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Arbués A, Schmidiger S, Reinhard M, Borrell S, Gagneux S, Portevin D. Soluble immune mediators orchestrate protective in vitro granulomatous responses across Mycobacterium tuberculosis complex lineages. eLife 2025; 13:RP99062. [PMID: 40162896 PMCID: PMC11957536 DOI: 10.7554/elife.99062] [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] [Indexed: 04/02/2025] Open
Abstract
The members of the Mycobacterium tuberculosis complex (MTBC) causing human tuberculosis comprise 10 phylogenetic lineages that differ in their geographical distribution. The human consequences of this phylogenetic diversity remain poorly understood. Here, we assessed the phenotypic properties at the host-pathogen interface of 14 clinical strains representing five major MTBC lineages. Using a human in vitro granuloma model combined with bacterial load assessment, microscopy, flow cytometry, and multiplexed-bead arrays, we observed considerable intra-lineage diversity. Yet, modern lineages were overall associated with increased growth rate and more pronounced granulomatous responses. MTBC lineages exhibited distinct propensities to accumulate triglyceride lipid droplets-a phenotype associated with dormancy-that was particularly pronounced in lineage 2 and reduced in lineage 3 strains. The most favorable granuloma responses were associated with strong CD4 and CD8 T cell activation as well as inflammatory responses mediated by CXCL9, granzyme B, and TNF. Both of which showed consistent negative correlation with bacterial proliferation across genetically distant MTBC strains of different lineages. Taken together, our data indicate that different virulence strategies and protective immune traits associate with MTBC genetic diversity at lineage and strain level.
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Affiliation(s)
- Ainhoa Arbués
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Sarah Schmidiger
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Damien Portevin
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
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Wu Z, Liu W, Tan Q, Chen Y, Lai X, Hong J, Liang H, Wu H, Liang J, Chen X. Involvement of Mycobacterium smegmatis small noncoding RNA B11 in triacylglycerol accumulation and altered cell wall permeability. BMC Microbiol 2025; 25:124. [PMID: 40057673 PMCID: PMC11889869 DOI: 10.1186/s12866-025-03826-7] [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: 07/27/2024] [Accepted: 02/13/2025] [Indexed: 05/13/2025] Open
Abstract
BACKGROUND Pathways involving triacylglycerol (TAG) accumulation are thought to play a crucial regulatory role in bacterial growth and metabolism. Despite this understanding, little is known about the biological functions and regulatory mechanisms of small RNAs in Mycobacterium. Mycobacterium smegmatis (M. smegmatis), a type of Mycobacterium, serves as a model organism to investigate the molecular, physiological, and drug resistance features of M. tuberculosis. RESULTS In this study, we demonstrated that overexpression of B11 significantly affects bacterial growth and colony morphology, increases antibiotic sensitivity and sodium dodecyl sulfate (SDS) surface stress, decreases intracellular survival, and suppresses cytokine secretion in macrophages. Transcriptomic and lipidomic analyses revealed a metabolic downshift in the B11 overexpression strain, characterized by reduced levels of TAG. Furthermore, transmission electron microscopy showed that the B11 overexpression strain exhibited decreased cell wall thickness, leading to reduced biofilm formation and altered cell wall permeability. Additionally, we observed that B11 regulated certain target genes but did not directly bind to those proteins tested. CONCLUSIONS Taken together, these findings suggest that B11 plays important roles in Mycobacterium survival under antibiotic and SDS stresses, TAG accumulation, and contributes to antibiotic sensitivity through altered cell wall permeability.
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Affiliation(s)
- Zhuhua Wu
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Weilong Liu
- Institute of Hepatology, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Qiuchan Tan
- School of Basic Medical Sciences, Guangzhou Health Science College, Guangzhou, Guangdong, China
| | - Yuhui Chen
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiaoyu Lai
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Jianming Hong
- The Sixth People's Hospital of Dongguan, Dongguan, Guangdong, China
| | - Hongdi Liang
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Huizhong Wu
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China.
| | - Jing Liang
- The Sixth People's Hospital of Dongguan, Dongguan, Guangdong, China.
| | - Xunxun Chen
- Key Laboratory of Translational Medicine of Guangdong, Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China.
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3
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Tan Q, Huang CC, Calderon R, Lecca L, Mendoza M, Rocha GR, Tintaya K, Tovar X, Feng JY, Pan SW, Tseng YH, Huang JR, Zhang Z, Murray MB. Microbiological aspects and clinical impact of lower lung field tuberculosis: An observational cohort study in Peru. Int J Infect Dis 2025; 150:107284. [PMID: 39491717 PMCID: PMC11694351 DOI: 10.1016/j.ijid.2024.107284] [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: 09/04/2024] [Revised: 10/17/2024] [Accepted: 10/23/2024] [Indexed: 11/05/2024] Open
Abstract
OBJECTIVES Approximately 40% of tuberculosis (TB) cases remain undiagnosed globally. Lower lung field TB (LLF TB) presents atypically and is often misidentified as other lung diseases, leading to diagnostic delays in resource-limited settings. It may contribute to increased TB transmission and mortality. We aimed to identify microbiological determinants of LLF TB and evaluate treatment responses to optimize care. METHODS We conducted an observational cohort study in Lima, Peru, enrolling adults with microbiologically confirmed pulmonary TB (PTB) diagnosed by GeneXpert MTB/RIF assay or sputum culture. Mycobacterium tuberculosis (MTB) lineage was determined using whole-genome sequencing. Due to the delayed chest radiograph changes in LLF TB compared to non-LLF TB, we measured changes in the St. George's Respiratory Questionnaire (SGRQ) score at 2-month treatment mark and evaluated World Health Organization-specified final treatment outcomes. We used logistic regression to evaluate the associations between LLF TB and microbiological determinants and treatment outcomes. We used linear regression to assess whether the change in SGRQ scores over the first 2 months of treatment varied by LLF TB status. RESULTS Among 1316 PTB patients, 84 (6%) had LLF TB. Compared to non-LLF TB patients, LLF TB patients were more likely to be smear-negative (adjusted odds ratio [aOR] [95% CI] = 2.04 [1.28-3.23], P = 0.002) and to be infected with Lineage 2 (aOR [95% CI] = 1.95 [95% CI: 1.07-3.41; P = 0.024]). People with LLF TB had less improvement in SGRQ scores after 2 months of treatment (adjusted score difference [95% CI] = -6.29 [-10.99 to -1.59], P = 0.009), while they experienced better final outcomes compared to non-LLF TB patients, though this difference did not reach statistical significance (aOR = 0.43 [95% CI: 0.13-1.05], P = 0.103). CONCLUSION Patients with LLF TB are more likely than those with upper lung lesions to be sputum-negative on conventional tests, to be infected with Lineage 2, and to show less clinical improvement after treatment.
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Affiliation(s)
- Qi Tan
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA; Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Leonid Lecca
- Partners In Health-Socios En Salud Sucursal, Lima, Peru
| | | | | | - Karen Tintaya
- Partners In Health-Socios En Salud Sucursal, Lima, Peru
| | - Ximena Tovar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Jia-Yih Feng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sheng-Wei Pan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Han Tseng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jhong-Ru Huang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Zibiao Zhang
- Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA; Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Mvubu NE, Govender D, Pillay M. Comparative Transcriptomics Reveal Differential Expression of Coding and Non-Coding RNAs in Clinical Strains of Mycobacterium tuberculosis. Int J Mol Sci 2024; 26:217. [PMID: 39796078 PMCID: PMC11720245 DOI: 10.3390/ijms26010217] [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: 11/06/2024] [Revised: 12/24/2024] [Accepted: 12/25/2024] [Indexed: 01/13/2025] Open
Abstract
Coding and non-coding RNAs (ncRNAs) are potential novel markers that can be exploited for TB diagnostics in the fight against Mycobacterium tuberculosis. The current study investigated the mechanisms of transcript regulation and ncRNA signatures through Total RNA Seq and small (smRNA) RNA Seq followed by Bioinformatics analysis in Beijing and F15/LAM4/KZN (KZN) clinical strains compared to the laboratory strain. Total RNA Seq revealed differential regulation of RNA transcripts in Beijing (n = 1095) and KZN (n = 856) strains compared to the laboratory H37Rv strain. The KZN vs. H37Rv coding transcripts uniquely enriched fatty acids, steroid degradation, fructose, and mannose metabolism as well as a bacterial secretion system. In contrast, Tuberculosis and biosynthesis of siderophores KEGG pathways were enriched by the Beijing vs. H37Rv-specific transcripts. Novel sense and antisense ncRNAs, as well as the expression of these transcripts, were observed, and these targeted RNA transcripts are involved in cell wall synthesis and bacterial metabolism in a strain-specific manner. RNA transcripts identified in the current study offer insights into gene regulation of transcripts involved in the growth and metabolism of the clinically relevant KZN and Beijing strains compared to the laboratory H37Rv strain and thus can be exploited in the fight against Tuberculosis.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Divenita Govender
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Manormoney Pillay
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
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Tarekegn BG, Tientcheu LD, Decker J, Bell AJ, Mukamolova GV, Kampmann B, Messele G, Abeje T, Aseffa A, Dockrell HM, Haldar P, Barer MR, Garton NJ. Host and pathogen factors that influence variability of Mycobacterium tuberculosis lipid body content in sputum from patients with tuberculosis: an observational study. THE LANCET. MICROBE 2024; 5:100885. [PMID: 38906163 DOI: 10.1016/s2666-5247(24)00108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND High proportions of Mycobacterium tuberculosis cells in sputum containing triacylglycerol-rich lipid bodies have been shown to be associated with treatment failure or relapse following antituberculous chemotherapy. Although lipid body determination is a potential biomarker for supporting clinical trial and treatment decisions, factors influencing variability in sputum frequencies of lipid body-positive (%LB+) M tuberculosis in patients are unknown. We aimed to test our hypothesis that exposure to host-generated NO and M tuberculosis strains are factors associated with differences in sputum %LB+. METHODS In this observational study, we determined %LB+ frequencies before treatment by microscopy in patients with smear-positive tuberculosis from two separate prospective observational study settings (Gondar, Ethiopia, recruited between May 1, 2010, and April 30, 2011, and Fajara, The Gambia, who provided sputum samples before treatment between May 5, 2010, and Dec 22, 2011). In Ethiopia, fractional exhaled nitric oxide (FeNO) was measured as a biomarker of host NO, and M tuberculosis strain differences were determined by spoligotyping. Treatment response was assessed by percentage weight change after 7 months. In The Gambia, treatment responses were assessed as change in BMI and radiographic burden of disease after 6 months. Sputum M tuberculosis isolates were studied in vitro for their %LB+ and triacylglycerol synthase 1 (tgs1) mRNA responses to NO exposure. Propidium iodide staining was used as a measure of NO strain toxicity. Correlation between in vitro %LB+ frequencies following NO exposure and those of the same strain in sputum was examined with linear regression and Dunnett's multiple comparison test. FINDINGS In Ethiopia, 73 patients who were smear positive for pulmonary tuberculosis were recruited (43 [59%] were male and 30 [41%] were female). Of these, the %LB+ in the sputum of 59 patients showed linear correlation with log10 FeNO (r2=0·28; p<0·0001) and an association with strain spoligotype was suggested. Seven M tuberculosis strains from The Gambia showed different dose-responses to NO in vitro, demonstrated by changing lipid body content, tgs1 transcription, and bacterial toxicity. In sputum %LB+ frequencies correlated with in vitro %LB+ responses to NO of the corresponding isolate. In a subset of 34 patients across both cohorts, higher sputum %LB+ frequencies before treatment were associated with weaker responses to treatment than lower sputum %LB+ frequencies. INTERPRETATION M tuberculosis strain and exposure to host-generated NO are associated with sputum %LB+. Our results support the use of M tuberculosis strain-dependent sputum %LB+ as a predictive biomarker of treatment response. FUNDING The Medical Research Council, the University of Leicester, and the University of Gondar.
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Affiliation(s)
- Baye G Tarekegn
- Department of Respiratory Sciences, University of Leicester, Leicester, UK; Department of Medical Microbiology, University of Gondar, Gondar, Ethiopia
| | - Leopold D Tientcheu
- Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Vaccines and Immunity Theme, Fajara, The Gambia; Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jonathan Decker
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Andrew J Bell
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Galina V Mukamolova
- Department of Respiratory Sciences, University of Leicester, Leicester, UK; Leicester Tuberculosis Research Group, University of Leicester, Leicester, UK; National Institute for Health and Care Research Leicester Biomedical Research Centre, Leicester, UK
| | - Beate Kampmann
- Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Vaccines and Immunity Theme, Fajara, The Gambia; Institut für Internationale Gesundheit and Centre for Global Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gashaw Messele
- Department of Surgery, University of Gondar, Gondar, Ethiopia
| | - Tadeye Abeje
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Hazel M Dockrell
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Pranabashis Haldar
- Department of Respiratory Sciences, University of Leicester, Leicester, UK; Leicester Tuberculosis Research Group, University of Leicester, Leicester, UK; National Institute for Health and Care Research Leicester Biomedical Research Centre, Leicester, UK
| | - Michael R Barer
- Department of Respiratory Sciences, University of Leicester, Leicester, UK; Leicester Tuberculosis Research Group, University of Leicester, Leicester, UK; National Institute for Health and Care Research Leicester Biomedical Research Centre, Leicester, UK; Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Natalie J Garton
- Department of Respiratory Sciences, University of Leicester, Leicester, UK; Leicester Tuberculosis Research Group, University of Leicester, Leicester, UK; National Institute for Health and Care Research Leicester Biomedical Research Centre, Leicester, UK.
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Doz-Deblauwe E, Bounab B, Carreras F, Fahel JS, Oliveira SC, Lamkanfi M, Le Vern Y, Germon P, Pichon J, Kempf F, Paget C, Remot A, Winter N. Dual neutrophil subsets exacerbate or suppress inflammation in tuberculosis via IL-1β or PD-L1. Life Sci Alliance 2024; 7:e202402623. [PMID: 38803236 PMCID: PMC11109925 DOI: 10.26508/lsa.202402623] [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: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Neutrophils can be beneficial or deleterious during tuberculosis (TB). Based on the expression of MHC-II and programmed death ligand 1 (PD-L1), we distinguished two functionally and transcriptionally distinct neutrophil subsets in the lungs of mice infected with mycobacteria. Inflammatory [MHC-II-, PD-L1lo] neutrophils produced inflammasome-dependent IL-1β in the lungs in response to virulent mycobacteria and "accelerated" deleterious inflammation, which was highly exacerbated in IFN-γR-/- mice. Regulatory [MHC-II+, PD-L1hi] neutrophils "brake" inflammation by suppressing T-cell proliferation and IFN-γ production. Such beneficial regulation, which depends on PD-L1, is controlled by IFN-γR signaling in neutrophils. The hypervirulent HN878 strain from the Beijing genotype curbed PD-L1 expression by regulatory neutrophils, abolishing the braking function and driving deleterious hyperinflammation in the lungs. These findings add a layer of complexity to the roles played by neutrophils in TB and may explain the reactivation of this disease observed in cancer patients treated with anti-PD-L1.
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Affiliation(s)
| | | | | | - Julia S Fahel
- INRAE, Université de Tours, Nouzilly, France
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sergio C Oliveira
- Department of Immunology, University of Sao Paolo, Sao Paulo, Brazil
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Mohamed Lamkanfi
- Laboratory of Medical Immunology, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | | | | | | | - Christophe Paget
- INSERM, U1100, Centre d'Étude des Pathologies Respiratoires, Tours, France
- Faculté de Médecine, Université de Tours, Tours, France
| | - Aude Remot
- INRAE, Université de Tours, Nouzilly, France
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Gordhan BG, Padarath K, Sewcharran A, McIvor A, VanNieuwenhze MS, Waja Z, Martinson N, Kana BD. Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State. Pathogens 2024; 13:318. [PMID: 38668273 PMCID: PMC11054447 DOI: 10.3390/pathogens13040318] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Growing evidence points to the presence of differentially culturable tubercle bacteria (DCTB) in clinical specimens from individuals with active tuberculosis (TB) disease. These bacteria are unable to grow on solid media but can resuscitate in liquid media. Given the epidemiological success of certain clinical genotype families of Mycobacterium tuberculosis, we hypothesize that different strains may have distinct mechanisms of adaptation and tolerance. We used an in vitro carbon starvation model to determine the propensity of strains from lineages 2 and 4 that included the Beijing and LAM families respectively, to generate DCTB. Beijing strains were associated with a greater propensity to produce DCTB compared to LAM strains. Furthermore, LAM strains required culture filtrate (CF) for resuscitation whilst starved Beijing strains were not dependent on CF. Moreover, Beijing strains showed improved resuscitation with cognate CF, suggesting the presence of unique growth stimulatory molecules in this family. Analysis of starved Beijing and LAM strains showed longer cells, which with resuscitation were restored to a shorter length. Cell wall staining with fluorescent D-amino acids identified strain-specific incorporation patterns, indicating that cell surface remodeling during resuscitation was distinct between clinical strains. Collectively, our data demonstrate that M. tuberculosis clinical strains from different genotype lineages have differential propensities to generate DCTB, which may have implications for TB treatment success.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Kiyasha Padarath
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Amanda McIvor
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | | | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
| | - Neil Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg 2017, South Africa; (Z.W.); (N.M.)
- Center for TB Research, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bavesh Davandra Kana
- Department of Science and Innovation and the National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2017, South Africa; (B.G.G.); (K.P.); (A.S.); (A.M.)
- National Health Laboratory Service, Johannesburg 2000, South Africa
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8
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Mvubu NE, Jacoby K. Mycobacterium tuberculosis complex molecular networks and their regulation: Implications of strain heterogeneity on epigenetic diversity and transcriptome regulation. Heliyon 2023; 9:e22611. [PMID: 38046135 PMCID: PMC10686871 DOI: 10.1016/j.heliyon.2023.e22611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tuberculosis has been a public health crisis since the 1900, which has caused the highest mortalities due to a single bacterial infection worldwide, that was recently further complicated by the Coronavirus disease 2019 pandemic. The causative agent of Tuberculosis, Mycobacterium tuberculosis, belongs to a genetically well-characterized family of strains known as the Mycobacterium tuberculosis complex, which has complicated progress made towards eradicating Tuberculosis due to pathogen-specific phenotypic differences in the members of this complex. Mycobacterium tuberculosis complex strains are genetically diverse human- and animal-adapted pathogens belonging to 7 lineages (Indo-Oceanic, East-Asian, East-African Indian, Euro-American, M. africanum West Africa 1, M. africanum West Africa 2 and Ethopia), respectively and the recently identified Lineage 8 and M. africanum Lineage 9. Genomic studies have revealed that Mycobacterium tuberculosis complex members are ∼99 % similar, however, due to selective pressure and adaptation to human host, they are prone to mutations that have resulted in development of drug resistance and phenotypic heterogeneity that impact strain virulence. Furthermore, members of the Mycobacterium tuberculosis complex have preferred geographic locations and possess unique phenotypic characteristics that is linked to their pathogenicity. Due to the recent advances in development next generation sequencing platforms, several studies have revealed epigenetic changes in genomic regions combined with "unique" gene regulatory mechanisms through non-coding RNAs that are responsible for strain-specific behaviour on in vitro and in vivo infection models. The current review provides up to date epigenetic patterns, gene regulation through non-coding RNAs, together with implications of these mechanisms in down-stream proteome and metabolome, which may be responsible for "unique" responses to infection by members of the Mycobacterium tuberculosis complex. Understanding lineage-specific molecular mechanisms during infection may provide novel drug targets and disease control measures towards World Health organization END-TB strategy.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Kieran Jacoby
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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9
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Dargham T, Mallick I, Kremer L, Santucci P, Canaan S. Intrabacterial lipid inclusion-associated proteins: a core machinery conserved from saprophyte Actinobacteria to the human pathogen Mycobacterium tuberculosis. FEBS Open Bio 2023; 13:2306-2323. [PMID: 37872001 PMCID: PMC10699116 DOI: 10.1002/2211-5463.13721] [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: 09/05/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the aetiologic agent of tuberculosis (TB), stores triacylglycerol (TAG) in the form of intrabacterial lipid inclusions (ILI) to survive and chronically persist within its host. These highly energetic molecules represent a major source of carbon to support bacterial persistence and reactivation, thus playing a leading role in TB pathogenesis. However, despite its physiological and clinical relevance, ILI metabolism in Mtb remains poorly understood. Recent discoveries have suggested that several ILI-associated proteins might be widely conserved across TAG-producing prokaryotes, but still very little is known regarding the nature and the biological functions of these proteins. Herein, we performed an in silico analysis of three independent ILI-associated proteomes previously reported to computationally define a potential core ILI-associated proteome, referred to as ILIome. Our investigation revealed the presence of 70 orthologous proteins that were strictly conserved, thereby defining a minimal ILIome core. We further narrowed our analysis to proteins involved in lipid metabolism and discuss here their putative biological functions, along with their molecular interactions and dynamics at the surface of these bacterial organelles. We also highlight the experimental limitations of the original proteomic investigations and of the present bioinformatic analysis, while describing new technological approaches and presenting biological perspectives in the field. The in silico investigation presented here aims at providing useful datasets that could constitute a scientific resource of broad interest for the mycobacterial community, with the ultimate goal of enlightening ILI metabolism in prokaryotes with a special emphasis on Mtb pathogenesis.
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Affiliation(s)
- Tonia Dargham
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
- IHU Méditerranée InfectionAix‐Marseille Univ.France
| | - Ivy Mallick
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM)Université de MontpellierFrance
- INSERM, Institut de Recherche en Infectiologie de MontpellierFrance
| | - Pierre Santucci
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
| | - Stéphane Canaan
- Aix‐Marseille Univ, CNRS, LISM UMR 7255, IMM FR3479, IM2BFrance
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10
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Adhyapak P, Liang K, Duan M, Kapoor S. Effect of Host Cholesterol on the Membrane Dynamics of Outer Membrane Lipids of Mycobacteria. Chem Asian J 2023; 18:e202300697. [PMID: 37846643 PMCID: PMC7616960 DOI: 10.1002/asia.202300697] [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: 08/09/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
The ability of Mycobacterium tuberculosis to remain dormant after primary infection represents the prime cause of new TB cases throughout the world. Hence, diagnosis and treatment of individuals hosting dormant mycobacterium is one of the crucial strategies to be adopted for the prevention of Tuberculosis. Among many strategies unleashed by the latent bacterium, one of them is scavenging host cholesterol for carbon source. Cholesterol modifies lipid membranes over many scales and here, its effect on mycobacterial membrane biophysics and the subsequent effect on partitioning of antibiotics into cholesterol- enriched mycobacterial membranes was investigated. Our research showed that cholesterol alters the phase state behavior of mycobacterial outer membrane lipids by enhancing the overall membrane order at the headgroup and acyl chain region and is integrated into both ordered and disordered domains/phases, with a preference for the latter. Exogenous cholesterol further alters the drug partitioning behavior of structurally different drugs, pointing to a larger clinical potential of using more hydrophobic medications to target dormant bacteria.
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Affiliation(s)
- Pranav Adhyapak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076 (India)
| | - Kuan Liang
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071 Hubei (China)
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071 Hubei (China)
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076 (India)
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11
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Schami A, Islam MN, Belisle JT, Torrelles JB. Drug-resistant strains of Mycobacterium tuberculosis: cell envelope profiles and interactions with the host. Front Cell Infect Microbiol 2023; 13:1274175. [PMID: 38029252 PMCID: PMC10664572 DOI: 10.3389/fcimb.2023.1274175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
In the past few decades, drug-resistant (DR) strains of Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), have become increasingly prevalent and pose a threat to worldwide public health. These strains range from multi (MDR) to extensively (XDR) drug-resistant, making them very difficult to treat. Further, the current and future impact of the Coronavirus Disease 2019 (COVID-19) pandemic on the development of DR-TB is still unknown. Although exhaustive studies have been conducted depicting the uniqueness of the M.tb cell envelope, little is known about how its composition changes in relation to drug resistance acquisition. This knowledge is critical to understanding the capacity of DR-M.tb strains to resist anti-TB drugs, and to inform us on the future design of anti-TB drugs to combat these difficult-to-treat strains. In this review, we discuss the complexities of the M.tb cell envelope along with recent studies investigating how M.tb structurally and biochemically changes in relation to drug resistance. Further, we will describe what is currently known about the influence of M.tb drug resistance on infection outcomes, focusing on its impact on fitness, persister-bacteria, and subclinical TB.
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Affiliation(s)
- Alyssa Schami
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - John T. Belisle
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- International Center for the Advancement of Research & Education, International Center for the Advancement of Research & Education, Texas Biomedical Research Institute, San Antonio, TX, United States
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12
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Ufimtseva EG, Eremeeva NI. Drug-Tolerant Mycobacterium tuberculosis Adopt Different Survival Strategies in Alveolar Macrophages of Patients with Pulmonary Tuberculosis. Int J Mol Sci 2023; 24:14942. [PMID: 37834390 PMCID: PMC10573496 DOI: 10.3390/ijms241914942] [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: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The rapid spread of drug-resistant M. tuberculosis (Mtb) strains and the phenomenon of phenotypic tolerance to drugs present challenges toward achieving the goal of tuberculosis (TB) elimination worldwide. By using the ex vivo cultures of alveolar macrophages obtained from lung tissues of TB patients after intensive antimicrobial chemotherapy before surgery, different subpopulations of multidrug-tolerant Mtb with a spectrum of phenotypic and growth features were identified in the same TB lesions. Our results are indicative of not only passive mechanisms generating nonheritable resistance of Mtb to antibiotics, which are associated mainly with a lack of Mtb growth, but also some active mechanisms of Mtb persistence, such as cell wall and metabolic pathway remodeling. In one of the subpopulations, non-acid-fast Mtb have undergone significant reprogramming with the restoration of acid-fastness, lipoarabinomannan expression and replication in host cells of some patients after withdrawal of anti-TB drugs. Our data indicate the universal stress protein Rv2623 as a clinically relevant biomarker of Mtb that has lost acid-fastness in human lungs. The studies of Mtb survival, persistence, dormancy, and resumption and the identification of biomarkers characterizing these phenomena are very important concerning the development of vaccines and drug regimens with individualized management of patients for overcoming the resistance/tolerance crisis in anti-TB therapy.
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Affiliation(s)
- Elena G Ufimtseva
- Laboratory of Medical Biotechnology, Research Institute of Biochemistry, Federal Research Center of Fundamental and Translational Medicine, 2 Timakova Street, 630117 Novosibirsk, Russia
| | - Natalya I Eremeeva
- Institute of Disinfectology, F.F. Erisman Federal Scientific Center of Hygiene of the Federal Service on Surveillance for Consumer Rights Protection and Human Well-Being, 18a Nauchniy Proezd, 117246 Moscow, Russia
- Scientific Department, Ural Research Institute for Phthisiopulmonology, National Medical Research Center of Tuberculosis and Infectious Diseases of Ministry of Health of the Russian Federation, 50 XXII Partsyezda Street, 620039 Yekaterinburg, Russia
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13
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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14
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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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15
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Fines DM, Schichnes D, Knight M, Anaya-Sanchez A, Thuong N, Cox J, Stanley SA. Mycobacterial formation of intracellular lipid inclusions is a dynamic process associated with rapid replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552809. [PMID: 37609245 PMCID: PMC10441389 DOI: 10.1101/2023.08.10.552809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intracellular lipid inclusions (ILI) are triacylglyceride rich organelles produced by mycobacteria thought to serve as energy reservoirs. It is believed that ILI are formed as a result of a dosR mediated transition from replicative growth to non-replicating persistence (NRP). ILI rich Mycobacterium tuberculosis (Mtb) bacilli have been reported during infection and in sputum, establishing their importance in Mtb pathogenesis. Studies conducted in mycobacteria such as Mycobacterium smegmatis, Mycobacterium abscessus, or lab Mtb strains have demonstrated ILI formation in the presence of hypoxic, nitric oxide, nutrient limitation, or low nitrogen stress, conditions believed to emulate the host environment within which Mtb resides. Here, we show that M. marinum and clinical Mtb isolates make ILI during active replication in axenic culture independent of environmental stressors. By tracking ILI formation dynamics we demonstrate that ILI are quickly formed in the presence of fresh media or exogenous fatty acids but are rapidly depleted while bacteria are still actively replicating. We also show that the cell envelope is an alternate site for neutral lipid accumulation observed during stationary phase. In addition, we screen a panel of 60 clinical isolates and observe variation in ILI production during early log phase growth between and among Mtb lineages. Finally, we show that dosR expression level does not strictly correlate with ILI accumulation in fresh clinical isolates. Taken together, our data provide evidence of an active ILI formation pathway in replicating mycobacteria cultured in the absence of stressors, suggesting a decoupling of ILI formation from NRP.
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16
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Moopanar K, Nyide ANG, Senzani S, Mvubu NE. Clinical strains of Mycobacterium tuberculosis exhibit differential lipid metabolism-associated transcriptome changes in in vitro cholesterol and infection models. Pathog Dis 2022; 81:6889515. [PMID: 36509392 PMCID: PMC9936260 DOI: 10.1093/femspd/ftac046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/30/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Many studies have identified host-derived lipids, characterised by the abundance of cholesterol, as a major source of carbon nutrition for Mycobacterium tuberculosis during infection. Members of the Mycobacterium tuberculosis complex are biologically different with regards to degree of disease, host range, pathogenicity and transmission. Therefore, the current study aimed at elucidating transcriptome changes during early infection of pulmonary epithelial cells and on an in vitro cholesterol-rich minimal media, in M. tuberculosis clinical strains F15/LAM4/KZN and Beijing, and the laboratory H37Rv strain. Infection of pulmonary epithelial cells elicited the upregulation of fadD28 and hsaC in both the F15/LAM4/KZN and Beijing strains and the downregulation of several other lipid-associated genes. Growth curve analysis revealed F15/LAM4/KZN and Beijing to be slow growers in 7H9 medium and cholesterol-supplemented media. RNA-seq analysis revealed strain-specific transcriptomic changes, thereby affecting different metabolic processes in an in vitro cholesterol model. The differential expression of these genes suggests that the genetically diverse M. tuberculosis clinical strains exhibit strain-specific behaviour that may influence their ability to metabolise lipids, specifically cholesterol, which may account for phenotypic differences observed during infection.
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Affiliation(s)
- Kynesha Moopanar
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Asanda Nomfundo Graduate Nyide
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Sibusiso Senzani
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st floor, Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - Nontobeko Eunice Mvubu
- Corresponding author. Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa.Tel: +27 31 260 7404; E-mail:
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17
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Shaku MT, Bishai WR. Mycobacterium tuberculosis: A Pathogen That Can Hold Its Breath a Long Time. Am J Respir Crit Care Med 2022; 206:10-12. [PMID: 35442854 PMCID: PMC9954324 DOI: 10.1164/rccm.202203-0432ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Moagi T. Shaku
- School of MedicineJohns Hopkins UniversityBaltimore, Maryland,Centre of Excellence for Biomedical TB ResearchFaculty of Health SciencesUniversity of the WitwatersrandJohannesburg, South Africa,National Health Laboratory ServiceJohannesburg, South Africa
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18
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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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19
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Gisch N, Utpatel C, Gronbach LM, Kohl TA, Schombel U, Malm S, Dobos KM, Hesser DC, Diel R, Götsch U, Gerdes S, Shuaib YA, Ntinginya NE, Khosa C, Viegas S, Kerubo G, Ali S, Al-Hajoj SA, Ndung'u PW, Rachow A, Hoelscher M, Maurer FP, Schwudke D, Niemann S, Reiling N, Homolka S. Sub-Lineage Specific Phenolic Glycolipid Patterns in the Mycobacterium tuberculosis Complex Lineage 1. Front Microbiol 2022; 13:832054. [PMID: 35350619 PMCID: PMC8957993 DOI: 10.3389/fmicb.2022.832054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 12/01/2022] Open
Abstract
“Ancestral” Mycobacterium tuberculosis complex (MTBC) strains of Lineage 1 (L1, East African Indian) are a prominent tuberculosis (TB) cause in countries around the Indian Ocean. However, the pathobiology of L1 strains is insufficiently characterized. Here, we used whole genome sequencing (WGS) of 312 L1 strains from 43 countries to perform a characterization of the global L1 population structure and correlate this to the analysis of the synthesis of phenolic glycolipids (PGL) – known MTBC polyketide-derived virulence factors. Our results reveal the presence of eight major L1 sub-lineages, whose members have specific mutation signatures in PGL biosynthesis genes, e.g., pks15/1 or glycosyltransferases Rv2962c and/or Rv2958c. Sub-lineage specific PGL production was studied by NMR-based lipid profiling and strains with a completely abolished phenolphthiocerol dimycoserosate biosynthesis showed in average a more prominent growth in human macrophages. In conclusion, our results show a diverse population structure of L1 strains that is associated with the presence of specific PGL types. This includes the occurrence of mycoside B in one sub-lineage, representing the first description of a PGL in an M. tuberculosis lineage other than L2. Such differences may be important for the evolution of L1 strains, e.g., allowing adaption to different human populations.
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Affiliation(s)
- Nicolas Gisch
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Lisa M Gronbach
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Ursula Schombel
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sven Malm
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Karen M Dobos
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Danny C Hesser
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Roland Diel
- Lung Clinic Grosshansdorf, Airway Disease Center North (ARCN), German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Udo Götsch
- Municipal Health Authority Frankfurt am Main, Frankfurt am Main, Germany
| | - Silke Gerdes
- Municipal Health Authority Hannover, Hanover, Germany
| | - Yassir A Shuaib
- College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum, Sudan.,WHO-Supranational Reference Laboratory of Tuberculosis, Institute of Microbiology and Laboratory Medicine (IML Red), Gauting, Germany
| | - Nyanda E Ntinginya
- National Institute for Medical Research Tanzania - Mbeya Medical Research Center, Mbeya, Tanzania
| | - Celso Khosa
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Sofia Viegas
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Glennah Kerubo
- Department of Medical Microbiology and Parasitology, School of Medicine, Kenyatta University, Nairobi, Kenya
| | - Solomon Ali
- Department of Microbiology, Immunology, and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Sahal A Al-Hajoj
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Perpetual W Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Centre for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Schwudke
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Norbert Reiling
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Microbial Interface Biology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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20
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Yokobori N, López B, Ritacco V. The host-pathogen-environment triad: Lessons learned through the study of the multidrug-resistant Mycobacterium tuberculosis M strain. Tuberculosis (Edinb) 2022; 134:102200. [PMID: 35339874 DOI: 10.1016/j.tube.2022.102200] [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: 12/30/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
Multidrug-resistant tuberculosis is one of the major obstacles that face the tuberculosis eradication efforts. Drug-resistant Mycobacterium tuberculosis clones were initially disregarded as a public health threat, because they were assumed to have paid a high fitness cost in exchange of resistance acquisition. However, some genotypes manage to overcome the impact of drug-resistance conferring mutations, retain transmissibility and cause large outbreaks. In Argentina, the HIV-AIDS epidemics fuelled the expansion of the so-called M strain in the early 1990s, which is responsible for the largest recorded multidrug-resistant tuberculosis cluster of Latin America. The aim of this work is to review the knowledge gathered after nearly three decades of multidisciplinary research on epidemiological, microbiological and immunological aspects of this highly successful strain. Collectively, our results indicate that the successful transmission of the M strain could be ascribed to its unaltered virulence, low Th1/Th17 response, a low fitness cost imposed by the resistance conferring mutations and a high resistance to host-related stress. In the early 2000s, the incident cases due to the M strain steadily declined and stabilized in the latest years. Improvements in the management, diagnosis and treatment of multidrug-resistant tuberculosis along with societal factors such as the low domestic and international mobility of the patients affected by this strain probably contributed to the outbreak containment. This stresses the importance of sustaining the public health interventions to avoid the resurgence of this conspicuous multidrug-resistant strain.
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Affiliation(s)
- Noemí Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
| | - Beatriz López
- Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina.
| | - Viviana Ritacco
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
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21
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Allué-Guardia A, Garcia-Vilanova A, Olmo-Fontánez AM, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and Age-Dependent Transcriptional Changes in Mycobacterium tuberculosis Cell Envelope Biosynthesis Genes after Exposure to Human Alveolar Lining Fluid. Int J Mol Sci 2022; 23:ijms23020983. [PMID: 35055170 PMCID: PMC8780516 DOI: 10.3390/ijms23020983] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis (M.tb), resulted in almost 1.4 million deaths in 2019, and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M.tb comes into close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic, innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M.tb upon contact, defining subsequent M.tb-host cell interactions and infection outcomes in vitro and in vivo. We also demonstrated that ALF from 60+ year old elders (E-ALF) vs. healthy 18- to 45-year-old adults (A-ALF) is dysfunctional, with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay shows that M.tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M.tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M.tb exposure to E-ALF shows a lesser transcriptional response, with most of the M.tb genes unchanged or downregulated. Overall, this study indicates that M.tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status, determined by factors such as age, might play an important role in determining infection outcome.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Andreu Garcia-Vilanova
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
| | - Angélica M. Olmo-Fontánez
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jay Peters
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Diego J. Maselli
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA;
| | - Joanne Turner
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Larry S. Schlesinger
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
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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: 12] [Impact Index Per Article: 3.0] [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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Mycobacterial MCE proteins as transporters that control lipid homeostasis of the cell wall. Tuberculosis (Edinb) 2021; 132:102162. [PMID: 34952299 DOI: 10.1016/j.tube.2021.102162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023]
Abstract
Mammalian cell entry (mce) genes are not only present in genomes of pathogenic mycobacteria, including Mycobacterium tuberculosis (the causative agent of tuberculosis), but also in saprophytic and opportunistic mycobacterial species. MCE are conserved cell-wall proteins encoded by mce operons, which maintain an identical structure in all mycobacteria: two yrbE genes (A and B) followed by six mce genes (A, B, C, D, E and F). Although these proteins are known to participate in the virulence of pathogenic mycobacteria, the presence of the operons in nonpathogenic mycobacteria and other bacteria indicates that they play another role apart from host cell invasion. In this respect, more recent studies suggest that they are functionally similar to ABC transporters and form part of lipid transporters in Actinobacteria. To date, most reviews on mce operons in the literature discuss their role in virulence. However, according to data from transcriptional studies, mce genes, particularly the mce1 and mce4 operons, modify their expression according to the carbon source and upon hypoxia, starvation, surface stress and oxidative stress; which suggests a role of MCE proteins in the response of Mycobacteria to external stressors. In addition to these data, this review also summarizes the studies demonstrating the role of MCE proteins as lipid transporters as well as the relevance of their transport function in the interaction of pathogenic Mycobacteria with the hosts. Altogether, the evidence to date would indicate that MCE proteins participate in the response to the stress conditions that mycobacteria encounter during infection, by participating in the cell wall remodelling and possibly contributing to lipid homeostasis.
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24
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Mekonnen D, Derbie A, Mihret A, Yimer SA, Tønjum T, Gelaw B, Nibret E, Munshae A, Waddell SJ, Aseffa A. Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids Health Dis 2021; 20:129. [PMID: 34602073 PMCID: PMC8487580 DOI: 10.1186/s12944-021-01550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa.Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome.The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov, 0412, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, PO Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endalkachew Nibret
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshae
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
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25
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Allué-Guardia A, Garcia-Vilanova A, M Olmo-Fontánez A, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and age-dependent transcriptional changes in Mycobacterium tuberculosis cell envelope biosynthesis genes after exposure to human alveolar lining fluid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.09.08.459334. [PMID: 34580670 PMCID: PMC8475962 DOI: 10.1101/2021.09.08.459334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis ( M . tb ), resulted in almost 1.4 million deaths in 2019 and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M . tb comes in close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M . tb upon contact, defining subsequent M . tb -host cell interactions and infection outcomes in vitro and in vivo . We also demonstrated that ALF from 60+ year old elders (E-ALF) vs . healthy 18- to 45-year-old adults (A-ALF) is dysfunctional with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay demonstrates that M . tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M . tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M . tb exposure to E-ALF shows lesser transcriptional response, with most of the M . tb genes unchanged or downregulated. Overall, this study indicates that M . tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status determined by factors such as age might play an important role in determining infection outcome.
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26
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Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli. Biochem J 2021; 478:3079-3098. [PMID: 34350952 DOI: 10.1042/bcj20210268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022]
Abstract
DevR/DosR response regulator is believed to participate in virulence, dormancy adaptation and antibiotic tolerance mechanisms of Mycobacterium tuberculosis by regulating the expression of the dormancy regulon. We have previously shown that the interaction of DevR with RNA polymerase is essential for the expression of DevR-regulated genes. Here, we developed a M. tuberculosis-specific in vivo transcription system to enrich our understanding of DevR-RNA polymerase interaction. This in vivo assay involves co-transforming E. coli with two plasmids that express α, β, β' and σA subunits of M. tuberculosis RNA polymerase and a third plasmid that harbors a DevR expression cassette and a GFP reporter gene under the DevR-regulated fdxA promoter. We show that DevR-dependent transcription is sponsored exclusively by M. tuberculosis RNA polymerase and regulated by α and σA subunits of M. tuberculosis RNA polymerase. Using this E. coli triple plasmid system to express mutant variants of M. tuberculosis RNA polymerase, we identified E280 residue in C-terminal domain of α and K513 and R515 residues of σA to participate in DevR-dependent transcription. In silico modeling of a ternary complex of DevR, σA domain 4 and fdxA promoter suggest an interaction of Q505, R515 and K513 residues of σA with E178 and D172 residues of DevR and E471 of σA, respectively. These findings provide us with new insights into the interactions between DevR and RNA polymerase of M. tuberculosis which can be targeted for intercepting DevR function. Finally, we demonstrate the utility of this system for screening of anti-DevR compounds.
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Crotta Asis A, Savoretti F, Cabruja M, Gramajo H, Gago G. Characterization of key enzymes involved in triacylglycerol biosynthesis in mycobacteria. Sci Rep 2021; 11:13257. [PMID: 34168231 PMCID: PMC8225852 DOI: 10.1038/s41598-021-92721-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Phosphatidic acid phosphatase (PAP) catalyzes the dephosphorylation of phosphatidic acid (PA) yielding diacylglycerol (DAG), the lipid precursor for triacylglycerol (TAG) biosynthesis. PAP activity has a key role in the regulation of PA flux towards TAG or glycerophospholipid synthesis. In this work we have characterized two Mycobacterium smegmatis genes encoding for functional PAP proteins. Disruption of both genes provoked a sharp reduction in de novo TAG biosynthesis in early growth phase cultures under stress conditions. In vivo labeling experiments demonstrated that TAG biosynthesis was restored in the ∆PAP mutant when bacteria reached exponential growth phase, with a concomitant reduction of phospholipid synthesis. In addition, comparative lipidomic analysis showed that the ∆PAP strain had increased levels of odd chain fatty acids esterified into TAGs, suggesting that the absence of PAP activity triggered other rearrangements of lipid metabolism, like phospholipid recycling, in order to maintain the wild type levels of TAG. Finally, the lipid changes observed in the ∆PAP mutant led to defective biofilm formation. Understanding the interaction between TAG synthesis and the lipid composition of mycobacterial cell envelope is a key step to better understand how lipid homeostasis is regulated during Mycobacterium tuberculosis infection.
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Affiliation(s)
- Agostina Crotta Asis
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Savoretti
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Matías Cabruja
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Stanford University, Stanford, USA
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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28
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Mallick I, Santucci P, Poncin I, Point V, Kremer L, Cavalier JF, Canaan S. Intrabacterial lipid inclusions in mycobacteria: unexpected key players in survival and pathogenesis? FEMS Microbiol Rev 2021; 45:6283747. [PMID: 34036305 DOI: 10.1093/femsre/fuab029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterial species, including Mycobacterium tuberculosis, rely on lipids to survive and chronically persist within their hosts. Upon infection, opportunistic and strict pathogenic mycobacteria exploit metabolic pathways to import and process host-derived free fatty acids, subsequently stored as triacylglycerols under the form of intrabacterial lipid inclusions (ILI). Under nutrient-limiting conditions, ILI constitute a critical source of energy that fuels the carbon requirements and maintain redox homeostasis, promoting bacterial survival for extensive periods of time. In addition to their basic metabolic functions, these organelles display multiple other biological properties, emphasizing their central role in the mycobacterial lifecycle. However, despite of their importance, the dynamics of ILI metabolism and their contribution to mycobacterial adaptation/survival in the context of infection has not been thoroughly documented. Herein, we provide an overview of the historical ILI discoveries, their characterization, and current knowledge regarding the micro-environmental stimuli conveying ILI formation, storage and degradation. We also review new biological systems to monitor the dynamics of ILI metabolism in extra- and intracellular mycobacteria and describe major molecular actors in triacylglycerol biosynthesis, maintenance and breakdown. Finally, emerging concepts regarding to the role of ILI in mycobacterial survival, persistence, reactivation, antibiotic susceptibility and inter-individual transmission are also discuss.
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Affiliation(s)
- Ivy Mallick
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, Montpellier, France.,IRIM, INSERM, Montpellier, France
| | | | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
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29
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Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:2628. [PMID: 33514768 PMCID: PMC7846770 DOI: 10.1038/s41598-021-81223-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022] Open
Abstract
While persistence in a dormant state is crucial for the life cycle of Mycobacterium tuberculosis, no investigation regarding dormancy survival of different strains across different lineages was performed so far. We analyzed responses to oxygen starvation and recovery in terms of growth, metabolism, and transcription. All different strains belonging to the Euro-American lineage (L4) showed similar survival and resuscitation characteristics. Different clinical isolates from the Beijing (L2), East African-Indian (L3), and Delhi/Central Asian (L1) lineage did not survive oxygen starvation. We show that dormancy survival is lineage-dependent. Recovery from O2 starvation was only observed in strains belonging to the Euro-American (L4) lineage but not in strains belonging to different lineages (L1, L2, L3). Thus, resuscitation from dormancy after oxygen starvation is not a general feature of all M. tuberculosis strains as thought before. Our findings are of key importance to understand infection dynamics of non-Euro-American vs Euro-American strains and to develop drugs targeting the dormant state.
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30
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Modlin SJ, Conkle-Gutierrez D, Kim C, Mitchell SN, Morrissey C, Weinrick BC, Jacobs WR, Ramirez-Busby SM, Hoffner SE, Valafar F. Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife 2020; 9:58542. [PMID: 33107429 PMCID: PMC7591249 DOI: 10.7554/elife.58542] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
This study assembles DNA adenine methylomes for 93 Mycobacterium tuberculosis complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling. Second, heterogeneity analysis of partially active methyltransferase alleles revealed that intracellular stochastic methylation generates a mosaic of methylomes within isogenic cultures, which we formalize as ‘intercellular mosaic methylation’ (IMM). Mutation-driven IMM was nearly ubiquitous in the globally prominent Beijing sublineage. Third, promoter methylation is widespread and associated with differential expression in the ΔhsdM transcriptome, suggesting promoter HsdM-methylation directly influences transcription. Finally, comparative and functional analyses identified 351 sites hypervariable across isolates and numerous putative regulatory interactions. This multi-omic integration revealed features of methylomic variability in clinical isolates and provides a rational basis for hypothesizing the functions of DNA adenine methylation in MTBC physiology and adaptive evolution.
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Affiliation(s)
- Samuel J Modlin
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Derek Conkle-Gutierrez
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Calvin Kim
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Scott N Mitchell
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Christopher Morrissey
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | | | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Sarah M Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Sven E Hoffner
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States.,Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
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31
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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32
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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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33
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Ly A, Liu J. Mycobacterial Virulence Factors: Surface-Exposed Lipids and Secreted Proteins. Int J Mol Sci 2020; 21:ijms21113985. [PMID: 32498243 PMCID: PMC7312605 DOI: 10.3390/ijms21113985] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 01/15/2023] Open
Abstract
The clinically important Mycobacterium tuberculosis (M. tb) and related mycobacterial pathogens use various virulence mechanisms to survive and cause disease in their hosts. Several well-established virulence factors include the surface-exposed lipids in the mycobacterial outer membrane, as well as the Esx family proteins and the Pro-Glu (PE)/ Pro-Pro-Glu (PPE) family proteins secreted by type VII secretion systems (T7SS). Five ESX T7SS exist in M. tb and three—EsxA secretion system-1 (ESX-1), ESX-3, and ESX-5—have been implicated in virulence, yet only the structures of ESX-3 and ESX-5 have been solved to date. Here, we summarize the current research on three outer membrane lipids—phthiocerol dimycocerosates, phenolic glycolipids, and sulfolipids—as well as the secretion machinery and substrates of three mycobacterial T7SS—ESX-1, ESX-3, and ESX-5. We propose a structural model of the M. tb ESX-1 system based on the latest structural findings of the ESX-3 and ESX-5 secretion apparatuses to gain insight into the transport mechanism of ESX-associated virulence factors.
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Affiliation(s)
| | - Jun Liu
- Correspondence: ; Tel.: +1-416-946-5067
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Moopanar K, Mvubu NE. Lineage-specific differences in lipid metabolism and its impact on clinical strains of Mycobacterium tuberculosis. Microb Pathog 2020; 146:104250. [PMID: 32407863 DOI: 10.1016/j.micpath.2020.104250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of TB and its incidences has been on the rise since 1993. Lipid metabolism is an imperative metabolic process, which grants M. tb the ability to utilize host-derived lipids as a secondary source of nutrition during infection. In addition to degrading host lipids, M. tb is proficient at using lipids, such as cholesterol, to facilitate its entry into macrophages. Mycolic acids, constituents of the mycobacterial cell wall, offer protection and aid in persistence of the bacterium. These are effectively synthesized using a complex fatty acid synthase system. Many pathogenesis studies have reported differences in lipid-metabolism of clinical strains of M. tb that belongs to diverse lineages of the Mycobacterium tuberculosis complex (MTBC). East-Asian and Euro-American lineages possess "unique" cell wall-associated lipids compared to the less transmissible Ethiopian lineage, which may offer these lineages a competitive advantage. Therefore, it is crucial to comprehend the complexities among the MTBC lineages with lipid metabolism and their impact on virulence, transmissibility and pathogenesis. Thus, this review provides an insight into lipid metabolism in various lineages of the MTBC and their impact on virulence and persistence during infection, as this may provide critical insight into developing novel therapeutics to combat TB.
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Affiliation(s)
- K Moopanar
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
| | - N E Mvubu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
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A Phenotypic Characterization of Two Isolates of a Multidrug-Resistant Outbreak Strain of Mycobacterium tuberculosis with Opposite Epidemiological Fitness. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4741237. [PMID: 32337252 PMCID: PMC7168692 DOI: 10.1155/2020/4741237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB) is an infectious disease, caused by Mycobacterium tuberculosis, primarily affecting the lungs. The M. tuberculosis strain of the Haarlem family named M was responsible for a large multidrug-resistant TB (MDR-TB) outbreak in Buenos Aires. This outbreak started in the early 1990s and in the mid 2000s still accounted for 29% of all MDR-TB cases in Argentina. By contrast, a clonal variant of strain M, named 410, has caused a single tuberculosis case since the onset of the outbreak. The molecular bases of the high epidemiological fitness of the M strain remain unclear. To assess its unique molecular properties, herein, we performed a comparative protein and lipid analysis of a representative clone of the M strain (Mp) and the nonprosperous M variant 410. We also evaluated their growth in low pH. The variant 410 had higher levels of latency proteins under standard conditions and delayed growth at low pH, suggesting that it is more sensitive to stress stimuli than Mp. Moreover, Mp showed higher levels of mycolic acids covalently attached to the cell wall and lower accumulation of free mycolic acids in the outer layer than the 410 strain. The low expression of latency proteins together with the reduced content of surface mycolic acids may facilitate Mp to evade the host immune responses.
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Wang WF, Lu MYJ, Cheng TJR, Tang YC, Teng YC, Hwa TY, Chen YH, Li MY, Wu MH, Chuang PC, Jou R, Wong CH, Li WH. Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome. Genome Biol Evol 2020; 12:3890-3905. [PMID: 31971587 PMCID: PMC7058165 DOI: 10.1093/gbe/evaa009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, kills over 1 million people worldwide annually. Development of drug resistance (DR) in the pathogen is a major challenge for TB control. We conducted whole-genome analysis of seven Taiwan M. tuberculosis isolates: One drug susceptible (DS) and five DR Beijing lineage isolates and one DR Euro-American lineage isolate. Developing a new method for DR mutation identification and applying it to the next-generation sequencing (NGS) data from the 6 Beijing lineage isolates, we identified 13 known and 6 candidate DR mutations and provided experimental support for 4 of them. We assembled the genomes of one DS and two DR Beijing lineage isolates and the Euro-American lineage isolate using NGS data. Moreover, using both PacBio and NGS sequencing data, we obtained a high-quality assembly of an extensive DR Beijing lineage isolate. Comparative analysis of these five newly assembled genomes and two published complete genomes revealed a large number of genetic changes, including gene gains and losses, indels and translocations, suggesting rapid evolution of M. tuberculosis. We found the MazEF toxin-antitoxin system in all the seven isolates studied and several interesting mutations in MazEF proteins. Finally, we used the four assembled Beijing lineage genomes to construct a high-quality Beijing lineage reference genome that is DS and contains all the genes in the four genomes. It contains 212 genes not found in the standard reference H37Rv, which is Euro-American. It is therefore a better reference than H37Rv for the Beijing lineage, the predominant lineage in Asia.
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Affiliation(s)
- Woei-Fuh Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Ching Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Chuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Teh-Yang Hwa
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Hua Wu
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Pei-Chun Chuang
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Chi-Huey Wong
- Genome Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Illinois
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Garcia-Vilanova A, Chan J, Torrelles JB. Underestimated Manipulative Roles of Mycobacterium tuberculosis Cell Envelope Glycolipids During Infection. Front Immunol 2019; 10:2909. [PMID: 31921168 PMCID: PMC6930167 DOI: 10.3389/fimmu.2019.02909] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
The Mycobacterium tuberculosis cell envelope has been evolving over time to make the bacterium transmissible and adaptable to the human host. In this context, the M. tuberculosis cell envelope contains a peripheral barrier full of lipids, some of them unique, which confer M. tuberculosis with a unique shield against the different host environments that the bacterium will encounter at the different stages of infection. This lipid barrier is mainly composed of glycolipids that can be characterized by three different subsets: trehalose-containing, mannose-containing, and 6-deoxy-pyranose-containing glycolipids. In this review, we explore the roles of these cell envelope glycolipids in M. tuberculosis virulence and pathogenesis, drug resistance, and further, how these glycolipids may dictate the M. tuberculosis cell envelope evolution from ancient to modern strains. Finally, we address how these M. tuberculosis cell envelope glycolipids are impacted by the host lung alveolar environment, their role in vaccination and masking host immunity, and subsequently the impact of these glycolipids in shaping how M. tuberculosis interacts with host cells, manipulating their immune response to favor the establishment of an infection.
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Affiliation(s)
- Andreu Garcia-Vilanova
- Population Health Program, TB Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - John Chan
- Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY, United States
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY, United States
| | - Jordi B. Torrelles
- Population Health Program, TB Group, Texas Biomedical Research Institute, San Antonio, TX, United States
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Liu DQ, Zhang JL, Pan ZF, Mai JT, Mei HJ, Dai Y, Zhang L, Wang QZ. Over-expression of Tgs1 in Mycobacterium marinum enhances virulence in adult zebrafish. Int J Med Microbiol 2019; 310:151378. [PMID: 31757695 DOI: 10.1016/j.ijmm.2019.151378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/28/2019] [Accepted: 11/04/2019] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), can persist in the host for decades without causing TB symptoms and can cause a latent infection, which is an intricate challenge of current TB control. The DosR regulon, which contains approximately 50 genes, is crucial in the non-replicating persistence of Mtb. tgs1 is one of the most powerfully induced genes in this regulon during Mtb non-replicating persistence. The gene encodes a triacyl glycerol synthase catalyzing synthesis of triacyl glycerol (TAG), which is proposed as an energy source during bacilli persistence. Here, western blotting showed that the Tgs1 protein was upregulated in clinical Mtb strains. To detect its physiological effects on mycobacterium, we constructed serial recombinant M. marinum including over-expressed Tgs1(Tgs1-H), reduced-expressed Tgs1(Tgs1-L), and wild type M. marinum strains as controls. Tgs1 over-expression did not influence M. marinum growth under aerobic shaking and in hypoxic cultures, while growth advantages were observed at an early stage under nutrient starvation. Transmission electron microscopy revealed more lipid droplets in Tgs1-H than the other two strains; the droplets filled the cytoplasm. Two-dimensional thin-layer chromatography revealed more phosphatidyl-myo-inositol mannosides in the Tgs1-H cell wall. To assess the virulence of recombinant M. marinum in the natural host, adult zebrafish were infected with Tgs1-H or wild type strains. Hypervirulence of Tgs1-H was characterized by markedly increased bacterial load and early death of adult zebrafish. Remarkably, zebrafish infected with Tgs1-H developed necrotizing granulomas much more rapidly and in higher amounts, which facilitated mycobacterial replication and dissemination among organs and eventual tissue destruction in zebrafish. RNA sequencing analysis showed Tgs1-H induced 13 genes differentially expressed under aerobiosis. Among them, PE_PGRS54 (MMAR_5307),one of the PE_PGRS family of antigens, was markedly up-regulated, while 110 coding genes were down-regulated in Tgs1-L.The 110 genes included 22 member genes of the DosR regulon. The collective results indicate an important role for the Tgs1 protein of M. marinumin progression of infection in the natural host. Tgs1 signaling may be involved in a previously unknown behavior of M. marinum under hypoxia/aerobiosis.
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Affiliation(s)
- Ding-Qian Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China; Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Jun-Li Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Zhi-Fen Pan
- The Tuberculosis Division of the First Hospital of Jiaxing, Jiaxing, Zhejiang, China
| | - Jun-Tao Mai
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Heng-Jun Mei
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yue Dai
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.
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Tong J, Liu Q, Wu J, Jiang Y, Takiff HE, Gao Q. Mycobacterium tuberculosis strains of the modern Beijing sublineage excessively accumulate triacylglycerols in vitro. Tuberculosis (Edinb) 2019; 120:101892. [PMID: 31783320 DOI: 10.1016/j.tube.2019.101892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) strains of modern Beijing sublineage appear to be more transmissible and cause more severe disease than strains of other sublineages, but the responsible pathogenic mechanisms remain unclear. We previously identified genetic changes that are specific for the modern Beijing sublineage, and here we characterize the lipidome and transcriptome differences between modern and ancient Beijing sublineages. We report that modern Beijing strains accumulated 2.89 (95%CI: 2.05-3.73) times more triacylglycerol (TAG) than ancient Beijing strains in vitro. We also observed that modern Beijing strains had a 2.64-fold (95%CI: 1.29-4.00) upregulation of tgs2 (annotated as TAG synthetase 2), whose role in TAG accumulation was further confirmed in Mycobacterium marinum (Mm). Because TAG serves as a crucial carbon source and reservoir of free fatty acids, the results suggest that the excessive accumulation of TAG might fuel the growth of modern Beijing strains after infection and lead to rapid development of disease.
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Affiliation(s)
- Jingfeng Tong
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China
| | - Jie Wu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China
| | - Yuan Jiang
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France; Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China.
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Kirubakar G, Murugaiyan J, Schaudinn C, Dematheis F, Holland G, Eravci M, Weise C, Roesler U, Lewin A. Proteome Analysis of a M. avium Mutant Exposes a Novel Role of the Bifunctional Protein LysX in the Regulation of Metabolic Activity. J Infect Dis 2019; 218:291-299. [PMID: 29471363 DOI: 10.1093/infdis/jiy100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/16/2018] [Indexed: 11/14/2022] Open
Abstract
Lysyl-phosphatidylglycerol is one of the components of the mycobacterial membrane that contributes to the resistance to cationic antimicrobial peptides, a host-induced frontline defense against invading pathogens. Its production is catalyzed by LysX, a bifunctional protein with lysyl transferase and lysyl transfer RNA synthetase activity. Comparative proteome analysis of a lysX mutant of Mycobacterium avium strain 104 and the wild type indicated that the lysX mutant strain undergoes a transition in phenotype by switching the carbon metabolism to β-oxidation of fatty acids, along with accumulation of lipid inclusions. Surprisingly, proteins associated with intracellular survival were upregulated in the lysX mutant, even during extracellular growth, preparing bacteria for the conditions occurring inside host cells. In line with this, the lysX mutant exhibited enhanced intracellular growth in human-blood-derived monocytes. Thus, our study exposes the significance of lysX in the metabolism and virulence of the environmental pathogen M. avium hominissuis.
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Affiliation(s)
- Greana Kirubakar
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Jayaseelan Murugaiyan
- Institute for Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Berlin, Germany
| | - Christoph Schaudinn
- Division ZBS 4, Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | | | - Gudrun Holland
- Division ZBS 4, Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Murat Eravci
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Berlin, Germany
| | - Astrid Lewin
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
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41
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Role of α-glucan-induced oxygen species in dendritic cells and its impact in immune response against tuberculosis. Int J Med Microbiol 2019; 309:151328. [PMID: 31324524 DOI: 10.1016/j.ijmm.2019.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/25/2019] [Accepted: 07/07/2019] [Indexed: 11/24/2022] Open
Abstract
With 10 million new cases and three million deaths estimated to occur yearly ̶ more than any time in history ̶ tuberculosis (TB) remains the single most widespread and deadly infectious disease. Until recently, it was thought that both latent and active TB was primarily related to host factors. Nonetheless, the participation of bacterial factors is becoming increasingly evident. Minimal variations in genes related to Mycobacterium tuberculosis (Mtb) virulence and pathogenesis can lead to marked differences in immunogenicity. Dendritic cells (DC) are professional antigen presenting cells whose maturation can vary depending on the cell wall composition of each particular Mtb strain being critical for the onset of the immune response against Mtb. Here we evaluated the role played by α-glucan, in the endogenous production of reactive oxygen species, ROS, and the impact on DC maturation and function. Results showed that α-glucans on Mtb induce ROS production leading to DC maturation and lymphocyte proliferation. Even more, α-glucans induced Syk activation but were not essential in non-opsonized phagocytosis. In summary, α-glucans of Mtb participates in ROS production and the subsequent DC maturation and antigen presentation, suggesting a relevant role of α-glucans for the onset of the protective immune response against TB.
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42
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Santucci P, Johansen MD, Point V, Poncin I, Viljoen A, Cavalier JF, Kremer L, Canaan S. Nitrogen deprivation induces triacylglycerol accumulation, drug tolerance and hypervirulence in mycobacteria. Sci Rep 2019; 9:8667. [PMID: 31209261 PMCID: PMC6572852 DOI: 10.1038/s41598-019-45164-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022] Open
Abstract
Mycobacteria share with other actinomycetes the ability to produce large quantities of triacylglycerol (TAG), which accumulate as intracytoplasmic lipid inclusions (ILI) also known as lipid droplets (LD). Mycobacterium tuberculosis (M. tb), the etiologic agent of tuberculosis, acquires fatty acids from the human host which are utilized to synthesize TAG, subsequently stored in the form of ILI to meet the carbon and nutrient requirements of the bacterium during long periods of persistence. However, environmental factors governing mycobacterial ILI formation and degradation remain poorly understood. Herein, we demonstrated that in the absence of host cells, carbon excess and nitrogen starvation promote TAG accumulation in the form of ILI in M. smegmatis and M. abscessus, used as surrogate species of M. tb. Based on these findings, we developed a simple and reversible in vitro model to regulate ILI biosynthesis and hydrolysis in mycobacteria. We also showed that TAG formation is tgs1 dependent and that lipolytic enzymes mediate TAG breakdown. Moreover, we confirmed that the nitrogen-deprived and ILI-rich phenotype was associated with an increased tolerance towards several drugs used for treating mycobacterial infections. Importantly, we showed that the presence of ILI substantially enhanced the bacterial burden and granuloma abundance in zebrafish embryos infected with lipid-rich M. abscessus as compared to embryos infected with lipid-poor M. abscessus, suggesting that ILI are actively contributing to mycobacterial virulence and pathogenesis.
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Affiliation(s)
- Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Matt D Johansen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France
| | | | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293, Montpellier, France.,INSERM, IRIM, 34293, Montpellier, France
| | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.
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Selective delipidation of Mycobacterium bovis BCG enables direct pulmonary vaccination and enhances protection against Mycobacterium tuberculosis. Mucosal Immunol 2019; 12:805-815. [PMID: 30778118 PMCID: PMC6462255 DOI: 10.1038/s41385-019-0148-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/02/2019] [Accepted: 01/27/2019] [Indexed: 02/04/2023]
Abstract
Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), is the leading killer due to an infectious organism. Mycobacterium bovis bacillus Calmette-Guérin (BCG) is the only vaccine approved against TB, however, its efficacy against pulmonary TB is poor. While BCG is currently inoculated intradermally, the natural route of M.tb infection is through the lung. Excessive lung pathology caused by pulmonary inoculation of BCG has prevented the use of this immunization route. Here, we show that selective chemical treatment of BCG with petroleum ether removes inflammatory lipids from the bacterial surface while keeping BCG viable. Pulmonary vaccination using this modified BCG attenuated inflammatory responses, prevented immunopathology of the lung, and significantly increased protection against M.tb infection in mice. We further directly linked IL-17A as the responsible contributor of improved immunity against M.tb infection. These results provide evidence that selective removal of cytotoxic lipids from the BCG surface attenuates inflammation and offers a safer and superior vaccine against TB causing less damage post-infectious challenge with M.tb.
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An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. Sci Rep 2019; 9:5204. [PMID: 30914757 PMCID: PMC6435705 DOI: 10.1038/s41598-019-41692-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/14/2019] [Indexed: 01/01/2023] Open
Abstract
Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a complex disease, with a spectrum of outcomes. Genomic, transcriptomic and methylation studies have revealed differences between Mtb lineages, likely to impact on transmission, virulence and drug resistance. However, so far no studies have integrated sequence-based genomic, transcriptomic and methylation characterisation across a common set of samples, which is critical to understand how DNA sequence and methylation affect RNA expression and, ultimately, Mtb pathogenesis. Here we perform such an integrated analysis across 22 M. tuberculosis clinical isolates, representing ancient (lineage 1) and modern (lineages 2 and 4) strains. The results confirm the presence of lineage-specific differential gene expression, linked to specific SNP-based expression quantitative trait loci: with 10 eQTLs involving SNPs in promoter regions or transcriptional start sites; and 12 involving potential functional impairment of transcriptional regulators. Methylation status was also found to have a role in transcription, with evidence of differential expression in 50 genes across lineage 4 samples. Lack of methylation was associated with three novel variants in mamA, likely to cause loss of function of this enzyme. Overall, our work shows the relationship of DNA sequence and methylation to RNA expression, and differences between ancient and modern lineages. Further studies are needed to verify the functional consequences of the identified mechanisms of gene expression regulation.
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Maurya RK, Bharti S, Krishnan MY. Triacylglycerols: Fuelling the Hibernating Mycobacterium tuberculosis. Front Cell Infect Microbiol 2019; 8:450. [PMID: 30687647 PMCID: PMC6333902 DOI: 10.3389/fcimb.2018.00450] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/18/2018] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) has the remarkable ability to persist with a modified metabolic status and phenotypic drug tolerance for long periods in the host without producing symptoms of active tuberculosis. These persisters may reactivate to cause active disease when the immune system becomes disrupted or compromised. Thus, the infected hosts with the persisters serve as natural reservoir of the deadly pathogen. Understanding the host and bacterial factors contributing to Mtb persistence is important to devise strategies to tackle the Mtb persisters. Host lipids act as the major source of carbon and energy for Mtb. Fatty acids derived from the host cells are converted to triacylglycerols (triglycerides or TAG) and stored in the bacterial cytoplasm. TAG serves as a dependable, long-term energy source of lesser molecular mass than other storage molecules like glycogen. TAG are found in substantial amounts in the mycobacterial cell wall. This review discusses the production, accumulation and possible roles of TAG in mycobacteria, pointing out the aspects that remain to be explored. Finally, the essentiality of TAG synthesis for Mtb is discussed with implications for identification of intervention strategies.
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Affiliation(s)
- Rahul Kumar Maurya
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Suman Bharti
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Manju Y Krishnan
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
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Kaufmann E, Sanz J, Dunn JL, Khan N, Mendonça LE, Pacis A, Tzelepis F, Pernet E, Dumaine A, Grenier JC, Mailhot-Léonard F, Ahmed E, Belle J, Besla R, Mazer B, King IL, Nijnik A, Robbins CS, Barreiro LB, Divangahi M. BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis. Cell 2018; 172:176-190.e19. [PMID: 29328912 DOI: 10.1016/j.cell.2017.12.031] [Citation(s) in RCA: 786] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/06/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022]
Abstract
The dogma that adaptive immunity is the only arm of the immune response with memory capacity has been recently challenged by several studies demonstrating evidence for memory-like innate immune training. However, the underlying mechanisms and location for generating such innate memory responses in vivo remain unknown. Here, we show that access of Bacillus Calmette-Guérin (BCG) to the bone marrow (BM) changes the transcriptional landscape of hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), leading to local cell expansion and enhanced myelopoiesis at the expense of lymphopoiesis. Importantly, BCG-educated HSCs generate epigenetically modified macrophages that provide significantly better protection against virulent M. tuberculosis infection than naïve macrophages. By using parabiotic and chimeric mice, as well as adoptive transfer approaches, we demonstrate that training of the monocyte/macrophage lineage via BCG-induced HSC reprogramming is sustainable in vivo. Our results indicate that targeting the HSC compartment provides a novel approach for vaccine development.
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Affiliation(s)
- Eva Kaufmann
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Joaquin Sanz
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Jonathan L Dunn
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nargis Khan
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Laura E Mendonça
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Alain Pacis
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Fanny Tzelepis
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Erwan Pernet
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Anne Dumaine
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | | | - Eisha Ahmed
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Jad Belle
- Department of Physiology, Complex Traits Group, McGill University, Montreal, QC H3G 0B1, Canada
| | - Rickvinder Besla
- Department of Immunology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Bruce Mazer
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Irah L King
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Anastasia Nijnik
- Department of Physiology, Complex Traits Group, McGill University, Montreal, QC H3G 0B1, Canada
| | - Clinton S Robbins
- Department of Immunology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1C5, Canada.
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, QC H4A 3J1, Canada.
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Varghese B, Enani M, Alrajhi A, Al Johani S, Albarak A, Althawadi S, Elkhizzi N, AlGhafli H, Shoukri M, Al-Hajoj S. Impact of Mycobacterium tuberculosis complex lineages as a determinant of disease phenotypes from an immigrant rich moderate tuberculosis burden country. Respir Res 2018; 19:259. [PMID: 30587190 PMCID: PMC6307224 DOI: 10.1186/s12931-018-0966-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/16/2018] [Indexed: 02/04/2023] Open
Abstract
Background Growing evidences suggested that the Mycobacterium tuberculosis complex (MTBC) lineages can determine the clinical outcome of pulmonary and extra-pulmonary tuberculosis. However, limited data only available revealing such association of bacterial genotypes and clinical phenotypes from immigrant rich countries. Methods A multicenter study has been carried out on a collection of 2092 (1003 extrapulmonary and 1089 pulmonary) MTBC isolates. Genotyping of all the isolates were carried out by spoligotyping and 24 loci based MIRU-VNTR typing. Results Demographically domination of young Saudi nationals (61.4%) and men (61.2%) were found in this cohort. Lymph nodes (62.4%) and gastrointestinal sites (16.7%) were the most common anatomical sites of infection. The predominant lineages were Delhi/CAS (26.9%), EAI (14.2%) and Ghana (9.9%). Mycobacterium africanum type I and II were reported for the first time in the country among extrapulmonary cases. ‘Ancestral’ lineages M.bovis (OR-5.22; 95% CI-2.23-8.22, p- < 0.001) and Delhi/CAS (OR-0.57; 95% CI-0.411-0.734, p- < 0.001) were directly associated with lymph node tuberculosis and gastrointestinal tuberculosis (M. bovis-OR-0.33; 95% CI-0.085-0.567, p-0.001 and Delhi/CAS-OR-1.87; 95% CI-1.22-2.53, p- < 0.001) respectively. Among the ‘Modern’ lineages, EAI showed significant association to central nervous system tuberculosis (OR-1.98; 95% CI-0.76-3.19, p-0.04) and Uganda-I to gastrointestinal tuberculosis (OR-2.41; 95% CI-0.77-4.06, p-0.02). Conclusions The findings substantially contribute to the emerging evidences that MTBC lineages influence disease phenotypes and epidemiological consequences. Electronic supplementary material The online version of this article (10.1186/s12931-018-0966-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bright Varghese
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia
| | - Mushira Enani
- Medical Specialties Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Alrajhi
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sameera Al Johani
- Department of Microbiology, King Abdul Aziz Medical City, Riyadh, Saudi Arabia
| | - Ali Albarak
- Department of Medicine, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Sahar Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Noura Elkhizzi
- Department of Microbiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hawra AlGhafli
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia
| | - Mohammed Shoukri
- National Biotechnology Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, MBC-03, King Faisal Specialist Hospital and Research Centre, Post Box # 3354, Riyadh, 11211, Saudi Arabia.
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Vashist A, Malhotra V, Sharma G, Tyagi JS, Clark-Curtiss JE. Interplay of PhoP and DevR response regulators defines expression of the dormancy regulon in virulent Mycobacterium tuberculosis. J Biol Chem 2018; 293:16413-16425. [PMID: 30181216 PMCID: PMC6200940 DOI: 10.1074/jbc.ra118.004331] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022] Open
Abstract
The DevR response regulator of Mycobacterium tuberculosis is an established regulator of the dormancy response in mycobacteria and can also be activated during aerobic growth conditions in avirulent strains, suggesting a complex regulatory system. Previously, we reported culture medium-specific aerobic induction of the DevR regulon genes in avirulent M. tuberculosis H37Ra that was absent in the virulent H37Rv strain. To understand the underlying basis of this differential response, we have investigated aerobic expression of the Rv3134c-devR-devS operon using M. tuberculosis H37Ra and H37Rv devR overexpression strains, designated as LIX48 and LIX50, respectively. Overexpression of DevR led to the up-regulation of a large number of DevR regulon genes in aerobic cultures of LIX48, but not in LIX50. To ascertain the involvement of PhoP response regulator, also known to co-regulate a subset of DevR regulon genes, we complemented the naturally occurring mutant phoPRa gene of LIX48 with the WT phoPRv gene. PhoPRv dampened the induced expression of the DevR regulon by >70-80%, implicating PhoP in the negative regulation of devR expression. Electrophoretic mobility shift assays confirmed phosphorylation-independent binding of PhoPRv to the Rv3134c promoter and further revealed that DevR and PhoPRv proteins exhibit differential DNA binding properties to the target DNA. Through co-incubations with DNA, ELISA, and protein complementation assays, we demonstrate that DevR forms a heterodimer with PhoPRv but not with the mutant PhoPRa protein. The study puts forward a new possible mechanism for coordinated expression of the dormancy regulon, having implications in growth adaptations critical for development of latency.
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Affiliation(s)
- Atul Vashist
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vandana Malhotra
- the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and
- From the Department of Biochemistry, Sri Venkateswara College, University of Delhi, New Delhi 110021, India
| | - Gunjan Sharma
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jaya Sivaswami Tyagi
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Josephine E Clark-Curtiss
- the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and
- the School of Life Sciences, Arizona State University, Tempe, Arizona 85287, and
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49
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Maarsingh JD, Haydel SE. Mycobacterium smegmatis PrrAB two-component system influences triacylglycerol accumulation during ammonium stress. Microbiology (Reading) 2018; 164:1276-1288. [DOI: 10.1099/mic.0.000705] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Jason D. Maarsingh
- 1School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Shelley E. Haydel
- 2Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA
- 1School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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50
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Mali PC, Meena LS. Triacylglycerol: nourishing molecule in endurance of Mycobacterium tuberculosis. J Biosci 2018; 43:149-154. [PMID: 29485123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ability of Mycobacterium tuberculosis (M. tuberculosis) to accumulate lipid-rich molecules as an energy source obtained from host cell debris remains interesting. Additionally, the potential of M. tuberculosis to survive under different stress conditions leading to its dormant state in pathogenesis remains elusive. The exact mechanism by which these lipid bodies generated in M. tuberculosis infection and utilized by bacilli inside infected macrophage for its survival is still not understood. In this, during bacillary infection, many metabolic pathways are involved that influence the survival of M. tuberculosis for their own support. However, the exact energy source derived from infecting host cells remain elusive. Therefore, this study highlights several alternative energy sources in the form of triacylglycerol (TAG) and fatty acids, i.e. oleic acids accumulation, which are essential in dormancy-like state under M. tuberculosis infection. The prominent stage in tuberculosis (TB) infection is re-establishment of M. tuberculosis under stress conditions and deployment of a confined strategy to utilize these biomolecules for its persistence survival. So, growing in our understanding of these pathways will help us in accelerating therapies, which could reduce TB prevalence world widely.
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Affiliation(s)
- Pratap C Mali
- Department of Zoology, University of Rajasthan, Jaipur 322 219, India
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