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Medikonda J, Wankar N, Asalla S, Raja SO, Yandrapally S, Jindal H, Agarwal A, Pant C, Kalivendi SV, Kumar Dubey H, Mohareer K, Gulyani A, Banerjee S. Rv0547c, a functional oxidoreductase, supports Mycobacterium tuberculosis persistence by reprogramming host mitochondrial fatty acid metabolism. Mitochondrion 2024; 78:101931. [PMID: 38986924 DOI: 10.1016/j.mito.2024.101931] [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: 04/06/2024] [Revised: 07/01/2024] [Accepted: 07/07/2024] [Indexed: 07/12/2024]
Abstract
Mycobacterium tuberculosis (Mtb) successfully thrives in the host by adjusting its metabolism and manipulating the host environment. In this study, we investigated the role of Rv0547c, a protein that carries mitochondria-targeting sequence (MTS), in mycobacterial persistence. We show that Rv0547c is a functional oxidoreductase that targets host-cell mitochondria. Interestingly, the localization of Rv0547c to mitochondria was independent of the predicted MTS but depended on specific arginine residues at the N- and C-terminals. As compared to the mitochondria-localization defective mutant, Rv0547c-2SDM, wild-type Rv0547c increased mitochondrial membrane fluidity and spare respiratory capacity. To comprehend the possible reason, comparative lipidomics was performed that revealed a reduced variability of long-chain and very long-chain fatty acids as well as altered levels of phosphatidylcholine and phosphatidylinositol class of lipids upon expression of Rv0547c, explaining the increased membrane fluidity. Additionally, the over representation of propionate metabolism and β-oxidation intermediates in Rv0547c-targeted mitochondrial fractions indicated altered fatty acid metabolism, which corroborated with changes in oxygen consumption rate (OCR) upon etomoxir treatment in HEK293T cells transiently expressing Rv0547c, resulting in enhanced mitochondrial fatty acid oxidation capacity. Furthermore, Mycobacterium smegmatis over expressing Rv0547c showed increased persistence during infection of THP-1 macrophages, which correlated with its increased expression in Mtb during oxidative and nutrient starvation stresses. This study identified for the first time an Mtb protein that alters mitochondrial metabolism and aids in survival in host macrophages by altering fatty acid metabolism to its benefit and, at the same time increases mitochondrial spare respiratory capacity to mitigate infection stresses and maintain cell viability.
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Affiliation(s)
- Jayashankar Medikonda
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Nandini Wankar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Suman Asalla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Sufi O Raja
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Haneesh Jindal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Anushka Agarwal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Chitrakshi Pant
- CSIR-Indian Institute of Chemical Technology (IICT), Uppal Road, Hyderabad, India 500007
| | - Shasi V Kalivendi
- CSIR-Indian Institute of Chemical Technology (IICT), Uppal Road, Hyderabad, India 500007
| | - Harish Kumar Dubey
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Krishnaveni Mohareer
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Akash Gulyani
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India 500046.
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Vadankula GR, Nilkanth VV, Rizvi A, Yandrapally S, Agarwal A, Chirra H, Biswas R, Arifuddin M, Nema V, Mallika A, Mande SC, Banerjee S. Confronting Tuberculosis: A Synthetic Quinoline-Isonicotinic Acid Hydrazide Hybrid Compound as a Potent Lead Molecule Against Mycobacterium tuberculosis. ACS Infect Dis 2024; 10:2288-2302. [PMID: 38717380 DOI: 10.1021/acsinfecdis.4c00277] [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: 06/15/2024]
Abstract
The current tuberculosis (TB) treatment is challenged by a complex first-line treatment for drug-sensitive (DS) TB. Additionally, the prevalence of multidrug (MDR)- and extensively drug (XDR)-resistant TB necessitates the search for new drug prototypes. We synthesized and screened 30 hybrid compounds containing aminopyridine and 2-chloro-3-formyl quinoline to arrive at a compound with potent antimycobacterial activity, UH-NIP-16. Subsequently, antimycobacterial activity against DS and MDR Mycobacterium tuberculosis (M.tb) strains were performed. It demonstrated an MIC50 value of 1.86 ± 0.21 μM for laboratory pathogenic M.tb strain H37Rv and 3.045 ± 0.813 μM for a clinical M.tb strain CDC1551. UH-NIP-16 also decreased the MIC50 values of streptomycin, isoniazid, ethambutol, and bedaquiline to about 45, 55, 68, and 76%, respectively, when used in combination, potentiating their activities. The molecule was active against a clinical MDR M.tb strain. Cytotoxicity on PBMCs from healthy donors and on human cell lines was found to be negligible. Further, blind docking of UH-NIP-16 using Auto Dock Vina and MGL tools onto diverse M.tb proteins showed high binding affinities with multiple M.tb proteins, the top five targets being metabolically critical proteins CelA1, DevS, MmaA4, lysine acetyltransferase, and immunity factor for tuberculosis necrotizing toxin. These bindings were confirmed by fluorescence spectroscopy using a representative protein, MmaA4. Envisaging that a pathogen will have a lower probability of developing resistance to a hybrid molecule with multiple targets, we propose that UH-NIP-16 can be further developed as a lead molecule with the bacteriostatic potential against M.tb, both alone and in combination with first-line drugs.
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Affiliation(s)
- Govinda Raju Vadankula
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
| | - Vipul V Nilkanth
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Arshad Rizvi
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
| | - Sriram Yandrapally
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
| | - Anushka Agarwal
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
| | - Hepshibha Chirra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Rashmita Biswas
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Vijay Nema
- Molecular Biology Division, ICMR-National Institute for Translational Virology and AIDS Research, Pune 411026, India
| | - Alvala Mallika
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Shekhar C Mande
- National Centre for Cell Science, Pune 411007, India
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Sharmistha Banerjee
- Laboratory of Molecular Pathogenesis, Department of Biochemistry, School of Life Sciences, University of Hyderabad (UoH), Hyderabad 500046, India
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Gao S, Wang Y, Yuan S, Zuo J, Jin W, Shen Y, Grenier D, Yi L, Wang Y. Cooperation of quorum sensing and central carbon metabolism in the pathogenesis of Gram-positive bacteria. Microbiol Res 2024; 282:127655. [PMID: 38402726 DOI: 10.1016/j.micres.2024.127655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 02/27/2024]
Abstract
Quorum sensing (QS), an integral component of bacterial communication, is essential in coordinating the collective response of diverse bacterial pathogens. Central carbon metabolism (CCM), serving as the primary metabolic hub for substances such as sugars, lipids, and amino acids, plays a crucial role in the life cycle of bacteria. Pathogenic bacteria often utilize CCM to regulate population metabolism and enhance the synthesis of specific cellular structures, thereby facilitating in adaptation to the host microecological environment and expediting infection. Research has demonstrated that QS can both directly or indirectly affect the CCM of numerous pathogenic bacteria, thus altering their virulence and pathogenicity. This article reviews the interplay between QS and CCM in Gram-positive pathogenic bacteria, details the molecular mechanisms by which QS modulates CCM, and lays the groundwork for investigating bacterial pathogenicity and developing innovative infection treatment drugs.
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Affiliation(s)
- Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Shuo Yuan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Wenjie Jin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec, Canada
| | - Li Yi
- Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China; College of Life Science, Luoyang Normal University, Luoyang 471934, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China.
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Gong J, Song L, Zhang Z, Dong J, Zhang S, Zhang W, Dong X, Hu Y, Liu Y. Correlations between root phosphorus acquisition and foliar phosphorus allocation reveal how grazing promotes plant phosphorus utilization. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108467. [PMID: 38412704 DOI: 10.1016/j.plaphy.2024.108467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/17/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Overgrazing and phosphorus (P) deficiency are two major factors limiting the sustainable development of grassland ecosystems. Exploring plant P utilization and acquisition strategies under grazing can provide a solid basis for determining a reasonable grazing intensity. Both foliar P allocation and root P acquisition are crucial mechanisms for plants to adapt to environmental P availability; however, their changing characteristics and correlation under grazing remain unknown. Here, we investigated foliar P fractions, root P-acquisition traits and gene expression, as well as rhizosphere and bulk soil properties of two dominant plant species, Leymus chinensis (a rhizomatous grass) and Stipa grandis (a bunchgrass), in a field grazing intensity gradient site in Inner Mongolia. Grazing induced different degrees of compensatory growth in the two dominant plant species, increased rhizosphere P availability, and alleviated plant P limitation. Under grazing, the foliar metabolite P of L. chinensis increased, whereas the nucleic acid P of S. grandis increased. Increased P fractions in L. chinensis were positively correlated with increased root exudates and rapid inorganic P absorption. For S. grandis, increased foliar P fractions were positively correlated with more fine roots, more root exudates, and up-regulated expression of genes involved in defense and P metabolism. Overall, efficient root P mobilization and uptake traits, as well as increases in leaf metabolic activity-related P fractions, supported plant compensatory growth under grazing, a process that differed between tiller types. The highest plant productivity and leaf metabolic activity-related P concentrations under medium grazing intensity clarify the underlying basis for sustainable livestock production.
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Affiliation(s)
- Jirui Gong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Liangyuan Song
- Institute of Land and Urban-Rural Development, Zhejiang University of Finance & Economics, Hangzhou, 310018, China.
| | - Zihe Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Jiaojiao Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Siqi Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Weiyuan Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xuede Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Yuxia Hu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Yingying Liu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, MOE Engineering Research Center of Desertification and Blown-sand Control, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
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Gao Y, Tariq A, Zeng F, Li X, Sardans J, Liu C, Peñuelas J. Fine-root traits are devoted to the allocation of foliar phosphorus fractions of desert species under water and phosphorus-poor environments. PHYSIOLOGIA PLANTARUM 2023; 175:e14105. [PMID: 38148234 DOI: 10.1111/ppl.14105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023]
Abstract
Traits of leaves and fine roots are expected to predict the responses and adaptation of plants to their environments. Whether and how fine-root traits (FRTs) are associated with the allocation of foliar phosphorus (P) fractions of desert species in water- and P-poor environments, however, remains unclear. We exposed seedlings of Alhagi sparsifolia Shap. (hereafter Alhagi) treated with two water and four P-supply levels for three years in open-air pot experiments and measured the concentrations of foliar P fractions, foliar traits, and FRTs. The allocation proportion of foliar nucleic acid-P and acid phosphatase (APase) activity of fine roots were significantly higher by 45.94 and 53.3% in drought and no-P treatments relative to well-watered and high-P treatments, whereas foliar metabolic-P and structural-P were significantly lower by 3.70 and 5.26%. Allocation proportions of foliar structural-P and residual-P were positively correlated with fine-root P (FRP) concentration, but nucleic acid-P concentration was negatively correlated with FRP concentration. A tradeoff was found between the allocation proportion to all foliar P fractions relative to the FRP concentration, fine-root APase activity, and amounts of carboxylates, followed by fine-root morphological traits. The requirement for a link between the aboveground and underground tissues of Alhagi was generally higher in the drought than the well-watered treatment. Altering FRTs and the allocation of P to foliar nucleic acid-P were two coupled strategies of Alhagi under conditions of drought and/or low-P. These results advance our understanding of the strategies for allocating foliar P by mediating FRTs in drought and P-poor environments.
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Affiliation(s)
- Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| | - Chenggang Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
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Yandrapally S, Agarwal A, Chatterjee A, Sarkar S, Mohareer K, Banerjee S. Mycobacterium tuberculosis EspR modulates Th1-Th2 shift by transcriptionally regulating IL-4, steering increased mycobacterial persistence and HIV propagation during co-infection. Front Immunol 2023; 14:1276817. [PMID: 37928551 PMCID: PMC10621737 DOI: 10.3389/fimmu.2023.1276817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) and HIV are known to mutually support each other during co-infection by multiple mechanisms. This synergistic influence could be either by direct interactions or indirectly through secreted host or pathogen factors that work in trans. Mtb secretes several virulence factors to modulate the host cellular environment for its persistence and escaping cell-intrinsic immune responses. We hypothesized that secreted Mtb transcription factors that target the host nucleus can directly interact with host DNA element(s) or HIV LTR during co-infection, thereby modulating immune gene expression, or driving HIV transcription, helping the synergistic existence of Mtb and HIV. Here, we show that the Mtb-secreted protein, EspR, a transcription regulator, increased mycobacterial persistence and HIV propagation during co-infection. Mechanistically, EspR localizes to the nucleus of the host cells during infection, binds to its putative cognate motif on the promoter region of the host IL-4 gene, activating IL-4 gene expression, causing high IL-4 titers that induce a Th2-type microenvironment, shifting the macrophage polarization to an M2 state as evident from CD206 dominant population over CD64. This compromised the clearance of the intracellular mycobacteria and enhanced HIV propagation. It was interesting to note that EspR did not bind to HIV LTR, although its transient expression increased viral propagation. This is the first report of an Mtb transcription factor directly regulating a host cytokine gene. This augments our understanding of the evolution of Mtb immune evasion strategies and unveils how Mtb aggravates comorbidities, such as HIV co-infection, by modulating the immune microenvironment.
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Borah Slater K, Beyß M, Xu Y, Barber J, Costa C, Newcombe J, Theorell A, Bailey MJ, Beste DJV, McFadden J, Nöh K. One-shot 13 C 15 N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux. Mol Syst Biol 2023; 19:e11099. [PMID: 36705093 PMCID: PMC9996240 DOI: 10.15252/msb.202211099] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13 C15 N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi-atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA-based 13 C15 N-metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system.
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Affiliation(s)
| | - Martin Beyß
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany.,Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Ye Xu
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jim Barber
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Catia Costa
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, UK
| | - Jane Newcombe
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Axel Theorell
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
| | - Melanie J Bailey
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, UK
| | - Dany J V Beste
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Johnjoe McFadden
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Katharina Nöh
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
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Li D, Zhao Q. Study of carbon fixation and carbon partitioning of evolved Chlorella sp.'s strain under different carbon dioxide conditions. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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9
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Ashokcoomar S, Reedoy KS, Loots DT, Beukes D, van Reenen M, Pillay B, Pillay M. M. tuberculosis curli pili (MTP) facilitates a reduction of microbicidal activity of infected THP-1 macrophages during early stages of infection. Comp Immunol Microbiol Infect Dis 2022; 90-91:101907. [DOI: 10.1016/j.cimid.2022.101907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
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Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome. Appl Environ Microbiol 2022; 88:e0059622. [PMID: 35862686 PMCID: PMC9361814 DOI: 10.1128/aem.00596-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The human microbiota, which comprises an ensemble of taxonomically and functionally diverse but often mutually cooperating microorganisms, benefits its host by shaping the host immunity, energy harvesting, and digestion of complex carbohydrates as well as production of essential nutrients. Dysbiosis in the human microbiota, especially the gut microbiota, has been reported to be linked to several diseases and metabolic disorders. Recent studies have further indicated that tracking these dysbiotic variations could potentially be exploited as biomarkers of disease states. However, the human microbiota is not geography agnostic, and hence a taxonomy-based (microbiome) biomarker for disease diagnostics has certain limitations. In comparison, (microbiome) function-based biomarkers are expected to have a wider applicability. Given that (i) the host physiology undergoes certain changes in the course of a disease and (ii) host-associated microbial communities need to adapt to this changing microenvironment of their host, we hypothesized that signatures emanating from the abundance of bacterial proteins associated with the signal transduction system (herein referred to as sensory proteins [SPs]) might be able to distinguish between healthy and diseased states. To test this hypothesis, publicly available metagenomic data sets corresponding to three diverse health conditions, namely, colorectal cancer, type 2 diabetes mellitus, and schizophrenia, were analyzed. Results demonstrated that SP signatures (derived from host-associated metagenomic samples) indeed differentiated among healthy individual and patients suffering from diseases of various severities. Our finding was suggestive of the prospect of using SP signatures as early biomarkers for diagnosing the onset and progression of multiple diseases and metabolic disorders. IMPORTANCE The composition of the human microbiota, a collection of host-associated microbes, has been shown to differ among healthy and diseased individuals. Recent studies have investigated whether tracking these variations could be exploited for disease diagnostics. It has been noted that compared to microbial taxonomies, the ensemble of functional proteins encoded by microbial genes are less likely to be affected by changes in ethnicity and dietary preferences. These functions are expected to help the microbe adapt to changing environmental conditions. Thus, healthy individuals might harbor a different set of genes than diseased individuals. To test this hypothesis, we analyzed metagenomes from healthy and diseased individuals for signatures of a particular group of proteins called sensory proteins (SP), which enable the bacteria to sense and react to changes in their microenvironment. Results demonstrated that SP signatures indeed differentiate among healthy individuals and those suffering from diseases of various severities.
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Chung WY, Abdul Rahim N, Mahamad Maifiah MH, Hawala Shivashekaregowda NK, Zhu Y, Wong EH. In silico genome-scale metabolic modeling and in vitro static time-kill studies of exogenous metabolites alone and with polymyxin B against Klebsiella pneumoniae. Front Pharmacol 2022; 13:880352. [PMID: 35991875 PMCID: PMC9386545 DOI: 10.3389/fphar.2022.880352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae is a top-prioritized Gram-negative pathogen with a high incidence in hospital-acquired infections. Polymyxins have resurged as a last-line therapy to combat Gram-negative “superbugs”, including MDR K. pneumoniae. However, the emergence of polymyxin resistance has increasingly been reported over the past decades when used as monotherapy, and thus combination therapy with non-antibiotics (e.g., metabolites) becomes a promising approach owing to the lower risk of resistance development. Genome-scale metabolic models (GSMMs) were constructed to delineate the altered metabolism of New Delhi metallo-β-lactamase- or extended spectrum β-lactamase-producing K. pneumoniae strains upon addition of exogenous metabolites in media. The metabolites that caused significant metabolic perturbations were then selected to examine their adjuvant effects using in vitro static time–kill studies. Metabolic network simulation shows that feeding of 3-phosphoglycerate and ribose 5-phosphate would lead to enhanced central carbon metabolism, ATP demand, and energy consumption, which is converged with metabolic disruptions by polymyxin treatment. Further static time–kill studies demonstrated enhanced antimicrobial killing of 10 mM 3-phosphoglycerate (1.26 and 1.82 log10 CFU/ml) and 10 mM ribose 5-phosphate (0.53 and 0.91 log10 CFU/ml) combination with 2 mg/L polymyxin B against K. pneumoniae strains. Overall, exogenous metabolite feeding could possibly improve polymyxin B activity via metabolic modulation and hence offers an attractive approach to enhance polymyxin B efficacy. With the application of GSMM in bridging the metabolic analysis and time–kill assay, biological insights into metabolite feeding can be inferred from comparative analyses of both results. Taken together, a systematic framework has been developed to facilitate the clinical translation of antibiotic-resistant infection management.
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Affiliation(s)
- Wan Yean Chung
- School of Pharmacy, Taylor’s University, Subang Jaya, Selangor, Malaysia
| | | | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), Gombak, Selangor, Malaysia
| | | | - Yan Zhu
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- *Correspondence: Yan Zhu, ; Eng Hwa Wong,
| | - Eng Hwa Wong
- School of Medicine, Taylor’s University, Subang Jaya, Selangor, Malaysia
- *Correspondence: Yan Zhu, ; Eng Hwa Wong,
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12
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Santamaria G, Ruiz-Rodriguez P, Renau-Mínguez C, Pinto FR, Coscollá M. In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes. Biomolecules 2022; 12:376. [PMID: 35327567 PMCID: PMC8945471 DOI: 10.3390/biom12030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/29/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is composed of several lineages characterized by a genome identity higher than 99%. Although the majority of the lineages are associated with humans, at least four lineages are adapted to other mammals, including different M. tuberculosis ecotypes. Host specificity is associated with higher virulence in its preferred host in ecotypes such as M. bovis. Deciphering what determines the preference of the host can reveal host-specific virulence patterns. However, it is not clear which genomic determinants might be influencing host specificity. In this study, we apply a combination of unsupervised and supervised classification methods on genomic data of ~27,000 M. tuberculosis clinical isolates to decipher host-specific genomic determinants. Host-specific genomic signatures are scarce beyond known lineage-specific mutations. Therefore, we integrated lineage-specific mutations into the iEK1011 2.0 genome-scale metabolic model to obtain lineage-specific versions of it. Flux distributions sampled from the solution spaces of these models can be accurately separated according to host association. This separation correlated with differences in cell wall processes, lipid, amino acid and carbon metabolic subsystems. These differences were observable when more than 95% of the samples had a specific growth rate significantly lower than the maximum achievable by the models. This suggests that these differences might manifest at low growth rate settings, such as the restrictive conditions M. tuberculosis suffers during macrophage infection.
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Affiliation(s)
- Guillem Santamaria
- ISysBio, University of Valencia-FISABIO Joint Unit, 46980 Paterna, Spain; (G.S.); (P.R.-R.); (C.R.-M.)
- BioISI—Biosciences & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Paula Ruiz-Rodriguez
- ISysBio, University of Valencia-FISABIO Joint Unit, 46980 Paterna, Spain; (G.S.); (P.R.-R.); (C.R.-M.)
| | - Chantal Renau-Mínguez
- ISysBio, University of Valencia-FISABIO Joint Unit, 46980 Paterna, Spain; (G.S.); (P.R.-R.); (C.R.-M.)
| | - Francisco R. Pinto
- BioISI—Biosciences & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Mireia Coscollá
- ISysBio, University of Valencia-FISABIO Joint Unit, 46980 Paterna, Spain; (G.S.); (P.R.-R.); (C.R.-M.)
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13
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Molecular perturbations in pulmonary tuberculosis patients identified by pathway-level analysis of plasma metabolic features. PLoS One 2022; 17:e0262545. [PMID: 35073339 PMCID: PMC8786114 DOI: 10.1371/journal.pone.0262545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023] Open
Abstract
Insight into the metabolic biosignature of tuberculosis (TB) may inform clinical care, reduce adverse effects, and facilitate metabolism-informed therapeutic development. However, studies often yield inconsistent findings regarding the metabolic profiles of TB. Herein, we conducted an untargeted metabolomics study using plasma from 63 Korean TB patients and 50 controls. Metabolic features were integrated with the data of another cohort from China (35 TB patients and 35 controls) for a global functional meta-analysis. Specifically, all features were matched to a known biological network to identify potential endogenous metabolites. Next, a pathway-level gene set enrichment analysis-based analysis was conducted for each study and the resulting p-values from the pathways of two studies were combined. The meta-analysis revealed both known metabolic alterations and novel processes. For instance, retinol metabolism and cholecalciferol metabolism, which are associated with TB risk and outcome, were altered in plasma from TB patients; proinflammatory lipid mediators were significantly enriched. Furthermore, metabolic processes linked to the innate immune responses and possible interactions between the host and the bacillus showed altered signals. In conclusion, our proof-of-concept study indicated that a pathway-level meta-analysis directly from metabolic features enables accurate interpretation of TB molecular profiles.
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14
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Kim JK, Park EJ, Jo EK. Itaconate, Arginine, and Gamma-Aminobutyric Acid: A Host Metabolite Triad Protective Against Mycobacterial Infection. Front Immunol 2022; 13:832015. [PMID: 35185924 PMCID: PMC8855927 DOI: 10.3389/fimmu.2022.832015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Immune metabolic regulation shapes the host-pathogen interaction during infection with Mycobacterium tuberculosis (Mtb), the pathogen of human tuberculosis (TB). Several immunometabolites generated by metabolic remodeling in macrophages are implicated in innate immune protection against Mtb infection by fine-tuning defensive pathways. Itaconate, produced by the mitochondrial enzyme immunoresponsive gene 1 (IRG1), has antimicrobial and anti-inflammatory effects, restricting intracellular mycobacterial growth. L-arginine, a component of the urea cycle, is critical for the synthesis of nitric oxide (NO) and is implicated in M1-mediated antimycobacterial responses in myeloid cells. L-citrulline, a by-product of NO production, contributes to host defense and generates L-arginine in myeloid cells. In arginase 1-expressing cells, L-arginine can be converted into ornithine, a polyamine precursor that enhances autophagy and antimicrobial protection against Mtb in Kupffer cells. Gamma-aminobutyric acid (GABA), a metabolite and neurotransmitter, activate autophagy to induce antimycobacterial host defenses. This review discusses the recent updates of the functions of the three metabolites in host protection against mycobacterial infection. Understanding the mechanisms by which these metabolites promote host defense will facilitate the development of novel host-directed therapeutics against Mtb and drug-resistant bacteria.
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Affiliation(s)
- Jin Kyung Kim
- Department of Microbiology, Chungnam National University College of Medicine, Daejeon, South Korea
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Eun-Jin Park
- Department of Microbiology, Chungnam National University College of Medicine, Daejeon, South Korea
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University College of Medicine, Daejeon, South Korea
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon, South Korea
- *Correspondence: Eun-Kyeong Jo,
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15
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Machine learning analysis of SERS fingerprinting for the rapid determination of Mycobacterium tuberculosis infection and drug resistance. Comput Struct Biotechnol J 2022; 20:5364-5377. [PMID: 36212533 PMCID: PMC9526180 DOI: 10.1016/j.csbj.2022.09.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Handheld Raman spectrometer is able to generate SERS spectra with sufficient quality for Mycobacterium tuberculosis detection. It is feasible to accurately discriminate Mtb-positive sputum from Mtb-negative sputum through SERS spectrometry. Pulmonary and extra-pulmonary Mtb strains were able to be accurately distinguished via SERS spectral analysis. Profiling of antibiotic resistance of Mtb strains was successfully achieved through machine learning analysis of SERS spectra.
Over the past decades, conventional methods and molecular assays have been developed for the detection of tuberculosis (TB). However, these techniques suffer limitations in the identification of Mycobacterium tuberculosis (Mtb), such as long turnaround time and low detection sensitivity, etc., not even mentioning the difficulty in discriminating antibiotics-resistant Mtb strains that cause great challenges in TB treatment and prevention. Thus, techniques with easy implementation for rapid diagnosis of Mtb infection are in high demand for routine TB diagnosis. Due to the label-free, low-cost and non-invasive features, surface enhanced Raman spectroscopy (SERS) has been extensively investigated for its potential in bacterial pathogen identification. However, at current stage, few studies have recruited handheld Raman spectrometer to discriminate sputum samples with or without Mtb, separate pulmonary Mtb strains from extra-pulmonary Mtb strains, or profile Mtb strains with different antibiotic resistance characteristics. In this study, we recruited a set of supervised machine learning algorithms to dissect different SERS spectra generated via a handheld Raman spectrometer with a focus on deep learning algorithms, through which sputum samples with or without Mtb strains were successfully differentiated (5-fold cross-validation accuracy = 94.32%). Meanwhile, Mtb strains isolated from pulmonary and extra-pulmonary samples were effectively separated (5-fold cross-validation accuracy = 99.86%). Moreover, Mtb strains with different drug-resistant profiles were also competently distinguished (5-fold cross-validation accuracy = 99.59%). Taken together, we concluded that, with the assistance of deep learning algorithms, handheld Raman spectrometer has a high application potential for rapid point-of-care diagnosis of Mtb infections in future.
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16
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Singh R, Dutta A, Bose T, Mande SS. A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100127. [PMID: 35909605 PMCID: PMC9325735 DOI: 10.1016/j.crmicr.2022.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/30/2022] Open
Abstract
Simulated growth of 803 gut microbes in mono- and co-cultures in 13 distinct diets. Inferred symbiotic relationships and metabolic co-operation among gut microbes. Diet-based variations in metabolic co-operation among gut microbes. Validation of in silico findings against existing literature evidence.
Gut health is intimately linked to dietary habits and the microbial community (microbiota) that flourishes within. The delicate dependency of the latter on nutritional availability is also strongly influenced by interactions (such as, parasitic or mutualistic) between the resident microbes, often affecting their growth rate and ability to produce key metabolites. Since, cultivating the entire repertoire of gut microbes is a challenging task, metabolic models (genome-based metabolic reconstructions) could be employed to predict their growth patterns and interactions. Here, we have used 803 gut microbial metabolic models from the Virtual Metabolic Human repository, and subsequently optimized and simulated them to grow on 13 dietary compositions. The presented pairwise interaction data (https://osf.io/ay8bq/) and the associated bacterial growth rates are expected to be useful for (a) deducing microbial association patterns, (b) diet-based inference of personalised gut profiles, and (c) as a steppingstone for studying multi-species metabolic interactions.
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17
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Conde R, Laires R, Gonçalves LG, Rizvi A, Barroso C, Villar M, Macedo R, Simões MJ, Gaddam S, Lamosa P, Puchades-Carrasco L, Pineda-Lucena A, Patel AB, Mande SC, Barnejee S, Matzapetakis M, Coelho AV. Discovery of serum biomarkers for diagnosis of tuberculosis by NMR metabolomics including cross-validation with a second cohort. Biomed J 2021; 45:654-664. [PMID: 34314900 PMCID: PMC9486122 DOI: 10.1016/j.bj.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background Tuberculosis (TB) is a disease with worldwide presence and a major cause of death in several developing countries. Current diagnostic methodologies often lack specificity and sensitivity, whereas a long time is needed to obtain a conclusive result. Methods In an effort to develop better diagnostic methods, this study aimed at the discovery of a biomarker signature for TB diagnosis using a Nuclear Magnetic Resonance based metabolomics approach. In this study, we acquired 1H NMR spectra of blood serum samples of groups of healthy subjects, individuals with latent TB and of patients with pulmonary and extra-pulmonary TB. The resulting data were treated with uni- and multivariate statistical analysis. Results Six metabolites (inosine, hypoxanthine, mannose, asparagine, aspartate and glutamate) were validated by an independent cohort, all of them related with metabolic processes described as associated with TB infection. Conclusion The findings of the study are according with the WHO Target Product Profile recommendations for a triage test to rule-out active TB.
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Affiliation(s)
- R Conde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - R Laires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L G Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - C Barroso
- CDP Almada-Seixal, ARSLVT, Portugal.
| | - M Villar
- CDP Venda Nova, ARSLVT, Portugal.
| | | | | | - S Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research Center, Hyderabad, India; Department of Genetics, Osmania University, Hyderabad, India.
| | - P Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - L Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - A Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain.
| | - A B Patel
- CSIR- Centre for Cellular Molecular Biology, Hyderabad, India.
| | - S C Mande
- National Centre For Cell Science, Pune, India; Present address: Council of Scientific and Industrial Research, New Delhi, India.
| | - S Barnejee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - M Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - A V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
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Usnic Acid Treatment Changes the Composition of Mycobacterium tuberculosis Cell Envelope and Alters Bacterial Redox Status. mSystems 2021; 6:6/3/e00097-21. [PMID: 33947802 PMCID: PMC8269206 DOI: 10.1128/msystems.00097-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mycobacterium tuberculosis developed efficient adaptation mechanisms in response to different environmental conditions. This resulted in the ability to survive in human macrophages and in resistance to numerous antibiotics. To get insight into bacterial responses to potent antimycobacterial natural compounds, we tested how usnic acid, a lichen-derived secondary metabolite, would influence mycobacteria at transcriptomic and metabolomic levels. The analysis of expression of sigma factors revealed a profound impact of usnic acid on one of the primary genetic regulatory systems of M. tuberculosis Combined liquid chromatography-mass spectrometry and nuclear magnetic resonance analyses allowed us to observe the perturbations in metabolic pathways, as well as in lipid composition, which took place within 24 h of exposure. Early bacterial response was related to redox homeostasis, lipid synthesis, and nucleic acid repair. Usnic acid treatment provoked disturbances of redox state in mycobacterial cells and increased production of structural elements of the cell wall and cell membrane. In addition, to increase the number of molecules related to restoration of redox balance, the rearrangements of the cell envelope were the first defense mechanisms observed under usnic acid treatment.IMPORTANCE The evaluation of mechanisms of mycobacterial response to natural products has been barely studied. However, it might be helpful to reveal bacterial adaptation strategies, which are eventually crucial for the discovery of new drug targets and, hence, understanding the resistance mechanisms. This study showed that the first-line mycobacterial defense against usnic acid, a potent antimicrobial agent, is the remodeling of the cell envelope and restoring redox homeostasis. Transcriptomic data correlated with metabolomics analysis. The observed metabolic changes appeared similar to those exerted by antibiotics.
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19
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Bioprospecting of the agaricomycete Ganoderma australe GPC191 as novel source for L-asparaginase production. Sci Rep 2021; 11:6192. [PMID: 33737513 PMCID: PMC7973716 DOI: 10.1038/s41598-021-84949-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 11/21/2022] Open
Abstract
l-Asparaginase is a therapeutically and industrially-competent enzyme, acting predominantly as an anti-neoplastic and anti-cancerous agent. The existing formulations of prokaryotic l-asparaginase are often toxic and contain l-glutaminase and urease residues, thereby increasing the purification steps. Production of l-glutaminase and urease free l-asparaginase is thus desired. In this research, bioprospecting of isolates from the less explored class Agaricomycetes was undertaken for l-asparaginase production. Plate assay (using phenol red and bromothymol blue dyes) was performed followed by estimation of l-asparaginase, l-glutaminase and urease activities by Nesslerization reaction for all the isolates. The isolate displaying the desired enzyme production was subjected to morphological, molecular identification, and phylogenetic analysis with statistical validation using Jukes-Cantor by Neighbour-joining tree of Maximum Likelihood statistical method. Among the isolates, Ganoderma australe GPC191 with significantly high zone index value (5.581 ± 0.045 at 120 h) and enzyme activity (1.57 ± 0.006 U/mL), devoid of l-glutaminase and urease activity was selected. The present study for the first-time reported G. australe as the potential source of l-glutaminase and urease-free l-asparaginase and also is one of the few studies contributing to the literature of G. australe in India. Hence, it can be postulated that it may find its future application in pharmaceutical and food industries.
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20
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Chang DPS, Guan XL. Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy. Metabolites 2021; 11:88. [PMID: 33540752 PMCID: PMC7913082 DOI: 10.3390/metabo11020088] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/16/2021] [Accepted: 01/29/2021] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a highly successful intracellular pathogen with the ability to withstand harsh conditions and reside long-term within its host. In the dormant and persistent states, the bacterium tunes its metabolism and is able to resist the actions of antibiotics. One of the main strategies Mtb adopts is through its metabolic versatility-it is able to cometabolize a variety of essential nutrients and direct these nutrients simultaneously to multiple metabolic pathways to facilitate the infection of the host. Mtb further undergo extensive remodeling of its metabolic pathways in response to stress and dormancy. In recent years, advancement in systems biology and its applications have contributed substantially to a more coherent view on the intricate metabolic networks of Mtb. With a more refined appreciation of the roles of metabolism in mycobacterial infection and drug resistance, and the success of drugs targeting metabolism, there is growing interest in further development of anti-TB therapies that target metabolism, including lipid metabolism and oxidative phosphorylation. Here, we will review current knowledge revolving around the versatility of Mtb in remodeling its metabolism during infection and dormancy, with a focus on central carbon metabolism and lipid metabolism.
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Affiliation(s)
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore;
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21
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Albors-Vaquer A, Rizvi A, Matzapetakis M, Lamosa P, Coelho AV, Patel AB, Mande SC, Gaddam S, Pineda-Lucena A, Banerjee S, Puchades-Carrasco L. Active and prospective latent tuberculosis are associated with different metabolomic profiles: clinical potential for the identification of rapid and non-invasive biomarkers. Emerg Microbes Infect 2020; 9:1131-1139. [PMID: 32486916 PMCID: PMC7448900 DOI: 10.1080/22221751.2020.1760734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/19/2020] [Indexed: 12/22/2022]
Abstract
Although 23% of world population is infected with Mycobacterium tuberculosis (M. tb), only 5-10% manifest the disease. Individuals surely exposed to M. tb that remain asymptomatic are considered potential latent TB (LTB) cases. Such asymptomatic M. tb.-exposed individuals represent a reservoir for active TB cases. Although accurate discrimination and early treatment of patients with active TB and asymptomatic M. tb.-exposed individuals are necessary to control TB, identifying those individuals at risk of developing active TB still remains a tremendous clinical challenge. This study aimed to characterize the differences in the serum metabolic profile specifically associated to active TB infected individuals or to asymptomatic M. tb.-exposed population. Interestingly, significant changes in a specific set of metabolites were shared when comparing either asymptomatic house-hold contacts of active TB patients (HHC-TB) or active TB patients (A-TB) to clinically healthy controls (HC). Furthermore, this analysis revealed statistically significant lower serum levels of aminoacids such as alanine, lysine, glutamate and glutamine, and citrate and choline in patients with A-TB, when compared to HHC-TB. The predictive ability of these metabolic changes was also evaluated. Although further validation in independent cohorts and comparison with other pulmonary infectious diseases will be necessary to assess the clinical potential, this analysis enabled the discrimination between HHC-TB and A-TB patients with an AUC value of 0.904 (confidence interval 0.81-1.00, p-value < 0.0001). Overall, the strategy described in this work could provide a sensitive, specific, and minimally invasive method that could eventually be translated into a clinical tool for TB control.
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Affiliation(s)
- A. Albors-Vaquer
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - A. Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | | | | | | | - S. C. Mande
- National Centre For Cell Science, Pune, India
- Council of Scientific and Industrial Research, New Delhi, India
| | - S. Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research Center, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - A. Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain
| | - S. Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - L. Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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22
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Reedoy KS, Loots DT, Beukes D, Reenen MV, Pillay B, Pillay M. Mycobacterium tuberculosis curli pili (MTP) is associated with significant host metabolic pathways in an A549 epithelial cell infection model and contributes to the pathogenicity of Mycobacterium tuberculosis. Metabolomics 2020; 16:116. [PMID: 33084984 DOI: 10.1007/s11306-020-01736-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION A clear understanding of the metabolome of Mycobacterium tuberculosis and its target host cell during infection is fundamental for the development of novel diagnostic tools, effective drugs and vaccines required to combat tuberculosis. The surface-located Mycobacterium tuberculosis curli pili (MTP) adhesin forms initial contact with the host cell and is therefore important for the establishment of infection. OBJECTIVE The aim of this investigation was to determine the role of MTP in modulating pathogen and host metabolic pathways in A549 epithelial cells infected with MTP proficient and deficient strains of M. tuberculosis. METHODS Uninfected A549 epithelial cells, and those infected with M. tuberculosis V9124 wild-type strain, Δmtp and the mtp-complemented strains, were subjected to metabolite extraction, two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS) and bioinformatic analyses. Univariate and multivariate statistical tests were used to identify metabolites that were significantly differentially produced in the WT-infected and ∆mtp-infected A549 epithelial cell models, comparatively. RESULTS A total of 46 metabolites occurred in significantly lower relative concentrations in the Δmtp-infected cells, indicating a reduction in nucleic acid synthesis, amino acid metabolism, glutathione metabolism, oxidative stress, lipid metabolism and peptidoglycan, compared to those cells infected with the WT strain. CONCLUSION The absence of MTP was associated with significant changes to the host metabolome, suggesting that this adhesin is an important contributor to the pathogenicity of M. tuberculosis, and supports previous findings of its potential as a suitable drug, vaccine and diagnostic target.
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Affiliation(s)
- K S Reedoy
- Medical Microbiology School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 1st Floor, Congella, Private Bag 7, Durban, 4013, South Africa
| | - D T Loots
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - D Beukes
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - M van Reenen
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - B Pillay
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - M Pillay
- Medical Microbiology School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 1st Floor, Congella, Private Bag 7, Durban, 4013, South Africa.
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23
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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24
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Prakash C, Pandey M, Talwar S, Singh Y, Kanojiya S, Pandey AK, Kumar N. Extra-ribosomal functions of Mtb RpsB in imparting stress resilience and drug tolerance to mycobacteria. Biochimie 2020; 177:87-97. [PMID: 32828823 DOI: 10.1016/j.biochi.2020.08.007] [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: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 01/21/2023]
Abstract
Emerging observations suggest that ribosomal proteins (RPs) play important extra-ribosomal roles in maintenance of cellular homeostasis. However, the mechanistic insights into these processes have not been extensively explored, especially in pathogenic bacteria. Here, we present our findings on potential extra-ribosomal functions of Mycobacterium tuberculosis (Mtb) RPs. We observed that Mtb RpsB and RpsQ are differentially localized to cell wall fraction in M. tuberculosis (H37Rv), while their M. smegmatis (Msm) homologs are primarily cytosolic. Cellular fractionation of ectopically expressed Mtb RPs in surrogate host (M. smegmatis) also shows their association with cell membrane/cell wall without any gross changes in cell morphology. M. smegmatis expressing Mtb RpsB exhibited altered redox homeostasis, decreased drug-induced ROS, reduced cell wall permeability and increased tolerance to various proteotoxic stress (oxidative stress, SDS and starvation). Mtb RpsB expression was also associated with increased resistance specifically towards Isoniazid, Ethionamide and Streptomycin. The enhanced drug tolerance was specific to Mtb RpsB and not observed upon ectopic expression of M. smegmatis homolog (Msm RpsB). Interestingly, C-terminus deletion in Mtb RpsB affected its localization and reversed the stress-resilient phenotypes. We also observed that M. tuberculosis (H37Rv) with upregulated RpsB levels had higher intracellular survival in macrophage. All these observations hint towards existence of moonlighting roles of Mtb RpsB in imparting stress resilience to mycobacteria. This work open avenues for further exploration of alternative pathways associated with fitness and drug tolerance in mycobacteria.
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Affiliation(s)
- Chetan Prakash
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Manitosh Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India; Department of Life Sciences, ITM University, Gwalior 475001, Madhya Pradesh, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yatendra Singh
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Sanjeev Kanojiya
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Amit Kumar Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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25
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Chew BLA, Tanoto FR, Luo D. LC-MS assay targeting the mycobacterial indirect aminoacylation pathway uncovers glutaminase activities of the nondiscriminating aspartyl-synthetase. FEBS Lett 2020; 594:2159-2167. [PMID: 32279326 DOI: 10.1002/1873-3468.13786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/28/2020] [Accepted: 03/26/2020] [Indexed: 11/08/2022]
Abstract
The synthesis of asparagine (Asn)-tRNAAsn in most prokaryotes uses an indirect aminoacylation pathway involving a nondiscriminating aspartyl synthetase (ND-AspRS) and a glutamine amidotransferase (GatCAB). This was recently implicated as an adaptive mistranslation mechanism for antimicrobial resistance in Mycobacterium tuberculosis, but it remains poorly understood. We report an accessible liquid chromatography-mass spectrometry method with unparalleled chemical specificity, sensitivity, and quantification over the current assays to enable the direct analysis and drug screening campaigns of this pathway. Through this method, we show that the mycobacterial ND-AspRS stimulates the glutaminase activity of GatCAB. We further uncover novel glutaminase activity of the synthetase. These biological insights help better understand the indirect aminoacylation biology and allude to new roles beyond protein translation.
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Affiliation(s)
- Bing Liang Alvin Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore City, Singapore
| | | | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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26
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Larsen MH, Lacourciere K, Parker TM, Kraigsley A, Achkar JM, Adams LB, Dupnik KM, Hall-Stoodley L, Hartman T, Kanipe C, Kurtz SL, Miller MA, Salvador LCM, Spencer JS, Robinson RT. The Many Hosts of Mycobacteria 8 (MHM8): A conference report. Tuberculosis (Edinb) 2020; 121:101914. [PMID: 32279870 PMCID: PMC7428850 DOI: 10.1016/j.tube.2020.101914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/18/2022]
Abstract
Mycobacteria are important causes of disease in human and animal hosts. Diseases caused by mycobacteria include leprosy, tuberculosis (TB), nontuberculous mycobacteria (NTM) infections and Buruli Ulcer. To better understand and treat mycobacterial disease, clinicians, veterinarians and scientists use a range of discipline-specific approaches to conduct basic and applied research, including conducting epidemiological surveys, patient studies, wildlife sampling, animal models, genetic studies and computational simulations. To foster the exchange of knowledge and collaboration across disciplines, the Many Hosts of Mycobacteria (MHM) conference series brings together clinical, veterinary and basic scientists who are dedicated to advancing mycobacterial disease research. Started in 2007, the MHM series recently held its 8th conference at the Albert Einstein College of Medicine (Bronx, NY). Here, we review the diseases discussed at MHM8 and summarize the presentations on research advances in leprosy, NTM and Buruli Ulcer, human and animal TB, mycobacterial disease comorbidities, mycobacterial genetics and 'omics, and animal models. A mouse models workshop, which was held immediately after MHM8, is also summarized. In addition to being a resource for those who were unable to attend MHM8, we anticipate this review will provide a benchmark to gauge the progress of future research concerning mycobacteria and their many hosts.
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Affiliation(s)
- Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karen Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Tina M Parker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Alison Kraigsley
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN, USA
| | - Jacqueline M Achkar
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Linda B Adams
- Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Programs, Baton Rouge, LA, USA
| | - Kathryn M Dupnik
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Travis Hartman
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carly Kanipe
- Department of Immunobiology, Iowa State University, Ames, IA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Sherry L Kurtz
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Washington, DC, USA
| | - Michele A Miller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Liliana C M Salvador
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
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