andrés-Martín
- Servicio de Inmunología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Rafael Gonzalo-Gobernado
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Carlos Correa
- Unidad de Cirugía Experimental y Animalario, Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Francisco Urbano
- Servicio Interdepartamental de Investigación (SIdI), Facultad de Medicina, Universidad Autónoma, 28029 Madrid, Spain
| | - Diego Gómez-Coronado
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| |
Collapse
|
2
|
Moukendza Koundi L, Ekomi Moure UA, Boni FG, Hamdi I, Fan L, Xie J. Mycobacterium tuberculosis Rv2617c is involved in stress response and phage infection resistance. Heliyon 2024; 10:e27400. [PMID: 38495141 PMCID: PMC10943396 DOI: 10.1016/j.heliyon.2024.e27400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is the pathogen of human tuberculosis (TB). Resistance to numerous in vivo stresses, including oxidative stress, is determinant for M. tuberculosis intracellular survival, and understanding associated mechanisms is crucial for developing new therapeutic strategies. M. tuberculosis Rv2617c has been associated with oxidative stress response when interacting with other proteins in M. tuberculosis; however, its functional promiscuity and underlying molecular mechanisms remain elusive. In this study, we investigated the phenotypic changes of Mycobacterium smegmatis (M. smegmatis) expressing Rv2617c (Ms_Rv2617c) and its behavior in the presence of various in vitro stresses and phage infections. We found that Rv2617c conferred resistance to SDS and diamide while sensitizing M. smegmatis to oxidative stress (H2O2) and altered mycobacterial phenotypic properties (single-cell clone and motility), suggestive of reprogrammed mycobacterial cell wall lipid contents exemplified by increased cell wall permeability. Interestingly, we also found that Rv2617c promoted M. smegmatis resistance to infection by phages (SWU1, SWU2, D29, and TM4) and kept phage TM4 from destroying mycobacterial biofilms. Our findings provide new insights into the role of Rv2617c in resistance to oxide and acid stresses and report for the first time on its role in phage resistance in Mycobacterium.
Collapse
Affiliation(s)
- Liadrine Moukendza Koundi
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Ulrich Aymard Ekomi Moure
- The Ninth People's Hospital of Chongqing, Affiliated Hospital of Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, 400716, Chongqing, China
| | - Funmilayo Grâce Boni
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Insaf Hamdi
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Lin Fan
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Key Laboratory of Tuberculosis, Shanghai, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| |
Collapse
|
3
|
Ning B, Shen J, Liu F, Zhang H, Jiang X. Baicalein Suppresses NLRP3 and AIM2 Inflammasome-Mediated Pyroptosis in Macrophages Infected by Mycobacterium tuberculosis via Induced Autophagy. Microbiol Spectr 2023; 11:e0471122. [PMID: 37125940 PMCID: PMC10269511 DOI: 10.1128/spectrum.04711-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) continues to pose a significant threat to global health because it causes granulomas and systemic inflammatory responses during active tuberculosis (TB). Mtb can induce macrophage pyroptosis, which results in the release of IL-1β and causes tissue damage, thereby promoting its spread. In the absence of anti-TB drugs, host-directed therapy (HDT) has been demonstrated to be an effective strategy against TB. In this study, we used an in vitro Mtb-infected macrophage model to assess the effect of baicalein, derived from Scutellariae radix, on pyroptosis induced in Mtb-infected macrophages. Further, we investigated the molecular mechanisms underlying the actions of baicalein. The results of the study suggest that baicalein inhibits pyroptosis in Mtb-infected macrophages by downregulating the assembly of AIM2 and NLRP3 inflammasome and promoting autophagy. Further research has also shown that the mechanism by which baicalein promotes autophagy may involve the inhibition of the activation of the Akt/mTOR pathway and the inhibition of the AIM2 protein, which affects the levels of CHMP2A protein required to promote autophagy. Thus, our data show that baicalein can inhibit Mtb infection-induced macrophage pyroptosis and has the potential to be a new adjunctive HDT drug. IMPORTANCE Current strategies for treating drug-resistant tuberculosis have limited efficacy and undesirable side effects; hence, research on new treatments, including innovative medications, is required. Host-directed therapy (HDT) has emerged as a viable strategy for modulating host cell responses in order to enhance protective immunity against infections. Baicalein, extracted from Scutellariae radix, was shown to inhibit pyroptosis caused by Mycobacterium tuberculosis-infected macrophages and was associated with autophagy. Our findings reveal that baicalein can be used as an adjunctive treatment for tuberculosis or other inflammatory diseases by regulating immune function and enhancing the antibacterial ability of the host. It also provides a new idea for exploring the anti-inflammatory mechanism of baicalein.
Collapse
Affiliation(s)
- Bangzuo Ning
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jingjing Shen
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fanglin Liu
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hemin Zhang
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Jiang
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
4
|
ppe51 Variants Enable Growth of Mycobacterium tuberculosis at Acidic pH by Selectively Promoting Glycerol Uptake. J Bacteriol 2022; 204:e0021222. [PMID: 36226966 PMCID: PMC9664963 DOI: 10.1128/jb.00212-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In defined media supplemented with single carbon sources, Mycobacterium tuberculosis (Mtb) exhibits carbon source specific growth restriction. When supplied with glycerol as the sole carbon source at pH 5.7, Mtb establishes a metabolically active state of nonreplicating persistence known as acid growth arrest. We hypothesized that acid growth arrest on glycerol is not a metabolic restriction, but rather an adaptive response. To test this hypothesis, we selected for and identified several Mtb mutants that could grow under these restrictive conditions. All mutations were mapped to the ppe51 gene and resulted in variants with 3 different amino acid substitutions- S211R, E215K, and A228D. Expression of the ppe51 variants in Mtb promoted growth at acidic pH showing that the mutant alleles are sufficient to cause the dominant gain-of-function, Enhanced Acid Growth (EAG) phenotype. Testing growth on other single carbon sources showed the PPE51 variants specifically enhanced growth on glycerol, suggesting PPE51 plays a role in glycerol uptake. Using radiolabeled glycerol, enhanced glycerol uptake was observed in Mtb expressing the PPE51 (S211R) variant, with glycerol overaccumulation in triacylglycerol. Notably, the EAG phenotype is deleterious for growth in macrophages, where the mutants have selectively faster replication and reduced survival in activated macrophages compared to resting macrophages. Recombinant PPE51 protein exhibited differential thermostability in the wild type (WT) or S211R variants in the presence of glycerol, supporting the model that EAG substitutions alter PPE51-glycerol interactions. Together, these findings support that PPE51 variants selectively promote glycerol uptake and that slowed growth at acidic pH is an important adaptive mechanism required for macrophage pathogenesis. IMPORTANCE It is puzzling why Mycobacterium tuberculosis (Mtb) cannot grow on glycerol at acidic pH, as it has a carbon source and oxygen, everything it needs to grow. In this study, we found that Mtb limits uptake of glycerol at acidic pH to restrict its growth and that mutations in ppe51 promote uptake of glycerol at acidic pH and enable growth. That is, Mtb can grow well at acidic pH on glycerol, but has adapted instead to stop growth. Notably, ppe51 variants exhibit enhanced replication and reduced survival in activated macrophages, supporting a role for pH-dependent slowed growth during macrophage pathogenesis.
Collapse
|
5
|
Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis. Microbiol Spectr 2021; 9:e0071621. [PMID: 34937194 PMCID: PMC8694153 DOI: 10.1128/spectrum.00716-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies involving the pathogenic organism Mycobacterium tuberculosis routinely require advanced biosafety laboratory facilities, which might not be readily available in rural areas where tuberculosis burdens are high. Attempts to adapt heat inactivation techniques have led to inconsistent conclusions, and the risk of protein denaturation due to extensive heating is impractical for subsequent mass spectrometry (MS)-based protein analyses. In this study, 240 specimens with one or two loops of M. tuberculosis strain H37Rv biomass and specific inactivated solutions were proportionally assigned to six heat inactivation methods in a thermal block at 80°C and 95°C for 20, 30, and 90 min. Twenty untreated specimens served as a positive control, and bacterial growth was followed up for 12 weeks. Our results showed that 90 min of heat inactivation was necessary for samples with two loops of biomass. Further protein extraction and a matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS assay demonstrated adequate scores for bacterial identification (≥1.7), with the highest score achieved in the 80°C/90 min and 95°C/30 min treatment groups. A proteomics study also confidently identified 648 proteins with ∼93% to 96% consistent protein abundances following heating at 95°C for 20, 30, and 90 min. Heat inactivation at 95°C for 90 min yielded the most quantifiable proteins, and a functional analysis revealed proteins located in the ribosomal subunit. In summary, we proposed a heat inactivation method for the M. tuberculosis strain H37Rv and studied the preservation of protein components for subsequent bacterial identification and protein-related assays. IMPORTANCE Inactivation of Mycobacterium tuberculosis is an important step to guarantee biosafety for subsequent M. tuberculosis identification and related research, notably in areas of endemicity with minimal resources. However, certain biomolecules might be denatured or hydrolyzed because of the harsh inactivation process, and a standardized protocol is yet to be determined. We evaluated distinct heating conditions to report the inactivation efficiency and performed downstream mass spectrometry-based M. tuberculosis identification and proteomics study. The results are important and useful for both basic and clinical M. tuberculosis studies.
Collapse
|
6
|
Li J, Liu Z, Hong M, Sun C, Zhang T, Zhang H, Ju J, Ma J. Semi-Synthesis of Marine-Derived Ilamycin F Derivatives and Their Antitubercular Activities. Front Chem 2021; 9:774555. [PMID: 34778219 PMCID: PMC8586704 DOI: 10.3389/fchem.2021.774555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is still a global disease threatening people’s lives. With the emergence of multi-drug-resistant Mycobacterium tuberculosis the prevention and control of tuberculosis faces new challenges, and the burden of tuberculosis treatment is increasing among the world. Ilamycins are novel cyclopeptides with potent anti-TB activities, which have a unique target protein against M. tuberculosis and drug-resistant strains. Herein, ilamycin F, a major secondary metabolite isolated from the marine-derived mutant strain Streptomyces atratus SCSIO ZH16 ΔilaR, is used as a scaffold to semi-synthesize eighteen new ilamycin derivatives (ilamycin NJL1–NJL18, 1–18). Our study reveals that four of ilamycin NJLs (1, 6, 8, and 10) have slightly stronger anti-TB activities against Mtb H37Rv (minimum inhibitory concentration, 1.6–1.7 μM) compared with that of ilamycin F on day 14th, but obviously display more potent activities than ilamycin F on day 3rd, indicating anti-TB activities of these derivatives with fast-onset effect. In addition, cytotoxic assays show most ilamycin NJLs with low cytotoxicity except ilamycin NJL1 (1). These findings will promote the further exploration of structure-activity relationships for ilamycins and the development of anti-TB drugs.
Collapse
Affiliation(s)
- Jun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhiyong Liu
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mingye Hong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tianyu Zhang
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
7
|
Wang H, Wan L, Shi J, Zhang T, Zhu H, Jiang S, Meng S, Wu S, Sun J, Chang L, Zhang L, Wan K, Yang J, Zhao X, Liu H, Zhang Y, Dai E, Xu P. Quantitative proteomics reveals that dormancy-related proteins mediate the attenuation in mycobacterium strains. Virulence 2021; 12:2228-2246. [PMID: 34634997 PMCID: PMC8923072 DOI: 10.1080/21505594.2021.1965703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that we obtained deep-coverage protein identification and high quantification. Although 272 genetic variations were reported in H37Ra and H37Rv, they showed very little expression difference in log and stationary phase. Quantitative comparison revealed H37Ra and H37Rv had significantly dysregulation in log phase (227) compared with stationary phase (61). While BCG and H37Rv, and BCG and H37Ra showed notable differences in stationary phase (1171 and 1124) with respect to log phase (381 and 414). In the log phase, similar patterns of protein abundance were observed between H37Ra and BCG, whereas a more similar expression pattern was observed between H37Rv and H37Ra in the stationary phase. Bioinformatic analysis revealed that the upregulated proteins detected for H37Rv and H37Ra in log phase were virulence-related factors. In both log and stationary phases, the dysregulated proteins detected for BCG, which have also been identified as M. tuberculosis response proteins under dormancy conditions. We accordingly describe the proteomic profiles of H37Rv, H37Ra, and BCG, which we believe will potentially provide a better understanding of H37Rv pathogenesis, H37Ra attenuation, and BCG immuno protection.
Collapse
Affiliation(s)
- Hong Wang
- School of Public Health, North China University of Science and Technology, Tangshan, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,The Fifth Hospital of Shijiazhuang, School of Public Health, North China University of Science and Technology, Shijiazhuang, China
| | - Li Wan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Hebei, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Huiming Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,Department of Biomedicine, School of Medicine, Guizhou University, Guiyang, China
| | - Songhao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Hebei, China
| | - Shuhong Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Hebei, China
| | - Shujia Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jinshuai Sun
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Hebei, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Liqun Zhang
- Department of Tuberculosis, Capital Medical University, Beijing Chest Hospital, Beijing, China
| | - Kanglin Wan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiaqi Yang
- School of Public Health, North China University of Science and Technology, Tangshan, China.,The Fifth Hospital of Shijiazhuang, School of Public Health, North China University of Science and Technology, Shijiazhuang, China
| | - Xiuqin Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Erhei Dai
- School of Public Health, North China University of Science and Technology, Tangshan, China.,The Fifth Hospital of Shijiazhuang, School of Public Health, North China University of Science and Technology, Shijiazhuang, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Hebei, China.,Department of Biomedicine, School of Medicine, Guizhou University, Guiyang, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
8
|
Bendre AD, Peters PJ, Kumar J. Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM. J Membr Biol 2021; 254:321-341. [PMID: 33954837 PMCID: PMC8099146 DOI: 10.1007/s00232-021-00179-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/23/2021] [Indexed: 12/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.
Collapse
Affiliation(s)
- Ameya D Bendre
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra, 411007, India.
| |
Collapse
|
9
|
Identification of CTL Epitopes on Efflux Pumps of the ATP-Binding Cassette and the Major Facilitator Superfamily of Mycobacterium tuberculosis. J Immunol Res 2021; 2021:8899674. [PMID: 33490292 PMCID: PMC7803423 DOI: 10.1155/2021/8899674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/30/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis is the world's most deadly infectious disease, with 10 million people falling ill and 1.5 million people dying from the disease every year. With the increasing number of drug-resistant Mycobacterium tuberculosis (MTB) strains and prevalence of coinfection of MTB with human immunodeficiency virus, many challenges remain in the prevention and treatment of tuberculosis. Therefore, the development of safe and effective tuberculosis vaccines is an urgent issue. In this study, we identified cytotoxic T lymphocyte epitopes on drug resistance-associated membrane protein efflux pumps of MTB, the ATP-binding cassette and the major facilitator superfamilies. First, three online software were used to predict HLA-A2-restricted epitopes. Then, the candidate epitopes were confirmed with the T2A2 cell binding affinity and peptide/MHC (pMHC) complex stability assays and in vitro immune activity experiments. Two drug-resistant T lymphocyte epitopes, designated Rv1218c-p24 and Rv2477c-p182, were selected, and their immunogenic activities studied in vivo in genetically engineered mice. The immune activities of these two epitopes were improved with the help of complete Freund's adjuvant (CFA). The epitopes identified here provide a foundation for the diagnosis and treatment of patients infected with drug resistant and the future development of a multiepitope vaccine.
Collapse
|
10
|
Bespyatykh J, Arapidi G, Shitikov E. Proteogenomic Approach for Mycobacterium tuberculosis Investigation. Methods Mol Biol 2021; 2259:191-201. [PMID: 33687716 DOI: 10.1007/978-1-0716-1178-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent advances in MS/MS technology have made it possible to use proteomic data to predict protein-coding sequences. This approach is called proteogenomics, and it allows to correctly translate start and stop sites and to reveal new open reading frames. Here, we focus on using proteogenomics to improve the annotation of Mycobacteriumtuberculosis strains. We also describe detail procedures of the extraction of proteins and their further preparation for LC-MS/MS analysis and outline the main steps of data analysis.
Collapse
Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
11
|
Strong EJ, Jurcic Smith KL, Saini NK, Ng TW, Porcelli SA, Lee S. Identification of Autophagy-Inhibiting Factors of Mycobacterium tuberculosis by High-Throughput Loss-of-Function Screening. Infect Immun 2020; 88:e00269-20. [PMID: 32989037 PMCID: PMC7671894 DOI: 10.1128/iai.00269-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
The interaction of host cells with mycobacteria is complex and can lead to multiple outcomes ranging from bacterial clearance to progressive or latent infection. Autophagy is recognized as one component of host cell responses that has an essential role in innate and adaptive immunity to intracellular bacteria. Many microbes, including Mycobacterium tuberculosis, have evolved to evade or exploit autophagy, but the precise mechanisms and virulence factors are mostly unknown. Through a loss-of-function screening of an M. tuberculosis transposon mutant library, we identified 16 genes that contribute to autophagy inhibition, six of which encoded the PE/PPE protein family. Their expression in Mycobacterium smegmatis confirmed that these PE/PPE proteins inhibit autophagy and increase intracellular bacterial persistence or replication in infected cells. These effects were associated with increased mammalian target of rapamycin (mTOR) activity and also with decreased production of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β). We also confirmed that the targeted deletion of the pe/ppe genes in M. tuberculosis resulted in enhanced autophagy and improved intracellular survival rates compared to those of wild-type bacteria in the infected macrophages. Differential expression of these PE/PPE proteins was observed in response to various stress conditions, suggesting that they may confer advantages to M. tuberculosis by modulating its interactions with host cells under various conditions. Our findings demonstrated that multiple M. tuberculosis PE/PPE proteins are involved in inhibiting autophagy during infection of host phagocytes and may provide strategic targets in developing therapeutics or vaccines against tuberculosis.
Collapse
Affiliation(s)
- Emily J Strong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Neeraj K Saini
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tony W Ng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sunhee Lee
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
12
|
Hermann C, Karamchand L, Blackburn JM, Soares NC. Cell Envelope Proteomics of Mycobacteria. J Proteome Res 2020; 20:94-109. [PMID: 33140963 DOI: 10.1021/acs.jproteome.0c00650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The World Health Organization (WHO) estimates that Mycobacterium tuberculosis, the most pathogenic mycobacterium species to humans, has infected up to a quarter of the world's population, with the occurrence of multidrug-resistant strains on the rise. Research into the detailed composition of the cell envelope proteome in mycobacteria over the last 20 years has formed a key part of the efforts to understand host-pathogen interactions and to control the current tuberculosis epidemic. This is due to the great importance of the cell envelope proteome during infection and during the development of antibiotic resistance as well as the search of surface-exposed proteins that could be targeted by therapeutics and vaccines. A variety of experimental approaches and mycobacterial species have been used in proteomic studies thus far. Here we provide for the first time an extensive summary of the different approaches to isolate the mycobacterial cell envelope, highlight some of the limitations of the studies performed thus far, and comment on how the recent advances in membrane proteomics in other fields might be translated into the field of mycobacteria to provide deeper coverage.
Collapse
Affiliation(s)
- Clemens Hermann
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Leshern Karamchand
- National Research Council Canada, Nanotechnology Research Centre, Biomedical Nanotechnologies, 11421 Saskatchewan Drive NW, Edmonton, Alberta T6G 2M9, Canada
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.,College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates
| |
Collapse
|
13
|
Abstract
Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery.
Collapse
|
14
|
Choi HH, Kwon KW, Han SJ, Kang SM, Choi E, Kim A, Cho SN, Shin SJ. PPE39 of the Mycobacterium tuberculosis strain Beijing/K induces Th1-cell polarization through dendritic cell maturation. J Cell Sci 2019; 132:jcs.228700. [PMID: 31371491 DOI: 10.1242/jcs.228700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/17/2019] [Indexed: 12/22/2022] Open
Abstract
In a previous study, we have identified MTBK_24820, the complete protein form of PPE39 in the hypervirulent Mycobacterium tuberculosis (Mtb) strain Beijing/K by using comparative genomic analysis. PPE39 exhibited vaccine potential against Mtb challenge in a murine model. Thus, in this present study, we characterize PPE39-induced immunological features by investigating the interaction of PPE39 with dendritic cells (DCs). PPE39-treated DCs display reduced dextran uptake and enhanced MHC-I, MHC-II, CD80 and CD86 expression, indicating that this PPE protein induces phenotypic DC maturation. In addition, PPE39-treated DCs produce TNF-α, IL-6 and IL-12p70 to a similar and/or greater extent than lipopolysaccharide-treated DCs in a dose-dependent manner. The activating effect of PPE39 on DCs was mediated by TLR4 through downstream MAPK and NF-κB signaling pathways. Moreover, PPE39-treated DCs promoted naïve CD4+ T-cell proliferation accompanied by remarkable increases of IFN-γ and IL-2 secretion levels, and an increase in the Th1-related transcription factor T-bet but not in Th2-associated expression of GATA-3, suggesting that PPE39 induces Th1-type T-cell responses through DC activation. Collectively, the results indicate that the complete form of PPE39 is a so-far-unknown TLR4 agonist that induces Th1-cell biased immune responses by interacting with DCs.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Hong-Hee Choi
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Kee Woong Kwon
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Seung Jung Han
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Soon Myung Kang
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Eunsol Choi
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Ahreum Kim
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sang-Nae Cho
- Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, South Korea .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea.,Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul 03722, South Korea
| |
Collapse
|
15
|
Bisht D, Sharma D, Sharma D, Singh R, Gupta VK. Recent insights intoMycobacterium tuberculosisthrough proteomics and implications for the clinic. Expert Rev Proteomics 2019; 16:443-456. [DOI: 10.1080/14789450.2019.1608185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| |
Collapse
|
16
|
Miryala SK, Anbarasu A, Ramaiah S. Impact of bedaquiline and capreomycin on the gene expression patterns of multidrug‐resistant
Mycobacterium tuberculosis
H37Rv strain and understanding the molecular mechanism of antibiotic resistance. J Cell Biochem 2019; 120:14499-14509. [DOI: 10.1002/jcb.28711] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Sravan Kumar Miryala
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Anand Anbarasu
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Sudha Ramaiah
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| |
Collapse
|
17
|
Cell wall enrichment unveils proteomic changes in the cell wall during treatment of Mycobacterium smegmatis with sub-lethal concentrations of rifampicin. J Proteomics 2019; 191:166-179. [DOI: 10.1016/j.jprot.2018.02.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 12/21/2022]
|
18
|
PE17 protein from Mycobacterium tuberculosis enhances Mycobacterium smegmatis survival in macrophages and pathogenicity in mice. Microb Pathog 2019; 126:63-73. [DOI: 10.1016/j.micpath.2018.10.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 01/26/2023]
|
19
|
Kai-Cheen A, Lay-Harn G. Comparison of aqueous soluble proteins profile of Mycobacterium tuberculosis H37Rv and H37Ra and a Malaysian clinical isolate. Biotechnol Appl Biochem 2018; 65:876-882. [PMID: 30132993 DOI: 10.1002/bab.1687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/15/2018] [Indexed: 11/06/2022]
Abstract
Differentially expressed aqueous soluble proteins between Mycobacterium tuberculosis H37Ra and H37Rv were identified. The protein extracts were separated by two-dimensional gel electrophoresis followed by tandem mass spectrometric analysis. Twelve proteins were detected to be differentially expressed significantly between virulent strain H37Rv and attenuated strain H37Ra. The differentially expression of these proteins was validated by a recently isolated clinical virulent strains of M. tuberculosis, TB138. Out of the 12 proteins identified, which consisted of ten upregulated and two downregulated proteins, nine were belonged to intermediate metabolism and respiration protein group, two were in lipid metabolism, and one protein was involved in information pathways and virulence. Among these proteins, two of the upregulated proteins, namely, mmsA and pntAa, showed a consistent expression pattern in both virulent mycobacterium strains. These proteins can serve as potential biomarkers for the intervention treatment of TB.
Collapse
Affiliation(s)
- Ang Kai-Cheen
- School of Pharmaceutical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
| | - Gam Lay-Harn
- School of Pharmaceutical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
| |
Collapse
|
20
|
|
21
|
Pinto SM, Verma R, Advani J, Chatterjee O, Patil AH, Kapoor S, Subbannayya Y, Raja R, Gandotra S, Prasad TSK. Integrated Multi-Omic Analysis of Mycobacterium tuberculosis H37Ra Redefines Virulence Attributes. Front Microbiol 2018; 9:1314. [PMID: 29971057 PMCID: PMC6018540 DOI: 10.3389/fmicb.2018.01314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
H37Ra is a virulence attenuated strain of Mycobacterium tuberculosis widely employed as a model to investigate virulence mechanisms. Comparative high-throughput studies have earlier correlated its avirulence to the presence of specific mutations or absence of certain proteins. However, a recent sequencing study of H37Ra, has disproved several genomic differences earlier reported to be associated with virulence. This warrants further investigations on the H37Ra proteome as well. In this study, we carried out an integrated analysis of the genome, transcriptome, and proteome of H37Ra. In addition to confirming single nucleotide variations (SNVs) and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. We also provide transcriptional and proteomic evidence for 3,900 genes representing ~80% of the total predicted gene count including 408 proteins that have not been identified previously. We identified 9 genes whose coding potential was hitherto reported to be absent in H37Ra. These include 2 putative virulence factors belonging to ESAT-6 like family of proteins. Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. A majority of these were found to be conserved in the virulent strain H37Rv as well as in other mycobacterial species suggesting that the differences in the virulent and avirulent strains of M. tuberculosis are not entirely dependent on the expression of certain proteins or their absence but may possibly be ascertained to functional changes.
Collapse
Affiliation(s)
- Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Oishi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Arun H Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Saketh Kapoor
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India
| |
Collapse
|
22
|
Das S, Hameed S, Fatima Z. Potential Drug Targets in Mycobacterial Cell Wall: Non-Lipid Perspective. Curr Drug Discov Technol 2018; 17:147-153. [PMID: 29875004 DOI: 10.2174/1570163815666180605113609] [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: 03/10/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB), still remains a deadly disease worldwide. With prolonged usage of anti-TB drugs, the current therapeutic regimes are becoming ineffective, particularly due to emergence of drug resistance in MTB. Under such compelling circumstances, it is pertinent to look for new drug targets. The cell wall envelope of MTB is composed of unique lipids that are frequently targeted for anti-TB therapy. This is evident from the fact that most of the commonly used front line drugs (Isoniazid and Ethambutol) act on lipid machinery of MTB. Thus, despite the fact that much of the attention is towards understanding the MTB lipid biology, in search for identification of new drug targets, our knowledge of bacterial cell wall non-lipid components remains rudimentary and underappreciated. Better understanding of such components of mycobacterial cell structure will help in the identification of new drug targets that can be utilized on the persistent mycobacterium. This review at a common platform summarizes some of the non-lipid cell wall components in MTB that have potential to be exploited as future drug targets.
Collapse
Affiliation(s)
- Shrayanee Das
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
| |
Collapse
|
23
|
Sharma D, Bisht D, Khan AU. Potential Alternative Strategy against Drug Resistant Tuberculosis: A Proteomics Prospect. Proteomes 2018; 6:E26. [PMID: 29843395 PMCID: PMC6027512 DOI: 10.3390/proteomes6020026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest human pathogen of the tuberculosis diseases. Drug resistance leads to emergence of multidrug-resistant and extremely drug resistant strains of M. tuberculosis. Apart from principal targets of resistance, many explanations have been proposed for drug resistance but some resistance mechanisms are still unknown. Recently approved line probe assay (LPA) diagnostics for detecting the resistance to first and second line drugs are unable to diagnose the drug resistance in M. tuberculosis isolates which do not have the mutations in particular genes responsible for resistance. Proteomics and bioinformatic tools emerged as direct approaches for identification and characterization of novel proteins which are directly and indirectly involved in drug resistance that could be used as potential targets in future. In future, these novel targets might reveal new mechanism of resistance and can be used in diagnostics or as drug targets.
Collapse
Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
| |
Collapse
|
24
|
Gel-free sample preparation techniques and bioinformatic enrichment analysis to in depth characterise the cell wall proteome of mycobacteria. MethodsX 2018; 5:475-484. [PMID: 30622917 PMCID: PMC6314971 DOI: 10.1016/j.mex.2018.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/18/2018] [Indexed: 11/20/2022] Open
Abstract
The comprehensive characterisation of the cell wall proteome of mycobacteria is of considerable relevance to both the discovery of new drug targets as well as to the design of new vaccines against Mycobacterium tuberculosis. However, due to its extremely hydrophobic nature, the coverage of proteomic studies of this subcellular compartment is still far from complete. Here, we report novel gel-free cell wall sample preparation procedures and quantitative LC–MS/MS measurements on a Q Exactive mass spectrometer. We combine these with a novel post-measurement bioinformatic analysis to filter out likely cytosolic contaminants. This reveals a subset of proteins that are highly enriched for cell wall proteins. The success of this approach is verified by peptide-centric measurement of the abundance of known subcellular markers, as well as analysis of the percentage of predicted membrane proteins within the purified fraction. While M. smegmatis was used during this study to establish and optimise the sample preparation procedures, these can easily be applied to other mycobacterial species, such as M. bovis BCG or M. tuberculosis. Improved gel-free cell wall sample preparation gives higher yields of tryptic peptides for LC–MS/MS measurement. Higher yields of tryptic peptides provide better quantitation and coverage of cell wall proteome. Post-measurement enrichment analysis filters out high abundance cytosolic contaminants that have carried through the experimental analysis.
Collapse
|
25
|
Comparative study of Mycobacterium tuberculosis and Mycobacterium bovis protein profiles. JOURNAL OF SURGERY AND MEDICINE 2018. [DOI: 10.28982/josam.417158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Muthu M, Deenadayalan A, Ramachandran D, Paul D, Gopal J, Chun S. A state-of-art review on the agility of quantitative proteomics in tuberculosis research. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Tan HW, Xu YM, Wu DD, Lau ATY. Recent insights into human bronchial proteomics - how are we progressing and what is next? Expert Rev Proteomics 2018; 15:113-130. [PMID: 29260600 DOI: 10.1080/14789450.2017.1417847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries. Areas covered: We overview the recent achievements and discoveries in human bronchial proteomics by outlining how some of the different proteomic techniques/strategies are developed and applied in LC, TB, COPD, and CF. Also, the future roles of bronchial proteomics in predictive proteomics and precision medicine are discussed. Expert commentary: Much progress has been made in bronchial proteomics. Owing to the advances in proteomics, we now have better ability to isolate proteins from desired cellular compartments, greater protein separation methods, more powerful protein detection technologies, and more sophisticated bioinformatic techniques. These all contributed to our further understanding of lung diseases and for biomarker and therapeutic target discoveries.
Collapse
Affiliation(s)
- Heng Wee Tan
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Yan-Ming Xu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Dan-Dan Wu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Andy T Y Lau
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| |
Collapse
|
28
|
Karuppusamy S, Mutharia L, Kelton D, Karrow N, Kirby G. Identification of antigenic proteins from Mycobacterium avium subspecies paratuberculosis cell envelope by comparative proteomic analysis. MICROBIOLOGY-SGM 2018; 164:322-337. [PMID: 29458660 DOI: 10.1099/mic.0.000606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Johne's disease (JD) is a contagious, chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). The aim of this study was to identify antigenic proteins from the MAP cell envelope (i.e. cell wall and cytoplasmic membranes) by comparing MAP, M. avium subsp. hominissuis (MAH) and M. smegmatis (MS) cell envelope protein profiles using a proteomic approach. Composite two-dimensional (2D) difference gel electrophoresis images revealed 13 spots present only in the image of the MAP cell envelope proteins. Using serum from MAP-infected cattle, immunoblot analysis of 2D gels revealed that proteins in the 13 spots were antigenic. These proteins were identified by liquid chromatography tandem mass spectrometry as products of the following genes: sdhA, fadE25_2, mkl, citA, gapdh, fadE3_2, moxR1, mmp, purC, mdh, atpG, fbpB and desA2 as well as two proteins without gene names identified as transcriptional regulator (MAP0035) protein and hypothetical protein (MAP1233). Protein functions ranged from energy generation, cell wall biosynthesis, protein maturation, bacterial replication and invasion of epithelial cells, functions considered essential to MAP virulence and intracellular survival. Five MAP cell envelope proteins, i.e. SdhA, FadE25_2, FadE3_2, MAP0035 and DesA2 were recombinantly expressed, three of which, i.e. SdhA, FadE25_2 and DesA2, were of sufficient purity and yield to generate polyclonal antibodies. Immunoblot analysis revealed antibodies reacted specifically to the respective MAP cell envelope proteins with minimal cross-reactivity with MAH and MS cell envelope proteins. Identification and characterization of MAP-specific proteins and antibodies to those proteins may be useful in developing new diagnostic tests for JD diagnosis.
Collapse
Affiliation(s)
| | - Lucy Mutharia
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - David Kelton
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Niel Karrow
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Gordon Kirby
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
29
|
Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol 2017; 39:64-72. [PMID: 29032348 DOI: 10.1016/j.mib.2017.09.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.
Collapse
Affiliation(s)
- Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
30
|
Myllymäki H, Niskanen M, Oksanen KE, Sherwood E, Ahava M, Parikka M, Rämet M. Identification of novel antigen candidates for a tuberculosis vaccine in the adult zebrafish (Danio rerio). PLoS One 2017; 12:e0181942. [PMID: 28742838 PMCID: PMC5526617 DOI: 10.1371/journal.pone.0181942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) remains a major global health challenge and the development of a better vaccine takes center stage in fighting the disease. For this purpose, animal models that are capable of replicating the course of the disease and are suitable for the early-stage screening of vaccine candidates are needed. A Mycobacterium marinum infection in adult zebrafish resembles human TB. Here, we present a pre-clinical screen for a DNA-based tuberculosis vaccine in the adult zebrafish using an M. marinum infection model. We tested 15 antigens representing different types of mycobacterial proteins, including the Resuscitation Promoting factors (Rpf), PE/PPE protein family members, other membrane proteins and metabolic enzymes. The antigens were expressed as GFP fusion proteins, facilitating the validation of their expression in vivo. The efficiency of the antigens was tested against a low-dose intraperitoneal M. marinum infection (≈ 40 colony forming units), which mimics a primary M. tuberculosis infection. While none of the antigens was able to completely prevent a mycobacterial infection, four of them, namely RpfE, PE5_1, PE31 and cdh, led to significantly reduced bacterial burdens at four weeks post infection. Immunization with RpfE also improved the survival of the fish against a high-dose intraperitoneal injection with M. marinum (≈ 10.000 colony forming units), resembling the disseminated form of the disease. This study shows that the M. marinum infection model in adult zebrafish is suitable for the pre-clinical screening of tuberculosis vaccines and presents RpfE as a potential antigen candidate for further studies.
Collapse
Affiliation(s)
- Henna Myllymäki
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- * E-mail:
| | - Mirja Niskanen
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Kaisa Ester Oksanen
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Eleanor Sherwood
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Maarit Ahava
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mataleena Parikka
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Oral and Maxillofacial Unit, Tampere University Hospital, Tampere, Finland
| | - Mika Rämet
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| |
Collapse
|
31
|
Touchette MH, Van Vlack ER, Bai L, Kim J, Cognetta AB, Previti ML, Backus KM, Martin DW, Cravatt BF, Seeliger JC. A Screen for Protein-Protein Interactions in Live Mycobacteria Reveals a Functional Link between the Virulence-Associated Lipid Transporter LprG and the Mycolyltransferase Antigen 85A. ACS Infect Dis 2017; 3:336-348. [PMID: 28276676 DOI: 10.1021/acsinfecdis.6b00179] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Outer membrane lipids in pathogenic mycobacteria are important for virulence and survival. Although the biosynthesis of these lipids has been extensively studied, mechanisms responsible for their assembly in the outer membrane are not understood. In the study of Gram-negative outer membrane assembly, protein-protein interactions define transport mechanisms, but analogous interactions have not been explored in mycobacteria. Here we identified interactions with the lipid transport protein LprG. Using site-specific photo-cross-linking in live mycobacteria, we mapped three major interaction interfaces within LprG. We went on to identify proteins that cross-link at the entrance to the lipid binding pocket, an area likely relevant to LprG transport function. We verified LprG site-specific interactions with two hits, the conserved lipoproteins LppK and LppI. We further showed that LprG interacts physically and functionally with the mycolyltransferase Ag85A, as loss of either protein leads to similar defects in cell growth and mycolylation. Overall, our results support a model in which protein interactions coordinate multiple pathways in outer membrane biogenesis and connect lipid biosynthesis to transport.
Collapse
Affiliation(s)
- Megan H. Touchette
- Department of Pharmacological Sciences, Stony Brook University, Stony
Brook, New York 11794, United States
| | - Erik R. Van Vlack
- Department of Chemistry, Stony Brook University, Stony
Brook, New York 11790, United States
| | - Lu Bai
- Department of Chemistry, Stony Brook University, Stony
Brook, New York 11790, United States
| | - Jia Kim
- Department of Pharmacological Sciences, Stony Brook University, Stony
Brook, New York 11794, United States
| | - Armand B. Cognetta
- Department of Chemical Physiology, The
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony
Brook, New York 11794, United States
| | - Keriann M. Backus
- Department of Chemical Physiology, The
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - Dwight W. Martin
- Department of Medicine, Stony Brook University, Stony
Brook, New York 11794, United States
- Proteomics Center, Stony Brook University, Stony
Brook, New York 11794, United States
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony
Brook, New York 11794, United States
| |
Collapse
|
32
|
Elghraoui A, Modlin SJ, Valafar F. SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics 2017; 18:302. [PMID: 28415976 PMCID: PMC5393005 DOI: 10.1186/s12864-017-3687-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. Further, one of the sequencing errors in H37Ra masks a true variant in common with the clinical strain CDC1551 which, when considered in the context of previous work, corresponds to a sequencing error in the H37Rv reference genome. CONCLUSIONS Our results constrain the set of genomic differences possibly affecting virulence by more than half, which focuses laboratory investigation on pertinent targets and demonstrates the power of SMRT sequencing for producing high-quality reference genomes.
Collapse
Affiliation(s)
- Afif Elghraoui
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Samuel J Modlin
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Faramarz Valafar
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA.
| |
Collapse
|
33
|
Bespyatykh JA, Shitikov EA, Ilina EN. Proteomics for the Investigation of Mycobacteria. Acta Naturae 2017; 9:15-25. [PMID: 28461970 PMCID: PMC5406656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 10/25/2022] Open
Abstract
The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
Collapse
Affiliation(s)
- J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| |
Collapse
|
34
|
Biological and Epidemiological Consequences of MTBC Diversity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:95-116. [PMID: 29116631 DOI: 10.1007/978-3-319-64371-7_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis is caused by different groups of bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). The combined action of human factors, environmental conditions and bacterial virulence determine the extent and form of human disease. MTBC virulence is a composite of different clinical phenotypes such as transmission rate and disease severity among others. Clinical phenotypes are also influenced by cellular and immunological phenotypes. MTBC phenotypes are determined by the genotype, therefore finding genotypes responsible for clinical phenotypes would allow discovering MTBC virulence factors. Different MTBC strains display different cellular and clinical phenotypes. Strains from Lineage 5 and Lineage 6 are metabolically different, grow slower, and are less virulent. Also, at least certain groups of Lineage 2 and Lineage 4 strains are more virulent in terms of disease severity and human-to-human transmission. Because phenotypic differences are ultimately caused by genotypic differences, different genomic loci have been related to various cellular and clinical phenotypes. However, defining the impact of specific bacterial genomic loci on virulence when other bacterial determinants, human and environmental factors are also impacting the phenotype would contribute to a better knowledge of tuberculosis virulence and ultimately benefit tuberculosis control.
Collapse
|
35
|
Muniyan R, Gurunathan J. Lauric acid and myristic acid from Allium sativum inhibit the growth of Mycobacterium tuberculosis H37Ra: in silico analysis reveals possible binding to protein kinase B. PHARMACEUTICAL BIOLOGY 2016; 54:2814-2821. [PMID: 27307092 DOI: 10.1080/13880209.2016.1184691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 01/21/2016] [Accepted: 04/27/2016] [Indexed: 06/06/2023]
Abstract
CONTEXT The bulb of Allium sativum Linn (Alliaceae) has numerous medicinal values. Though the petroleum ether extract of the bulb has shown to exhibit antimycobacterial activity, the phytochemical(s) responsible for this inhibitory activity is not known. OBJECTIVE To characterize the bioactive compounds in the petroleum ether extract of Allium sativum (garlic) that inhibit the growth of Mycobacterium tuberculosis H37Ra. MATERIALS AND METHODS Bioactivity-guided fractionation was employed to isolate the bioactive compounds. Antimycobacterial activity was evaluated by well-diffusion method and microplate alamar blue assay (MABA). Infrared spectroscopy, mass spectrometry and nuclear magnetic resonance spectroscopy were used to characterize the bioactive compounds. Autodock was used to obtain information on molecular recognition, and molecular dynamics simulation was performed using GROMACS. RESULTS The bioactive compounds that inhibited the growth of M. tuberculosis H37Ra were found to be lauric acid (LA) and myristic acid (MA). The minimal inhibitory concentration of LA and MA was found to be 22.2 and 66.7 μg/mL, respectively. In silico analysis revealed that these fatty acids could bind at the cleft between the N-terminal and C-terminal lobes of the cytosolic domain of serine/threonine protein kinase B (PknB). DISCUSSION AND CONCLUSION The inhibition activity was dependent on the alkyl chain length of the fatty acid, and the amino acid residues involved in binding to fatty acid was found to be conserved across the Pkn family of proteins. The study indicates the possibility of using fatty acid derivatives, involving Pkn family of proteins, to inhibit the signal transduction processes in M. tuberculosis.
Collapse
Affiliation(s)
- Rajiniraja Muniyan
- a School of Bio Sciences and Technology, VIT University , Vellore , Tamil Nadu , India
| | - Jayaraman Gurunathan
- a School of Bio Sciences and Technology, VIT University , Vellore , Tamil Nadu , India
| |
Collapse
|
36
|
Proteomic analysis of drug-resistant Mycobacterium tuberculosis by one-dimensional gel electrophoresis and charge chromatography. Arch Microbiol 2016; 199:9-15. [PMID: 27417316 DOI: 10.1007/s00203-016-1267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/03/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a form of TB caused by Mycobacterium tuberculosis (M. tuberculosis) that do not respond to, at least, isoniazid and rifampicin, the two most powerful, first-line (or standard) anti-TB drugs. Novel intervention strategies for eliminating this disease were based on finding proteins that can be used for designing new drugs or new and reliable kits for diagnosis. The aim of this study was to compare the protein profiles of MDR-TB with sensitive isolates. Proteomic analysis of M. tuberculosis MDR-TB and sensitive isolates was obtained with ion exchange chromatography coupled with MALDI-TOF-TOF (matrix-assisted laser desorption/ionization) in order to identify individual proteins that have different expression in MDR-TB to be used as a drug target or diagnostic marker for designing valuable TB vaccines or TB rapid tests. We identified eight proteins in MDR-TB isolates, and analyses showed that these proteins are absent in M. tuberculosis-sensitive isolates: (Rv2140c, Rv0009, Rv1932, Rv0251c, Rv2558, Rv1284, Rv3699 and MMP major membrane proteins). These data will provide valuable clues in further investigation for suitable TB rapid tests or drug targets against drug-resistant and sensitive M. tuberculosis isolates.
Collapse
|
37
|
Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V. Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 2016; 6:28985. [PMID: 27356881 PMCID: PMC4928086 DOI: 10.1038/srep28985] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022] Open
Abstract
Beijing B0/W148, a "successful" clone of Mycobacterium tuberculosis, is widespread in the Russian Federation and some countries of the former Soviet Union. Here, we used label-free gel-LC-MS/MS shotgun proteomics to discover features of Beijing B0/W148 strains that could explain their success. Qualitative and quantitative proteome analyses of Beijing B0/W148 strains allowed us to identify 1,868 proteins, including 266 that were differentially abundant compared with the control strain H37Rv. To predict the biological effects of the observed differences in protein abundances, we performed Gene Ontology analysis together with analysis of protein-DNA interactions using a gene regulatory network. Our results demonstrate that Beijing B0/W148 strains have increased levels of enzymes responsible for long-chain fatty acid biosynthesis, along with a coincident decrease in the abundance of proteins responsible for their degradation. Together with high levels of HsaA (Rv3570c) protein, involved in steroid degradation, these findings provide a possible explanation for the increased transmissibility of Beijing B0/W148 strains and their survival in host macrophages. Among other, we confirmed a very low level of the SseA (Rv3283) protein in Beijing B0/W148 characteristic for all «modern» Beijing strains, which could lead to increased DNA oxidative damage, accumulation of mutations, and potentially facilitate the development of drug resistance.
Collapse
Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Ilya Altukhov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitry Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | | | - Peter Yablonsky
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| |
Collapse
|
38
|
Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KVS, Kumar D, Nandicoori VK. Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns. J Biol Chem 2016; 291:14257-14273. [PMID: 27151218 PMCID: PMC4933181 DOI: 10.1074/jbc.m115.666123] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as well as active disease-causing states. Here, we report systematic proteomic analyses of four strains, H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and drug resistance. Resolution of lysates of the four strains by liquid chromatography, coupled to mass spectrometry analysis, identified a total of 2161 protein groups covering ∼54% of the predicted M. tuberculosis proteome. Label-free quantification analysis of the data revealed 257 differentially expressed protein groups. The differentially expressed protein groups could be classified into seven K-means cluster bins, which broadly delineated strain-specific variations. Analysis of the data for possible mechanisms responsible for drug resistance phenotype of JAL suggested that it could be due to a combination of overexpression of proteins implicated in drug resistance and the other factors. Expression pattern analyses of transcription factors and their downstream targets demonstrated substantial differential modulation in JAL, suggesting a complex regulatory mechanism. Results showed distinct variations in the protein expression patterns of Esx and mce1 operon proteins in JAL and BND strains, respectively. Abrogating higher levels of ESAT6, an important Esx protein known to be critical for virulence, in the JAL strain diminished its virulence, although it had marginal impact on the other strains. Taken together, this study reveals that strain-specific variations in protein expression patterns have a meaningful impact on the biology of the pathogen.
Collapse
Affiliation(s)
- Gagan Deep Jhingan
- National Institute of Immunology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Sangeeta Kumari
- National Institute of Immunology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Shilpa V Jamwal
- Drug Discovery Research Center, Translational Health Science and Technology Institute, Faridabad, Haryana 121004
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Divya Arora
- National Institute of Immunology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Neharika Jain
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | | | - Areejit Samal
- Institute of Mathematical Sciences, Chennai 600113, India
| | - Kanury V S Rao
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067
| | - Vinay Kumar Nandicoori
- National Institute of Immunology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067.
| |
Collapse
|
39
|
Vemula MH, Ganji R, Sivangala R, Jakkala K, Gaddam S, Penmetsa S, Banerjee S. Mycobacterium tuberculosis Zinc Metalloprotease-1 Elicits Tuberculosis-Specific Humoral Immune Response Independent of Mycobacterial Load in Pulmonary and Extra-Pulmonary Tuberculosis Patients. Front Microbiol 2016; 7:418. [PMID: 27065979 PMCID: PMC4814508 DOI: 10.3389/fmicb.2016.00418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/15/2016] [Indexed: 11/20/2022] Open
Abstract
Conventionally, facultative intracellular pathogen, Mycobacterium tuberculosis, the tuberculosis (TB) causing bacilli in human is cleared by cell-mediated immunity (CMI) with CD4+ T cells playing instrumental role in protective immunity, while antibody-mediated immunity (AMI) is considered non-protective. This longstanding convention has been challenged with recent evidences of increased susceptibility of hosts with compromised AMI and monoclonal antibodies conferring passive protection against TB and other intracellular pathogens. Therefore, novel approaches toward vaccine development include strategies aiming at induction of humoral response along with CMI. This necessitates the identification of mycobacterial proteins with properties of immunomodulation and strong immunogenicity. In this study, we determined the immunogenic potential of M. tuberculosis Zinc metalloprotease-1 (Zmp1), a secretory protein essential for intracellular survival and pathogenesis of M. tuberculosis. We observed that Zmp1 was secreted by in vitro grown M. tuberculosis under granuloma-like stress conditions (acidic, oxidative, iron deficiency, and nutrient deprivation) and generated Th2 cytokine microenvironment upon exogenous treatment of peripheral blood mononulear cells PBMCs with recombinant Zmp1 (rZmp1). This was supported by recording specific and robust humoral response in TB patients in a cohort of 295. The anti-Zmp1 titers were significantly higher in TB patients (n = 121) as against healthy control (n = 62), household contacts (n = 89) and non-specific infection controls (n = 23). A significant observation of the study is the presence of equally high titers of anti-Zmp1 antibodies in a range of patients with high bacilli load (sputum bacilli load of 300+ per mL) to paucibacillary smear-negative pulmonary tuberculosis (PTB) cases. This clearly indicated the potential of Zmp1 to evoke an effective humoral response independent of mycobacterial load. Such mycobacterial proteins can be explored as antigen candidates for prime-boost vaccination strategies or extrapolated as markers for disease detection and progression.
Collapse
Affiliation(s)
- Mani H Vemula
- Department of Biochemistry, School of Life Sciences, University of Hyderabad Hyderabad, India
| | - Rakesh Ganji
- Department of Biochemistry, School of Life Sciences, University of Hyderabad Hyderabad, India
| | - Ramya Sivangala
- Department of Immunology, Bhagwan Mahavir Medical Research Center Hyderabad, India
| | - Kiran Jakkala
- Department of Biochemistry, School of Life Sciences, University of Hyderabad Hyderabad, India
| | - Sumanlatha Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research CenterHyderabad, India; Department of Genetics, Osmania UniversityHyderabad, India
| | | | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad Hyderabad, India
| |
Collapse
|
40
|
Sharma D, Kumar B, Lata M, Joshi B, Venkatesan K, Shukla S, Bisht D. Comparative Proteomic Analysis of Aminoglycosides Resistant and Susceptible Mycobacterium tuberculosis Clinical Isolates for Exploring Potential Drug Targets. PLoS One 2015; 10:e0139414. [PMID: 26436944 PMCID: PMC4593609 DOI: 10.1371/journal.pone.0139414] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
Aminoglycosides, amikacin (AK) and kanamycin (KM) are second line anti-tuberculosis drugs used to treat tuberculosis (TB) and resistance to them affects the treatment. Membrane and membrane associated proteins have an anticipated role in biological processes and pathogenesis and are potential targets for the development of new diagnostics/vaccine/therapeutics. In this study we compared membrane and membrane associated proteins of AK and KM resistant and susceptible Mycobacterium tuberculosis isolates by 2DE coupled with MALDI-TOF/TOF-MS and bioinformatic tools. Twelve proteins were found to have increased intensities (PDQuest Advanced Software) in resistant isolates and were identified as ATP synthase subunit alpha (Rv1308), Trigger factor (Rv2462c), Dihydrolipoyl dehydrogenase (Rv0462), Elongation factor Tu (Rv0685), Transcriptional regulator MoxR1(Rv1479), Universal stress protein (Rv2005c), 35kDa hypothetical protein (Rv2744c), Proteasome subunit alpha (Rv2109c), Putative short-chain type dehydrogenase/reductase (Rv0148), Bacterioferritin (Rv1876), Ferritin (Rv3841) and Alpha-crystallin/HspX (Rv2031c). Among these Rv2005c, Rv2744c and Rv0148 are proteins with unknown functions. Docking showed that both drugs bind to the conserved domain (Usp, PspA and SDR domain) of these hypothetical proteins and GPS-PUP predicted potential pupylation sites within them. Increased intensities of these proteins and proteasome subunit alpha might not only be neutralized/modulated the drug molecules but also involved in protein turnover to overcome the AK and KM resistance. Besides that Rv1876, Rv3841 and Rv0685 were found to be associated with iron regulation signifying the role of iron in resistance. Further research is needed to explore how these potential protein targets contribute to resistance of AK and KM.
Collapse
MESH Headings
- Amikacin/pharmacology
- Amino Acid Motifs
- Anti-Bacterial Agents/pharmacology
- Antitubercular Agents/pharmacology
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Bacterial Proteins/physiology
- Cell Membrane/metabolism
- Conserved Sequence
- Drug Delivery Systems
- Drug Resistance, Microbial/genetics
- Drug Resistance, Microbial/physiology
- Electrophoresis, Gel, Two-Dimensional
- Humans
- Iron/physiology
- Kanamycin/pharmacology
- Kanamycin Resistance/genetics
- Kanamycin Resistance/physiology
- Membrane Proteins/genetics
- Membrane Proteins/physiology
- Models, Molecular
- Molecular Docking Simulation
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Protein Conformation
- Protein Processing, Post-Translational
- Protein Structure, Tertiary
- Proteomics
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
- Tuberculosis/microbiology
- Ubiquitins/metabolism
Collapse
Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Bhavnesh Kumar
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Beenu Joshi
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Sangeeta Shukla
- School of Studies in Zoology, Jiwaji University, Gwalior, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
- * E-mail:
| |
Collapse
|
41
|
Calder B, Soares NC, de Kock E, Blackburn JM. Mycobacterial proteomics: analysis of expressed proteomes and post-translational modifications to identify candidate virulence factors. Expert Rev Proteomics 2015; 12:21-35. [PMID: 25603863 DOI: 10.1586/14789450.2015.1007046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Mycobacterium tuberculosis bacillus has a number of unique features that make it a particularly effective human pathogen. Although genomic analysis has added to our current understanding of the molecular basis by which M. tuberculosis damages its host, proteomics may be better suited to describe the dynamic interactions between mycobacterial and host systems that underpin this disease. The M. tuberculosis proteome has been investigated using proteomics for over a decade, with increasingly sophisticated mass spectrometry technology and sensitive methods for comparative proteomic profiling. Deeper coverage of the M. tuberculosis proteome has led to the identification of hundreds of putative virulence determinants, as well as an unsurpassed coverage of post-translational modifications. Proteomics is therefore uniquely poised to contribute to our understanding of this pathogen, which may ultimately lead to better management of the disease.
Collapse
Affiliation(s)
- Bridget Calder
- Division of Medical Biochemistry, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Rd, Observatory, Cape Town 7925, South Africa
| | | | | | | |
Collapse
|
42
|
Patil S, Giribhattanavar P, Patil M, Kumar K. Immunoconfirmation of central nervous system tuberculosis by blotting: A study of 300 cases. Int J Mycobacteriol 2015; 4:124-30. [DOI: 10.1016/j.ijmyco.2015.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 11/25/2022] Open
|
43
|
Fishbein S, van Wyk N, Warren RM, Sampson SL. Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. Mol Microbiol 2015; 96:901-16. [PMID: 25727695 DOI: 10.1111/mmi.12981] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 01/08/2023]
Abstract
The pe/ppe genes represent one of the most intriguing aspects of the Mycobacterium tuberculosis genome. These genes are especially abundant in pathogenic mycobacteria, with more than 160 members in M. tuberculosis. Despite being discovered over 15 years ago, their function remains unclear, although various lines of evidence implicate selected family members in mycobacterial virulence. In this review, we use PE/PPE phylogeny as a framework within which we examine the diversity and putative functions of these proteins. We report on the evolution and diversity of the respective gene families, as well as the implications thereof for function and host immune recognition. We summarize recent findings on pe/ppe gene regulation, also placing this in the context of PE/PPE phylogeny. We collate data from several large proteomics datasets, providing an overview of PE/PPE localization, and discuss the implications this may have for host responses. Assessment of the current knowledge of PE/PPE diversity suggests that these proteins are not variable antigens as has been so widely speculated; however, they do clearly play important roles in virulence. Viewing the growing body of pe/ppe literature through the lens of phylogeny reveals trends in features and function that may be associated with the evolution of mycobacterial pathogenicity.
Collapse
Affiliation(s)
- S Fishbein
- Harvard School of Public Health, Boston, MA, USA.,DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - N van Wyk
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - R M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| | - S L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, South Africa
| |
Collapse
|
44
|
Feltcher ME, Gunawardena HP, Zulauf KE, Malik S, Griffin JE, Sassetti CM, Chen X, Braunstein M. Label-free Quantitative Proteomics Reveals a Role for the Mycobacterium tuberculosis SecA2 Pathway in Exporting Solute Binding Proteins and Mce Transporters to the Cell Wall. Mol Cell Proteomics 2015; 14:1501-16. [PMID: 25813378 DOI: 10.1074/mcp.m114.044685] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 01/18/2023] Open
Abstract
Mycobacterium tuberculosis is an example of a bacterial pathogen with a specialized SecA2-dependent protein export system that contributes to its virulence. Our understanding of the mechanistic basis of SecA2-dependent export and the role(s) of the SecA2 pathway in M. tuberculosis pathogenesis has been hindered by our limited knowledge of the proteins exported by the pathway. Here, we set out to identify M. tuberculosis proteins that use the SecA2 pathway for their export from the bacterial cytoplasm to the cell wall. Using label-free quantitative proteomics involving spectral counting, we compared the cell wall and cytoplasmic proteomes of wild type M. tuberculosis to that of a ΔsecA2 mutant. This work revealed a role for the M. tuberculosis SecA2 pathway in the cell wall localization of solute binding proteins that work with ABC transporters to import solutes. Another discovery was a profound effect of SecA2 on the cell wall localization of the Mce1 and Mce4 lipid transporters, which contribute to M. tuberculosis virulence. In addition to the effects on solute binding proteins and Mce transporter export, our label-free quantitative analysis revealed an unexpected relationship between SecA2 and the hypoxia-induced DosR regulon, which is associated with M. tuberculosis latency. Nearly half of the transcriptionally controlled DosR regulon of cytoplasmic proteins were detected at higher levels in the ΔsecA2 mutant versus wild type M. tuberculosis. By increasing the list of M. tuberculosis proteins known to be affected by the SecA2 pathway, this study expands our appreciation of the types of proteins exported by this pathway and guides our understanding of the mechanism of SecA2-dependent protein export in mycobacteria. At the same time, the newly identified SecA2-dependent proteins are helpful for understanding the significance of this pathway to M. tuberculosis virulence and physiology.
Collapse
Affiliation(s)
| | - Harsha P Gunawardena
- §Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina, 27599
| | | | - Seidu Malik
- From the ‡Department of Microbiology and Immunology
| | - Jennifer E Griffin
- ¶Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Christopher M Sassetti
- ¶Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655; ‖Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815
| | - Xian Chen
- §Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina, 27599;
| | | |
Collapse
|
45
|
Toll-like receptor 2-dependent extracellular signal-regulated kinase signaling in Mycobacterium tuberculosis-infected macrophages drives anti-inflammatory responses and inhibits Th1 polarization of responding T cells. Infect Immun 2015; 83:2242-54. [PMID: 25776754 DOI: 10.1128/iai.00135-15] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/12/2015] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis survives within macrophages and employs immune evasion mechanisms to persist in the host. Protective T helper type 1 (Th1) responses are induced, and the immune response in most individuals is sufficient to restrict M. tuberculosis to latent infection, but most infections are not completely resolved. As T cells and macrophages respond, a balance is established between protective Th1-associated and other proinflammatory cytokines, such as interleukin-12 (IL-12), interferon gamma (IFN-γ), and tumor necrosis factor alpha, and anti-inflammatory cytokines, such as IL-10. The mechanisms by which M. tuberculosis modulates host responses to promote its survival remain unclear. In these studies, we demonstrate that M. tuberculosis induction of IL-10, suppression of IL-12, and inhibition of class II major histocompatibility complex (MHC-II) molecules in infected macrophages are all driven by Toll-like receptor 2 (TLR2)-dependent activation of the extracellular signal-regulated kinases (ERK). Elimination of ERK signaling downstream of TLR2 by pharmacologic inhibition with U0126 or genetic deletion of Tpl2 blocks IL-10 secretion and enhances IL-12 p70 secretion. We demonstrate that M. tuberculosis regulation of these pathways in macrophages affects T cell responses to infected macrophages. Thus, genetic blockade of the ERK pathway in Tpl2(-/-) macrophages enhances Th1 polarization and IFN-γ production by antigen-specific CD4(+) T cells responding to M. tuberculosis infection. These data indicate that M. tuberculosis and its potent TLR2 ligands activate ERK signaling in macrophages to promote anti-inflammatory macrophage responses and blunt Th1 responses against the pathogen.
Collapse
|
46
|
Phong TQ, Ha DTT, Volker U, Hammer E. Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis. Indian J Microbiol 2015; 55:219-30. [PMID: 25805910 DOI: 10.1007/s12088-015-0511-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/09/2015] [Indexed: 12/21/2022] Open
Abstract
Reports in recent years indicate that the increasing emergence of resistance to drugs be using to TB treatment. The resistance to them severely affects to options for effective treatment. The emergence of multidrug-resistant tuberculosis has increased interest in understanding the mechanism of drug resistance in M. tuberculosis and the development of new therapeutics, diagnostics and vaccines. In this study, a label-free quantitative proteomics approach has been used to analyze proteome of multidrug-resistant and susceptible clinical isolates of M. tuberculosis and identify differences in protein abundance between the two groups. With this approach, we were able to identify a total of 1,583 proteins. The majority of identified proteins have predicted roles in lipid metabolism, intermediary metabolism, cell wall and cell processes. Comparative analysis revealed that 68 proteins identified by at least two peptides showed significant differences of at least twofolds in relative abundance between two groups. In all protein differences, the increase of some considering proteins such as NADH dehydrogenase, probable aldehyde dehydrogenase, cyclopropane mycolic acid synthase 3, probable arabinosyltransferase A, putative lipoprotein, uncharacterized oxidoreductase and six membrane proteins in resistant isolates might be involved in the drug resistance and to be potential diagnostic protein targets. The decrease in abundance of proteins related to secretion system and immunogenicity (ESAT-6-like proteins, ESX-1 secretion system associated proteins, O-antigen export system and MPT63) in the multidrug-resistant strains can be a defensive mechanism undertaken by the resistant cell.
Collapse
Affiliation(s)
- Truong Quoc Phong
- Center for Research and Development in Biotechnology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Do Thi Thu Ha
- Center for Research and Development in Biotechnology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Uwe Volker
- Interfaculty Institute for Genetic and Functional Genomic, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetic and Functional Genomic, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
47
|
Schubert OT, Aebersold R. Microbial Proteome Profiling and Systems Biology: Applications to Mycobacterium tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:235-54. [PMID: 26621471 DOI: 10.1007/978-3-319-23603-2_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Each year, 1.3 million people die from tuberculosis, an infectious disease caused by Mycobacterium tuberculosis. Systems biology-based strategies might significantly contribute to the knowledge-guided development of more effective vaccines and drugs to prevent and cure infectious diseases. To build models simulating the behaviour of a system in response to internal or external stimuli and to identify potential targets for therapeutic intervention, systems biology approaches require the acquisition of quantitative molecular profiles on many perturbed states. Here we review the current state of proteomic analyses in Mycobacterium tuberculosis and discuss the potential of recently emerging targeting mass spectrometry-based techniques which enable fast, sensitive and accurate protein measurements.
Collapse
Affiliation(s)
- Olga T Schubert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, CH-8093, Switzerland.
- Systems Biology Graduate School, Zurich, CH-8057, Switzerland.
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, CH-8093, Switzerland.
- Faculty of Science, University of Zurich, Zurich, CH-8057, Switzerland.
| |
Collapse
|
48
|
Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
Collapse
Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
| | | | | |
Collapse
|
49
|
Rees MA, Kleifeld O, Crellin PK, Ho B, Stinear TP, Smith AI, Coppel RL. Proteomic Characterization of a Natural Host–Pathogen Interaction: Repertoire of in Vivo Expressed Bacterial and Host Surface-Associated Proteins. J Proteome Res 2014; 14:120-32. [DOI: 10.1021/pr5010086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Timothy P. Stinear
- Department
of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | |
Collapse
|
50
|
Comparative proteomic analysis of Mycobacterium tuberculosis strain H37Rv versus H37Ra. Int J Mycobacteriol 2013; 2:220-6. [PMID: 26786126 DOI: 10.1016/j.ijmyco.2013.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) H37Ra is an attenuated tubercle bacillus closely related to the virulent type strain MTB H37Rv. In spite of extensive study, variation in virulence between the MTB H37Rv and MTB H37Ra strains is still to be understood. The difference in protein expression or structure due to mutation may probably be an important factor for the virulence property of MTB H37Rv strain. METHODS In this study, a whole proteome comparison between these two strains was carried out using bioinformatics approaches to elucidate differences in their protein sequences. RESULTS On comparison of whole proteome using NCBI standalone BLAST program between these two strains, 3759 identical proteins in both the strains out of 4003 proteins were revealed in MTB H37Rv and 4034 proteins were revealed in MTB H37Ra; 244 proteins of MTB H37Rv and 260 proteins of MTB H37Ra were found to be non-identical. A total of 172 proteins were identified with mutations (Insertions/deletions/substitutions) in MTB H37Ra while 53 proteins of MTB H37Rv and 85 proteins of MTB H37Ra were found to be distinct. Among 244 non-identical proteins, 19 proteins were reported to have an important biological function; In this study, mutation was shown in these proteins of MTB H37Ra. CONCLUSION This study reports the protein differences with mutations between MTB H37Rv and H37Ra, which may help in better understanding the pathogenesis and virulence properties of MTB H37Rv.
Collapse
|