1
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Chugh S, Bahal RK, Dhiman R, Singh R. Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development. NPJ Vaccines 2024; 9:57. [PMID: 38461350 PMCID: PMC10924964 DOI: 10.1038/s41541-024-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024] Open
Abstract
In its myriad devastating forms, Tuberculosis (TB) has existed for centuries, and humanity is still affected by it. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of TB, was the foremost killer among infectious agents until the COVID-19 pandemic. One of the key healthcare strategies available to reduce the risk of TB is immunization with bacilli Calmette-Guerin (BCG). Although BCG has been widely used to protect against TB, reports show that BCG confers highly variable efficacy (0-80%) against adult pulmonary TB. Unwavering efforts have been made over the past 20 years to develop and evaluate new TB vaccine candidates. The failure of conventional preclinical animal models to fully recapitulate human response to TB, as also seen for the failure of MVA85A in clinical trials, signifies the need to develop better preclinical models for TB vaccine evaluation. In the present review article, we outline various approaches used to identify protective mycobacterial antigens and recent advancements in preclinical models for assessing the efficacy of candidate TB vaccines.
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Affiliation(s)
- Saurabh Chugh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
| | - Ritika Kar Bahal
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Ramandeep Singh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India.
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2
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Kotimoole C, Antil N, Kasaragod S, Behera S, Arvind A, Reiling N, Flo T, Prasad T. Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis. Mol Cell Proteomics 2023; 22:100533. [PMID: 36948415 PMCID: PMC10149365 DOI: 10.1016/j.mcpro.2023.100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Mycobacterium avium is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. M. avium has ∼4,500 predicted protein-coding regions on average, which can help discover several variants at the proteome level. Many of them are potentially associated with virulence; thus, identifying such proteins can be a helpful feature in developing panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of M. avium with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using i) a protein database for Mycobacterium tuberculosis, ii) a M. avium genome six-frame translated database, and iii) a variant protein database of M. avium. A search of mass spectrometry data against M. avium protein database resulted in identifying 2,954 proteins. Further, proteogenomic analyses aided in identifying 1,301 novel peptide sequences and correcting translation start sites for 15 proteins. Ultimately, we created a spectral library of M. avium proteins, including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the M. avium proteome. Thus, we present an M. avium spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.
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Affiliation(s)
- ChinmayaNarayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Neelam Antil
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - SantoshKumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Anjana Arvind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany; German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - TrudeHelen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, 424.04.035, Øya, Norway
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3
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Barreiro C, Ibáñez AM. Bidimensional Analyses of the Intra- and Extracellular Proteomes of Steroid Producer Mycobacteria. Methods Mol Biol 2023; 2704:115-141. [PMID: 37642841 DOI: 10.1007/978-1-0716-3385-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. However, those industrially relevant mycobacteria have received less attention, even though the steroid market sales in 2021 were estimated in $56.45 billion.The extracellular proteome, due to its relevance in the sterol processing and uptake, and the intracellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. Both, monodimensional gels, as preparatory analysis, and bidimensional gels as proteome analysis are described. As a proof of concept, the protein extraction methods for both sub-proteomes of Mycobacterium are described. Thus, procedures and relevant key points of these proteome analyses are fully detailed.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain.
| | - Ana M Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, León, Spain
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, Valladolid, Spain
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4
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M.tb-Rv2462c of Mycobacterium tuberculosis Shows Chaperone-like Activity and Plays a Role in Stress Adaptation and Immunomodulation. BIOLOGY 2022; 12:biology12010069. [PMID: 36671761 PMCID: PMC9855790 DOI: 10.3390/biology12010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Mycobacterium tuberculosis (M.tb)-encoded factors protect it against host-generated stresses and support its survival in the hostile host environment. M.tb possesses two peptidyl-prolyl cis-trans isomerases and a probable trigger factor encoded by Rv2462c which has an FKBP-like PPIase domain. PPIases are known to assist the folding of peptidyl-prolyl bonds and are involved in various cellular processes important for bacterial survival in host-generated stresses. In this study, we aim to functionally characterize Rv2462c of M.tb. Our data suggest that the trigger factor of M.tb exhibits chaperone activity both in vitro and in vivo. Heterologous expression of M.tb-Rv2462c locus into Mycobacterium smegmatis enhanced its survival within macrophages, adaptation to oxidative stress and biofilm formation. M.tb-trigger factor has strong immunomodulatory potential and modifies the cytokine profile of the host towards the proinflammatory axis.
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5
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Klein BY, Greenblatt CL, Gofrit ON, Bercovier H. Bacillus Calmette–Guérin in Immuno-Regulation of Alzheimer’s Disease. Front Aging Neurosci 2022; 14:861956. [PMID: 35832066 PMCID: PMC9271739 DOI: 10.3389/fnagi.2022.861956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Bacillus Calmette–Guérin is frequently the treatment of choice of superficial bladder cancer. Exposing the urinary bladder of elderly patients with bladder cancer to the BCG vaccine reduced the risk of Alzheimer’s disease (AD) substantially. Vaccines against other infectious microorganisms by other vaccination methods showed a similar but a lesser effect. This suggests that immune effects on AD are antigenically non-specific, likely being a metabolic result of immune system activation, similar to that shown for Juvenile diabetes. In this mini review we point to the benefit of BCG vaccine. We then briefly highlight the pathological involvement of the immune system in the AD both, in the peripheral and the central (brain) compartments. Given the uncertain prophylactic mechanism of the BCG effect against AD we propose to take advantage of the therapeutically planned bladder exposure to BCG. Based on pathological aggregation of wrongly cleaved amyloid precursor protein (APP) resistant to the unfolded protein response (UPR) which results in amyloid beta plaques we predict that BCG may impact the UPR signaling cascade. In addition pathways of innate immunity training concerned with energy metabolism, predict capability of activated immune cells to substitute deranged astrocytes that fail to support neuronal energy metabolism. This mini review points to ways through which immune cells can mediate between BCG vaccination and AD to support the wellness of the central nervous system.
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Affiliation(s)
- Benjamin Y. Klein
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Benjamin Y. Klein,
| | - Charles L. Greenblatt
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofer N. Gofrit
- Department of Urology, Hadassah Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hervé Bercovier
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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6
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López Medrano R, Burgos Asurmendi I, Rivero Lezcano OM. A rapid proteomic system (MALDI-TOF) for nontuberculous-mycobacteria identification. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:385-387. [PMID: 35537995 DOI: 10.1016/j.eimce.2022.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Proteomic techniques relaying upon mass spectrometry (MALDI_TOF) applied to nontuberculous mycobacteria (NTM) identification, constitute a difficult goal. Cell wall structure features complicates the protein extraction procedure. A total of 106 isolates belonging to a variety of MNTs species isolated from clinical samples taken at the Complejo Asistencial Universitario de León for a two years period (2019-20) were identified following a simplified method (MALDI-TOF Biotyper Bruker®) developped in our laboratory. The resultant identification was compared to a parallel one ruled on the Centro de Referencia de Majadahonda. A total of 22different MNTs species were tested, obtaining an agreement of 92,45%. Only 8 minor discrepancies between species belonging to same taxonomic group of MNTs were detected. The score obtained in the 67.92% of the cases was higher than 1.8. A time-saving of 24min compared to the manufacturer's proceeding was achieved.
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Affiliation(s)
- Ramiro López Medrano
- Servicio de Microbiología, Complejo Asistencial Universitario de León, León, Spain.
| | - Isabel Burgos Asurmendi
- Servicio de Anestesiología y Reanimación, Complejo Asistencial Universitario de León, León, Spain
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7
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Weaver SD, Schuster-Little N, Whelan RJ. Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1103-1110. [PMID: 35175250 PMCID: PMC9210495 DOI: 10.1039/d1ay02145a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Reversed-phase liquid chromatography (RPLC) is widely used to reduce sample complexity prior to mass spectrometry (MS) analysis in bottom-up proteomics. Improving peptide separation in complex samples enables lower-abundance proteins to be identified. Multidimensional separations that combine orthogonal separation modes improve protein and peptide identifications over RPLC alone. Here we report a preparative capillary electrophoresis (CE) fractionation method that combines CE and RPLC separations. Using this method, we demonstrate improved protein and peptide identification in a tryptic digest of E. coli cell lysate, with 132 ± 33% more protein identifications and 185 ± 65% more peptide identifications over non-fractionated samples. Fractionation enables detection of lower-abundance proteins in this complex sample. We demonstrate improved coverage of ovarian cancer biomarker MUC16 isolated from conditioned cell media, with 6.73% sequence coverage using CE fractionation compared to 2.74% coverage without preparative fractionation. This new method will allow researchers performing bottom-up proteomics to harness the advantages of CE separations while using widely available LC-MS/MS instrumentation.
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Affiliation(s)
- Simon D Weaver
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
| | - Naviya Schuster-Little
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
| | - Rebecca J Whelan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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8
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Gong W, Wu X. Differential Diagnosis of Latent Tuberculosis Infection and Active Tuberculosis: A Key to a Successful Tuberculosis Control Strategy. Front Microbiol 2021; 12:745592. [PMID: 34745048 PMCID: PMC8570039 DOI: 10.3389/fmicb.2021.745592] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 12/16/2022] Open
Abstract
As an ancient infectious disease, tuberculosis (TB) is still the leading cause of death from a single infectious agent worldwide. Latent TB infection (LTBI) has been recognized as the largest source of new TB cases and is one of the biggest obstacles to achieving the aim of the End TB Strategy. The latest data indicate that a considerable percentage of the population with LTBI and the lack of differential diagnosis between LTBI and active TB (aTB) may be potential reasons for the high TB morbidity and mortality in countries with high TB burdens. The tuberculin skin test (TST) has been used to diagnose TB for > 100 years, but it fails to distinguish patients with LTBI from those with aTB and people who have received Bacillus Calmette–Guérin vaccination. To overcome the limitations of TST, several new skin tests and interferon-gamma release assays have been developed, such as the Diaskintest, C-Tb skin test, EC-Test, and T-cell spot of the TB assay, QuantiFERON-TB Gold In-Tube, QuantiFERON-TB Gold-Plus, LIAISON QuantiFERON-TB Gold Plus test, and LIOFeron TB/LTBI. However, these methods cannot distinguish LTBI from aTB. To investigate the reasons why all these methods cannot distinguish LTBI from aTB, we have explained the concept and definition of LTBI and expounded on the immunological mechanism of LTBI in this review. In addition, we have outlined the research status, future directions, and challenges of LTBI differential diagnosis, including novel biomarkers derived from Mycobacterium tuberculosis and hosts, new models and algorithms, omics technologies, and microbiota.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
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9
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Borah K, Xu Y, McFadden J. Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches. Front Immunol 2021; 12:762315. [PMID: 34795672 PMCID: PMC8593131 DOI: 10.3389/fimmu.2021.762315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/18/2021] [Indexed: 01/10/2023] Open
Abstract
Tuberculosis (TB) is a devastating infectious disease that kills over a million people every year. There is an increasing burden of multi drug resistance (MDR) and extensively drug resistance (XDR) TB. New and improved therapies are urgently needed to overcome the limitations of current treatment. The causative agent, Mycobacterium tuberculosis (Mtb) is one of the most successful pathogens that can manipulate host cell environment for adaptation, evading immune defences, virulence, and pathogenesis of TB infection. Host-pathogen interaction is important to establish infection and it involves a complex set of processes. Metabolic cross talk between the host and pathogen is a facet of TB infection and has been an important topic of research where there is growing interest in developing therapies and drugs that target these interactions and metabolism of the pathogen in the host. Mtb scavenges multiple nutrient sources from the host and has adapted its metabolism to survive in the intracellular niche. Advancements in systems-based omic technologies have been successful to unravel host-pathogen interactions in TB. In this review we discuss the application and usefulness of omics in TB research that provides promising interventions for developing anti-TB therapies.
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Affiliation(s)
- Khushboo Borah
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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10
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López Medrano R, Burgos Asurmendi I, Rivero Lezcano OM. A rapid proteomic system (MALDI-TOF) for nontuberculous-mycobacteria identification. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00203-2. [PMID: 34266677 DOI: 10.1016/j.eimc.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/24/2022]
Abstract
Proteomic techniques relaying upon mass spectrometry (MALDI_TOF) applied to nontuberculous mycobacteria (NTM) identification, constitute a difficult goal. Cell wall structure features complicates the protein extraction procedure. A total of 106 isolates belonging to a variety of MNTs species isolated from clinical samples taken at the Complejo Asistencial Universitario de León for a two years period (2019-20) were identified following a simplified method (MALDI-TOF Biotyper Bruker®) developped in our laboratory. The resultant identification was compared to a parallel one ruled on the Centro de Referencia de Majadahonda. A total of 22 different MNTs species were tested, obtaining an agreement of 91,5%. Only 9 minor discrepancies between species belonging to the same taxonomic group of MNTs were detected. The score obtained in the 67.92% of the cases was higher than 1.8. A time-saving of 24 minutes compared to the manufacturer's proceeding was achieved.
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Affiliation(s)
- Ramiro López Medrano
- Servicio de Microbiología. Complejo Asistencial Universitario de León, León, España.
| | - Isabel Burgos Asurmendi
- Servicio de Anestesiología y Reanimación. Complejo Asistencial Universitario de León, León, España
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11
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Lee KI, Choi S, Choi HG, Gurmessa SK, Dang TB, Back YW, Park HS, Kim HJ. Recombinant Rv1654 protein of Mycobacterium tuberculosis induces mitochondria-mediated apoptosis in macrophage. Microbiol Immunol 2021; 65:178-188. [PMID: 33565648 DOI: 10.1111/1348-0421.12880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/10/2021] [Accepted: 02/08/2021] [Indexed: 02/04/2023]
Abstract
Mycobacterium tuberculosis contains diverse immunologically active components. This study investigated the biological function of a newly identified component, Rv1654, with the potential to induce apoptosis in macrophages. Recombinant Rv1654 induced macrophage apoptosis in a caspase-9/3-dependent manner through the production of reactive oxygen species (ROS) and interaction with Toll-like receptor 4. In addition, Rv1654 induced the production of tumor necrosis factor-α, interleukin-6, and monocyte chemoattractant protein-1 through the mitogen-activated protein kinase pathway. Furthermore, Rv1654-induced c-Jun N-terminal kinase (JNK) activation was inhibited by the ROS scavenger and Rv1654-induced apoptosis was inhibited by the JNK inhibitor. Moreover, it was found that treatment of macrophages with Rv1654 led to the loss of mitochondrial membrane potential, release of cytochrome c into the cytosol, and translocation of Bax into the mitochondria. Finally, Rv1654-mediated apoptosis was inhibited in macrophages transfected with Bax siRNA. These results suggest that Rv1654 induces macrophage apoptosis through a mitochondrial-dependent pathway and ROS-mediated JNK activation.
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Affiliation(s)
- Kang-In Lee
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Seunga Choi
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Han-Gyu Choi
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Sintayehu Kebede Gurmessa
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Thi Binh Dang
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Yong Woo Back
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hye-Soo Park
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hwa-Jung Kim
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Department of Translational Immunology Institute, College of Medicine, Chungnam National University, Daejeon, South Korea.,Infection Control Convergence Research Center, College of Medicine, Chungnam National University, Daejeon, South Korea
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12
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Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
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13
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Covián C, Retamal-Díaz A, Bueno SM, Kalergis AM. Could BCG Vaccination Induce Protective Trained Immunity for SARS-CoV-2? Front Immunol 2020; 11:970. [PMID: 32574258 PMCID: PMC7227382 DOI: 10.3389/fimmu.2020.00970] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Trained immunity is a type of non-specific memory-like immune response induced by some pathogens and vaccines, such as BCG, which can confer antigen-independent protection against a wide variety of pathogens. The BCG vaccine has been extensively used to protect against tuberculosis for almost a 100 years. Interestingly, this vaccine reduces children's mortality caused by infections unrelated to Mycobacterium tuberculosis infection, a phenomenon thought to be due to the induction of trained immunity. The SARS-CoV-2 pandemic has infected, as of April 22, 2020, 2,623,231 people globally, causing a major public health problem worldwide. Currently, no vaccine or treatment is available to control this pandemic. We analyzed the number of positive cases and deaths in different countries and correlated them with the inclusion of BCG vaccination at birth in their national vaccination programs. Interestingly, those countries where BCG vaccination is given at birth have shown a lower contagion rate and fewer COVID-19-related deaths, suggesting that this vaccine may induce trained immunity that could confer some protection for SARS-CoV-2.
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Affiliation(s)
- Camila Covián
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Angello Retamal-Díaz
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M. Bueno
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Departamento de Endocrinología, Facultad de Medicina, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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14
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Macalino SJY, Billones JB, Organo VG, Carrillo MCO. In Silico Strategies in Tuberculosis Drug Discovery. Molecules 2020; 25:E665. [PMID: 32033144 PMCID: PMC7037728 DOI: 10.3390/molecules25030665] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) remains a serious threat to global public health, responsible for an estimated 1.5 million mortalities in 2018. While there are available therapeutics for this infection, slow-acting drugs, poor patient compliance, drug toxicity, and drug resistance require the discovery of novel TB drugs. Discovering new and more potent antibiotics that target novel TB protein targets is an attractive strategy towards controlling the global TB epidemic. In silico strategies can be applied at multiple stages of the drug discovery paradigm to expedite the identification of novel anti-TB therapeutics. In this paper, we discuss the current TB treatment, emergence of drug resistance, and the effective application of computational tools to the different stages of TB drug discovery when combined with traditional biochemical methods. We will also highlight the strengths and points of improvement in in silico TB drug discovery research, as well as possible future perspectives in this field.
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Affiliation(s)
- Stephani Joy Y. Macalino
- Chemistry Department, De La Salle University, 2401 Taft Avenue, Manila 0992, Philippines;
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Junie B. Billones
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Voltaire G. Organo
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Maria Constancia O. Carrillo
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
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15
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Meza AN, Cambui CCN, Moreno ACR, Fessel MR, Balan A. Mycobacterium tuberculosis CysA2 is a dual sulfurtransferase with activity against thiosulfate and 3-mercaptopyruvate and interacts with mammalian cells. Sci Rep 2019; 9:16791. [PMID: 31727914 PMCID: PMC6856128 DOI: 10.1038/s41598-019-53069-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/17/2019] [Indexed: 11/18/2022] Open
Abstract
Cyanide is a toxic compound that is converted to the non-toxic thiocyanate by a rhodanese enzyme. Rhodaneses belong to the family of transferases (sulfurtransferases), which are largely studied. The sulfur donor defines the subfamily of these enzymes as thiosulfate:cyanide sulfurtransferases or rhodaneses (TSTs) or 3-mercaptopyruvate sulfurtransfeases (MSTs). In Mycobacterium tuberculosis, the causative agent of tuberculosis, the gene Rv0815c encodes the protein CysA2, a putative uncharacterized thiosulfate:cyanide sulfurtransferase that belongs to the essential sulfur assimilation pathway in the bacillus and is secreted during infection. In this work, we characterized the functional and structural properties of CysA2 and its kinetic parameters. The recombinant CysA2 is a α/β protein with two rhodanese-like domains that maintains the functional motifs and a catalytic cysteine. Sulfurtransferase activity was determined using thiosulfate and 3-mercaptopyruvate as sulfur donors. The assays showed Km values of 2.89 mM and 7.02 mM for thiosulfate and 3-mercaptopyruvate, respectively, indicating the protein has dual activity as TST and MST. Immunological assays revealed that CysA2 interacted with pulmonary cells, and it was capable to activate macrophages and dendritic cells, indicating the stimulation of the immune response, which is important for its use as an antigen for vaccine development and immunodiagnostic.
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Affiliation(s)
- A N Meza
- Department of Microbiology, Institute of Biomedical Sciences, Applied Structural Biology Laboratory, LBEA, University of São Paulo, São Paulo, SP, Brazil
- Institute of Biology, Post-graduate Program in Genetics and Molecular Biology, University of Campinas, UNICAMP, Campinas, SP, Brazil
| | - C C N Cambui
- Department of Microbiology, Institute of Biomedical Sciences, Applied Structural Biology Laboratory, LBEA, University of São Paulo, São Paulo, SP, Brazil
| | - A C R Moreno
- Department of Microbiology, Vaccine Development Laboratory, Biomedical Sciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - M R Fessel
- Department of Microbiology, Institute of Biomedical Sciences, Applied Structural Biology Laboratory, LBEA, University of São Paulo, São Paulo, SP, Brazil
| | - A Balan
- Department of Microbiology, Institute of Biomedical Sciences, Applied Structural Biology Laboratory, LBEA, University of São Paulo, São Paulo, SP, Brazil.
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16
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Stamm CE, Pasko BL, Chaisavaneeyakorn S, Franco LH, Nair VR, Weigele BA, Alto NM, Shiloh MU. Screening Mycobacterium tuberculosis Secreted Proteins Identifies Mpt64 as a Eukaryotic Membrane-Binding Bacterial Effector. mSphere 2019; 4:e00354-19. [PMID: 31167949 PMCID: PMC6553557 DOI: 10.1128/msphere.00354-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/19/2019] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is one of the most successful human pathogens. One reason for its success is that Mtb can reside within host macrophages, a cell type that normally functions to phagocytose and destroy infectious bacteria. However, Mtb is able to evade macrophage defenses in order to survive for prolonged periods of time. Many intracellular pathogens secrete virulence factors targeting host membranes and organelles to remodel their intracellular environmental niche. We hypothesized that Mtb secreted proteins that target host membranes are vital for Mtb to adapt to and manipulate the host environment for survival. Thus, we characterized 200 secreted proteins from Mtb for their ability to associate with eukaryotic membranes using a unique temperature-sensitive yeast screen and to manipulate host trafficking pathways using a modified inducible secretion screen. We identified five Mtb secreted proteins that both associated with eukaryotic membranes and altered the host secretory pathway. One of these secreted proteins, Mpt64, localized to the endoplasmic reticulum during Mtb infection of murine and human macrophages and impaired the unfolded protein response in macrophages. These data highlight the importance of secreted proteins in Mtb pathogenesis and provide a basis for further investigation into their molecular mechanisms.IMPORTANCE Advances have been made to identify secreted proteins of Mycobacterium tuberculosis during animal infections. These data, combined with transposon screens identifying genes important for M. tuberculosis virulence, have generated a vast resource of potential M. tuberculosis virulence proteins. However, the function of many of these proteins in M. tuberculosis pathogenesis remains elusive. We have integrated three cell biological screens to characterize nearly 200 M. tuberculosis secreted proteins for eukaryotic membrane binding, host subcellular localization, and interactions with host vesicular trafficking. In addition, we observed the localization of one secreted protein, Mpt64, to the endoplasmic reticulum (ER) during M. tuberculosis infection of macrophages. Interestingly, although Mpt64 is exported by the Sec pathway, its delivery into host cells was dependent upon the action of the type VII secretion system. Finally, we observed that Mpt64 impairs the ER-mediated unfolded protein response in macrophages.
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Affiliation(s)
- Chelsea E Stamm
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Breanna L Pasko
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sujittra Chaisavaneeyakorn
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Luis H Franco
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Vidhya R Nair
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bethany A Weigele
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael U Shiloh
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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17
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Gough ME, Graviss EA, Chen TA, Obasi EM, May EE. Compounding effect of vitamin D 3 diet, supplementation, and alcohol exposure on macrophage response to mycobacterium infection. Tuberculosis (Edinb) 2019; 116S:S42-S58. [PMID: 31126718 DOI: 10.1016/j.tube.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
Vitamin D3 is known to be a key component in the defense against Mycobacterium tuberculosis (Mtb) infection through the regulation of cytokine and effector molecules. Conversely, alcohol exposure has been recognized as an immune dysregulator. Macrophages were extracted from D3 deficient and sufficient diet mice and supplemented with D3 or exposed to ethanol during ex vivo infection using M. bovis BCG, as a surrogate for Mtb. Results of our study indicate that while exogenous supplementation or alcohol exposure did alter immune response, in vivo diet was the greatest determinant of cytokine and effector molecule production. Alcohol exposure was found to profoundly dysregulate primary murine macrophages, with ethanol-exposed cells generally characterized as hyper- or hyporesponsive. Exogenous D3 supplementation had a normative effect for diet deficient host, however supplementation was not sufficient to compensate for the effects of diet deficiency. Vitamin D3 sufficient diet resulted in reduced cell cytotoxicity for the majority of time points. Results provide insight into the ramifications of both the individual and combined health risks of D3 deficiency or alcohol exposure. Given the clinical relevance of D3 deficiency and alcohol use comorbidities, outcomes of this study have implications in therapeutic approaches for the treatment of tuberculosis disease.
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Affiliation(s)
- Maya E Gough
- Biomedical Engineering Department, University of Houston, USA
| | - Edward A Graviss
- Pathology & Genomic Medicine, Houston Methodist Research Institute, USA
| | - Tzu-An Chen
- HEALTH Research Institute, University of Houston, USA
| | - Ezemenari M Obasi
- HEALTH Research Institute, University of Houston, USA; Psychological, Health, & Learning Sciences Department, University of Houston, USA
| | - Elebeoba E May
- Biomedical Engineering Department, University of Houston, USA; HEALTH Research Institute, University of Houston, USA.
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18
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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
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19
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Mehmood A, Kouser L, Kaur A, Holmskov U, Al-Ahdal MN, Sim RB, Kishore U, Tsolaki AG. Complement Dependent and Independent Interaction Between Bovine Conglutinin and Mycobacterium bovis BCG: Implications in Bovine Tuberculosis. Front Immunol 2019; 9:3159. [PMID: 30804949 PMCID: PMC6370948 DOI: 10.3389/fimmu.2018.03159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022] Open
Abstract
Bovine conglutinin, the first animal collectin to be discovered, is structurally very similar to Surfactant Protein D (SP-D). SP-D is known to interact with Mycobacterium tuberculosis, and the closely-related M. bovis, the causative agent of bovine tuberculosis. We speculated that due to the overall similarities between conglutinin and SP-D, conglutinin is likely to have a protective influence in bovine tuberculosis. We set out to investigate the role of conglutinin in host-pathogen interaction during mycobacterial infection. We show here that a recombinant truncated form of conglutinin (rfBC), composed of the neck and C-type lectin domains, binds specifically and in a dose-dependent manner to the model organism Mycobacterium bovis BCG. rfBC showed a significant direct bacteriostatic effect on the growth of M. bovis BCG in culture. In addition, rfBC inhibited the uptake of M. bovis BCG by THP-1 macrophages (human monocyte lineage cell line) and suppressed the subsequent pro-inflammatory response. Conglutinin is well-known as a binder of the complement activation product, iC3b. rfBC was also able to inhibit the uptake of complement-coated M. bovis BCG by THP-1 macrophages, whilst modulating the pro-inflammatory response. It is likely that rfBC inhibits the phagocytosis of mycobacteria by two distinct mechanisms: firstly, rfBC interferes with mannose receptor-mediated uptake by masking lipoarabinomannan (LAM) on the mycobacterial surface. Secondly, since conglutinin binds iC3b, it can interfere with complement receptor-mediated uptake via CR3 and CR4, by masking interactions with iC3b deposited on the mycobacterial surface. rfBC was also able to modulate the downstream pro-inflammatory response in THP-1 cells, which is important for mobilizing the adaptive immune response, facilitating containment of mycobacterial infection. In conclusion, we show that conglutinin possesses complement-dependent and complement-independent anti-mycobacterial activities, interfering with both known mechanisms of mycobacterial uptake by macrophages. As mycobacteria are specialized intracellular pathogens, conglutinin may inhibit M. bovis and M. tuberculosis from establishing an intracellular niche within macrophages, and thus, negatively affect the long-term survival of the pathogen in the host.
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Affiliation(s)
- Arshad Mehmood
- Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Lubna Kouser
- Allergy and Clinical Immunology, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Anuvinder Kaur
- Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Uffe Holmskov
- Department of Cancer and Inflammation, University of Southern Denmark, Odense, Denmark
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Robert B Sim
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Uday Kishore
- Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Anthony G Tsolaki
- Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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20
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Alanine dehydrogenases in mycobacteria. J Microbiol 2019; 57:81-92. [PMID: 30706339 DOI: 10.1007/s12275-019-8543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Since NAD(H)-dependent L-alanine dehydrogenase (EC 1.1.4.1; Ald) was identified as one of the major antigens present in culture filtrates of Mycobacterium tuberculosis, many studies on the enzyme have been conducted. Ald catalyzes the reversible conversion of pyruvate to alanine with concomitant oxidation of NADH to NAD+ and has a homohexameric quaternary structure. Expression of the ald genes was observed to be strongly upregulated in M. tuberculosis and Mycobacterium smegmatis grown in the presence of alanine. Furthermore, expression of the ald genes in some mycobacteria was observed to increase under respiration-inhibitory conditions such as oxygen-limiting and nutrient-starvation conditions. Upregulation of ald expression by alanine or under respiration-inhibitory conditions is mediated by AldR, a member of the Lrp/AsnC family of transcriptional regulators. Mycobacterial Alds were demonstrated to be the enzymes required for utilization of alanine as a nitrogen source and to help mycobacteria survive under respiration-inhibitory conditions by maintaining cellular NADH/NAD+ homeostasis. Several inhibitors of Ald have been developed, and their application in combination with respiration-inhibitory antitubercular drugs such as Q203 and bedaquiline was recently suggested.
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21
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Kasempimolporn S, Premchaiporn P, Thaveekarn W, Boonchang S, Sitprija V. Comparative Proteomic Profiling of Mycobacterium tuberculosis and the Thai Vaccine Strain Mycobacterium bovis Bacille Calmette-Guerin Tokyo172: Diverse Biomarker Candidates for Species Differentiation. J Glob Infect Dis 2018; 10:196-200. [PMID: 30581260 PMCID: PMC6276322 DOI: 10.4103/jgid.jgid_149_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: Bacille Calmette–Guerin (BCG)-related complications can occur in vaccinated children. Comparison of the composition of cellular proteins of virulent Mycobacterium tuberculosis (MTB) H37Rv with of attenuated Mycobacterium bovis BCG Tokyo172 vaccine strain used in Thailand and identify protein candidates of value for differentiation between the two mycobacterial species may facilitate the diagnosis of etiologic agent of mycobacterial disease in vaccinated children, as most cases have been believed to have originated from BCG vaccine. Materials and Methods: The two-dimensional electrophoresis (2DE) proteomic profiles of cellular proteins from the Thai vaccine strain M. bovis BCG Tokyo172 and MTB were compared and the matched spots in 2DE gels were submitted to mass spectrometry analysis. Results: There were a number of similar protein contents with different intensity or position between MTB and M. bovis BCG Tokyo172. A higher expression of some immunogenic proteins was shown in BGG Tokyo172 when compared to MTB, while some were shown the opposite pattern. Conclusions: Proteomic approach reveals key proteins participating in different species of Mycobacteria, and may be useful for discrimination between MTB and the BCG Tokyo172 infection.
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Affiliation(s)
- Songsri Kasempimolporn
- Department of Research and Development, Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Pornpimol Premchaiporn
- Department of Research and Development, Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Wichit Thaveekarn
- Department of Research and Development, Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Supatsorn Boonchang
- Department of Research and Development, Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Visith Sitprija
- Department of Research and Development, Queen Saovabha Memorial Institute, Thai Red Cross Society, Bangkok 10330, Thailand
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Yao J, Du X, Chen S, Shao Y, Deng K, Jiang M, Liu J, Shen Z, Chen X, Feng G. Rv2346c enhances mycobacterial survival within macrophages by inhibiting TNF-α and IL-6 production via the p38/miRNA/NF-κB pathway. Emerg Microbes Infect 2018; 7:158. [PMID: 30232332 PMCID: PMC6145905 DOI: 10.1038/s41426-018-0162-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022]
Abstract
The intracellular survival of Mycobacterium tuberculosis (Mtb) has a central role in the pathogenesis of tuberculosis. Mtb Rv2346c is a member of 6-kDa early secreted antigenic target family of proteins, which are known to inhibit the host immune responses to promote bacillary persistence in macrophages. However, the mechanism through which Rv2346c participates in Mtb pathogenesis is unclear. In the present study, recombinant Rv2346c protein was synthesized and used to treat Bacillus Calmette–Guérin (BCG)-infected macrophages. The results showed that Rv2346c inhibited the proliferation of BCG-infected macrophages and enhanced the survival of BCG in macrophages. Tumor necrosis factor-α (TNF-α) and interleukin (IL)-6 were upregulated during BCG infection but downregulated by Rv2346c. Additional experiments showed that nuclear transcription factor-κB (NF-κB) in BCG-infected macrophages induced the production of TNF-α and IL-6. In addition, miR-155 and miR-99b had a suppressive effect on NF-κB, and the expression of these miRNAs was promoted by p38. Furthermore, Rv2346c was shown to decrease the activation of NF-κB, whereas it enhanced the phosphorylation of p38 and the expression of miR-155 and miR-99b. The function of Rv2346c was also verified in Mtb-infected mice. The results showed that Rv2346c increased the observed bacterial load and lung injury and downregulated TNF-α and IL-6 in vivo. Overall, our results reveal that Rv2346c enhances mycobacterial survival in macrophages via inhibiting the production of TNF-α and IL-6 in a p38/miRNA/NF-κB pathway-dependent manner, suggesting that Rv2346c acts as a crucial virulence factor in Mtb infection and has potential use as a target for anti-tuberculosis therapy.
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Affiliation(s)
- Jing Yao
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Xingran Du
- Department of Infectious Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Sixia Chen
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Yan Shao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, 210009, China
| | - Kaili Deng
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Mingzi Jiang
- Department of Respiratory Medicine, the First People's Hospital of Kunshan, Kunshan, Jiangsu, 215300, China
| | - Jingning Liu
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Ziyan Shen
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China
| | - Xiaolin Chen
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing, Jiangsu, 211100, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, China.
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23
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Trutneva K, Shleeva M, Nikitushkin V, Demina G, Kaprelyants A. Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology. Front Microbiol 2018; 9:2083. [PMID: 30233550 PMCID: PMC6131537 DOI: 10.3389/fmicb.2018.02083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/14/2018] [Indexed: 01/07/2023] Open
Abstract
Mycobacteria are able to form dormant cells, which survive for a long time without multiplication. The molecular mechanisms behind prolonged survival of dormant cells are not fully described. In particular, little information is known on biochemical processes which might take place in cells under dormancy. To gain insight into this problem, Mycobacterium smegmatis cells in deep dormant state were obtained after gradual acidification of the growth medium in prolonged stationary phase followed by 1 month of storage at room temperature. Such cells were characterized by low metabolic activity, including respiration, resistance to antibiotics, and altered morphology. The protein composition of cytoplasm and membrane fractions obtained from active and dormant cells were compared by 2D electrophoresis. Almost half of the proteins found in the proteome of dormant cells were absent in that of active cells. This result differs significantly from published results obtained in other studies employing different models of mycobacterium dormancy. This discrepancy could be explained by a deeper dormancy developed in the present model. A feature of a “dormant proteome” is high representation of enzymes involved in glycolysis and defense systems that inactivate or detoxify reactive oxygen and nitrogen species, aldehydes, and oxidized lipids. Dormant mycobacteria are enriched by degradative enzymes, which could eliminate damaged molecules, or the products of such degradation could be reutilized by the cell during prolonged storage. We suggest that some enzymes in dormant cells are inactive, having been used upon transition to the dormant state, or proteins stored in dormant cells for further cell reactivation. At the same time, some proteins could be functional and play roles in maintenance of cell metabolism, albeit at a very slow rate. This study provides a clue as to which biochemical processes could be active under dormancy to ensure long-term viability of dormant mycobacteria.
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Affiliation(s)
- Kseniya Trutneva
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia
| | - Margarita Shleeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim Nikitushkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia
| | - Galina Demina
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia
| | - Arseny Kaprelyants
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia
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Coppola M, Ottenhoff TH. Genome wide approaches discover novel Mycobacterium tuberculosis antigens as correlates of infection, disease, immunity and targets for vaccination. Semin Immunol 2018; 39:88-101. [PMID: 30327124 DOI: 10.1016/j.smim.2018.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023]
Abstract
Every day approximately six thousand people die of Tuberculosis (TB). Its causative agent, Mycobacterium tuberculosis (Mtb), is an ancient pathogen that through its evolution developed complex mechanisms to evade immune surveillance and acquire the ability to establish persistent infection in its hosts. Currently, it is estimated that one-fourth of the human population is latently infected with Mtb and among those infected 3-10% are at risk of developing active TB disease during their lifetime. The currently available diagnostics are not able to detect this risk group for prophylactic treatment to prevent transmission. Anti-TB drugs are available but only as long regimens with considerable side effects, which could both be reduced if adequate tests were available to monitor the response of TB to treatment. New vaccines are also urgently needed to substitute or boost Bacille Calmette-Guérin (BCG), the only approved TB vaccine: although BCG prevents disseminated TB in infants, it fails to impact the incidence of pulmonary TB in adults, and therefore has little effect on TB transmission. To achieve TB eradication, the discovery of Mtb antigens that effectively correlate with the human response to infection, with the curative host response following TB treatment, and with natural as well as vaccine induced protection will be critical. Over the last decade, many new Mtb antigens have been found and proposed as TB biomarkers and vaccine candidates, but only a very small number of these is being used in commercial diagnostic tests or is being assessed as candidate TB vaccine antigens in human clinical trials, aiming to prevent infection, disease or disease recurrence following treatment. Most of these antigens were discovered decades ago, before the complete Mtb genome sequence became available, and thus did not harness the latest insights from post-genomic antigen discovery strategies and genome wide approaches. These have, for example, revealed critical phase variation in Mtb replication and accompanying gene -and therefore antigen- expression patterns. In this review, we present a brief overview of past methodologies, and subsequently focus on the most important recent Mtb antigen discovery studies which have mined the Mtb antigenome through "unbiased" genome wide approaches. We compare the results for these approaches -as far as we know for the first time-, highlight Mtb antigens that have been identified independently by different strategies and present a comprehensive overview of the Mtb antigens thus discovered.
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Affiliation(s)
- Mariateresa Coppola
- Dept. Infectious Diseases, LUMC, PO Box 9600, 2300RC Leiden, The Netherlands.
| | - Tom Hm Ottenhoff
- Dept. Infectious Diseases, LUMC, PO Box 9600, 2300RC Leiden, The Netherlands
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Dutta D. Advance in Research on Mycobacterium tuberculosis FabG4 and Its Inhibitor. Front Microbiol 2018; 9:1184. [PMID: 29946302 PMCID: PMC6008564 DOI: 10.3389/fmicb.2018.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence from recent reports of drug-resistant mycobacterial strains poses a challenge worldwide. Drug-resistant strains often undergo mutations, adopt alternative pathways, and express drug efflux pumps to reduce or eliminate drug doses. Besides these intrinsic resistance mechanisms, bacteria can evade drug doses by forming biofilms. Biofilms are the concerted growth of adherent microorganisms, which can also be formed at the air-water interface. The growth is supported by the extracellular polymer matrix which is self-produced by the microorganisms. Reduced metabolic activity in a nutrient-deficient environment in the biofilm may cause the microorganisms to take alternative pathways that can make the microorganisms recalcitrant to the drug doses. Recent works have shown that Mycobacterium tuberculosis expresses several proteins during its growth in biofilm, those when deleted, did not show any effect on mycobacterial growth in normal nutrient-sufficient conditions. Studying these unconventional proteins in mycobacterial biofilms is therefore of utmost importance. In this article, I will discuss one such mycobacterial biofilm-related protein FabG4 that is recently shown to be important for mycobacterial survival in the presence of antibiotic stressors and limited nutrient condition. In an attempt to find more effective FabG4 inhibitors and its importance in biofilm forming M. tuberculosis, present knowledge about FabG4 and its known inhibitors are discussed. Based on the existing data, a putative role of FabG4 is also suggested.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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26
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Ravindran MS, Wenk MR. Activity-Based Lipid Esterase Profiling of M. bovis BCG at Different Metabolic States Using Tetrahydrolipstatin (THL) as Bait. Methods Mol Biol 2018; 1491:75-85. [PMID: 27778282 DOI: 10.1007/978-1-4939-6439-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ. THL possesses bactericidal activities, but its precise spectrum of molecular targets is poorly characterized. Here, we used THL analogs functionalized to enable Huisgen-base cycloaddition, commonly known as "click chemistry," to identify target proteins after enrichment from mycobacterial cell lysates obtained from different physiological conditions.
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Affiliation(s)
- Madhu Sudhan Ravindran
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Markus R Wenk
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Department of Biological Sciences, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Swiss Tropical and Public Health Institute, University of Basel, 4051, Basel, Switzerland.
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27
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Shi P, Fu X, Shen Q, Liu M, Pan Q, Tang Y, Jiang W, Lv Z, Yan T, Ma Y, Chen M, Hao X, Liu P, Li L, Sun X, Tang K. The roles of AaMIXTA1 in regulating the initiation of glandular trichomes and cuticle biosynthesis in Artemisia annua. THE NEW PHYTOLOGIST 2018; 217:261-276. [PMID: 28940606 DOI: 10.1111/nph.14789] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/14/2017] [Indexed: 05/24/2023]
Abstract
The glandular secretory trichomes (GSTs) on Artemisia annua leaves have the capacity to secrete and store artemisinin, a compound which is the most effective treatment for uncomplicated malaria. An effective strategy to improve artemisinin content is therefore to increase the density of GSTs in A. annua. However, the formation mechanism of GSTs remains poorly understood. To explore the mechanisms of GST initiation in A. annua, we screened myeloblastosis (MYB) transcription factor genes from a GST transcriptome database and identified a MIXTA transcription factor, AaMIXTA1, which is expressed predominantly in the basal cells of GST in A. annua. Overexpression and repression of AaMIXTA1 resulted in an increase and decrease, respectively, in the number of GSTs as well as the artemisinin content in transgenic plants. Transcriptome analysis and cuticular lipid profiling showed that AaMIXTA1 is likely to be responsible for activating cuticle biosynthesis. In addition, dual-luciferase reporter assays further demonstrated that AaMIXTA1 could directly activate the expression of genes related to cuticle biosynthesis. Taken together, AaMIXTA1 regulated cuticle biosynthesis and prompted GST initiation without any abnormal impact on the morphological structure of the GSTs and so provides a new way to improve artemisinin content in this important medicinal plant.
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Affiliation(s)
- Pu Shi
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Fu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Shen
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Meng Liu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qifang Pan
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yueli Tang
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weimin Jiang
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zongyou Lv
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tingxiang Yan
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanan Ma
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Minghui Chen
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolong Hao
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pin Liu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ling Li
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofen Sun
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kexuan Tang
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Vollmer AC, Bark SJ. Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:1-36. [PMID: 29680123 DOI: 10.1016/bs.aambs.2017.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR two-component signaling pathways. These and other foundational studies suggest Usps serve regulatory and protective roles to enable adaptation and survival under external stresses. Despite these foundational studies, many bacterial species have multiple paralogs of genes encoding these proteins and ablation of the genes does not provide a distinct phenotype. This outcome has limited our understanding of the biochemical functions of these proteins. Here, we summarize the current knowledge of Usps in general and UspA in particular across different genera as well as conclusions about their functions from seminal studies in diverse organisms. Our objective has been to organize the foundational studies in this field to identify the significant impediments to further understanding of Usp functions at the molecular level. We propose ideas and experimental approaches that may overcome these impediments and drive future development of molecular approaches to understand and target Usps as central regulators of stress adaptation and survival. Despite the fact that the full functions of Usps are still not known, creative many applications have already been proposed, tested, and used. The complementary approaches of basic research and applications, along with new technology and analytic tools, may yield the elusive yet critical functions of universal stress proteins in diverse systems.
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29
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Bespyatykh JA, Manicheva OA, Smolyakov AV, Dogonadze MZ, Zhuravlev VY, Shitikov EA, Ilina EN. [Influence of cultivation conditions on the proteomic profile of Mycobacterium tuberculosis H37RV]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:334-340. [PMID: 28862605 DOI: 10.18097/pbmc20176304334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Comparative proteomic profiling of M. tuberculosis H37Rv strains cultured on two different nutrient media, Levenstein-Jensen and Middlebrook 7H11, was performed using a label-free LC-MS/MS approach. It was shown that results obtained from two media possessed high convergence. The only difference was observed in the representation of fumarate reductase FrdB, its abundance was higher in the mycobacterial cells cultured on Levenstein-Jensen medium. The correlation analysis of biological repeats revealed the high convergence of the results obtained from Middlebrook 7H11 medium. Thus, we can conclude that the use of the Middlebrook 7H11 medium is most appropriate in the scientific laboratory.
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Affiliation(s)
- J A Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - O A Manicheva
- Research Institute of Phtisiopulmonology, St. Petersburg, Russia
| | - A V Smolyakov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - M Z Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russia
| | - V Yu Zhuravlev
- Research Institute of Phtisiopulmonology, St. Petersburg, Russia
| | - E A Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - E N Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
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30
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Kumar G, Shankar H, Sharma D, Sharma P, Bisht D, Katoch VM, Joshi B. Proteomics of Culture Filtrate of Prevalent Mycobacterium tuberculosis Strains: 2D-PAGE Map and MALDI-TOF/MS Analysis. SLAS DISCOVERY 2017; 22:1142-1149. [PMID: 28683213 DOI: 10.1177/2472555217717639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Although diverse efforts have been done to identify biomarkers for control of tuberculosis using laboratory strain Mycobacterium tuberculosis H37Rv, the disease still poses a threat to mankind. There are many emerging M. tuberculosis strains, and proteomic profiling of these strains might be important to find out potential targets for diagnosis and/or prevention of tuberculosis. We evaluated the comparative proteomic profiling of culture filtrate (CF) proteins from prevalent M. tuberculosis strains (Central Asian or Delhi type; CAS1_Del, East African-Indian; EAI-3 and Beijing family) by 2D polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. As a result, we could identify 12 CF proteins (Rv0066c, Rv1310, Rv3375, Rv1415, Rv0567, Rv1886c, Rv3803c, Rv3804c, Rv2031c, Rv1038c, Rv2809, and Rv1911c), which were consistently increased in all prevalent M. tuberculosis strains, and interestingly, two CF proteins (Rv2809, Rv1911c) were identified with unknown functions. Consistent increased intensity of these proteins suggests their critical role for survival of prevalent M. tuberculosis isolates, and some of these proteins may also have potential as diagnostic and vaccine candidates for tuberculosis, which needs to be further explored by immunological analysis.
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Affiliation(s)
- Gavish Kumar
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India.,Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Hari Shankar
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Prashant Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
| | - Vishwa M Katoch
- Department of Health Research (Ministry of Health and Family Welfare), Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India
| | - Beenu Joshi
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Taj Ganj, Agra, Uttar Pradesh, India
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31
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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.
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Barreiro C, Morales A, Vázquez-Iglesias I, Sola-Landa A. Intra- and Extra-cellular Proteome Analyses of Steroid-Producer Mycobacteria. Methods Mol Biol 2017; 1645:73-92. [PMID: 28710622 DOI: 10.1007/978-1-4939-7183-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. In contrast, those industrially relevant mycobacteria have received less attention, even though the steroids market sales in 2011, in example, were estimated in $8 billion.The extra-cellular proteome, due to its relevance in the sterols processing and uptake; as well as the intra-cellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. As a proof of concept, the obtaining methods for both sub-proteomes of Mycobacterium neoaurum NRRL B-3805, a relevant industrial strain involved in steroids production, have been developed. Thus, procedures and relevant key points of these proteomes analyses are fully described.
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Affiliation(s)
- Carlos Barreiro
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain.
- Área de Microbiología, Departamento de Biología Molecular, Campus de Ponferrada, Universidad de León, Avda. Astorga, s/n, 24400, Ponferrada, Spain.
| | - Alejandro Morales
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Inés Vázquez-Iglesias
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
| | - Alberto Sola-Landa
- Instituto de Biotecnología de León (INBIOTEC), Parque Científico de León, Avda. Real 1, 24006, León, Spain
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Rabodoarivelo MS, Aerts M, Vandamme P, Palomino JC, Rasolofo V, Martin A. Optimizing of a protein extraction method for Mycobacterium tuberculosis proteome analysis using mass spectrometry. J Microbiol Methods 2016; 131:144-147. [DOI: 10.1016/j.mimet.2016.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 01/11/2023]
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34
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Long J, Basu Roy R, Zhang YJ, Antrobus R, Du Y, Smith DL, Weekes MP, Javid B. Plasma Membrane Profiling Reveals Upregulation of ABCA1 by Infected Macrophages Leading to Restriction of Mycobacterial Growth. Front Microbiol 2016; 7:1086. [PMID: 27462310 PMCID: PMC4940386 DOI: 10.3389/fmicb.2016.01086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 01/01/2023] Open
Abstract
The plasma membrane represents a critical interface between the internal and extracellular environments, and harbors multiple proteins key receptors and transporters that play important roles in restriction of intracellular infection. We applied plasma membrane profiling, a technique that combines quantitative mass spectrometry with selective cell surface aminooxy-biotinylation, to Bacille Calmette–Guérin (BCG)-infected THP-1 macrophages. We quantified 559 PM proteins in BCG-infected THP-1 cells. One significantly upregulated cell-surface protein was the cholesterol transporter ABCA1. We showed that ABCA1 was upregulated on the macrophage cell-surface following infection with pathogenic mycobacteria and knockdown of ABCA1 resulted in increased mycobacterial survival within macrophages, suggesting that it may be a novel mycobacterial host-restriction factor.
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Affiliation(s)
- Jing Long
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University Beijing, China
| | | | | | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge Cambridge, UK
| | - Yuxian Du
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University Beijing, China
| | - Duncan L Smith
- Cancer Research UK Manchester Institute, University of Manchester Manchester, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge Cambridge, UK
| | - Babak Javid
- Collaboration Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua UniversityBeijing, China; Harvard TH Chan School of Public Health, BostonMA, USA
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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 03/17/2016] [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.
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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.
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36
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Comparative Analysis of Human B Cell Epitopes Based on BCG Genomes. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3620141. [PMID: 27382565 PMCID: PMC4921132 DOI: 10.1155/2016/3620141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/16/2016] [Indexed: 12/02/2022]
Abstract
Background. Tuberculosis is a huge global health problem. BCG is the only vaccine used for about 100 years against TB, but the reasons for protection variability in populations remain unclear. To improve BCG efficacy and develop a strategy for new vaccines, the underlying genetic differences among BCG subtypes should be understood urgently. Methods and Findings. Human B cell epitope data were collected from the Immune Epitope Database. Epitope sequences were mapped with those of 15 genomes, including 13 BCGs, M. bovis AF2122/97, and M. tuberculosis H37Rv, to identify epitopes distribution. Among 398 experimentally verified B cell epitopes, 321 (80.7%) were conserved, while the remaining 77 (19.3%) were lost to varying degrees in BCGs. The variable protective efficacy of BCGs may result from the degree of B cell epitopes deficiency. Conclusions. Here we firstly analyzed the genetic characteristics of BCGs based on B cell epitopes and found that B cell epitopes distribution may contribute to vaccine efficacy. Restoration of important antigens or effective B cell epitopes in BCG could be a useful strategy for vaccine development.
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Abstract
The emerging field of proteomics has contributed greatly to improving our understanding of the human pathogen Mycobacterium tuberculosis over the last two decades. In this chapter we provide a comprehensive overview of mycobacterial proteome research and highlight key findings. First, studies employing a combination of two-dimensional gel electrophoresis and mass spectrometry (MS) provided insights into the proteomic composition, initially of the whole bacillus and subsequently of subfractions, such as the cell wall, cytosol, and secreted proteins. Comparison of results obtained under various culture conditions, i.e., acidic pH, nutrient starvation, and low oxygen tension, aiming to mimic facets of the intracellular lifestyle of M. tuberculosis, provided initial clues to proteins relevant for intracellular survival and manipulation of the host cell. Further attempts were aimed at identifying the biological functions of the hypothetical M. tuberculosis proteins, which still make up a quarter of the gene products of M. tuberculosis, and at characterizing posttranslational modifications. Recent technological advances in MS have given rise to new methods such as selected reaction monitoring (SRM) and data-independent acquisition (DIA). These targeted, cutting-edge techniques combined with a public database of specific MS assays covering the entire proteome of M. tuberculosis allow the simple and reliable detection of any mycobacterial protein. Most recent studies attempt not only to identify but also to quantify absolute amounts of single proteins in the complex background of host cells without prior sample fractionation or enrichment. Finally, we will discuss the potential of proteomics to advance vaccinology, drug discovery, and biomarker identification to improve intervention and prevention measures for tuberculosis.
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Singh VK, Srivastava R, Srivastava BS. Manipulation of BCG vaccine: a double-edged sword. Eur J Clin Microbiol Infect Dis 2016; 35:535-43. [PMID: 26810060 DOI: 10.1007/s10096-016-2579-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/07/2016] [Indexed: 12/27/2022]
Abstract
Mycobacterium bovis Bacillus Calmette-Guérin (BCG), an attenuated vaccine derived from M. bovis, is the only licensed vaccine against tuberculosis (TB). Despite its protection against TB in children, the protective efficacy in pulmonary TB is variable in adolescents and adults. In spite of the current knowledge of molecular biology, immunology and cell biology, infectious diseases such as TB and HIV/AIDS are still challenges for the scientific community. Genetic manipulation facilitates the construction of recombinant BCG (rBCG) vaccine that can be used as a highly immunogenic vaccine against TB with an improved safety profile, but, still, the manipulation of BCG vaccine to improve efficacy should be carefully considered, as it can bring in both favourable and unfavourable effects. The purpose of this review is not to comprehensively review the interaction between microorganisms and host cells in order to use rBCG expressing M. tuberculosis (Mtb) immunodominant antigens that are available in the public domain, but, rather, to also discuss the limitations of rBCG vaccine, expressing heterologous antigens, during manipulation that pave the way for a promising new vaccine approach.
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Affiliation(s)
- V K Singh
- Section for Immunology, Department of Experimental Medical Science, Lund University, BMC D14, 22184, Lund, Sweden.
| | - R Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - B S Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
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Majlessi L, Prados-Rosales R, Casadevall A, Brosch R. Release of mycobacterial antigens. Immunol Rev 2015; 264:25-45. [PMID: 25703550 DOI: 10.1111/imr.12251] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mycobacterium tuberculosis has evolved from a Mycobacterium canettii-like progenitor pool into one of the most successful and widespread human pathogens. The pathogenicity of M. tuberculosis is linked to its ability to secrete/export/release selected mycobacterial proteins, and it is also established that active release of mycobacterial antigens is a prerequisite for strong immune recognition. Recent research has enabled mycobacterial secretion systems and vesicle-based release of mycobacterial antigens to be elucidated, which together with host-related specificities constitute key variables that determine the outcome of infection. Here, we discuss recently discovered, novel aspects on the nature and the regulation of antigen release of the tuberculosis agent with particular emphasis on the biological characterization of mycobacteria-specific ESX/type VII secretion systems and their secreted proteins, belonging to the Esx, PE, and PPE categories. The importance of specific mycobacterial antigen release is probably best exemplified by the striking differences observed between the cellular events during infection with the ESX-1-deficient, attenuated Mycobacterium bovis BCG compared to the virulent M. tuberculosis, which are clearly important for design of more specific diagnostics and more efficient vaccines.
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Affiliation(s)
- Laleh Majlessi
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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40
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Zhou F, Xu X, Wu S, Cui X, Fan L, Pan W. Protein array identification of protein markers for serodiagnosis of Mycobacterium tuberculosis infection. Sci Rep 2015; 5:15349. [PMID: 26481294 PMCID: PMC4642701 DOI: 10.1038/srep15349] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 09/22/2015] [Indexed: 01/26/2023] Open
Abstract
The lack of effective and accurate diagnostic tools contributes to the high prevalence of tuberculosis (TB) worldwide. The current serodiagnostics for TB are inadequate mainly due to lack of TB-specific antigens with highly accurate diagnosis. In the current study, we aimed to identify novel diagnostic antigens using glutathione S-transferase (GST)-fusion protein technique. We determined the reactivity of these recombinant proteins arrayed in solution and on GSH-immobilized microplates with TB patient sera. Of 409 TB proteins produced, ninety-two yielded seropositive reactions, fourteen including eight novel proteins showed strong immunoreactivity. Further, six were selected and constructed as a multiple-antigen combination set through analysis of various combinations. A comparative study of the multiple-antigen combination set and a commercially available kit revealed that the combination set showed 66.3% (95% CI 60.5–71.8) sensitivity, which was significantly higher than that of the commercial kit [31.6% (95% CI 26.3–37.3)]. The specificity of both methods was similar at 89.6% (95% CI 83.3–95.4) and 90.6% (95% CI 83.0–95.6), respectively. This study provides a set of novel diagnostic protein markers with great potential for the development of novel diagnostic tools for active TB.
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Affiliation(s)
- Fangbin Zhou
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Sijia Wu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xiaobing Cui
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Lin Fan
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.,Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
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41
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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.
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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
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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:
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42
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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.
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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
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43
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Zheng YQ, Naguib YW, Dong Y, Shi YC, Bou S, Cui Z. Applications of bacillus Calmette–Guerin and recombinant bacillus Calmette–Guerin in vaccine development and tumor immunotherapy. Expert Rev Vaccines 2015. [DOI: 10.1586/14760584.2015.1068124] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuan-qiang Zheng
- 1Inner Mongolia Key Laboratory of Molecular Biology, Inner Mongolia Medical University, Hohhot 010059, China
| | - Youssef W Naguib
- 2Pharmaceutics Division, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yixuan Dong
- 2Pharmaceutics Division, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yan-chun Shi
- 1Inner Mongolia Key Laboratory of Molecular Biology, Inner Mongolia Medical University, Hohhot 010059, China
| | - Shorgan Bou
- 3National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, China
| | - Zhengrong Cui
- 1Inner Mongolia Key Laboratory of Molecular Biology, Inner Mongolia Medical University, Hohhot 010059, China
- 2Pharmaceutics Division, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
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44
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An inducible expression system for high-level expression of recombinant proteins in slow growing mycobacteria. Plasmid 2015; 81:27-31. [PMID: 26021569 DOI: 10.1016/j.plasmid.2015.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022]
Abstract
A novel protein expression vector utilising the inducible hspX promoter of Mycobacterium tuberculosis was constructed and evaluated in this study. High-level induction of three mycobacterial antigens, comprising up to 9% of bacterial sonicate, was demonstrated in recombinant Mycobacterium bovis BCG when grown under low-oxygen tension, which serves to enhance hspX promoter activity. Recombinant proteins were efficiently purified from bacterial lysates in a soluble form by virtue of a C-terminal 6-histidine tag. Purification of the immunodominant M. tuberculosis Ag85B antigen using this system resulted in a recombinant protein that stimulated significant IFN-γ release from Ag85B-reactive T cells generated after vaccination of mice with an Ag85B-expressing vaccine. Further, the M. tuberculosis L-alanine dehydrogenase (Ald) protein purified from recombinant BCG displayed strong enzymatic activity in recombinant form. This study demonstrated that high levels of native-like recombinant mycobacterial proteins can be produced in mycobacterial hosts, and this may aid the analysis of mycobacterial protein function and the development of new treatments.
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45
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Protection against Mycobacterium tuberculosis infection offered by a new multistage subunit vaccine correlates with increased number of IFN-γ+ IL-2+ CD4+ and IFN-γ+ CD8+ T cells. PLoS One 2015; 10:e0122560. [PMID: 25822536 PMCID: PMC4378938 DOI: 10.1371/journal.pone.0122560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/22/2015] [Indexed: 01/13/2023] Open
Abstract
Protein subunit vaccines present a compelling new area of research for control of tuberculosis (TB). Based on the interaction between Mycobacterium tuberculosis and its host, five stage-specific antigens of M. tuberculosis that participate in TB pathogenesis—Rv1813, Rv2660c, Ag85B, Rv2623, and HspX—were selected. These antigens were verified to be recognized by T cells from a total of 42 whole blood samples obtained from active TB patients, patients with latent TB infections (LTBIs), and healthy control donors. The multistage polyprotein A1D4 was developed using the selected five antigens as a potentially more effective novel subunit vaccine. The immunogenicity and protective efficacy of A1D4 emulsified in the adjuvant MTO [monophosphoryl lipid A (MPL), trehalose-6,6′-dibehenate (TDB), components of MF59] was compared with Bacillus Calmette-Guerin (BCG) in C57BL/6 mice. Our results demonstrated that A1D4/MTO could provide more significant protection against M. tuberculosis infection than the PBS control or MTO adjuvant alone judging from the A1D4-specific Th1-type immune response; however, its efficacy was inferior to BCG as demonstrated by the bacterial load in the lung and spleen, and by the pathological changes in the lung. Antigen-specific single IL-2-secreting cells and different combinations with IL-2-secreting CD4+ T cells were beneficial and correlated with BCG vaccine-induced protection against TB. Antigen-specific IFN-γ+IL-2+ CD4+ T cells were the only effective biomarker significantly induced by A1D4/MTO. Among all groups, A1D4/MTO immunization also conferred the highest number of antigen-specific single IFN-γ+ and IFN-γ+TNF-α+ CD4+ T cells, which might be related to the antigen load in vivo, and single IFN-γ+ CD8+ T cells by mimicking the immune patterns of LTBIs or curable TB patients. Our strategy seems promising for the development of a TB vaccine based on multistage antigens, and subunit antigen A1D4 suspended in MTO adjuvant warrants preclinical evaluation in animal models of latent infection and may boost BCG vaccination.
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46
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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.
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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
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47
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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.
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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.
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48
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de Keijzer J, de Haas PE, de Ru AH, van Veelen PA, van Soolingen D. Disclosure of selective advantages in the "modern" sublineage of the Mycobacterium tuberculosis Beijing genotype family by quantitative proteomics. Mol Cell Proteomics 2014; 13:2632-45. [PMID: 25022876 DOI: 10.1074/mcp.m114.038380] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mycobacterium tuberculosis Beijing genotype, consisting of the more ancient (atypical) and modern (typical) emerging sublineage, is one of the most prevalent and genetically conserved genotype families and has often been associated with multidrug resistance. In this study, we employed a 2D-LC-FTICR MS approach, combined with dimethylation of tryptic peptides, to systematically compare protein abundance levels of ancient and modern Beijing strains and identify differences that could be associated with successful spread of the modern sublineage. The data is available via ProteomeXchange using the identifier PXD000931. Despite the highly uniform protein abundance ratios in both sublineages, we identified four proteins as differentially regulated between both sublineages, which could explain the apparent increased adaptation of the modern Beijing strains. These proteins are; Rv0450c/MmpL4, Rv1269c, Rv3137, and Rv3283/sseA. Transcriptional and functional analysis of these proteins in a large cohort of 29 Beijing strains showed that the mRNA levels of Rv0450c/MmpL4 are significantly higher in modern Beijing strains, whereas we also provide evidence that Rv3283/sseA is less abundant in the modern Beijing sublineage. Our findings provide a possible explanation for the increased virulence and success of the modern Beijing sublineage. In addition, in the established dataset of 1817 proteins, we demonstrate the pre-existence of several, possibly unique, antibiotic efflux pumps in the proteome of the Beijing strains. This may reflect an increased ability of Beijing strains to escape exposure to antituberculosis drugs.
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Affiliation(s)
- Jeroen de Keijzer
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands;
| | - Petra E de Haas
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands
| | - Arnoud H de Ru
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Peter A van Veelen
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Dick van Soolingen
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands; ¶Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands
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49
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The proteomics quantification dilemma. J Proteomics 2014; 107:98-102. [PMID: 24681132 DOI: 10.1016/j.jprot.2014.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 11/22/2022]
Abstract
Proteomics is dominated today by the protein expression discourse, which favorites the bottom-up approach because of its high throughput and its high sensitivity. For quantification this proceeding is misleading, if a protein is present with more than one protein species in the sample to be analyzed. The protein speciation discourse considers this more realistic situation and affords the top-down procedures or at least a separation of the protein species in advance to identification and quantification. Today all of the top-down procedures are one order of magnitude less sensitive than the bottom-up ones. To increase sensitivity and to increase throughput are major challenges for proteomics of the next years. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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50
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Wu Y, Jin Y, Pan W, Ye C, Sun X, Sun Y, Hu B, Zhou J. Comparative proteomics analysis of host cells infected with Brucella abortus A19. Electrophoresis 2014; 35:1130-43. [PMID: 24519676 DOI: 10.1002/elps.201300378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/23/2014] [Accepted: 01/24/2014] [Indexed: 01/18/2023]
Abstract
We carried out a proteomic analysis of THP-1-derived macrophages with and without Brucella abortus A19 (B. abortus A19) infection in order to study the cellular responses to B. abortus A19. The proteins were analyzed at different time points after infection with 2DE followed by MALDI-TOF/TOF identification. Comparative analysis of multiple 2DE gels revealed that the majority of changes in protein abundance appeared between 48 and 96 h after infection. MS identified 44 altered proteins, including 20 proteins increased in abundance and 24 proteins decreased in abundance, which were found to be involved in cytoskeleton, signal transduction, energy metabolism, host macromolecular biosynthesis, and stress response. Moreover, 22 genes corresponding to the altered proteins were quantified by real-time RT-PCR to examine the transcriptional profiles between infected and uninfected THP-1-derived macrophages. Finally, we mapped the altered pathways and networks using ingenuity pathway analysis, which suggested that the altered protein species were heavily favored germ cell-Sertoli cell junction signaling as the primary pathway. Furthermore, mechanisms of viral exit from host cell and macrophage stimulating protein-recepteur d'origine nantais signaling appeared to be major pathways modulated in infected cells. This study effectively provides useful dynamic protein-related information concerning B. abortus infection in macrophages.
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Affiliation(s)
- Yongping Wu
- College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, P.R. China; Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P.R. China
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