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McCaffrey EF, Delmastro AC, Fitzhugh I, Ranek JS, Douglas S, Peters JM, Fullaway CC, Bosse M, Liu CC, Gillen C, Greenwald NF, Anzick S, Martens C, Winfree S, Bai Y, Sowers C, Goldston M, Kong A, Boonrat P, Bigbee CL, Venugopalan R, Maiello P, Klein E, Rodgers MA, Scanga CA, Lin PL, Kirschner D, Fortune S, Bryson BD, Butler JR, Mattila JT, Flynn JL, Angelo M. The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.18.638923. [PMID: 40027668 PMCID: PMC11870603 DOI: 10.1101/2025.02.18.638923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We previously discovered that human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the intriguing possibility that they promote tolerance to infection. In this study, our goal was to identify the prime drivers for establishing this tolerogenic niche and to determine if the magnitude of this response correlates with bacterial persistence. To do this, we conducted a multimodal spatial analysis of 52 granulomas from 16 non-human primates (NHP) who were infected with low dose Mtb for 9-12 weeks. Notably, each granuloma's bacterial burden was individually quantified allowing us to directly ask how granuloma spatial structure and function relate to infection control. We found that a universal feature of TB granulomas was partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment associated with pathologic immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlated with worsened bacterial burden. We conclude that hypoxia governs immune cell state and organization within granulomas and is a potent driver of subverted immunity during TB.
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Affiliation(s)
- Erin F. McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
- Spatial Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Alea C. Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Isobel Fitzhugh
- The Department of Biomedical Sciences and Technology, AdventHealth University, Orlando, FL
| | - Jolene S. Ranek
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Sarah Douglas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Joshua M. Peters
- Department of Biological Engineering, MIT, Cambridge, MA
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, MA
| | | | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Candace C. Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Craig Gillen
- The Department of Biomedical Sciences and Technology, AdventHealth University, Orlando, FL
| | - Noah F. Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Sarah Anzick
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT
| | - Craig Martens
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT
| | - Seth Winfree
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT
| | - Yunhao Bai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Cameron Sowers
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Mako Goldston
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Alex Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Potchara Boonrat
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Carolyn L. Bigbee
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Roopa Venugopalan
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Edwin Klein
- Division of Laboratory Animal Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark A. Rodgers
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Charles A. Scanga
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Philana Ling Lin
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Pediatrics, Division of Infectious Disease, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Denise Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Sarah Fortune
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, MA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bryan D. Bryson
- Department of Biological Engineering, MIT, Cambridge, MA
- Ragon Institute of Mass General, Harvard, and MIT, Cambridge, MA
| | - J. Russell Butler
- The Department of Biomedical Sciences and Technology, AdventHealth University, Orlando, FL
| | - Joshua T. Mattila
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
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Guo J, Qiu Y, Hu C, Cao Y, Li D, Du Y. Enhancing Antituberculosis Treatment Nanoparticles Encapsulated with Catalase and Levofloxacin Under Ultrasound Stimulation: A 3D Spheroid Study. Mol Pharm 2025; 22:747-759. [PMID: 39772621 DOI: 10.1021/acs.molpharmaceut.4c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB). Tuberculous granuloma is the central and key pathological structure of tuberculosis and is characterized by tissue hypoxia and ineffective drug delivery. To address these issues, this study fabricated a composite nanoparticle loaded with catalase (CAT) and levofloxacin (LEV) (CAT@LEV-NPs) and then combined it with ultrasound (US) to investigate the bactericidal effect and underlying mechanisms using TB spheroids. The TB spheroids were constructed using attenuated Bacillus Calmette-Guérin (BCG) instead of MTB to facilitate operation under general experimental conditions. This study examined the physical properties and oxygen production efficiency of CAT@LEV-NPs. Subsequently, we treated TB spheroids with nanoparticles alone or in combination with US and found that ultrasound significantly increased drug permeability and activated CAT@LEV-NPs to produce a large number of reactive oxygen species (ROS). The combined treatment showed excellent antibacterial effects, resulting in more severe damage to the bacterial structure than other treatments. Additionally, the combined treatment induced a higher M1 polarization of macrophages, increased the apoptosis rate, and improved the anoxic microenvironment in TB spheroids. These factors may be closely related to the enhanced bactericidal effects of combined treatment. In conclusion, our study suggests that US combined with CAT@LEV-NPs could serve as a novel, noninvasive, safe, and effective treatment modality for intractable MTB infections.
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Affiliation(s)
- Jiajun Guo
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yan Qiu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Can Hu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yuchao Cao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yonghong Du
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
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Carey CJ, Duggan N, Drabinska J, McClean S. Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis. FEMS Microbiol Rev 2025; 49:fuaf018. [PMID: 40312783 PMCID: PMC12071387 DOI: 10.1093/femsre/fuaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 04/04/2025] [Accepted: 04/29/2025] [Indexed: 05/03/2025] Open
Abstract
The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.
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Affiliation(s)
- Ciarán J Carey
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Niamh Duggan
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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Kim H, Shin SJ. Revolutionizing control strategies against Mycobacterium tuberculosis infection through selected targeting of lipid metabolism. Cell Mol Life Sci 2023; 80:291. [PMID: 37704889 PMCID: PMC11072447 DOI: 10.1007/s00018-023-04914-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Lipid species play a critical role in the growth and virulence expression of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). During Mtb infection, foamy macrophages accumulate lipids in granulomas, providing metabolic adaptation and survival strategies for Mtb against multiple stresses. Host-derived lipid species, including triacylglycerol and cholesterol, can also contribute to the development of drug-tolerant Mtb, leading to reduced efficacy of antibiotics targeting the bacterial cell wall or transcription. Transcriptional and metabolic analyses indicate that lipid metabolism-associated factors of Mtb are highly regulated by antibiotics and ultimately affect treatment outcomes. Despite the well-known association between major antibiotics and lipid metabolites in TB treatment, a comprehensive understanding of how altered lipid metabolites in both host and Mtb influence treatment outcomes in a drug-specific manner is necessary to overcome drug tolerance. The current review explores the controversies and correlations between lipids and drug efficacy in various Mtb infection models and proposes novel approaches to enhance the efficacy of anti-TB drugs. Moreover, the review provides insights into the efficacious control of Mtb infection by elucidating the impact of lipids on drug efficacy. This review aims to improve the effectiveness of current anti-TB drugs and facilitate the development of innovative therapeutic strategies against Mtb infection by making reverse use of Mtb-favoring lipid species.
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Affiliation(s)
- Hagyu Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea.
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Mouse Models for Mycobacterium tuberculosis Pathogenesis: Show and Do Not Tell. Pathogens 2022; 12:pathogens12010049. [PMID: 36678397 PMCID: PMC9865329 DOI: 10.3390/pathogens12010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/29/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Science has been taking profit from animal models since the first translational experiments back in ancient Greece. From there, and across all history, several remarkable findings have been obtained using animal models. One of the most popular models, especially for research in infectious diseases, is the mouse. Regarding research in tuberculosis, the mouse has provided useful information about host and bacterial traits related to susceptibility to the infection. The effect of aging, sexual dimorphisms, the route of infection, genetic differences between mice lineages and unbalanced immunity scenarios upon Mycobacterium tuberculosis infection and tuberculosis development has helped, helps and will help biomedical researchers in the design of new tools for diagnosis, treatment and prevention of tuberculosis, despite various discrepancies and the lack of deep study in some areas of these traits.
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Wang Z, Guo T, Jiang T, Zhao Z, Zu X, li L, Zhang Q, Hou Y, Song K, Xue Y. Regional distribution of Mycobacterium tuberculosis infection and resistance to rifampicin and isoniazid as determined by high-resolution melt analysis. BMC Infect Dis 2022; 22:812. [PMCID: PMC9620668 DOI: 10.1186/s12879-022-07792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/29/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Identifying the transmission mode and resistance mechanism of Mycobacterium tuberculosis (MTB) is key to prevent disease transmission. However, there is a lack of regional data. Therefore, the aim of this study was to identify risk factors associated with the transmission of MTB and regional patterns of resistance to isoniazid (INH) and rifampicin (RFP), as well as the prevalence of multidrug-resistant tuberculosis (MDR-TB). Methods High-resolution melt (HRM) analysis was conducted using sputum, alveolar lavage fluid, and pleural fluid samples collected from 17,515 patients with suspected or confirmed MTB infection in the downtown area and nine counties of Luoyang City from 2019 to 2021. Results Of the 17,515 patients, 82.6% resided in rural areas, and 96.0% appeared for an initial screening. The HRM positivity rate was 16.8%, with a higher rate in males than females (18.0% vs. 14.1%, p < 0.001). As expected, a positive sputum smear was correlated with a positive result for HRM analysis. By age, the highest rates of MTB infection occurred in males (22.9%) aged 26–30 years and females (28.1%) aged 21–25. The rates of resistance to RFP and INH and the incidence of MDR were higher in males than females (20.5% vs. 16.1%, p < 0.001, 15.9% vs. 12.0%, p < 0.001 and 12.9% vs. 10.2%, p < 0.001, respectively). The HRM positivity rate was much higher in previously treated patients than those newly diagnosed for MTB infection. Notably, males at the initial screening had significantly higher rates of HRM positive, INH resistance, RFP resistance, and MDR-TB than females (all, p < 0.05), but not those previously treated for MTB infection. The HRM positivity and drug resistance rates were much higher in the urban vs. rural population. By multivariate analyses, previous treatment, age < 51 years, residing in an urban area, and male sex were significantly and positively associated with drug resistance after adjusting for smear results and year of testing. Conclusion Males were at higher risks for MTB infection and drug resistance, while a younger age was associated with MTB infection, resistance to INH and RFP, and MDR-TB. Further comprehensive monitoring of resistance patterns is needed to control the spread of MTB infection and manage drug resistance locally.
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Affiliation(s)
- Zhenzhen Wang
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital and Clinical Medical College, Henan University of Science and Technology, 471000 Luo Yang, China ,grid.453074.10000 0000 9797 0900School of Medical Technology and Engineering, Henan University of Science and Technology, Luo Yang, 471000 China
| | - Tengfei Guo
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital and Clinical Medical College, Henan University of Science and Technology, 471000 Luo Yang, China
| | - Tao Jiang
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital and Clinical Medical College, Henan University of Science and Technology, 471000 Luo Yang, China
| | - Zhanqin Zhao
- grid.453074.10000 0000 9797 0900Animal Science and Technology, Henan University of Science and Technology, Luo Yang, 471000 China
| | - Xiangyang Zu
- grid.453074.10000 0000 9797 0900School of Medical Technology and Engineering, Henan University of Science and Technology, Luo Yang, 471000 China
| | - Long li
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital and Clinical Medical College, Henan University of Science and Technology, 471000 Luo Yang, China
| | - Qing Zhang
- grid.453074.10000 0000 9797 0900The First Affiliated Hospital and Clinical Medical College, Henan University of Science and Technology, 471000 Luo Yang, China
| | - Yi Hou
- Luoyang City CDC, Luo Yang, 471000 China
| | - Kena Song
- grid.453074.10000 0000 9797 0900School of Medical Technology and Engineering, Henan University of Science and Technology, Luo Yang, 471000 China
| | - Yun Xue
- grid.453074.10000 0000 9797 0900School of Medical Technology and Engineering, Henan University of Science and Technology, Luo Yang, 471000 China
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
| | | | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Mahatha AC, Banerjee SK, Ghosh A, Lata S, Saha S, Basu J, Kundu M. A systems approach to decipher a role of transcription factor RegX3 in the adaptation of Mycobacterium tuberculosis to hypoxic stress. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35980355 DOI: 10.1099/mic.0.001229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two-component systems (TCSs) are required for the ability of Mycobacterium tuberculosis to respond to stress. The paired TCS, SenX3-RegX3 is known to respond to phosphate starvation and acid stress. The other stress conditions under which RegX3 is required for M. tuberculosis to mount an appropriate response, remain incompletely understood. Here we have employed genome-wide microarray profiling to compare gene expression in a ΔregX3 mutant with the wild-type under phosphate stress, in order to gain information on the probable RegX3 regulon. We pulled out a set of 128 hypoxia-associated genes, which could potentially be regulated by RegX3, by overlapping the gene set downregulated at least twofold in ΔregX3 with the gene set reported in the literature to be associated with the response to hypoxia. We identified potential RegX3 binding inverted repeats at the loci of 41 of these genes, in silico. We also observed that ΔregX3 was attenuated in terms of its ability to withstand hypoxia, and this was reversed upon complementation with regX3, corroborating a role of RegX3 in the response of M. tuberculosis to hypoxia. We validated the binding of RegX3 at the upstream regions of a selected set of these genes. Electrophoretic mobility shift assays (EMSAs) confirmed that RegX3 binds to the upstream regions of the hypoxia-associated genes Rv3334, whiB7, Rv0195, Rv0196 and Rv1960c. Gene expression analyses showed that the expression of these genes is regulated by RegX3 under hypoxia. We also show that the expression of whiB7, Rv3334 and Rv0195 in macrophage-grown M. tuberculosis, is dependent on RegX3. Finally, we show that attenuation of survival of ΔregX3 under hypoxia is partly reversed upon overexpression of either Rv0195 or Rv3334, suggesting that the RegX3-Rv0195 and the RegX3-Rv3334 axis are involved in the adaptation of M. tuberculosis to a hypoxic environment.
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Affiliation(s)
- Amar Chandra Mahatha
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Srijon Kaushik Banerjee
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.,Present address: Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15217, USA
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Suruchi Lata
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Manikuntala Kundu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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Sarathy JP, Dartois V. Caseum: a Niche for Mycobacterium tuberculosis Drug-Tolerant Persisters. Clin Microbiol Rev 2020; 33:e00159-19. [PMID: 32238365 PMCID: PMC7117546 DOI: 10.1128/cmr.00159-19] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-recalcitrant persisting mycobacteria. Caseum is found in closed nodules and in open cavities connecting with an airway. Several commonly accepted characteristics of caseum were established during the preantibiotic era, when autopsies of deceased tuberculosis (TB) patients were common but methodologies were limited. These pioneering studies generated concepts such as acidic pH, low oxygen tension, and paucity of nutrients being the drivers of nonreplication and persistence in caseum. Here we review widely accepted beliefs about the caseum-specific stress factors thought to trigger the shift of Mycobacterium tuberculosis to drug tolerance. Our current state of knowledge reveals that M. tuberculosis is faced with a lipid-rich diet rather than nutrient deprivation in caseum. Variable caseum pH is seen across lesions, possibly transiently acidic in young lesions but overall near neutral in most mature lesions. Oxygen tension is low in the avascular caseum of closed nodules and high at the cavity surface, and a gradient of decreasing oxygen tension likely forms toward the cavity wall. Since caseum is largely made of infected and necrotized macrophages filled with lipid droplets, the microenvironmental conditions encountered by M. tuberculosis in foamy macrophages and in caseum bear many similarities. While there remain a few knowledge gaps, these findings constitute a solid starting point to develop high-throughput drug discovery assays that combine the right balance of oxygen tension, pH, lipid abundance, and lipid species to model the profound drug tolerance of M. tuberculosis in caseum.
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Affiliation(s)
- Jansy P Sarathy
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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Gao B, Wang J, Huang J, Huang X, Sha W, Qin L. The dynamic region of the peptidoglycan synthase gene, Rv0050, induces the growth rate and morphologic heterogeneity in Mycobacteria. INFECTION GENETICS AND EVOLUTION 2019; 72:86-92. [DOI: 10.1016/j.meegid.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022]
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Mycobacterium tuberculosis Rv0191 is an efflux pump of major facilitator superfamily transporter regulated by Rv1353c. Arch Biochem Biophys 2019; 667:59-66. [DOI: 10.1016/j.abb.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
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Yang H, Sha W, Liu Z, Tang T, Liu H, Qin L, Cui Z, Chen J, Liu F, Zheng R, Huang X, Wang J, Feng Y, Ge B. Lysine acetylation of DosR regulates the hypoxia response of Mycobacterium tuberculosis. Emerg Microbes Infect 2018; 7:34. [PMID: 29559631 PMCID: PMC5861037 DOI: 10.1038/s41426-018-0032-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 01/09/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) infection remains a large global public health problem. One striking characteristic of Mtb is its ability to adapt to hypoxia and trigger the ensuing transition to a dormant state for persistent infection, but how the hypoxia response of Mtb is regulated remains largely unknown. Here we performed a quantitative acetylome analysis to compare the acetylation profile of Mtb under aeration and hypoxia, and showed that 377 acetylation sites in 269 Mtb proteins were significantly changed under hypoxia. In particular, deacetylation of dormancy survival regulator (DosR) at K182 promoted the hypoxia response in Mtb and enhanced the transcription of DosR-targeted genes. Mechanistically, recombinant DosRK182R protein demonstrated enhanced DNA-binding activity in comparison with DosRK182Q protein. Moreover, Rv0998 was identified as an acetyltransferase that mediates the acetylation of DosR at K182. Deletion of Rv0998 also promoted the adaptation of Mtb to hypoxia and the transcription of DosR-targeted genes. Mice infected with an Mtb strain containing acetylation-defective DosRK182R had much lower bacterial counts and less severe histopathological impairments compared with those infected with the wild-type strain. Our findings suggest that hypoxia induces the deacetylation of DosR, which in turn increases its DNA-binding ability to promote the transcription of target genes, allowing Mtb to shift to dormancy under hypoxia.
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Affiliation(s)
- Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Wei Sha
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Tianqi Tang
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200049, PR China
| | - Haipeng Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Zhenling Cui
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Jianxia Chen
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Feng Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Yonghong Feng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, PR China. .,Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, 200049, PR China.
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