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Mulholland CV, Wiggins TJ, Cui J, Vilchèze C, Rajagopalan S, Shultis MW, Reyes-Fernández EZ, Jacobs WR, Berney M. Propionate prevents loss of the PDIM virulence lipid in Mycobacterium tuberculosis. Nat Microbiol 2024; 9:1607-1618. [PMID: 38740932 DOI: 10.1038/s41564-024-01697-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Phthiocerol dimycocerosate (PDIM) is an essential virulence lipid of Mycobacterium tuberculosis. In vitro culturing rapidly selects for spontaneous PDIM-negative mutants that have attenuated virulence and increased cell wall permeability, thus impacting the relevance of experimental findings. PDIM loss can also reduce the efficacy of the BCG Pasteur vaccine. Here we show that vancomycin susceptibility can rapidly screen for M. tuberculosis PDIM production. We find that metabolic deficiency of methylmalonyl-CoA impedes the growth of PDIM-producing bacilli, selecting for PDIM-negative variants. Supplementation with odd-chain fatty acids, cholesterol or vitamin B12 restores PDIM-positive bacterial growth. Specifically, we show that propionate supplementation enhances PDIM-producing bacterial growth and selects against PDIM-negative mutants, analogous to in vivo conditions. Our study provides a simple approach to screen for and maintain PDIM production, and reveals how discrepancies between the host and in vitro nutrient environments can attenuate bacterial pathogenicity.
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Affiliation(s)
- Claire V Mulholland
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Thomas J Wiggins
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Jinhua Cui
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Saranathan Rajagopalan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael W Shultis
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | | | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA.
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2
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Gong Z, Qu Z, Cai J. Gene cloning, expression, and enzyme kinetics analysis of Eimeria tenella 2- methylcitrate synthase. Vet Parasitol 2024; 328:110193. [PMID: 38704976 DOI: 10.1016/j.vetpar.2024.110193] [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: 01/16/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024]
Abstract
In prokaryotes and lower eukaryotes, 2-methylcitrate cycle (2-MCC) is the main pathway for propionate decomposition and transformation, but little is known about the 2-MCC pathway of Eimeria tenella. The analysis of genomic data found that the coding gene of 2- methylcitrate synthase (EC 2.3.3.5, PrpC) exists in E. tenella, which is a key enzyme of 2-MCC pathway. Through the search analysis of the database (ToxoDB), it was found that ETH_ 00026655 contains the complete putative sequence of EtprpC. In this study, we amplified the ORF sequence of EtprpC based on putative sequence. Then, prokaryotic expression, enzyme activity and kinetic analysis was performed. The results showed that the EtprpC ORF sequence was 1272 bp, encoding a 46.3 kDa protein comprising 424 amino acids. Enzyme activity assays demonstrate linearity between the initial reaction rate (OD/min) and EtPrpC concentration (ranging from 1.5 to 9 µg/reaction), with optimal enzyme activity observed at 41°C and pH 8.0. The results of enzymatic kinetic analysis showed that the Km of EtPrpC for propionyl-CoA, oxaloacetic acid, and acetyl-CoA was 5.239 ± 0.17 mM, 1.102 ± 0.08 μM, and 5.999 ± 1.24 μM, respectively. The Vmax was 191.11 ± 19.1 nmol/min/mg, 225.48 ± 14.4 nmol/min/mg, and 370.02 ± 25.8 nmol/min/mg when EtPrpC concentration at 4, 6, and 8 μg, respectively. Although the ability of EtPrpC to catalyze acetyl-CoA is only 0.11% of its ability to catalyze propionyl-CoA, it indicates that the 2-MCC pathway in E. tenella is similar to that in bacteria and may have a bypass function in the TCA cycle. This study can provide the theoretical foundation for the new drug targets and the development of new anticoccidial drugs.
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Affiliation(s)
- Zhenxing Gong
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia Province 750021, People's Republic of China; State Key Laboratory of Veterinary Etiological Biology, Lanzhou, Gansu Province 730046, People's Republic of China; Key Laboratory of Veterinary Parasitology of Gansu Province, 730046, People's Republic of China; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig, 730046, People's Republic of China; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China.
| | - Zigang Qu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou, Gansu Province 730046, People's Republic of China; Key Laboratory of Veterinary Parasitology of Gansu Province, 730046, People's Republic of China; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig, 730046, People's Republic of China; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China.
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou, Gansu Province 730046, People's Republic of China; Key Laboratory of Veterinary Parasitology of Gansu Province, 730046, People's Republic of China; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig, 730046, People's Republic of China; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China.
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3
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Isaiah S, Loots DT, van Furth AMT, Davoren E, van Elsland S, Solomons R, van der Kuip M, Mason S. Urinary markers of Mycobacterium tuberculosis and dysbiosis in paediatric tuberculous meningitis cases undergoing treatment. Gut Pathog 2024; 16:14. [PMID: 38475868 DOI: 10.1186/s13099-024-00609-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The pathogenesis of tuberculous meningitis (TBM) involves infection by Mycobacterium tuberculosis in the meninges and brain. However, recent studies have shown that the immune response and inflammatory processes triggered by TBM can have significant effects on gut microbiota. Disruptions in the gut microbiome have been linked to various systemic consequences, including altered immunity and metabolic dysregulation. Inflammation caused by TBM, antibiotic treatment, and changes in host immunity can all influence the composition of gut microbes. This complex relationship between TBM and the gut microbiome is of great importance in clinical settings. To gain a deeper understanding of the intricate interactions between TBM and the gut microbiome, we report innovative insights into the development of the disease in response to treatment. Ultimately, this could lead to improved outcomes, management strategies and quality of life for individuals affected by TBM. METHOD We used a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to investigate metabolites associated with gut metabolism in paediatric participants by analysing the urine samples collected from a control group (n = 40), and an experimental group (n = 35) with confirmed TBM, which were subdivided into TBM stage 1 (n = 8), stage 2 (n = 11) and stage 3 (n = 16). FINDINGS Our metabolomics investigation showed that, of the 78 initially selected compounds of microbiome origin, eight unique urinary metabolites were identified: 2-methylbutyrlglycine, 3-hydroxypropionic acid, 3-methylcrotonylglycine, 4-hydroxyhippuric acid, 5-hydroxyindoleacetic acid, 5-hydroxyhexanoic acid, isobutyrylglycine, and phenylacetylglutamine as urinary markers of dysbiosis in TBM. CONCLUSION These results - which are supported by previous urinary studies of tuberculosis - highlight the importance of gut metabolism and of identifying corresponding microbial metabolites as novel points for the foundation of improved management of TBM patients.
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Affiliation(s)
- Simon Isaiah
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Du Toit Loots
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - A Marceline Tutu van Furth
- Vrije Universiteit, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Centers, Emma Children's Hospital, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Elmarie Davoren
- Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Martijn van der Kuip
- Vrije Universiteit, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Centers, Emma Children's Hospital, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Shayne Mason
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa.
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4
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Sparks IL, Kado T, Prithviraj M, Nijjer J, Yan J, Morita YS. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nat Commun 2024; 15:2191. [PMID: 38467648 PMCID: PMC10928101 DOI: 10.1038/s41467-024-46565-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
The growth and division of mycobacteria, which include clinically relevant pathogens, deviate from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. The phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM) are cell envelope components critical for host-pathogen interactions, but their physiological functions in mycobacteria remained elusive. In this work, using biosynthetic mutants of these lipoglycans, we examine their roles in maintaining cell envelope integrity in Mycobacterium smegmatis and Mycobacterium tuberculosis. We find that mutants defective in producing mature LAM fail to maintain rod cell shape specifically at the new pole and para-septal regions whereas a mutant that produces a larger LAM becomes multi-septated. Therefore, LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell wall integrity and septal placement.
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Affiliation(s)
- Ian L Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
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5
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Campos-Pardos E, Uranga S, Picó A, Gómez AB, Gonzalo-Asensio J. Dependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution. Nat Commun 2024; 15:2161. [PMID: 38461302 PMCID: PMC10924821 DOI: 10.1038/s41467-024-46449-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
Human and animal tuberculosis is caused by the Mycobacterium tuberculosis Complex (MTBC), which has evolved a genomic decay of cobalamin (vitamin B12) biosynthetic genes. Accordingly, and in sharp contrast to environmental, opportunistic and ancestor mycobacteria; we demonstrate that M. tuberculosis (Mtb), M. africanum, and animal-adapted lineages, lack endogenous production of cobalamin, yet they retain the capacity for exogenous uptake. A B12 anemic model in immunocompromised and immunocompetent mice, demonstrates improved survival, and lower bacteria in organs, in B12 anemic animals infected with Mtb relative to non-anemic controls. Conversely, no differences were observed between mice groups infected with M. canettii, an ancestor mycobacterium which retains cobalamin biosynthesis. Interrogation of the B12 transcriptome in three MTBC strains defined L-methionine synthesis by metE and metH genes as a key phenotype. Expression of metE is repressed by a cobalamin riboswitch, while MetH requires the cobalamin cofactor. Thus, deletion of metE predominantly attenuates Mtb in anemic mice; although inactivation of metH exclusively causes attenuation in non-anemic controls. Here, we show how sub-physiological levels of B12 in the host antagonizes Mtb virulence, and describe a yet unknown mechanism of host-pathogen cross-talk with implications for B12 anemic populations.
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Affiliation(s)
- Elena Campos-Pardos
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Picó
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Belén Gómez
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain.
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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6
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog 2024; 20:e1012050. [PMID: 38422159 DOI: 10.1371/journal.ppat.1012050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved lldD2 variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of lldD2 mutations in adapting to host stress.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Young Yon Kwon
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Abigail M Frey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Andrew J Vickers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sheng Hui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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7
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Chugh S, Tiwari P, Suri C, Gupta SK, Singh P, Bouzeyen R, Kidwai S, Srivastava M, Rameshwaram NR, Kumar Y, Asthana S, Singh R. Polyphosphate kinase-1 regulates bacterial and host metabolic pathways involved in pathogenesis of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2024; 121:e2309664121. [PMID: 38170746 PMCID: PMC10786269 DOI: 10.1073/pnas.2309664121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Inorganic polyphosphate (polyP) is primarily synthesized by Polyphosphate Kinase-1 (PPK-1) and regulates numerous cellular processes, including energy metabolism, stress adaptation, drug tolerance, and microbial pathogenesis. Here, we report that polyP interacts with acyl CoA carboxylases, enzymes involved in lipid biosynthesis in Mycobacterium tuberculosis. We show that deletion of ppk-1 in M. tuberculosis results in transcriptional and metabolic reprogramming. In comparison to the parental strain, the Δppk-1 mutant strain had reduced levels of virulence-associated lipids such as PDIMs and TDM. We also observed that polyP deficiency in M. tuberculosis is associated with enhanced phagosome-lysosome fusion in infected macrophages and attenuated growth in mice. Host RNA-seq analysis revealed decreased levels of transcripts encoding for proteins involved in either type I interferon signaling or formation of foamy macrophages in the lungs of Δppk-1 mutant-infected mice relative to parental strain-infected animals. Using target-based screening and molecular docking, we have identified raloxifene hydrochloride as a broad-spectrum PPK-1 inhibitor. We show that raloxifene hydrochloride significantly enhanced the activity of isoniazid, bedaquiline, and pretomanid against M. tuberculosis in macrophages. Additionally, raloxifene inhibited the growth of M. tuberculosis in mice. This is an in-depth study that provides mechanistic insights into the regulation of mycobacterial pathogenesis by polyP deficiency.
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Affiliation(s)
- Saurabh Chugh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Prabhakar Tiwari
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Charu Suri
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Padam Singh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Rania Bouzeyen
- Institut Pasteur de Tunis, Laboratory of Transmission, Control and Immunobiology of Infections, LRII IPT02, Tunis1002, Tunisia
| | - Saqib Kidwai
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Nagender Rao Rameshwaram
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
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8
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Chen Y, MacGilvary NJ, Tan S. Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid metabolism regulator. PLoS Genet 2024; 20:e1011143. [PMID: 38266039 PMCID: PMC10843139 DOI: 10.1371/journal.pgen.1011143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/05/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
Successful colonization of the host requires Mycobacterium tuberculosis (Mtb) to sense and respond coordinately to disparate environmental cues during infection and adapt its physiology. However, how Mtb response to environmental cues and the availability of key carbon sources may be integrated is poorly understood. Here, by exploiting a reporter-based genetic screen, we have unexpectedly found that overexpression of transcription factors involved in Mtb lipid metabolism altered the dampening effect of low environmental potassium concentrations ([K+]) on the pH response of Mtb. Cholesterol is a major carbon source for Mtb during infection, and transcriptional analyses revealed that Mtb response to acidic pH was augmented in the presence of cholesterol and vice versa. Strikingly, deletion of the putative lipid regulator mce3R had little effect on Mtb transcriptional response to acidic pH or cholesterol individually, but resulted specifically in loss of cholesterol response augmentation in the simultaneous presence of acidic pH. Similarly, while mce3R deletion had little effect on Mtb response to low environmental [K+] alone, augmentation of the low [K+] response by the simultaneous presence of cholesterol was lost in the mutant. Finally, a mce3R deletion mutant was attenuated for growth in foamy macrophages and for colonization in a murine infection model that recapitulates caseous necrotic lesions and the presence of foamy macrophages. These findings reveal the critical coordination between Mtb response to environmental cues and cholesterol, a vital carbon source, and establishes Mce3R as a transcription factor that crucially serves to integrate these signals.
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Affiliation(s)
- Yue Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Nathan J. MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Current affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
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9
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Nakayasu M, Takamatsu K, Kanai K, Masuda S, Yamazaki S, Aoki Y, Shibata A, Suda W, Shirasu K, Yazaki K, Sugiyama A. Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids. mBio 2023; 14:e0059923. [PMID: 37772873 PMCID: PMC10653915 DOI: 10.1128/mbio.00599-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Saponins are a group of plant specialized metabolites with various bioactive properties, both for human health and soil microorganisms. Our previous works demonstrated that Sphingobium is enriched in both soils treated with a steroid-type saponin, such as tomatine, and in the tomato rhizosphere. Despite the importance of saponins in plant-microbe interactions in the rhizosphere, the genes involved in the catabolism of saponins and their aglycones (sapogenins) remain largely unknown. Here we identified several enzymes that catalyzed the degradation of steroid-type saponins in a Sphingobium isolate from tomato roots, RC1. A comparative genomic analysis of Sphingobium revealed the limited distribution of genes for saponin degradation in our saponin-degrading isolates and several other isolates, suggesting the possible involvement of the saponin degradation pathway in the root colonization of Sphingobium spp. The genes that participate in the catabolism of sapogenins could be applied to the development of new industrially valuable sapogenin molecules.
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Affiliation(s)
- Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Kyoko Takamatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Keiko Kanai
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Shinichi Yamazaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
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10
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Mulholland CV, Wiggins TJ, Cui J, Vilchèze C, Rajagopalan S, Shultis MW, Reyes-Fernández EZ, Jacobs WR, Berney M. The PDIM paradox of Mycobacterium tuberculosis: new solutions to a persistent problem. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562559. [PMID: 37905120 PMCID: PMC10614861 DOI: 10.1101/2023.10.16.562559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phthiocerol dimycocerosate (PDIM) is an essential virulence lipid of Mycobacterium tuberculosis. In vitro culturing rapidly selects for spontaneous mutations that cause PDIM loss leading to virulence attenuation and increased cell wall permeability. We discovered that PDIM loss is due to a metabolic deficiency of methylmalonyl-CoA that impedes the growth of PDIM-producing bacilli. This can be remedied by supplementation with odd-chain fatty acids, cholesterol, or vitamin B12. We developed a much-needed facile and scalable routine assay for PDIM production and show that propionate supplementation enhances the growth of PDIM-producing bacilli and selects against PDIM-negative mutants, analogous to in vivo conditions. Our results solve a major issue in tuberculosis research and exemplify how discrepancies between the host and in vitro nutrient environments can attenuate bacterial pathogenicity.
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Affiliation(s)
- Claire V. Mulholland
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
| | | | | | - Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
| | - Saranathan Rajagopalan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
| | - Michael W. Shultis
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
| | | | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine,
Bronx, New York, USA
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11
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Allué-Guardia A, Garcia-Vilanova A, Schami AM, Olmo-Fontánez AM, Hicks A, Peters J, Maselli DJ, Wewers MD, Wang Y, Torrelles JB. Exposure of Mycobacterium tuberculosis to human alveolar lining fluid shows temporal and strain-specific adaptation to the lung environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559381. [PMID: 37808780 PMCID: PMC10557635 DOI: 10.1101/2023.09.27.559381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Upon infection, Mycobacterium tuberculosis ( M.tb ) reaches the alveolar space and comes in close contact with human alveolar lining fluid (ALF) for an uncertain period of time prior to its encounter with alveolar cells. We showed that homeostatic ALF hydrolytic enzymes modify the M.tb cell envelope, driving M.tb -host cell interactions. Still, the contribution of ALF during M.tb infection is poorly understood. Here, we exposed 4 M.tb strains with different levels of virulence, transmissibility, and drug resistance (DR) to physiological concentrations of human ALF for 15-min and 12-h, and performed RNA sequencing. Gene expression analysis showed a temporal and strain-specific adaptation to human ALF. Differential expression (DE) of ALF-exposed vs. unexposed M.tb revealed a total of 397 DE genes associated with lipid metabolism, cell envelope and processes, intermediary metabolism and respiration, and regulatory proteins, among others. Most DE genes were detected at 12-h post-ALF exposure, with DR- M.tb strain W-7642 having the highest number of DE genes. Interestingly, genes from the KstR2 regulon, which controls the degradation of cholesterol C and D rings, were significantly upregulated in all strains post-ALF exposure. These results indicate that M.tb -ALF contact drives initial metabolic and physiologic changes in M.tb , with potential implications in infection outcome. IMPORTANCE Tuberculosis, caused by airborne pathogen Mycobacterium tuberculosis ( M.tb ), is one of the leading causes of mortality worldwide. Upon infection, M.tb reaches the alveoli and gets in contact with human alveolar lining fluid (ALF), where ALF hydrolases modify the M.tb cell envelope driving subsequent M.tb -host cell interactions. Still, the contributions of ALF during infection are poorly understood. We exposed 4 M.tb strains to ALF for 15-min and 12-h and performed RNA sequencing, demonstrating a temporal and strain-specific adaptation of M.tb to ALF. Interestingly, genes associated with cholesterol degradation were highly upregulated in all strains. This study shows for the first time that ALF drives global metabolic changes in M.tb during the initial stages of the infection, with potential implications in disease outcome. Biologically relevant networks and common and strain-specific bacterial determinants derived from this study could be further investigated as potential therapeutic candidates.
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12
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Pandey M, Talwar S, Pal R, Nain V, Johri S, Singhal A, Pandey AK. Transcription factor mce3R modulates antibiotics and disease persistence in Mycobacteriumtuberculosis. Res Microbiol 2023; 174:104082. [PMID: 37244349 DOI: 10.1016/j.resmic.2023.104082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
Transcription factors (TFs) of Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis, regulate a network of pathways that help prolong the survival of Mtb inside the host. In this study, we have characterized a transcription repressor gene (mce3R) from the TetR family, that encodes for Mce3R protein in Mtb. We demonstrated that the mce3R gene is dispensable for the growth of Mtb on cholesterol. Gene expression analysis suggests that the transcription of genes belonging to the mce3R regulon is independent of the carbon source. We found that, in comparison to the wild type, the mce3R deleted strain (Δmce3R) generated more intracellular ROS and demonstrated reduced susceptibility to oxidative stress. Total lipid analysis suggests that mce3R regulon encoded proteins modulate the biosynthesis of cell wall lipids in Mtb. Interestingly, the absence of Mce3R increased the frequency of generation of antibiotic persisters in Mtb and imparted in-vivo growth advantage phenotype in guinea pigs. In conclusion, genes belonging to the mce3R regulon modulate the frequency of generation of persisters in Mtb. Hence, targeting mce3R regulon encoded proteins could potentiate the current regimen by eliminating persisters during Mtb infection.
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Affiliation(s)
- Manitosh Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India; Department of Life Science, ITM University, Gwalior, Madhya Pradesh, India
| | - Sakshi Talwar
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Rahul Pal
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Vaibhav Nain
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Sonia Johri
- Department of Life Science, ITM University, Gwalior, Madhya Pradesh, India
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science Technology and Research (A∗STAR), Singapore 138648, Republic of Singapore; Singapore Immunology Network (SIgN), A∗STAR, Singapore 138648, Republic of Singapore
| | - Amit Kumar Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India.
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13
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Maxson ME, Das L, Goldberg MF, Porcelli SA, Chan J, Jacobs WR. Mycobacterium tuberculosis Central Metabolism Is Key Regulator of Macrophage Pyroptosis and Host Immunity. Pathogens 2023; 12:1109. [PMID: 37764917 PMCID: PMC10535942 DOI: 10.3390/pathogens12091109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Metabolic dysregulation in Mycobacterium tuberculosis results in increased macrophage apoptosis or pyroptosis. However, mechanistic links between Mycobacterium virulence and bacterial metabolic plasticity remain ill defined. In this study, we screened random transposon insertions of M. bovis BCG to identify mutants that induce pyroptotic death of the infected macrophage. Analysis of the transposon insertion sites identified a panel of fdr (functioning death repressor) genes, which were shown in some cases to encode functions central to Mycobacterium metabolism. In-depth studies of one fdr gene, fdr8 (BCG3787/Rv3727), demonstrated its important role in the maintenance of M. tuberculosis and M. bovis BCG redox balance in reductive stress conditions in the host. Our studies expand the subset of known Mycobacterium genes linking bacterial metabolic plasticity to virulence and also reveal that the broad induction of pyroptosis by an intracellular bacterial pathogen is linked to enhanced cellular immunity in vivo.
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Affiliation(s)
- Michelle E. Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Lahari Das
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | | | - Steven A. Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | - John Chan
- Department of Medicine, New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, USA;
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
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14
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Chen Y, MacGilvary NJ, Tan S. Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid utilization regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554309. [PMID: 37662244 PMCID: PMC10473576 DOI: 10.1101/2023.08.22.554309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
How bacterial response to environmental cues and nutritional sources may be integrated in enabling host colonization is poorly understood. Exploiting a reporter-based screen, we discovered that overexpression of Mycobacterium tuberculosis (Mtb) lipid utilization regulators altered Mtb acidic pH response dampening by low environmental potassium (K+). Transcriptional analyses unveiled amplification of Mtb response to acidic pH in the presence of cholesterol, a major carbon source for Mtb during infection, and vice versa. Strikingly, deletion of the putative lipid regulator mce3R resulted in loss of augmentation of (i) cholesterol response at acidic pH, and (ii) low [K+] response by cholesterol, with minimal effect on Mtb response to each signal individually. Finally, the ∆mce3R mutant was attenuated for colonization in a murine model that recapitulates lesions with lipid-rich foamy macrophages. These findings reveal critical coordination between bacterial response to environmental and nutritional cues, and establish Mce3R as a crucial integrator of this process.
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Affiliation(s)
- Yue Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Nathan J. MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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15
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Prithviraj M, Kado T, Mayfield JA, Young DC, Huang AD, Motooka D, Nakamura S, Siegrist MS, Moody DB, Morita YS. Tuberculostearic Acid Controls Mycobacterial Membrane Compartmentalization. mBio 2023; 14:e0339622. [PMID: 36976029 PMCID: PMC10127668 DOI: 10.1128/mbio.03396-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
The intracellular membrane domain (IMD) is a laterally discrete region of the mycobacterial plasma membrane, enriched in the subpolar region of the rod-shaped cell. Here, we report genome-wide transposon sequencing to discover the controllers of membrane compartmentalization in Mycobacterium smegmatis. The putative gene cfa showed the most significant effect on recovery from membrane compartment disruption by dibucaine. Enzymatic analysis of Cfa and lipidomic analysis of a cfa deletion mutant (Δcfa) demonstrated that Cfa is an essential methyltransferase for the synthesis of major membrane phospholipids containing a C19:0 monomethyl-branched stearic acid, also known as tuberculostearic acid (TBSA). TBSA has been intensively studied due to its abundant and genus-specific production in mycobacteria, but its biosynthetic enzymes had remained elusive. Cfa catalyzed the S-adenosyl-l-methionine-dependent methyltransferase reaction using oleic acid-containing lipid as a substrate, and Δcfa accumulated C18:1 oleic acid, suggesting that Cfa commits oleic acid to TBSA biosynthesis, likely contributing directly to lateral membrane partitioning. Consistent with this model, Δcfa displayed delayed restoration of subpolar IMD and delayed outgrowth after bacteriostatic dibucaine treatment. These results reveal the physiological significance of TBSA in controlling lateral membrane partitioning in mycobacteria. IMPORTANCE As its common name implies, tuberculostearic acid is an abundant and genus-specific branched-chain fatty acid in mycobacterial membranes. This fatty acid, 10-methyl octadecanoic acid, has been an intense focus of research, particularly as a diagnostic marker for tuberculosis. It was discovered in 1934, and yet the enzymes that mediate the biosynthesis of this fatty acid and the functions of this unusual fatty acid in cells have remained elusive. Through a genome-wide transposon sequencing screen, enzyme assay, and global lipidomic analysis, we show that Cfa is the long-sought enzyme that is specifically involved in the first step of generating tuberculostearic acid. By characterizing a cfa deletion mutant, we further demonstrate that tuberculostearic acid actively regulates lateral membrane heterogeneity in mycobacteria. These findings indicate the role of branched fatty acids in controlling the functions of the plasma membrane, a critical barrier for the pathogen to survive in its human host.
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Affiliation(s)
- Malavika Prithviraj
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jacob A. Mayfield
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David C. Young
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Annie D. Huang
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - M. Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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16
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McDowell JR, Bai G, Lasek-Nesselquist E, Eisele LE, Wu Y, Hurteau G, Johnson R, Bai Y, Chen Y, Chan J, McDonough KA. Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification. Mol Microbiol 2023; 119:401-422. [PMID: 36760076 PMCID: PMC10315211 DOI: 10.1111/mmi.15030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 02/11/2023]
Abstract
Cyclic AMP (cAMP) signaling is essential to Mycobacterium tuberculosis (Mtb) pathogenesis. However, the roles of phosphodiesterases (PDEs) Rv0805, and the recently identified Rv1339, in cAMP homeostasis and Mtb biology are unclear. We found that Rv0805 modulates Mtb growth within mice, macrophages and on host-associated carbon sources. Mycobacterium bovis BCG grown on a combination of propionate and glycerol as carbon sources showed high levels of cAMP and had a strict requirement for Rv0805 cNMP hydrolytic activity. Supplementation with vitamin B12 or spontaneous genetic mutations in the pta-ackA operon restored the growth of BCGΔRv0805 and eliminated propionate-associated cAMP increases. Surprisingly, reduction of total cAMP levels by ectopic expression of Rv1339 restored only 20% of growth, while Rv0805 complementation fully restored growth despite a smaller effect on total cAMP levels. Deletion of an Rv0805 localization domain also reduced BCG growth in the presence of propionate and glycerol. We propose that localized Rv0805 cAMP hydrolysis modulates activity of a specialized pathway associated with propionate metabolism, while Rv1339 has a broader role in cAMP homeostasis. Future studies will address the biological roles of Rv0805 and Rv1339, including their impacts on metabolism, cAMP signaling and Mtb pathogenesis.
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Affiliation(s)
- James R. McDowell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Immunology and Microbial Disease, MC-151, Albany Medical College, Albany, NY 12208-3479
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Yan Wu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Gregory Hurteau
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yinlan Bai
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yong Chen
- Albert Einstein College of Medicine, Bronx, NY
| | - John Chan
- Albert Einstein College of Medicine, Bronx, NY
| | - Kathleen A. McDonough
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
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17
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Bedard M, van der Niet S, Bernard EM, Babunovic G, Cheng TY, Aylan B, Grootemaat AE, Raman S, Botella L, Ishikawa E, O'Sullivan MP, O'Leary S, Mayfield JA, Buter J, Minnaard AJ, Fortune SM, Murphy LO, Ory DS, Keane J, Yamasaki S, Gutierrez MG, van der Wel N, Moody DB. A terpene nucleoside from M. tuberculosis induces lysosomal lipid storage in foamy macrophages. J Clin Invest 2023; 133:161944. [PMID: 36757797 PMCID: PMC10014106 DOI: 10.1172/jci161944] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Induction of lipid-laden foamy macrophages is a cellular hallmark of tuberculosis (TB) disease, which involves the transformation of infected phagolysosomes from a site of killing into a nutrient-rich replicative niche. Here, we show that a terpenyl nucleoside shed from Mycobacterium tuberculosis, 1-tuberculosinyladenosine (1-TbAd), caused lysosomal maturation arrest and autophagy blockade, leading to lipid storage in M1 macrophages. Pure 1-TbAd, or infection with terpenyl nucleoside-producing M. tuberculosis, caused intralysosomal and peribacillary lipid storage patterns that matched both the molecules and subcellular locations known in foamy macrophages. Lipidomics showed that 1-TbAd induced storage of triacylglycerides and cholesterylesters and that 1-TbAd increased M. tuberculosis growth under conditions of restricted lipid access in macrophages. Furthermore, lipidomics identified 1-TbAd-induced lipid substrates that define Gaucher's disease, Wolman's disease, and other inborn lysosomal storage diseases. These data identify genetic and molecular causes of M. tuberculosis-induced lysosomal failure, leading to successful testing of an agonist of TRPML1 calcium channels that reverses lipid storage in cells. These data establish the host-directed cellular functions of an orphan effector molecule that promotes survival in macrophages, providing both an upstream cause and detailed picture of lysosome failure in foamy macrophages.
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Affiliation(s)
- Melissa Bedard
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sanne van der Niet
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Elliott M Bernard
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gregory Babunovic
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Beren Aylan
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anita E Grootemaat
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Sahadevan Raman
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laure Botella
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Eri Ishikawa
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Mary P O'Sullivan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College, Dublin, Ireland
| | - Seónadh O'Leary
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College, Dublin, Ireland
| | - Jacob A Mayfield
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey Buter
- Department of Chemical Biology, Stratingh Institute for Chemistry, Groningen, Netherlands
| | - Adriaan J Minnaard
- Department of Chemical Biology, Stratingh Institute for Chemistry, Groningen, Netherlands
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Daniel S Ory
- Casma Therapeutics, Cambridge, Massachusetts, USA
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College, Dublin, Ireland
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Nicole van der Wel
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - D Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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18
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Zhang Y, Xiao P, Pan D, Zhou X. New Insights into the Modification of the Non-Core Metabolic Pathway of Steroids in Mycolicibacterium and the Application of Fermentation Biotechnology in C-19 Steroid Production. Int J Mol Sci 2023; 24:ijms24065236. [PMID: 36982310 PMCID: PMC10049677 DOI: 10.3390/ijms24065236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Androsta-4-ene-3,17-dione (AD), androsta-1,4-diene-3,17-dione (ADD), and 9α-hydroxy-4-androstene-3,17-dione (9-OHAD), which belong to C-19 steroids, are critical steroid-based drug intermediates. The biotransformation of phytosterols into C-19 steroids by Mycolicibacterium cell factories is the core step in the synthesis of steroid-based drugs. The production performance of engineered mycolicibacterial strains has been effectively enhanced by sterol core metabolic modification. In recent years, research on the non-core metabolic pathway of steroids (NCMS) in mycolicibacterial strains has made significant progress. This review discusses the molecular mechanisms and metabolic modifications of NCMS for accelerating sterol uptake, regulating coenzyme I balance, promoting propionyl-CoA metabolism, reducing reactive oxygen species, and regulating energy metabolism. In addition, the recent applications of biotechnology in steroid intermediate production are summarized and compared, and the future development trend of NCMS research is discussed. This review provides powerful theoretical support for metabolic regulation in the biotransformation of phytosterols.
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Affiliation(s)
- Yang Zhang
- School of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Peiyao Xiao
- School of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Delong Pan
- School of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Xiuling Zhou
- School of Life Science, Liaocheng University, Liaocheng 252000, China
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19
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Cyclic AMP-Mediated Inhibition of Cholesterol Catabolism in Mycobacterium tuberculosis by the Novel Drug Candidate GSK2556286. Antimicrob Agents Chemother 2023; 67:e0129422. [PMID: 36602336 PMCID: PMC9872607 DOI: 10.1128/aac.01294-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Despite the deployment of combination tuberculosis (TB) chemotherapy, efforts to identify shorter, nonrelapsing treatments have resulted in limited success. Recent evidence indicates that GSK2556286 (GSK286), which acts via Rv1625c, a membrane-bound adenylyl cyclase in Mycobacterium tuberculosis, shortens treatment in rodents relative to standard of care drugs. Moreover, GSK286 can replace linezolid in the three-drug, Nix-TB regimen. Given its therapeutic potential, we sought to better understand the mechanism of action of GSK286. The compound blocked growth of M. tuberculosis in cholesterol media and increased intracellular cAMP levels ~50-fold. GSK286 did not inhibit growth of an rv1625c transposon mutant in cholesterol media and did not induce cyclic AMP (cAMP) production in this mutant, suggesting that the compound acts on this adenylyl cyclase. GSK286 also induced cAMP production in Rhodococcus jostii RHA1, a cholesterol-catabolizing actinobacterium, when Rv1625c was heterologously expressed. However, these elevated levels of cAMP did not inhibit growth of R. jostii RHA1 in cholesterol medium. Mutations in rv1625c conferred cross-resistance to GSK286 and the known Rv1625c agonist, mCLB073. Metabolic profiling of M. tuberculosis cells revealed that elevated cAMP levels, induced using either an agonist or a genetic tool, did not significantly affect pools of steroid metabolites in cholesterol-incubated cells. Finally, the inhibitory effect of agonists was not dependent on the N-acetyltransferase MtPat. Together, these data establish that GSK286 is an Rv1625c agonist and sheds light on how cAMP signaling can be manipulated as a novel antibiotic strategy to shorten TB treatments. Nevertheless, the detailed mechanism of action of these compounds remains to be elucidated.
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20
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Larkins-Ford J, Aldridge BB. Advances in the design of combination therapies for the treatment of tuberculosis. Expert Opin Drug Discov 2023; 18:83-97. [PMID: 36538813 PMCID: PMC9892364 DOI: 10.1080/17460441.2023.2157811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Tuberculosis requires lengthy multi-drug therapy. Mycobacterium tuberculosis occupies different tissue compartments during infection, making drug access and susceptibility patterns variable. Antibiotic combinations are needed to ensure each compartment of infection is reached with effective drug treatment. Despite drug combinations' role in treating tuberculosis, the design of such combinations has been tackled relatively late in the drug development process, limiting the number of drug combinations tested. In recent years, there has been significant progress using in vitro, in vivo, and computational methodologies to interrogate combination drug effects. AREAS COVERED This review discusses the advances in these methodologies and how they may be used in conjunction with new successful clinical trials of novel drug combinations to design optimized combination therapies for tuberculosis. Literature searches for approaches and experimental models used to evaluate drug combination effects were undertaken. EXPERT OPINION We are entering an era richer in combination drug effect and pharmacokinetic/pharmacodynamic data, genetic tools, and outcome measurement types. Application of computational modeling approaches that integrate these data and produce predictive models of clinical outcomes may enable the field to generate novel, effective multidrug therapies using existing and new drug combination backbones.
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Affiliation(s)
- Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Current address: MarvelBiome Inc, Woburn, MA, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA
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21
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Mosquera-Restrepo SF, Zuberogoïtia S, Gouxette L, Layre E, Gilleron M, Stella A, Rengel D, Burlet-Schiltz O, Caro AC, Garcia LF, Segura C, Peláez Jaramillo CA, Rojas M, Nigou J. A Mycobacterium tuberculosis fingerprint in human breath allows tuberculosis detection. Nat Commun 2022; 13:7751. [PMID: 36517492 PMCID: PMC9751131 DOI: 10.1038/s41467-022-35453-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
An estimated one-third of tuberculosis (TB) cases go undiagnosed or unreported. Sputum samples, widely used for TB diagnosis, are inefficient at detecting infection in children and paucibacillary patients. Indeed, developing point-of-care biomarker-based diagnostics that are not sputum-based is a major priority for the WHO. Here, in a proof-of-concept study, we tested whether pulmonary TB can be detected by analyzing patient exhaled breath condensate (EBC) samples. We find that the presence of Mycobacterium tuberculosis (Mtb)-specific lipids, lipoarabinomannan lipoglycan, and proteins in EBCs can efficiently differentiate baseline TB patients from controls. We used EBCs to track the longitudinal effects of antibiotic treatment in pediatric TB patients. In addition, Mtb lipoarabinomannan and lipids were structurally distinct in EBCs compared to ex vivo cultured bacteria, revealing specific metabolic and biochemical states of Mtb in the human lung. This provides essential information for the rational development or improvement of diagnostic antibodies, vaccines and therapeutic drugs. Our data collectively indicate that EBC analysis can potentially facilitate clinical diagnosis of TB across patient populations and monitor treatment efficacy. This affordable, rapid and non-invasive approach seems superior to sputum assays and has the potential to be implemented at point-of-care.
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Affiliation(s)
- Sergio Fabián Mosquera-Restrepo
- grid.412881.60000 0000 8882 5269Cellular Immunology and Immunogenetics Group (GICIG), Institute of Medical Research, Faculty of Medicine, University Research Headquarters (SIU), University of Antioquia (UdeA), Medellin, Colombia
| | - Sophie Zuberogoïtia
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Lucie Gouxette
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Emilie Layre
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Martine Gilleron
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Alexandre Stella
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - David Rengel
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Odile Burlet-Schiltz
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Ana Cecilia Caro
- grid.412881.60000 0000 8882 5269Interdisciplinary Group for Molecular Studies (GIEM), Institute of Chemistry, Faculty of Exact and Natural Sciences. University of Antioquia (UdeA), Medellin, Colombia
| | - Luis F. Garcia
- grid.412881.60000 0000 8882 5269Cellular Immunology and Immunogenetics Group (GICIG), Institute of Medical Research, Faculty of Medicine, University Research Headquarters (SIU), University of Antioquia (UdeA), Medellin, Colombia
| | - César Segura
- grid.412881.60000 0000 8882 5269Malaria Group, University Research Headquarters, University of Antioquia (UdeA), Medellín, Colombia
| | - Carlos Alberto Peláez Jaramillo
- grid.412881.60000 0000 8882 5269Interdisciplinary Group for Molecular Studies (GIEM), Institute of Chemistry, Faculty of Exact and Natural Sciences. University of Antioquia (UdeA), Medellin, Colombia
| | - Mauricio Rojas
- grid.412881.60000 0000 8882 5269Cellular Immunology and Immunogenetics Group (GICIG), Institute of Medical Research, Faculty of Medicine, University Research Headquarters (SIU), University of Antioquia (UdeA), Medellin, Colombia ,grid.412881.60000 0000 8882 5269Flow Cytometry Core, University Research Headquarters (SIU), University of Antioquia, UdeA, Medellín, Colombia
| | - Jérôme Nigou
- grid.15781.3a0000 0001 0723 035XInstitute of Pharmacology and Structural Biology (IPBS), University of Toulouse, CNRS, University of Toulouse III-Paul Sabatier, Toulouse, France
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22
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Samuels AN, Wang ER, Harrison GA, Valenta JC, Stallings CL. Understanding the contribution of metabolism to Mycobacterium tuberculosis drug tolerance. Front Cell Infect Microbiol 2022; 12:958555. [PMID: 36072222 PMCID: PMC9441742 DOI: 10.3389/fcimb.2022.958555] [Citation(s) in RCA: 4] [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: 05/31/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Treatment of Mycobacterium tuberculosis (Mtb) infections is particularly arduous. One challenge to effectively treating tuberculosis is that drug efficacy in vivo often fails to match drug efficacy in vitro. This is due to multiple reasons, including inadequate drug concentrations reaching Mtb at the site of infection and physiological changes of Mtb in response to host derived stresses that render the bacteria more tolerant to antibiotics. To more effectively and efficiently treat tuberculosis, it is necessary to better understand the physiologic state of Mtb that promotes drug tolerance in the host. Towards this end, multiple studies have converged on bacterial central carbon metabolism as a critical contributor to Mtb drug tolerance. In this review, we present the evidence that changes in central carbon metabolism can promote drug tolerance, depending on the environment surrounding Mtb. We posit that these metabolic pathways could be potential drug targets to stymie the development of drug tolerance and enhance the efficacy of current antimicrobial therapy.
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Affiliation(s)
| | | | | | | | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States
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23
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Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
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Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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24
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Theriault ME, Pisu D, Wilburn KM, Lê-Bury G, MacNamara CW, Michael Petrassi H, Love M, Rock JM, VanderVen BC, Russell DG. Iron limitation in M. tuberculosis has broad impact on central carbon metabolism. Commun Biol 2022; 5:685. [PMID: 35810253 PMCID: PMC9271047 DOI: 10.1038/s42003-022-03650-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the cause of the human pulmonary disease tuberculosis (TB), contributes to approximately 1.5 million deaths every year. Prior work has established that lipids are actively catabolized by Mtb in vivo and fulfill major roles in Mtb physiology and pathogenesis. We conducted a high-throughput screen to identify inhibitors of Mtb survival in its host macrophage. One of the hit compounds identified in this screen, sAEL057, demonstrates highest activity on Mtb growth in conditions where cholesterol was the primary carbon source. Transcriptional and functional data indicate that sAEL057 limits Mtb’s access to iron by acting as an iron chelator. Furthermore, pharmacological and genetic inhibition of iron acquisition results in dysregulation of cholesterol catabolism, revealing a previously unappreciated linkage between these pathways. Characterization of sAEL057’s mode of action argues that Mtb’s metabolic regulation reveals vulnerabilities in those pathways that impact central carbon metabolism. An inhibitor of Mycobacterium tuberculosis (Mtb) survival acts as an iron chelator, demonstrating that iron deprivation alters Mtb cholesterol and central carbon metabolism.
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Affiliation(s)
- Monique E Theriault
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Davide Pisu
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kaley M Wilburn
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gabrielle Lê-Bury
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Case W MacNamara
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - H Michael Petrassi
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - Melissa Love
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - Jeremy M Rock
- Department of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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25
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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26
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Li M, Patel HV, Cognetta AB, Smith TC, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC. Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. Cell Chem Biol 2022; 29:883-896.e5. [PMID: 34599873 PMCID: PMC8964833 DOI: 10.1016/j.chembiol.2021.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/08/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening ∼200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.
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Affiliation(s)
- Michael Li
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Hiren V Patel
- Department of Microbiology and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Armand B Cognetta
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Ivy Mallick
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | | | - Mary L Previti
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA.
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27
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Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Proc Natl Acad Sci U S A 2022; 119:e2201632119. [PMID: 35380903 PMCID: PMC9169745 DOI: 10.1073/pnas.2201632119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Efforts to improve tuberculosis therapy include optimizing multidrug regimens to take advantage of drug–drug synergies. However, the complex host environment has a profound effect on bacterial metabolic state and drug activity, making predictions of optimal drug combinations difficult. In this study, we leverage a newly developed library of conditional knockdown Mycobacterium tuberculosis mutants in which genetic depletion of essential genes mimics the effect of drug therapy. This tractable system allowed us to assess the effect of growth condition on predicted drug–drug interactions. We found that these interactions can be differentially sensitive to the metabolic state, and select in vitro–defined interactions can be leveraged to accelerate bacterial killing during infection. These findings suggest strategies for optimizing tuberculosis therapy. Current chemotherapy against Mycobacterium tuberculosis (Mtb), an important human pathogen, requires a multidrug regimen lasting several months. While efforts have been made to optimize therapy by exploiting drug–drug synergies, testing new drug combinations in relevant host environments remains arduous. In particular, host environments profoundly affect the bacterial metabolic state and drug efficacy, limiting the accuracy of predictions based on in vitro assays alone. In this study, we utilized conditional Mtb knockdown mutants of essential genes as an experimentally tractable surrogate for drug treatment and probe the relationship between Mtb carbon metabolism and chemical–genetic interactions (CGIs). We examined the antitubercular drugs isoniazid, rifampicin, and moxifloxacin and found that CGIs are differentially responsive to the metabolic state, defining both environment-independent and -dependent interactions. Specifically, growth on the in vivo–relevant carbon source, cholesterol, reduced rifampicin efficacy by altering mycobacterial cell surface lipid composition. We report that a variety of perturbations in cell wall synthesis pathways restore rifampicin efficacy during growth on cholesterol, and that both environment-independent and cholesterol-dependent in vitro CGIs could be leveraged to enhance bacterial clearance in the mouse infection model. Our findings present an atlas of chemical–genetic–environmental interactions that can be used to optimize drug–drug interactions, as well as provide a framework for understanding in vitro correlates of in vivo efficacy.
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28
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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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29
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CRISPR Interference Reveals That All- Trans-Retinoic Acid Promotes Macrophage Control of Mycobacterium tuberculosis by Limiting Bacterial Access to Cholesterol and Propionyl Coenzyme A. mBio 2022; 13:e0368321. [PMID: 35038923 PMCID: PMC8764544 DOI: 10.1128/mbio.03683-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macrophages are a protective replicative niche for Mycobacterium tuberculosis (Mtb) but can kill the infecting bacterium when appropriately activated. To identify mechanisms of clearance, we compared levels of bacterial restriction by human macrophages after treatment with 26 compounds, including some currently in clinical trials for tuberculosis. All-trans-retinoic acid (ATRA), an active metabolite of vitamin A, drove the greatest increase in Mtb control. Bacterial clearance was transcriptionally and functionally associated with changes in macrophage cholesterol trafficking and lipid metabolism. To determine how these macrophage changes affected bacterial control, we performed the first Mtb CRISPR interference screen in an infection model, identifying Mtb genes specifically required to survive in ATRA-activated macrophages. These data showed that ATRA treatment starves Mtb of cholesterol and the downstream metabolite propionyl coenzyme A (propionyl-CoA). Supplementation with sources of propionyl-CoA, including cholesterol, abrogated the restrictive effect of ATRA. This work demonstrates that targeting the coupled metabolism of Mtb and the macrophage improves control of infection and that it is possible to genetically map the mode of bacterial death using CRISPR interference. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a leading cause of death due to infectious disease. Improving the immune response to tuberculosis holds promise for fighting the disease but is limited by our lack of knowledge as to how the immune system kills M. tuberculosis. Our research identifies a potent way to make relevant immune cells more effective at fighting M. tuberculosis and then uses paired human and bacterial genomic methods to determine the mechanism of that improved bacterial clearance.
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30
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Chandra P, Coullon H, Agarwal M, Goss CW, Philips JA. Macrophage global metabolomics identifies cholestenone as host/pathogen cometabolite present in human Mycobacterium tuberculosis infection. J Clin Invest 2022; 132:152509. [PMID: 35104812 PMCID: PMC8803325 DOI: 10.1172/jci152509] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/30/2021] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) causes an enormous burden of disease worldwide. As a central aspect of its pathogenesis, M. tuberculosis grows in macrophages, and host and microbe influence each other's metabolism. To define the metabolic impact of M. tuberculosis infection, we performed global metabolic profiling of M. tuberculosis-infected macrophages. M. tuberculosis induced metabolic hallmarks of inflammatory macrophages and a prominent signature of cholesterol metabolism. We found that infected macrophages accumulate cholestenone, a mycobacterial-derived, oxidized derivative of cholesterol. We demonstrated that the accumulation of cholestenone in infected macrophages depended on the M. tuberculosis enzyme 3β-hydroxysteroid dehydrogenase (3β-Hsd) and correlated with pathogen burden. Because cholestenone is not a substantial human metabolite, we hypothesized it might be diagnostic of M. tuberculosis infection in clinical samples. Indeed, in 2 geographically distinct cohorts, sputum cholestenone levels distinguished subjects with tuberculosis (TB) from TB-negative controls who presented with TB-like symptoms. We also found country-specific detection of cholestenone in plasma samples from M. tuberculosis-infected subjects. While cholestenone was previously thought to be an intermediate required for cholesterol degradation by M. tuberculosis, we found that M. tuberculosis can utilize cholesterol for growth without making cholestenone. Thus, the accumulation of cholestenone in clinical samples suggests it has an alternative role in pathogenesis and could be a clinically useful biomarker of TB infection.
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Affiliation(s)
- Pallavi Chandra
- Division of Infectious Diseases, Department of Medicine.,Department of Molecular Microbiology, and
| | - Héloise Coullon
- Division of Infectious Diseases, Department of Medicine.,Department of Molecular Microbiology, and
| | - Mansi Agarwal
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charles W Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer A Philips
- Division of Infectious Diseases, Department of Medicine.,Department of Molecular Microbiology, and
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31
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Wilburn KM, Montague CR, Qin B, Woods AK, Love MS, McNamara CW, Schultz PG, Southard TL, Huang L, Petrassi HM, VanderVen BC. Pharmacological and genetic activation of cAMP synthesis disrupts cholesterol utilization in Mycobacterium tuberculosis. PLoS Pathog 2022; 18:e1009862. [PMID: 35134095 PMCID: PMC8856561 DOI: 10.1371/journal.ppat.1009862] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/18/2022] [Accepted: 01/18/2022] [Indexed: 01/27/2023] Open
Abstract
There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3', 5'-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.
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Affiliation(s)
- Kaley M. Wilburn
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Christine R. Montague
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - Bo Qin
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Ashley K. Woods
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Melissa S. Love
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Case W. McNamara
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Peter G. Schultz
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Teresa L. Southard
- Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Lu Huang
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
| | - H. Michael Petrassi
- Calibr, a division of The Scripps Research Institute, San Diego, California, United States of America
| | - Brian C. VanderVen
- Microbiology & Immunology, Cornell University, Ithaca, New York, United States of America
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Pan X. Cholesterol Metabolism in Chronic Kidney Disease: Physiology, Pathologic Mechanisms, and Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1372:119-143. [PMID: 35503178 PMCID: PMC11106795 DOI: 10.1007/978-981-19-0394-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
High plasma levels of lipids and/or lipoproteins are risk factors for atherosclerosis, nonalcoholic fatty liver disease (NAFLD), obesity, and diabetes. These four conditions have also been identified as risk factors leading to the development of chronic kidney disease (CKD). Although many pathways that generate high plasma levels of these factors have been identified, most clinical and physiologic dysfunction results from aberrant assembly and secretion of lipoproteins. The results of several published studies suggest that elevated levels of low-density lipoprotein (LDL)-cholesterol are a risk factor for atherosclerosis, myocardial infarction, coronary artery calcification associated with type 2 diabetes, and NAFLD. Cholesterol metabolism has also been identified as an important pathway contributing to the development of CKD; clinical treatments designed to alter various steps of the cholesterol synthesis and metabolism pathway are currently under study. Cholesterol synthesis and catabolism contribute to a multistep process with pathways that are regulated at the cellular level in renal tissue. Cholesterol metabolism may also be regulated by the balance between the influx and efflux of cholesterol molecules that are capable of crossing the membrane of renal proximal tubular epithelial cells and podocytes. Cellular accumulation of cholesterol can result in lipotoxicity and ultimately kidney dysfunction and failure. Thus, further research focused on cholesterol metabolism pathways will be necessary to improve our understanding of the impact of cholesterol restriction, which is currently a primary intervention recommended for patients with dyslipidemia.
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Affiliation(s)
- Xiaoyue Pan
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, USA.
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33
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Yang F, Xu L, Liang L, Liang W, Li J, Lin D, Dai M, Zhou D, Li Y, Chen Y, Zhao H, Tian GB, Feng S. The Involvement of Mycobacterium Type III-A CRISPR-Cas System in Oxidative Stress. Front Microbiol 2021; 12:774492. [PMID: 34956138 PMCID: PMC8696179 DOI: 10.3389/fmicb.2021.774492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Type I and type II CRISPR-Cas systems are employed to evade host immunity by targeting interference of bacteria’s own genes. Although Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, possesses integrated type III-A CRISPR-Cas system, its role in mycobacteria remains obscure. Here, we observed that seven cas genes (csm2∼5, cas10, cas6) were upregulated in Mycobacterium bovis BCG under oxidative stress treatment, indicating the role of type III-A CRISPR-Cas system in oxidative stress. To explore the functional role of type III-A CRISPR-Cas system, TCC (Type III-A CRISPR-Cas system, including cas6, cas10, and csm2-6) mutant was generated. Deletion of TCC results in increased sensitivity in response to hydrogen peroxide and reduced cell envelope integrity. Analysis of RNA-seq dataset revealed that TCC impacted on the oxidation-reduction process and the composition of cell wall which is essential for mycobacterial envelop integrity. Moreover, disrupting TCC led to poor intracellular survival in vivo and in vitro. Finally, we showed for the first time that TCC contributed to the regulation of regulatory T cell population, supporting a role of TCC in modulating host immunity. Our finding reveals the important role of TCC in cell envelop homeostasis. Our work also highlights type III-A CRISPR-Cas system as an important factor for intracellular survival and host immunoregulation in mycobacteria, thus may be a potential target for therapy.
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Affiliation(s)
- Fan Yang
- Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Lingqing Xu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lujie Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Wanfei Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiachen Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Daixi Lin
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Dianrong Zhou
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yaxin Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yong Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Hui Zhao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. mBio 2021; 12:e0176621. [PMID: 34872348 PMCID: PMC8649757 DOI: 10.1128/mbio.01766-21] [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] [Indexed: 11/23/2022] Open
Abstract
The crucial transmission phase of tuberculosis (TB) relies on infectious sputum and yet cannot easily be modeled. We applied one-step RNA sequencing (RNA-Seq) to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission of Mycobacterium tuberculosis. In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses, including an interferon-driven proinflammatory response and a metabolic shift toward glycolysis, was observed in the host. Among all bacterial sequences in the sputum, approximately 1.5% originated from M. tuberculosis, and its transcript abundance was lower in HIV-1-coinfected patients. Commensal bacterial abundance was reduced in the presence of M. tuberculosis infection. Direct alignment to the genomes of the predominant microbiota species also reveals differential adaptation, whereby firmicutes (e.g., streptococci) displayed a nonreplicating phenotype with reduced transcription of ribosomal proteins and reduced activities of ATP synthases, while Neisseria and Prevotella spp. were less affected. The transcriptome of sputum M. tuberculosis more closely resembled aerobic replication and shared similarity in carbon metabolism to in vitro and in vivo models with significant upregulation of genes associated with cholesterol metabolism and downstream propionate detoxification pathways. In addition, and counter to previous reports on intracellular M. tuberculosis infection in vitro, M. tuberculosis in sputum was zinc, but not iron, deprived, and the phoP loci were also significantly downregulated, suggesting that the pathogen is likely extracellular in location.
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Lien KA, Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 2021; 10:e74358. [PMID: 34751132 PMCID: PMC8635971 DOI: 10.7554/elife.74358] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/18/2023] Open
Abstract
Encapsulin nanocompartments are an emerging class of prokaryotic protein-based organelle consisting of an encapsulin protein shell that encloses a protein cargo. Genes encoding nanocompartments are widespread in bacteria and archaea, and recent works have characterized the biochemical function of several cargo enzymes. However, the importance of these organelles to host physiology is poorly understood. Here, we report that the human pathogen Mycobacterium tuberculosis (Mtb) produces a nanocompartment that contains the dye-decolorizing peroxidase DyP. We show that this nanocompartment is important for the ability of Mtb to resist oxidative stress in low pH environments, including during infection of host cells and upon treatment with a clinically relevant antibiotic. Our findings are the first to implicate a nanocompartment in bacterial pathogenesis and reveal a new mechanism that Mtb uses to combat oxidative stress.
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Affiliation(s)
- Katie A Lien
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Kayla Dinshaw
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Robert J Nichols
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Matthew Knight
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Rahul Singh
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - David F Savage
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, BerkeleyBerkeleyUnited States
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36
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Wang N, Sarathy JP, Zimmerman M, Kaya F, Wang H, Dartois V, Carter CL. On-Slide Heat Sterilization Enables Mass Spectrometry Imaging of Tissue Infected with High-Threat Pathogens Outside of Biocontainment: A Study Directed at Mycobacterium tuberculosis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2664-2674. [PMID: 34672552 PMCID: PMC8653782 DOI: 10.1021/jasms.1c00205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 05/16/2023]
Abstract
Mass spectrometry imaging investigations of tissues infected with agents that require high-security biocontainment, such as Mycobacterium tuberculosis, have been limited due to incompatible sterilization techniques. Here we describe an on-slide heat sterilization method that enables mass spectrometry imaging investigations of pharmaceuticals, lipids, and metabolites in infected tissue samples outside of biocontainment. An evaluation of different temperatures and incubation times determined that 100 °C for 1 h was essential to sterilize 5 times the bacterial burden observed in tuberculosis (TB) cavity sections. Laser-capture microdissection combined with liquid chromatography with tandem mass spectrometry quantitation, in addition to mass spectrometry imaging, showed that no degradation was observed following the on-slide heat sterilization protocol for a variety of drug classes covering a range of physicochemical properties. Utilizing the tissue mimetic model, we demonstrated that the detection of lipid and metabolite ions was not impacted by heat sterilization and that, for several metabolites, the on-slide heat sterilization method improved the sensitivity when compared to control samples. An application of the on-slide heat sterilization to M. tuberculosis infected tissue enabled the first detection and spatial distribution of lipids indicative of a lysosomal storage disease phenotype within TB granuloma macrophages, in addition to the differential distribution of metabolites central to the fatty acid oxidation pathway. These initial investigations detected a pronounced heterogeneity within the cellular regions and necrotic cores of individual TB granulomas and across different evolving granulomas. This study provides the framework for mass spectrometry imaging investigations of high-threat pathogens outside of biocontainment.
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Affiliation(s)
- Ning Wang
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Jansy P. Sarathy
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Matthew Zimmerman
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Firat Kaya
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Han Wang
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Véronique Dartois
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
- Department
of Medical Sciences, Hackensack School of
Medicine, Nutley, New Jersey 07110, United States
| | - Claire L. Carter
- Center
for Discovery and Innovation, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
- Department
of Pathology, Hackensack School of Medicine, Nutley, New Jersey 07110, United States
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37
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Dutta E, DeJesus MA, Ruecker N, Zaveri A, Koh EI, Sassetti CM, Schnappinger D, Ioerger TR. An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence. PLoS One 2021; 16:e0257911. [PMID: 34597304 PMCID: PMC8486102 DOI: 10.1371/journal.pone.0257911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Chemical-genetics (C-G) experiments can be used to identify interactions between inhibitory compounds and bacterial genes, potentially revealing the targets of drugs, or other functionally interacting genes and pathways. C-G experiments involve constructing a library of hypomorphic strains with essential genes that can be knocked-down, treating it with an inhibitory compound, and using high-throughput sequencing to quantify changes in relative abundance of individual mutants. The hypothesis is that, if the target of a drug or other genes in the same pathway are present in the library, such genes will display an excessive fitness defect due to the synergy between the dual stresses of protein depletion and antibiotic exposure. While assays at a single drug concentration are susceptible to noise and can yield false-positive interactions, improved detection can be achieved by requiring that the synergy between gene and drug be concentration-dependent. We present a novel statistical method based on Linear Mixed Models, called CGA-LMM, for analyzing C-G data. The approach is designed to capture the dependence of the abundance of each gene in the hypomorph library on increasing concentrations of drug through slope coefficients. To determine which genes represent candidate interactions, CGA-LMM uses a conservative population-based approach in which genes with negative slopes are considered significant only if they are outliers with respect to the rest of the population (assuming that most genes in the library do not interact with a given inhibitor). We applied the method to analyze 3 independent hypomorph libraries of M. tuberculosis for interactions with antibiotics with anti-tubercular activity, and we identify known target genes or expected interactions for 7 out of 9 drugs where relevant interacting genes are known.
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Affiliation(s)
- Esha Dutta
- Department of Computer Science, Texas A&M University, College Station, TX, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, United States of America
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Eun-Ik Koh
- Department of Microbiology & Physiological Systems, University of Massachusetts Medical School, Worchester, MA, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology & Physiological Systems, University of Massachusetts Medical School, Worchester, MA, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX, United States of America
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38
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Intragenic Distribution of IS 6110 in Clinical Mycobacterium tuberculosis Strains: Bioinformatic Evidence for Gene Disruption Leading to Underdiagnosed Antibiotic Resistance. Microbiol Spectr 2021; 9:e0001921. [PMID: 34287057 PMCID: PMC8552512 DOI: 10.1128/spectrum.00019-21] [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] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance is a global challenge for tuberculosis control, and accelerating its diagnosis is critical for therapy decisions and controlling transmission. Genotype-based molecular diagnostics now play an increasing role in accelerating the detection of such antibiotic resistance, but their accuracy depends on the instructed detection of genetic variations. Genetic mobile elements such as IS6110 are established sources of genetic variation in Mycobacterium tuberculosis, but their implication in clinical antibiotic resistance has thus far been unclear. Here, we describe the discovery of an intragenic IS6110 insertion into Rv0678 that caused antibiotic resistance in an in vitro-selected M. tuberculosis isolate. The subsequent development of bioinformatics scripts allowed genome-wide analysis of intragenic IS6110 insertions causing gene disruptions in 6,426 clinical M. tuberculosis strains. This analysis identified 10,070 intragenic IS6110 insertions distributed among 333 different genes. Focusing on genes whose disruption leads to antibiotic resistance, 12 clinical isolates were identified with high confidence to be resistant to bedaquiline, clofazimine, pyrazinamide, ethionamide, and para-aminosalicylic acid because of an IS6110-mediated gene disruption event. A number of these IS6110-mediated resistant strains had identical genomic distributions of IS6110 elements and likely represent transmission events of a single resistant isolate. These data provide strong evidence that IS6110-mediated gene disruption is a clinically relevant mechanism of antibiotic resistance in M. tuberculosis that should be considered for molecular diagnostics. Concomitantly, this analysis provides a list of 333 IS6110-disrupted genes in clinical tuberculosis isolates that can be deemed nonessential for human infection. IMPORTANCE To help control the spread of drug-resistant tuberculosis and to guide treatment choices, it is important that rapid and accurate molecular diagnostic tools are used. Current molecular diagnostic tools detect the most common antibiotic-resistance-conferring mutations in the form of single nucleotide changes, small deletions, or insertions. Mobile genetic elements, named IS6110, are also known to move within the M. tuberculosis genome and cause significant genetic variations, although the role of this variation in clinical drug resistance remains unclear. In this work, we show that both in vitro and in data analyzed from 6,426 clinical M. tuberculosis strains, IS6110 elements are found that disrupt specific genes essential for the function of a number of pivotal antituberculosis drugs. By providing ample evidence of clinically relevant IS6110-mediated drug resistance, we believe that this shows that this form of genetic variation must not be overlooked in molecular diagnostics of drug resistance.
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Tanigawa K, Luo Y, Kawashima A, Kiriya M, Nakamura Y, Karasawa K, Suzuki K. Essential Roles of PPARs in Lipid Metabolism during Mycobacterial Infection. Int J Mol Sci 2021; 22:ijms22147597. [PMID: 34299217 PMCID: PMC8304230 DOI: 10.3390/ijms22147597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
The mycobacterial cell wall is composed of large amounts of lipids with varying moieties. Some mycobacteria species hijack host cells and promote lipid droplet accumulation to build the cellular environment essential for their intracellular survival. Thus, lipids are thought to be important for mycobacteria survival as well as for the invasion, parasitization, and proliferation within host cells. However, their physiological roles have not been fully elucidated. Recent studies have revealed that mycobacteria modulate the peroxisome proliferator-activated receptor (PPAR) signaling and utilize host-derived triacylglycerol (TAG) and cholesterol as both nutrient sources and evasion from the host immune system. In this review, we discuss recent findings that describe the activation of PPARs by mycobacterial infections and their role in determining the fate of bacilli by inducing lipid metabolism, anti-inflammatory function, and autophagy.
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Affiliation(s)
- Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (K.T.); (Y.N.); (K.K.)
| | - Yuqian Luo
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (Y.L.); (A.K.); (M.K.)
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, China
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (Y.L.); (A.K.); (M.K.)
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (Y.L.); (A.K.); (M.K.)
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (K.T.); (Y.N.); (K.K.)
| | - Ken Karasawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (K.T.); (Y.N.); (K.K.)
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan; (Y.L.); (A.K.); (M.K.)
- Correspondence: ; Tel.: +81-3-3964-1211
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Pawełczyk J, Brzostek A, Minias A, Płociński P, Rumijowska-Galewicz A, Strapagiel D, Zakrzewska-Czerwińska J, Dziadek J. Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis. Sci Rep 2021; 11:12396. [PMID: 34117327 PMCID: PMC8196197 DOI: 10.1038/s41598-021-91812-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that can adapt to the various nutrients available during its life cycle. However, in the nutritionally stringent environment of the macrophage phagolysosome, Mtb relies mainly on cholesterol. In previous studies, we demonstrated that Mtb can accumulate and utilize cholesterol as the sole carbon source. However, a growing body of evidence suggests that a lipid-rich environment may have a much broader impact on the pathogenesis of Mtb infection than previously thought. Therefore, we applied high-resolution transcriptome profiling and the construction of various mutants to explore in detail the global effect of cholesterol on the tubercle bacillus metabolism. The results allow re-establishing the complete list of genes potentially involved in cholesterol breakdown. Moreover, we identified the modulatory effect of vitamin B12 on Mtb transcriptome and the novel function of cobalamin in cholesterol metabolite dissipation which explains the probable role of B12 in Mtb virulence. Finally, we demonstrate that a key role of cholesterol in mycobacterial metabolism is not only providing carbon and energy but involves also a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment far before specific stress-inducing phagosomal signals occur.
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Affiliation(s)
- Jakub Pawełczyk
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Anna Brzostek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Alina Minias
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Przemysław Płociński
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland ,grid.10789.370000 0000 9730 2769Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Anna Rumijowska-Galewicz
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- grid.10789.370000 0000 9730 2769Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- grid.8505.80000 0001 1010 5103Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jarosław Dziadek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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de Lima JB, da Silva Fonseca LP, Xavier LP, de Matos Macchi B, Cassoli JS, da Silva EO, da Silva Valadares RB, do Nascimento JLM, Santos AV, de Sena CBC. Culture of Mycobacterium smegmatis in Different Carbon Sources to Induce In Vitro Cholesterol Consumption Leads to Alterations in the Host Cells after Infection: A Macrophage Proteomics Analysis. Pathogens 2021; 10:pathogens10060662. [PMID: 34071265 PMCID: PMC8230116 DOI: 10.3390/pathogens10060662] [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] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
During tuberculosis, Mycobacterium uses host macrophage cholesterol as a carbon and energy source. To mimic these conditions, Mycobacterium smegmatis can be cultured in minimal medium (MM) to induce cholesterol consumption in vitro. During cultivation, M. smegmatis consumes MM cholesterol and changes the accumulation of cell wall compounds, such as PIMs, LM, and LAM, which plays an important role in its pathogenicity. These changes lead to cell surface hydrophobicity modifications and H2O2 susceptibility. Furthermore, when M. smegmatis infects J774A.1 macrophages, it induces granuloma-like structure formation. The present study aims to assess macrophage molecular disturbances caused by M. smegmatis after cholesterol consumption, using proteomics analyses. Proteins that showed changes in expression levels were analyzed in silico using OmicsBox and String analysis to investigate the canonical pathways and functional networks involved in infection. Our results demonstrate that, after cholesterol consumption, M. smegmatis can induce deregulation of protein expression in macrophages. Many of these proteins are related to cytoskeleton remodeling, immune response, the ubiquitination pathway, mRNA processing, and immunometabolism. The identification of these proteins sheds light on the biochemical pathways involved in the mechanisms of action of mycobacteria infection, and may suggest novel protein targets for the development of new and improved treatments.
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Affiliation(s)
- Jaqueline Batista de Lima
- Laboratory of Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (J.B.d.L.); (E.O.d.S.)
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (L.P.X.); (A.V.S.)
| | | | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (L.P.X.); (A.V.S.)
| | - Barbarella de Matos Macchi
- Laboratory of Molecular and Cellular Neurochemistry, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (B.d.M.M.); (J.L.M.d.N.)
- National Institute of Science and Technology in Neuroimmunomodulation (INCT-NIM), Rio de Janeiro 21040-900, RJ, Brazil
| | - Juliana Silva Cassoli
- Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil;
| | - Edilene Oliveira da Silva
- Laboratory of Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (J.B.d.L.); (E.O.d.S.)
- National Institute of Science and Technology in Structural Biology and Bioimaging, Rio de Janeiro 21941-901, RJ, Brazil
| | | | - José Luiz Martins do Nascimento
- Laboratory of Molecular and Cellular Neurochemistry, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (B.d.M.M.); (J.L.M.d.N.)
- National Institute of Science and Technology in Neuroimmunomodulation (INCT-NIM), Rio de Janeiro 21040-900, RJ, Brazil
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (L.P.X.); (A.V.S.)
| | - Chubert Bernardo Castro de Sena
- Laboratory of Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, PA, Brazil; (J.B.d.L.); (E.O.d.S.)
- National Institute of Science and Technology in Neuroimmunomodulation (INCT-NIM), Rio de Janeiro 21040-900, RJ, Brazil
- Correspondence:
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Luo T, Xu P, Zhang Y, Porter JL, Ghanem M, Liu Q, Jiang Y, Li J, Miao Q, Hu B, Howden BP, Fyfe JAM, Globan M, He W, He P, Wang Y, Liu H, Takiff HE, Zhao Y, Chen X, Pan Q, Behr MA, Stinear TP, Gao Q. Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii. Nat Commun 2021; 12:2491. [PMID: 33941780 PMCID: PMC8093194 DOI: 10.1038/s41467-021-22760-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.
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Affiliation(s)
- Tao Luo
- grid.13291.380000 0001 0807 1581Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Peng Xu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China ,grid.417409.f0000 0001 0240 6969Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, Zunyi, China
| | - Yangyi Zhang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jessica L. Porter
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Marwan Ghanem
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Qingyun Liu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yuan Jiang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jing Li
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Qing Miao
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Benjamin P. Howden
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XMicrobiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000 Australia
| | - Janet A. M. Fyfe
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Maria Globan
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Wencong He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ping He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yiting Wang
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Houming Liu
- grid.263817.9Department of Clinical Laboratory, The Third People’s Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Howard E. Takiff
- grid.428999.70000 0001 2353 6535Unité de Pathogenetique Integrée Mycobacterienne, Institut Pasteur, Paris, France ,grid.418243.80000 0001 2181 3287Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela ,Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Yanlin Zhao
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xinchun Chen
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qichao Pan
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Marcel A. Behr
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Qian Gao
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Borah K, Mendum TA, Hawkins ND, Ward JL, Beale MH, Larrouy‐Maumus G, Bhatt A, Moulin M, Haertlein M, Strohmeier G, Pichler H, Forsyth VT, Noack S, Goulding CW, McFadden J, Beste DJV. Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis. Mol Syst Biol 2021; 17:e10280. [PMID: 33943004 PMCID: PMC8094261 DOI: 10.15252/msb.202110280] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
The co-catabolism of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady-state chemostat system. We demonstrate that Mtb efficiently co-metabolises either cholesterol or glycerol, in combination with two-carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.
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Affiliation(s)
- Khushboo Borah
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Tom A Mendum
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Nathaniel D Hawkins
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Jane L Ward
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Michael H Beale
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Gerald Larrouy‐Maumus
- MRC Centre for Molecular Bacteriology and InfectionDepartment of Life SciencesFaculty of Natural SciencesImperial College LondonLondonUK
| | - Apoorva Bhatt
- School of BiosciencesUniversity of BirminghamEdgbastonUK
| | - Martine Moulin
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Michael Haertlein
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Gernot Strohmeier
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
| | - Harald Pichler
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
- Institute of Molecular BiotechnologyNAWI GrazBioTechMed GrazGraz University of TechnologyGrazAustria
| | - V Trevor Forsyth
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
- Faculty of Natural SciencesKeele UniversityStaffordshireUK
| | - Stephan Noack
- Institute of Bio‐ and Geosciences 1: Biotechnology 2Forschungszentrum Jülich GmbHJülichGermany
| | - Celia W Goulding
- Department of Pharmaceutical Sciences & Molecular Biology & BiochemistryUniversity of California IrvineIrvineCAUSA
| | - Johnjoe McFadden
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Dany J V Beste
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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Dong W, Nie X, Zhu H, Liu Q, Shi K, You L, Zhang Y, Fan H, Yan B, Niu C, Lyu LD, Zhao GP, Yang C. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc Natl Acad Sci U S A 2021; 118:e2019305118. [PMID: 33853942 PMCID: PMC8072231 DOI: 10.1073/pnas.2019305118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Host-derived fatty acids are an important carbon source for pathogenic mycobacteria during infection. How mycobacterial cells regulate the catabolism of fatty acids to serve the pathogenicity, however, remains unknown. Here, we identified a TetR-family transcriptional factor, FdmR, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum by combining use of transcriptomics, chromatin immunoprecipitation followed by sequencing, dynamic 13C-based flux analysis, metabolomics, and lipidomics. An M. marinum mutant deficient in FdmR was severely attenuated in zebrafish larvae and adult zebrafish. The mutant showed defective growth but high substrate consumption on fatty acids. FdmR was identified as a long-chain acyl-coenzyme A (acyl-CoA)-responsive repressor of genes involved in fatty acid degradation and modification. We demonstrated that FdmR functions as a valve to direct the flux of exogenously derived fatty acids away from β-oxidation toward lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. Moreover, we found that FdmR suppresses degradation of long-chain acyl-CoAs endogenously synthesized through the type I fatty acid synthase. By modulating the supply of long-chain acyl-CoAs for lipogenesis, FdmR controls the abundance and chain length of virulence-associated lipids and mycolates and plays an important role in the impermeability of the cell envelope. These results reveal that despite the fact that host-derived fatty acids are used as an important carbon source, overactive catabolism of fatty acids is detrimental to mycobacterial cell growth and pathogenicity. This study thus presents FdmR as a potentially attractive target for chemotherapy.
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Affiliation(s)
- Wenyue Dong
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqun Nie
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hong Zhu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Kunxiong Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Linlin You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hongyan Fan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Bo Yan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Guo-Ping Zhao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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45
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Park JH, Shim D, Kim KES, Lee W, Shin SJ. Understanding Metabolic Regulation Between Host and Pathogens: New Opportunities for the Development of Improved Therapeutic Strategies Against Mycobacterium tuberculosis Infection. Front Cell Infect Microbiol 2021; 11:635335. [PMID: 33796480 PMCID: PMC8007978 DOI: 10.3389/fcimb.2021.635335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) causes chronic granulomatous lung disease in humans. Recently, novel strategies such as host-directed therapeutics and adjunctive therapies that enhance the effect of existing antibiotics have emerged to better control Mtb infection. Recent advances in understanding the metabolic interplay between host immune cells and pathogens have provided new insights into how their interactions ultimately influence disease outcomes and antibiotic-treatment efficacy. In this review, we describe how metabolic cascades in immune environments and relevant metabolites produced from immune cells during Mtb infection play critical roles in the progression of diseases and induction of anti-Mtb protective immunity. In addition, we introduce how metabolic alterations in Mtb itself can lead to the development of persister cells that are resistant to host immunity and can eventually evade antibiotic attacks. Further understanding of the metabolic link between host cells and Mtb may contribute to not only the prevention of Mtb persister development but also the optimization of host anti-Mtb immunity together with enhanced efficacy of existing antibiotics. Overall, this review highlights novel approaches to improve and develop host-mediated therapeutic strategies against Mtb infection by restoring and switching pathogen-favoring metabolic conditions with host-favoring conditions.
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Affiliation(s)
- Ji-Hae Park
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Dahee Shim
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Keu Eun San Kim
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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46
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Rens C, Chao JD, Sexton DL, Tocheva EI, Av-Gay Y. Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis. MICROBIOLOGY-SGM 2021; 167. [PMID: 33629944 DOI: 10.1099/mic.0.001042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The success of Mycobacterium tuberculosis as a pathogen is well established: tuberculosis is the leading cause of death by a single infectious agent worldwide. The threat of multi- and extensively drug-resistant bacteria has renewed global concerns about this pathogen and understanding its virulence strategies will be essential in the fight against tuberculosis. The current review will focus on phthiocerol dimycocerosates (PDIMs), a long-known and well-studied group of complex lipids found in the M. tuberculosis cell envelope. Numerous studies show a role for PDIMs in several key steps of M. tuberculosis pathogenesis, with recent studies highlighting its involvement in bacterial virulence, in association with the ESX-1 secretion system. Yet, the mechanisms by which PDIMs help M. tuberculosis to control macrophage phagocytosis, inhibit phagosome acidification and modulate host innate immunity, remain to be fully elucidated.
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Affiliation(s)
- Céline Rens
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Joseph D Chao
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Danielle L Sexton
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Elitza I Tocheva
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada.,Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
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47
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Laval T, Chaumont L, Demangel C. Not too fat to fight: The emerging role of macrophage fatty acid metabolism in immunity to Mycobacterium tuberculosis. Immunol Rev 2021; 301:84-97. [PMID: 33559209 DOI: 10.1111/imr.12952] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/23/2022]
Abstract
While the existence of a special relationship between Mycobacterium tuberculosis (Mtb) and host lipids has long been known, it remains a challenging enigma. It was clearly established that Mtb requires host fatty acids (FAs) and cholesterol to produce energy, build its distinctive lipid-rich cell wall, and produce lipid virulence factors. It was also observed that in infected hosts, Mtb constantly resides in a FA-rich environment that the pathogen contributes to generate by inducing a lipid-laden "foamy" phenotype in host macrophages. These observations and the proximity between lipid droplets and phagosomes containing bacteria within infected macrophages gave rise to the hypothesis that Mtb reprograms host cell lipid metabolism to ensure a continuous supply of essential nutrients and its long-term persistence in vivo. However, recent studies question this principle by indicating that in Mtb-infected macrophages, lipid droplet formation prevents bacterial acquisition of host FAs while supporting the production of FA-derived protective lipid mediators. Further, in vivo investigations reveal discrete macrophage phenotypes linking the FA metabolisms of host cell and intracellular pathogen. Notably, FA storage within lipid droplets characterizes both macrophages controlling Mtb infection and dormant intracellular Mtb. In this review, we integrate findings from immunological and microbiological studies illustrating the new concept that cytoplasmic accumulation of FAs is a metabolic adaptation of macrophages to Mtb infection, which potentiates their antimycobacterial responses and forces the intracellular pathogen to shift into fat-saving, survival mode.
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Affiliation(s)
- Thomas Laval
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Lise Chaumont
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
| | - Caroline Demangel
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
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48
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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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Gibson SER, Harrison J, Cox JAG. Drug Susceptibility Screening Using In Vitro Models of Hypoxic Non-Replicating Persistent Mycobacteria. Methods Mol Biol 2021; 2314:247-260. [PMID: 34235656 DOI: 10.1007/978-1-0716-1460-0_10] [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] [Indexed: 12/14/2022]
Abstract
Non-replicating persistence (NRP) is a functional adaptation that mycobacteria undergo in response to the stresses of the granuloma, facilitating antibiotic tolerance and long-term infection. These stresses, or NRP-inducing factors, include hypoxia, nutrient deprivation, and nitric oxide assault, which mycobacteria are well evolved to tolerate through a series of metabolic and physiological adaptations producing the NRP state. Most attempts to replicate these conditions in vitro have focused on only one of these factors at a time for ease and simplicity, but as a result, do not necessarily produce physiologically relevant phenotypes. Here, we provide the methods for two different in vitro NRP strategies that are useful for drug susceptibility testing and high-throughput screening.
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Affiliation(s)
| | - James Harrison
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Jonathan A G Cox
- School of Life and Health Sciences, Aston University, Birmingham, UK.
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Mondino S, Vázquez CL, Cabruja M, Sala C, Cazenave-Gassiot A, Blanco FC, Wenk MR, Bigi F, Cole ST, Gramajo H, Gago G. FasR Regulates Fatty Acid Biosynthesis and Is Essential for Virulence of Mycobacterium tuberculosis. Front Microbiol 2020; 11:586285. [PMID: 33193236 PMCID: PMC7652896 DOI: 10.3389/fmicb.2020.586285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/22/2020] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, is the world's leading cause of death from an infectious disease. One of the main features of this pathogen is the complex and dynamic lipid composition of the cell envelope, which adapts to the variable host environment and defines the fate of infection by actively interacting with and modulating immune responses. However, while much has been learned about the enzymes of the numerous lipid pathways, little knowledge is available regarding the proteins and metabolic signals regulating lipid metabolism during M. tuberculosis infection. In this work, we constructed and characterized a FasR-deficient mutant in M. tuberculosis and demonstrated that FasR positively regulates fas and acpS expression. Lipidomic analysis of the wild type and mutant strains revealed complete rearrangement of most lipid components of the cell envelope, with phospholipids, mycolic acids, sulfolipids, and phthiocerol dimycocerosates relative abundance severely altered. As a consequence, replication of the mutant strain was impaired in macrophages leading to reduced virulence in a mouse model of infection. Moreover, we show that the fasR mutant resides in acidified cellular compartments, suggesting that the lipid perturbation caused by the mutation prevented M. tuberculosis inhibition of phagolysosome maturation. This study identified FasR as a novel factor involved in regulation of mycobacterial virulence and provides evidence for the essential role that modulation of lipid homeostasis plays in the outcome of M. tuberculosis infection.
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Affiliation(s)
- Sonia Mondino
- Laboratory of Physiology and Genetics of Actinomycetes, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Matías Cabruja
- Laboratory of Physiology and Genetics of Actinomycetes, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Markus R. Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fabiana Bigi
- Instituto de Biotecnología-IABIMO (INTA-CONICET), Hurlingham, Argentina
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
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