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Campolattano N, D'Abrosca G, Russo L, De Siena B, Della Gala M, De Chiara I, Marasco R, Goff A, Waddell SJ, Sacco M, Muscariello L. Insight into the on/off switch that regulates expression of the MSMEG-3762/63 efflux pump in Mycobacterium smegmatis. Sci Rep 2023; 13:20332. [PMID: 37989843 PMCID: PMC10663510 DOI: 10.1038/s41598-023-47695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Drug resistance is one of the most difficult challenges facing tuberculosis (TB) control. Drug efflux is among the mechanisms leading to drug resistance. In our previous studies, we partially characterized the ABC-type MSMEG-3762/63 efflux pump in Mycobacterium smegmatis, which shares high percentage of identity with the Mycobacterium tuberculosis Rv1687/86c pump. MSMEG-3762/63 was shown to have extrusion activity for rifampicin and ciprofloxacin, used in first and second-line anti-TB treatments. Moreover, we described the functional role of the TetR-like MSMEG-3765 protein as a repressor of the MSMEG_3762/63/65 operon and orthologous Rv1687/86/85c in M. tuberculosis. Here we show that the operon is upregulated in the macrophage environment, supporting a previous observation of induction triggered by acid-nitrosative stress. Expression of the efflux pump was also induced by sub-inhibitory concentrations of rifampicin or ciprofloxacin. Both these drugs also prevented the binding of the MSMEG-3765 TetR repressor protein to its operator in the MSMEG_3762/63/65 operon. The hypothesis that these two drugs might be responsible for the induction of the efflux pump operon was assessed by bioinformatics analyses. Docking studies using a structural model of the regulator MSMEG-3765 showed that both antibiotics abolished the ability of this transcriptional repressor to recognize the efflux pump operon by interacting with the homodimer at different binding sites within the same binding pocket. Reduced binding of the repressor leads to induction of the efflux pump in M. smegmatis, and reduced efficacy of these two anti-mycobacterial drugs.
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Affiliation(s)
- Nicoletta Campolattano
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Gianluca D'Abrosca
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Barbara De Siena
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Milena Della Gala
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Ida De Chiara
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Rosangela Marasco
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Aaron Goff
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Margherita Sacco
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Lidia Muscariello
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy.
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Maxson ME, Das L, Goldberg MF, Porcelli SA, Chan J, Jacobs WR. Mycobacterium tuberculosis Central Metabolism Is Key Regulator of Macrophage Pyroptosis and Host Immunity. Pathogens 2023; 12:1109. [PMID: 37764917 PMCID: PMC10535942 DOI: 10.3390/pathogens12091109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Metabolic dysregulation in Mycobacterium tuberculosis results in increased macrophage apoptosis or pyroptosis. However, mechanistic links between Mycobacterium virulence and bacterial metabolic plasticity remain ill defined. In this study, we screened random transposon insertions of M. bovis BCG to identify mutants that induce pyroptotic death of the infected macrophage. Analysis of the transposon insertion sites identified a panel of fdr (functioning death repressor) genes, which were shown in some cases to encode functions central to Mycobacterium metabolism. In-depth studies of one fdr gene, fdr8 (BCG3787/Rv3727), demonstrated its important role in the maintenance of M. tuberculosis and M. bovis BCG redox balance in reductive stress conditions in the host. Our studies expand the subset of known Mycobacterium genes linking bacterial metabolic plasticity to virulence and also reveal that the broad induction of pyroptosis by an intracellular bacterial pathogen is linked to enhanced cellular immunity in vivo.
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Affiliation(s)
- Michelle E. Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Lahari Das
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | | | - Steven A. Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
| | - John Chan
- Department of Medicine, New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, USA;
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (L.D.); (S.A.P.)
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3
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Meng C, Liu J, Kang X, Xu Z, Xu S, Li X, Pan Z, Chen X, Jiao X. Discrepancy in Response of Mouse Dendritic Cells against BCG: Weak Immune Effects of Plasmacytoid Dendritic Cells Compared to Classical Dendritic Cells despite the Uptake of Bacilli. Trop Med Infect Dis 2023; 8:tropicalmed8030140. [PMID: 36977141 PMCID: PMC10057906 DOI: 10.3390/tropicalmed8030140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/25/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Tuberculosis (TB), a zoonosis characterized by chronic respiratory infections, is mainly caused by Mycobacterium tuberculosis and is associated with one of the heaviest disease burdens in the world. Dendritic cells (DCs) play a key role and act as a bridge between innate and adaptive immune responses against TB. DCs are divided into distinct subsets. Currently, the response of DCs to mycobacterial infections is poorly understood. Herein, we aimed to evaluate the responses of splenic conventional DCs (cDC) and plasmacytoid DCs (pDC), subsets to Bacillus Calmette–Guérin (BCG) infection in mice. Splenic pDC had a significantly higher infection rate and intracellular bacterial count than cDC and the CD8+ and CD8− cDC subsets after BCG infection. However, the expression levels of CD40, CD80, CD86, and MHC-II molecules were significantly upregulated in splenic cDC and the CD8 cDC subsets compared to pDC during BCG infection. Splenic cDC had a higher expression of IFN-γ and IL-12p70 than pDC, whereas pDC had higher levels of TNF-α and MCP-1 than cDC in mice infected with BCG. At early stages of immunization with BCG containing the Ag85A protein, splenic cDC and pDC could present the Ag85A peptide to a specific T hybridoma; however, cDC had a stronger antigen presenting activity than pDC. In summary, splenic cDC and pDC extensively participate in mouse immune responses against BCG infection in vivo. Although pDC had a higher BCG uptake, cDC induced stronger immunological effects, including activation and maturation, cytokine production, and antigen presentation.
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Affiliation(s)
- Chuang Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jun Liu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Xilong Kang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhengzhong Xu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Shuangyuan Xu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Xin Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.C.); (X.J.)
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.C.); (X.J.)
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Bi J, Guo Q, Zhou Z, Huang X, Qin L, Tao X, Ye T, Chen L, Li G, Wang Z, Liu L, Zhang G. Malonylome analysis uncovers the association of lysine malonylation with metabolism and acidic stress in pathogenic Mycobacterium tuberculosis. Microbiol Res 2022; 265:127209. [PMID: 36174356 DOI: 10.1016/j.micres.2022.127209] [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: 05/26/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the pathogenic agent of tuberculosis, remains a primary inducement of morbidity and mortality globally. Mtb have evolved mechanisms to recognize diverse signals, such as acidic pH within phagolysosomes and therefore to reprogram multiple physiological and metabolic processes to adapt to intracellular survival. Moreover, lysine malonylation has been suggested to participate in regulation of enzymes in carbon metabolism. However, lysine malonylation in Mtb and its association with acidic pH associated metabolism adaptation remain unknown. Here, we systematically characterized the comparative malonylome of Mtb H37Rv grown in normal (7H9-Tyloxapol (Ty)-7.4) and acidic (7H9-Ty-4.5) medium mimicking lysosome pH. In total, 2467 lysine malonylation sites within 1026 proteins were identified, which related to diverse biological processes, particularly accumulated in metabolic process. 1090 lysine malonylation sites from 562 proteins were quantified, among which 391 lysine malonylation sites in 273 protein were down-regulated while 40 lysine malonylation sites from 36 proteins were up-regulated in acidic medium, indicating that malonylation may participate in acidic pH associated metabolism. Accordingly, the enzyme activity of GlcB was reduced under acidic stress corresponding to decreased malonylation of GlcB compared with that of normal condition and this was further demonstrated by site-specific mutations. We further found that Mtb-CobB, a sirtuin-like deacetylase and desuccinylase, involved in demalonylase activity. Together, the Mtb malonylome not only indicates the critical role of malonylation in metabolism regulation, but may provide new insights of malonylation on metabolism adaptation to acidic micro-environment in vivo.
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Affiliation(s)
- Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Qinglong Guo
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Ziyuan Zhou
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Xiujing Huang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Linxiu Qin
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Xiaoyu Tao
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Taosheng Ye
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Liang Chen
- Guangdong Centre for Tuberculosis Control, Guangzhou 510430, China
| | - Guobao Li
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China.
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5
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Herrera MT, Guzmán-Beltrán S, Bobadilla K, Santos-Mendoza T, Flores-Valdez MA, Gutiérrez-González LH, González Y. Human Pulmonary Tuberculosis: Understanding the Immune Response in the Bronchoalveolar System. Biomolecules 2022; 12:biom12081148. [PMID: 36009042 PMCID: PMC9405639 DOI: 10.3390/biom12081148] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis, the causal agent of one of the most devastating infectious diseases worldwide, can evade or modulate the host immune response and remain dormant for many years. In this review, we focus on identifying the local immune response induced in vivo by M. tuberculosis in the lungs of patients with active tuberculosis by analyzing data from untouched cells from bronchoalveolar lavage fluid (BALF) or exhaled breath condensate (EBC) samples. The most abundant resident cells in patients with active tuberculosis are macrophages and lymphocytes, which facilitate the recruitment of neutrophils. The cellular response is characterized by an inflammatory state and oxidative stress produced mainly by macrophages and T lymphocytes. In the alveolar microenvironment, the levels of cytokines such as interleukins (IL), chemokines, and matrix metalloproteinases (MMP) are increased compared with healthy patients. The production of cytokines such as interferon (IFN)-γ and IL-17 and specific immunoglobulin (Ig) A and G against M. tuberculosis indicate that the adaptive immune response is induced despite the presence of a chronic infection. The role of epithelial cells, the processing and presentation of antigens by macrophages and dendritic cells, as well as the role of tissue-resident memory T cells (Trm) for in situ vaccination remains to be understood.
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Affiliation(s)
- María Teresa Herrera
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Silvia Guzmán-Beltrán
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Karen Bobadilla
- Laboratory of Transcriptomics and Molecular Immunology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
| | - Mario Alberto Flores-Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico
| | - Luis Horacio Gutiérrez-González
- Laboratory of Transcriptomics and Molecular Immunology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
- Correspondence: (L.H.G.-G.); (Y.G.); Tel.: +52-55-5487-1700 (ext. 5117) (Y.G.)
| | - Yolanda González
- Department of Microbiology, National Institute for Respiratory Diseases Ismael Cosío Villegas, Mexico City 14080, Mexico
- Correspondence: (L.H.G.-G.); (Y.G.); Tel.: +52-55-5487-1700 (ext. 5117) (Y.G.)
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6
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Rosas-García J, Ramón-Luing LA, Bobadilla K, Meraz-Ríos MA, Sevilla-Reyes EE, Santos-Mendoza T. Distinct Transcriptional Profile of PDZ Genes after Activation of Human Macrophages and Dendritic Cells. Int J Mol Sci 2022; 23:ijms23137010. [PMID: 35806015 PMCID: PMC9266728 DOI: 10.3390/ijms23137010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
The PDZ (PSD95, Dlg and ZO-1) genes encode proteins that primarily function as scaffolds of diverse signaling pathways. To date, 153 PDZ genes have been identified in the human genome, most of which have multiple protein isoforms widely studied in epithelial and neural cells. However, their expression and function in immune cells have been poorly studied. Herein, we aimed to assess the transcriptional profiles of 83 PDZ genes in human macrophages (Mɸ) and dendritic cells (DCs) and changes in their relative expression during cell PRR stimulation. Significantly distinct PDZ gene transcriptional profiles were identified under different stimulation conditions. Furthermore, a distinct PDZ gene transcriptional signature was found in Mɸ and DCs under the same phagocytic stimuli. Notably, more than 40 PDZ genes had significant changes in expression, with potentially relevant functions in antigen-presenting cells (APCs). Given that several PDZ proteins are targeted by viral products, our results support that many of these proteins might be viral targets in APCs as part of evasion mechanisms. Our results suggest a distinct requirement for PDZ scaffolds in Mɸ and DCs signaling pathways activation. More assessments on the functions of PDZ proteins in APCs and their role in immune evasion mechanisms are needed.
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Affiliation(s)
- Jorge Rosas-García
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
- Department of Molecular Biomedicine, CINVESTAV, Mexico City 07360, Mexico;
| | - Lucero A. Ramón-Luing
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Karen Bobadilla
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
| | | | - Edgar E. Sevilla-Reyes
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
- Correspondence: (E.E.S.-R.); (T.S.-M.)
| | - Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
- Correspondence: (E.E.S.-R.); (T.S.-M.)
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Kondratieva E, Majorov K, Grigorov A, Skvortsova Y, Kondratieva T, Rubakova E, Linge I, Azhikina T, Apt A. An In Vivo Model of Separate M. tuberculosis Phagocytosis by Neutrophils and Macrophages: Gene Expression Profiles in the Parasite and Disease Development in the Mouse Host. Int J Mol Sci 2022; 23:ijms23062961. [PMID: 35328388 PMCID: PMC8954342 DOI: 10.3390/ijms23062961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
The role of neutrophils in tuberculosis infection remains less well studied compared to that of the CD4+ T-lymphocytes and macrophages. Thus, alterations in Mycobacterium tuberculosis transcription profile following phagocytosis by neutrophils and how these shifts differ from those caused by macrophage phagocytosis remain unknown. We developed a mouse model that allows obtaining large amounts of either neutrophils or macrophages infected in vivo with M. tuberculosis for mycobacteria isolation in quantities sufficient for the whole genome RNA sequencing and aerosol challenge of mice. Here, we present: (i) the differences in transcription profiles of mycobacteria isolated from liquid cultures, neutrophils and macrophages infected in vivo; (ii) phenotypes of infection and lung inflammation (life span, colony forming units (CFU) counts in organs, lung pathology, immune cells infiltration and cytokine production) in genetically TB-susceptible mice identically infected via respiratory tract with neutrophil-passaged (NP), macrophage-passaged (MP) and conventionally prepared (CP) mycobacteria. Two-hour residence within neutrophils caused transcriptome shifts consistent with mycobacterial transition to dormancy and diminished their capacity to attract immune cells to infected lung tissue. Mycobacterial multiplication in organs did not depend upon pre-phagocytosis, whilst survival time of infected mice was shorter in the group infected with NP bacilli. We also discuss possible reasons for these phenotypic divergences.
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Affiliation(s)
- Elena Kondratieva
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Konstantin Majorov
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Artem Grigorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Yulia Skvortsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Tatiana Kondratieva
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Elvira Rubakova
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Irina Linge
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
| | - Tatyana Azhikina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (Y.S.); (T.A.)
| | - Alexander Apt
- Laboratory for Immunogenetics, Central Research TB Institute, 107564 Moscow, Russia; (E.K.); (K.M.); (T.K.); (E.R.); (I.L.)
- Correspondence:
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8
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Kottom TJ, Carmona EM, Limper AH. Gene Expression in Lung Epithelial Cells Following Interaction with Pneumocystis carinii and its Specific Life Forms Yields Insights into Host Gene Responses to Infection. Microbiol Immunol 2022; 66:238-251. [PMID: 35229348 PMCID: PMC9090966 DOI: 10.1111/1348-0421.12972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
Pneumocystis spp. interacts with epithelial cells in the alveolar spaces of the lung. It is thought that the binding of Pneumocystis to host cell epithelium is needed for life cycle completion and proliferation. The effect of this interaction on lung epithelial cells have previously shown that the trophic form of this organism greatly inhibits p34 cdc2 activity, a serine/threonine kinase required for transition from G2 to M phase in the cell cycle. To gain further insight into the host response during Pneumocystis pneumonia (PCP), we used microarray technology to profile epithelial cell (A549) gene expression patterns following Pneumocystis carinii interaction. Furthermore, we isolated separate populations of cyst and trophic forms of P. carinii, which were then applied to the lung epithelial cells. Differential expression of genes involved in various cellular functions dependent on the specific P. carinii life form in contact with the A549 cell were identified. The reliability of our data was further confirmed by Northern blot analysis on a number of selected up or down regulated transcripts. The transcriptional response to P. carinii was dominated by cytokines, apoptotic, and anti-apoptotic related genes. These results reveal several previously unknown effects of P. carinii on the lung epithelial cell and provide insight into the complex interactions of host and pathogen. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Theodore J Kottom
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
| | - Eva M Carmona
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
| | - Andrew H Limper
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
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9
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Medley J, Goff A, Bettencourt PJG, Dare M, Cole L, Cantillon D, Waddell SJ. Dissecting the Mycobacterium bovis BCG Response to Macrophage Infection to Help Prioritize Targets for Anti-Tuberculosis Drug and Vaccine Discovery. Vaccines (Basel) 2022; 10:vaccines10010113. [PMID: 35062774 PMCID: PMC8780277 DOI: 10.3390/vaccines10010113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
New strategies are required to reduce the worldwide burden of tuberculosis. Intracellular survival and replication of Mycobacterium tuberculosis after macrophage phagocytosis is a fundamental step in the complex host–pathogen interactions that lead to granuloma formation and disease. Greater understanding of how the bacterium survives and thrives in these environments will inform novel drug and vaccine discovery programs. Here, we use in-depth RNA sequencing of Mycobacterium bovis BCG from human THP-1 macrophages to describe the mycobacterial adaptations to the intracellular environment. We identify 329 significantly differentially regulated genes, highlighting cholesterol catabolism, the methylcitrate cycle and iron homeostasis as important for mycobacteria inside macrophages. Examination of multi-functional gene families revealed that 35 PE/PPE genes and five cytochrome P450 genes were upregulated 24 h after infection, highlighting pathways of potential significance. Comparison of the intracellular transcriptome to gene essentiality and immunogenicity studies identified 15 potential targets that are both required for intracellular survival and induced on infection, and eight upregulated genes that have been demonstrated to be immunogenic in TB patients. Further insight into these new and established targets will support drug and vaccine development efforts.
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Affiliation(s)
- Jamie Medley
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Aaron Goff
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Paulo J. G. Bettencourt
- Faculty of Medicine, Catholic University of Portugal, 1649-023 Lisbon, Portugal;
- Center for Interdisciplinary Research in Health, Catholic University of Portugal, 1649-023 Lisbon, Portugal
| | - Madelaine Dare
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Liam Cole
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Daire Cantillon
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Simon J. Waddell
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
- Correspondence:
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10
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Vilchèze C, Yan B, Casey R, Hingley-Wilson S, Ettwiller L, Jacobs WR. Commonalities of Mycobacterium tuberculosis Transcriptomes in Response to Defined Persisting Macrophage Stresses. Front Immunol 2022; 13:909904. [PMID: 35844560 PMCID: PMC9283954 DOI: 10.3389/fimmu.2022.909904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
As the goal of a bacterium is to become bacteria, evolution has imposed continued selections for gene expression. The intracellular pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis, has adopted a fine-tuned response to survive its host's methods to aggressively eradicate invaders. The development of microarrays and later RNA sequencing has led to a better understanding of biological processes controlling the relationship between host and pathogens. In this study, RNA-seq was performed to detail the transcriptomes of M. tuberculosis grown in various conditions related to stresses endured by M. tuberculosis during host infection and to delineate a general stress response incurring during persisting macrophage stresses. M. tuberculosis was subjected to long-term growth, nutrient starvation, hypoxic and acidic environments. The commonalities between these stresses point to M. tuberculosis maneuvering to exploit propionate metabolism for lipid synthesis or to withstand propionate toxicity whilst in the intracellular environment. While nearly all stresses led to a general shutdown of most biological processes, up-regulation of pathways involved in the synthesis of amino acids, cofactors, and lipids were observed only in hypoxic M. tuberculosis. This data reveals genes and gene cohorts that are specifically or exclusively induced during all of these persisting stresses. Such knowledge could be used to design novel drug targets or to define possible M. tuberculosis vulnerabilities for vaccine development. Furthermore, the disruption of specific functions from this gene set will enhance our understanding of the evolutionary forces that have caused the tubercle bacillus to be a highly successful pathogen.
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Affiliation(s)
- Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bo Yan
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - Rosalyn Casey
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzie Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Laurence Ettwiller
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- *Correspondence: William R. Jacobs Jr,
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11
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Pires D, Calado M, Velez T, Mandal M, Catalão MJ, Neyrolles O, Lugo-Villarino G, Vérollet C, Azevedo-Pereira JM, Anes E. Modulation of Cystatin C in Human Macrophages Improves Anti-Mycobacterial Immune Responses to Mycobacterium tuberculosis Infection and Coinfection With HIV. Front Immunol 2021; 12:742822. [PMID: 34867965 PMCID: PMC8637326 DOI: 10.3389/fimmu.2021.742822] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis owes its resurgence as a major global health threat mostly to the emergence of drug resistance and coinfection with HIV. The synergy between HIV and Mycobacterium tuberculosis (Mtb) modifies the host immune environment to enhance both viral and bacterial replication and spread. In the lung immune context, both pathogens infect macrophages, establishing favorable intracellular niches. Both manipulate the endocytic pathway in order to avoid destruction. Relevant players of the endocytic pathway to control pathogens include endolysosomal proteases, cathepsins, and their natural inhibitors, cystatins. Here, a mapping of the human macrophage transcriptome for type I and II cystatins during Mtb, HIV, or Mtb-HIV infection displayed different profiles of gene expression, revealing cystatin C as a potential target to control mycobacterial infection as well as HIV coinfection. We found that cystatin C silencing in macrophages significantly improves the intracellular killing of Mtb, which was concomitant with an increased general proteolytic activity of cathepsins. In addition, downmodulation of cystatin C led to an improved expression of the human leukocyte antigen (HLA) class II in macrophages and an increased CD4+ T-lymphocyte proliferation along with enhanced IFN-γ secretion. Overall, our results suggest that the targeting of cystatin C in human macrophages represents a promising approach to improve the control of mycobacterial infections including multidrug-resistant (MDR) TB.
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Affiliation(s)
- David Pires
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Marta Calado
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Tomás Velez
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Manoj Mandal
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Maria João Catalão
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Olivier Neyrolles
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Geanncarlo Lugo-Villarino
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Christel Vérollet
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Elsa Anes
- Host-Pathogen Interactions, Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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12
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Domínguez Cadena LC, Schultz TE, Zamoshnikova A, Donovan ML, Mathmann CD, Yu CH, Mori G, Stow JL, Blumenthal A. Rab6b localizes to the Golgi complex in murine macrophages and promotes tumor necrosis factor release in response to mycobacterial infection. Immunol Cell Biol 2021; 99:1067-1076. [PMID: 34555867 DOI: 10.1111/imcb.12503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022]
Abstract
The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in the host control of mycobacterial infections. Expression and release of TNF are tightly regulated, yet the molecular mechanisms that control the release of TNF by mycobacteria-infected host cells, in particular macrophages, are incompletely understood. Rab GTPases direct the transport of intracellular membrane-enclosed vesicles and are important regulators of macrophage cytokine secretion. Rab6b is known to be predominantly expressed in the brain where it functions in retrograde transport and anterograde vesicle transport for exocytosis. Whether it executes similar functions in the context of immune responses is unknown. Here we show that Rab6b is expressed by primary mouse macrophages, where it localized to the Golgi complex. Infection with Mycobacterium bovis bacille Calmette-Guérin (BCG) resulted in dynamic changes in Rab6b expression in primary mouse macrophages in vitro as well as in organs from infected mice in vivo. We further show that Rab6b facilitated TNF release by M. bovis BCG-infected macrophages, in the absence of discernible impact on Tnf messenger RNA and intracellular TNF protein expression. Our observations identify Rab6b as a positive regulator of M. bovis BCG-induced TNF trafficking and secretion by macrophages and positions Rab6b among the molecular machinery that orchestrates inflammatory cytokine responses by macrophages.
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Affiliation(s)
- Leslie C Domínguez Cadena
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas E Schultz
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Alina Zamoshnikova
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Meg L Donovan
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Carmen D Mathmann
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Chien-Hsiung Yu
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Giorgia Mori
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
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13
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Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis. Cell Discov 2021; 7:30. [PMID: 33947837 PMCID: PMC8096850 DOI: 10.1038/s41421-021-00259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.
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14
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Zn 2+ Intoxication of Mycobacterium marinum during Dictyostelium discoideum Infection Is Counteracted by Induction of the Pathogen Zn 2+ Exporter CtpC. mBio 2021; 12:mBio.01313-20. [PMID: 33531393 PMCID: PMC7858047 DOI: 10.1128/mbio.01313-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microelements are essential for the function of the innate immune system. A deficiency in zinc or copper results in an increased susceptibility to bacterial infections. Macrophages use diverse strategies to restrict intracellular pathogens, including either depriving the bacteria of (micro)nutrients such as transition metals or intoxicating them via metal accumulation. Little is known about the chemical warfare between Mycobacterium marinum, a close relative of Mycobacterium tuberculosis (Mtb), and its hosts. We use the professional phagocyte Dictyostelium discoideum to investigate the role of Zn2+ during M. marinum infection. We show that M. marinum senses toxic levels of Zn2+ and responds by upregulating one of its isoforms of the Zn2+ efflux transporter CtpC. Deletion of ctpC (MMAR_1271) leads to growth inhibition in broth supplemented with Zn2+ as well as reduced intracellular growth. Both phenotypes were fully rescued by constitutive ectopic expression of the Mtb CtpC orthologue demonstrating that MMAR_1271 is the functional CtpC Zn2+ efflux transporter in M. marinum. Infection leads to the accumulation of Zn2+ inside the Mycobacterium-containing vacuole (MCV), achieved by the induction and recruitment of the D. discoideum Zn2+ efflux pumps ZntA and ZntB. In cells lacking ZntA, there is further attenuation of M. marinum growth, presumably due to a compensatory efflux of Zn2+ into the MCV, carried out by ZntB, the main Zn2+ transporter in endosomes and phagosomes. Counterintuitively, bacterial growth is also impaired in zntB KO cells, in which MCVs appear to accumulate less Zn2+ than in wild-type cells, suggesting restriction by other Zn2+-mediated mechanisms. Absence of CtpC further epistatically attenuates the intracellular proliferation of M. marinum in zntA and zntB KO cells, confirming that mycobacteria face noxious levels of Zn2+.
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15
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Cantillon D, Wroblewska J, Cooper I, Newport MJ, Waddell SJ. Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance. NPJ Biofilms Microbiomes 2021; 7:12. [PMID: 33526771 PMCID: PMC7851154 DOI: 10.1038/s41522-021-00186-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Mycobacteria naturally grow as corded biofilms in liquid media without detergent. Such detergent-free biofilm phenotypes may reflect the growth pattern of bacilli in tuberculous lung lesions. New strategies are required to treat tuberculosis, which is responsible for more deaths each year than any other bacterial disease. The lengthy 6-month regimen for drug-sensitive tuberculosis is necessary to remove antimicrobial drug tolerant populations of bacilli that persist through drug therapy. The role of biofilm-like growth in the generation of these sub-populations remains poorly understood despite the hypothesised clinical significance and mounting evidence of biofilms in pathogenesis. We adapt a three-dimensional Rotary Cell Culture System to model M. bovis BCG biofilm growth in low-shear detergent-free liquid suspension. Importantly, biofilms form without attachment to artificial surfaces and without severe nutrient starvation or environmental stress. Biofilm-derived planktonic bacilli are tolerant to isoniazid and streptomycin, but not rifampicin. This phenotypic drug tolerance is lost after passage in drug-free media. Transcriptional profiling reveals induction of cell surface regulators, sigE and BCG_0559c alongside the ESX-5 secretion apparatus in these low-shear liquid-suspension biofilms. This study engineers and characterises mycobacteria grown as a suspended biofilm, illuminating new drug discovery pathways for this deadly disease.
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Affiliation(s)
- Daire Cantillon
- grid.12082.390000 0004 1936 7590Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Justyna Wroblewska
- grid.12082.390000 0004 1936 7590Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Ian Cooper
- grid.12477.370000000121073784School of Pharmacy & Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ UK
| | - Melanie J. Newport
- grid.12082.390000 0004 1936 7590Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Simon J. Waddell
- grid.12082.390000 0004 1936 7590Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
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16
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Maitra A, Evangelopoulos D, Chrzastek A, Martin LT, Hanrath A, Chapman E, Hailes HC, Lipman M, McHugh TD, Waddell SJ, Bhakta S. Carprofen elicits pleiotropic mechanisms of bactericidal action with the potential to reverse antimicrobial drug resistance in tuberculosis. J Antimicrob Chemother 2020; 75:3194-3201. [PMID: 32790867 PMCID: PMC7566368 DOI: 10.1093/jac/dkaa307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/10/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The rise of antimicrobial drug resistance in Mycobacterium tuberculosis coupled with the shortage of new antibiotics has elevated TB to a major global health priority. Repurposing drugs developed or used for other conditions has gained special attention in the current scenario of accelerated drug development for several global infectious diseases. In a similar effort, previous studies revealed that carprofen, a non-steroidal anti-inflammatory drug, selectively inhibited the growth of replicating, non-replicating and MDR clinical isolates of M. tuberculosis. OBJECTIVES We aimed to reveal the whole-cell phenotypic and transcriptomic effects of carprofen in mycobacteria. METHODS Integrative molecular and microbiological approaches such as resazurin microtitre plate assay, high-throughput spot-culture growth inhibition assay, whole-cell efflux inhibition, biofilm inhibition and microarray analyses were performed. Analogues of carprofen were also synthesized and assessed for their antimycobacterial activity. RESULTS Carprofen was found to be a bactericidal drug that inhibited mycobacterial drug efflux mechanisms. It also restricted mycobacterial biofilm growth. Transcriptome profiling revealed that carprofen likely acts by targeting respiration through the disruption of membrane potential. The pleiotropic nature of carprofen's anti-TB action may explain why spontaneous drug-resistant mutants could not be isolated in practice. CONCLUSIONS This immunomodulatory drug and its chemical analogues have the potential to reverse TB antimicrobial drug resistance, offering a swift path to clinical trials of novel TB drug combinations.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Dimitrios Evangelopoulos
- UCL Centre for Clinical Microbiology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| | - Alina Chrzastek
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Aidan Hanrath
- UCL Centre for Clinical Microbiology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| | - Ellie Chapman
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Marc Lipman
- Royal Free London NHS Foundation Trust, UCL-TB and UCL Respiratory, University College London, London NW3 2QG, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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17
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Rodrigues TS, Conti BJ, Fraga-Silva TFDC, Almeida F, Bonato VLD. Interplay between alveolar epithelial and dendritic cells and Mycobacterium tuberculosis. J Leukoc Biol 2020; 108:1139-1156. [PMID: 32620048 DOI: 10.1002/jlb.4mr0520-112r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
The innate response plays a crucial role in the protection against tuberculosis development. Moreover, the initial steps that drive the host-pathogen interaction following Mycobacterium tuberculosis infection are critical for the development of adaptive immune response. As alveolar Mϕs, airway epithelial cells, and dendritic cells can sense the presence of M. tuberculosis and are the first infected cells. These cells secrete mediators, which generate inflammatory signals that drive the differentiation and activation of the T lymphocytes necessary to clear the infection. Throughout this review article, we addressed the interaction between epithelial cells and M. tuberculosis, as well as the interaction between dendritic cells and M. tuberculosis. The understanding of the mechanisms that modulate those interactions is critical to have a complete view of the onset of an infection and may be useful for the development of dendritic cell-based vaccine or immunotherapies.
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Affiliation(s)
- Tamara Silva Rodrigues
- Basic and Applied Immunology Program, Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Bruno José Conti
- Basic and Applied Immunology Program, Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Thais Fernanda de Campos Fraga-Silva
- Basic and Applied Immunology Program, Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Fausto Almeida
- Basic and Applied Immunology Program, Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Vânia Luiza Deperon Bonato
- Basic and Applied Immunology Program, Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
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18
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Abstract
Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery.
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19
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Giraud-Gatineau A, Coya JM, Maure A, Biton A, Thomson M, Bernard EM, Marrec J, Gutierrez MG, Larrouy-Maumus G, Brosch R, Gicquel B, Tailleux L. The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection. eLife 2020; 9:e55692. [PMID: 32369020 PMCID: PMC7200153 DOI: 10.7554/elife.55692] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/04/2020] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are widely used in the treatment of bacterial infections. Although known for their microbicidal activity, antibiotics may also interfere with the host's immune system. Here, we analyzed the effects of bedaquiline (BDQ), an inhibitor of the mycobacterial ATP synthase, on human macrophages. Genome-wide gene expression analysis revealed that BDQ reprogramed cells into potent bactericidal phagocytes. We found that 579 and 1,495 genes were respectively differentially expressed in naive- and M. tuberculosis-infected macrophages incubated with the drug, with an over-representation of lysosome-associated genes. BDQ treatment triggered a variety of antimicrobial defense mechanisms, including phagosome-lysosome fusion, and autophagy. These effects were associated with activation of transcription factor EB, involved in the transcription of lysosomal genes, resulting in enhanced intracellular killing of different bacterial species that were naturally insensitive to BDQ. Thus, BDQ could be used as a host-directed therapy against a wide range of bacterial infections.
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Affiliation(s)
- Alexandre Giraud-Gatineau
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut PasteurParisFrance
- Université Paris Diderot, Sorbonne Paris Cité, Cellule PasteurParisFrance
| | | | - Alexandra Maure
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut PasteurParisFrance
- Université Paris Diderot, Sorbonne Paris Cité, Cellule PasteurParisFrance
| | - Anne Biton
- Bioinformatics and Biostatistics, Department of Computational Biology, USR 3756 CNRS, Institut PasteurParisFrance
| | - Michael Thomson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUnited Kingdom
| | - Elliott M Bernard
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Jade Marrec
- Mycobacterial Genetics Unit, Institut PasteurParisFrance
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Gérald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUnited Kingdom
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut PasteurParisFrance
| | - Brigitte Gicquel
- Mycobacterial Genetics Unit, Institut PasteurParisFrance
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease ControlShenzhenChina
| | - Ludovic Tailleux
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut PasteurParisFrance
- Mycobacterial Genetics Unit, Institut PasteurParisFrance
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20
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Wu K, Li M, Chen ZY, Lowrie DB, Fan XY. Probe Signal Values in mRNA Arrays Imply an Excessive Involvement of Neutrophil FCGR1 in Tuberculosis. Front Med (Lausanne) 2020; 7:19. [PMID: 32118006 PMCID: PMC7033432 DOI: 10.3389/fmed.2020.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/13/2020] [Indexed: 01/21/2023] Open
Abstract
The perturbed genes from transcriptomes are often presented in terms of relative expressions against control samples. However, the probe signal values (PSVs) of genes, implying protein abundances, are often ignored. Here, we explored the PSVs in tuberculosis (TB)-relevant signature genes. The signatures from Mycobacterium tuberculosis-infected THP-1 cells were defined as induced (TMtb-i, with a derived TMtb-iNet) and repressed (TMtb-r). The signature from human blood was defined as a pulmonary TB (PTB)-specific signature (PTBsig). The analysis showed that before infection, TMtb-i and TMtb-iNet had lower PSVs and TMtb-r genes had average PSVs. In the blood of healthy donors, PTBsig (divided into up-regulated PTBsigUp and down-regulated PTBsigDn) displayed average PSVs. This was partly due to masking by the cellular heterogeneity of blood; diverse PSVs were seen in constituent cell populations (CD4/8+ T, monocytes and neutrophils). Specifically, the PSVs of PTBsigUp in the neutrophils of healthy donors were higher (implying higher protein abundances), and much higher in the neutrophils of PTB (implying excessive protein abundances). Based on the PSV patterns of PTBsigUp in four cell populations, we identified three representative highly homologous genes (FCGR1A, FCGR1B, and the pseudogene FCGR1CP, which were often poorly distinguished), of which the summed PSVs were the highest in the neutrophils of PTB patients and healthy donors. The three genes were all up-regulated and responsive to chemotherapy in the blood of PTB, as validated in an RNA-seq-based analysis. This PSV-based study confirms the excessive involvement of neutrophil FCGR1 in PTB.
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Affiliation(s)
- Kang Wu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
| | - Meng Li
- Department of Life Science, Bengbu Medical College, Bengbu, China
| | - Zhen-Yan Chen
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Douglas B Lowrie
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
| | - Xiao-Yong Fan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.,TB Center, Shanghai Emerging and Re-emerging Institute, Shanghai, China
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21
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Knobloch P, Koliwer-Brandl H, Arnold FM, Hanna N, Gonda I, Adenau S, Personnic N, Barisch C, Seeger MA, Soldati T, Hilbi H. Mycobacterium marinum produces distinct mycobactin and carboxymycobactin siderophores to promote growth in broth and phagocytes. Cell Microbiol 2020; 22:e13163. [PMID: 31945239 DOI: 10.1111/cmi.13163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Mycobacterium marinum is a model organism for pathogenic Mycobacterium species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. These pathogens enter phagocytes and replicate within the Mycobacterium-containing vacuole, possibly followed by vacuole exit and growth in the host cell cytosol. Mycobacteria release siderophores called mycobactins to scavenge iron, an essential yet poorly soluble and available micronutrient. To investigate the role of M. marinum mycobactins, we purified by organic solvent extraction and identified by mass spectrometry the lipid-bound mycobactin (MBT) and the water-soluble variant carboxymycobactin (cMBT). Moreover, we generated by specialised phage transduction a defined M. marinum ΔmbtB deletion mutant predicted to be defective for mycobactin production. The M. marinum ΔmbtB mutant strain showed a severe growth defect in broth and phagocytes, which was partially complemented by supplying the mbtB gene on a plasmid. Furthermore, purified Fe-MBT or Fe-cMBT improved the growth of wild type as well as ΔmbtB mutant bacteria on minimal plates, but only Fe-cMBT promoted the growth of wild-type M. marinum during phagocyte infection. Finally, the intracellular growth of M. marinum ΔmbtB in Acanthamoeba castellanii amoebae was restored by coinfection with wild-type bacteria. Our study identifies and characterises the M. marinum MBT and cMBT siderophores and reveals the requirement of mycobactins for extra- and intracellular growth of the pathogen.
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Affiliation(s)
- Paulina Knobloch
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | | | - Fabian M Arnold
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Nabil Hanna
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Sophia Adenau
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Nicolas Personnic
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Caroline Barisch
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
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22
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Soni DK, Dubey SK, Bhatnagar R. ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development. Emerg Microbes Infect 2020; 9:207-220. [PMID: 31985348 PMCID: PMC7034087 DOI: 10.1080/22221751.2020.1714488] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nutrient procurement specifically from nutrient-limiting environment is essential for pathogenic bacteria to survive and/or persist within the host. Long-term survival or persistent infection is one of the main reasons for the overuse of antibiotics, and contributes to the development and spread of antibiotic resistance. Mycobacterium tuberculosis is known for long-term survival within the host, and develops multidrug resistance. Before and during infection, the pathogen encounters various harsh environmental conditions. To cope up with such nutrient-limiting conditions, it is crucial to uptake essential nutrients such as ions, sugars, amino acids, peptides, and metals, necessary for numerous vital biological activities. Among the various types of transporters, ATP-binding cassette (ABC) importers are essentially unique to bacteria, accessible as drug targets without penetrating the cytoplasmic membrane, and offer an ATP-dependent gateway into the cell by mimicking substrates of the importer and designing inhibitors against substrate-binding proteins, ABC importers endeavour for the development of successful drug candidates and antibiotics. Alternatively, the production of antibodies against substrate-binding proteins could lead to vaccine development. In this review, we will emphasize the role of M. tuberculosis ABC importers for survival and virulence within the host. Furthermore, we will elucidate their unique characteristics to discover emerging therapies to combat tuberculosis.
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Affiliation(s)
- Dharmendra Kumar Soni
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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23
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Bettencourt P, Müller J, Nicastri A, Cantillon D, Madhavan M, Charles PD, Fotso CB, Wittenberg R, Bull N, Pinpathomrat N, Waddell SJ, Stylianou E, Hill AVS, Ternette N, McShane H. Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 2020; 5:2. [PMID: 31908851 PMCID: PMC6941960 DOI: 10.1038/s41541-019-0148-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/25/2019] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb) is responsible for more deaths globally than any other pathogen. The only available vaccine, bacillus Calmette-Guérin (BCG), has variable efficacy throughout the world. A more effective vaccine is urgently needed. The immune response against tuberculosis relies, at least in part, on CD4+ T cells. Protective vaccines require the induction of antigen-specific CD4+ T cells via mycobacterial peptides presented by MHC class-II in infected macrophages. In order to identify mycobacterial antigens bound to MHC, we have immunoprecipitated MHC class-I and class-II complexes from THP-1 macrophages infected with BCG, purified MHC class-I and MHC class-II peptides and analysed them by liquid chromatography tandem mass spectrometry. We have successfully identified 94 mycobacterial peptides presented by MHC-II and 43 presented by MHC-I, from 76 and 41 antigens, respectively. These antigens were found to be highly expressed in infected macrophages. Gene ontology analysis suggests most of these antigens are associated with membranes and involved in lipid biosynthesis and transport. The sequences of selected peptides were confirmed by spectral match validation and immunogenicity evaluated by IFN-gamma ELISpot against peripheral blood mononuclear cell from volunteers vaccinated with BCG, M.tb latently infected subjects or patients with tuberculosis disease. Three antigens were expressed in viral vectors, and evaluated as vaccine candidates alone or in combination in a murine aerosol M.tb challenge model. When delivered in combination, the three candidate vaccines conferred significant protection in the lungs and spleen compared with BCG alone, demonstrating proof-of-concept for this unbiased approach to identifying new candidate antigens. Protective vaccines against Mycobacterium tuberculosis (M.tb), such as bacillus Calmette-Guérin (BCG), trigger strong CD4 T-cell responses specific to mycobacterium peptides, but their efficacy is variable. Paulo Bettencourt and colleagues now identify a set of mycobacterium peptides presented by BCG-infected macrophages via major compatibility complexes (MHC), and show that three of these antigens can be combined to formulate a vaccine that confers improved protection to Mtb infection in mice. After identifying 94 MHC-II-associated and 43 MHC-I-associated mycobacterium peptides, the researchers performed immunogenicity assays with peripheral blood mononuclear cells from BCG-vaccinated donors, latent Mtb-infected patients and patients with tuberculosis, and show that a set of these peptides was recognised by the immune cells, validating their potential as possible components for new Mtb vaccine formulations. These findings further support the value of immunopeptidomics for the identification of new antigens for effective vaccine alternatives.
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Affiliation(s)
| | - Julius Müller
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Annalisa Nicastri
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Daire Cantillon
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Meera Madhavan
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Philip D Charles
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Carine B Fotso
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Naomi Bull
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Simon J Waddell
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | | | | | - Nicola Ternette
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK.,2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Helen McShane
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
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24
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Maya-Hoyos M, Rosales C, Novoa-Aponte L, Castillo E, Soto CY. The P-type ATPase CtpF is a plasma membrane transporter mediating calcium efflux in Mycobacterium tuberculosis cells. Heliyon 2019; 5:e02852. [PMID: 31788573 PMCID: PMC6879984 DOI: 10.1016/j.heliyon.2019.e02852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/29/2019] [Accepted: 11/08/2019] [Indexed: 11/25/2022] Open
Abstract
Among the 12 P-type ATPases encoded by the genome of Mycobacterium tuberculosis (Mtb), CtpF responds to the greatest number of stress conditions, including oxidative stress, hypoxia, and infection. CtpF is the mycobacterial homolog of the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) of higher eukaryotes. Its expression is regulated by the global regulator of latency, DosR. However, the role that CtpF plays in the mycobacterial plasma membrane remains unknown. In this study, different functional analyses showed that CtpF is associated with calcium pumping from mycobacterial cells. Specifically, Mtb CtpF expression in Mycobacterium smegmatis cells prevents Ca2+ accumulation compared with wild type (WT) cells. In addition, plasma membrane vesicles from recombinant membranes, in which the direction of ion transport is inverted, accumulate more Ca2+ compared with vesicles obtained from the WT strain. This findings support the hypothesis that CtpF contributes to calcium efflux from mycobacterial cells. Accordingly, Mtb cells defective in ctpF (MtbΔctpF) accumulate more Ca2+ compared with WT cells, while the Ca2+-dependent ATPase activity is significantly lower in the mutant cells. Interestingly, the deletion of ctpF in Mtb impairs the tolerance of the bacteria to oxidative and nitrosative stress. Overall, our results indicate that CtpF is associated with calcium pumping from mycobacterial cells and the response to oxidative stress.
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Affiliation(s)
| | | | | | | | - Carlos Y. Soto
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia
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25
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Alqaseer K, Turapov O, Barthe P, Jagatia H, De Visch A, Roumestand C, Wegrzyn M, Bartek IL, Voskuil MI, O'Hare HM, Ajuh P, Bottrill AR, Witney AA, Cohen-Gonsaud M, Waddell SJ, Mukamolova GV. Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112. Mol Microbiol 2019; 112:1847-1862. [PMID: 31562654 PMCID: PMC6906086 DOI: 10.1111/mmi.14398] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/23/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is able to persist in the body through months of multi‐drug therapy. Mycobacteria possess a wide range of regulatory proteins, including the protein kinase B (PknB) which controls peptidoglycan biosynthesis during growth. Here, we observed that depletion of PknB resulted in specific transcriptional changes that are likely caused by reduced phosphorylation of the H‐NS‐like regulator Lsr2 at threonine 112. The activity of PknB towards this phosphosite was confirmed with purified proteins, and this site was required for adaptation of Mtb to hypoxic conditions, and growth on solid media. Like H‐NS, Lsr2 binds DNA in sequence‐dependent and non‐specific modes. PknB phosphorylation of Lsr2 reduced DNA binding, measured by fluorescence anisotropy and electrophoretic mobility shift assays, and our NMR structure of phosphomimetic T112D Lsr2 suggests that this may be due to increased dynamics of the DNA‐binding domain. Conversely, the phosphoablative T112A Lsr2 had increased binding to certain DNA sites in ChIP‐sequencing, and Mtb containing this variant showed transcriptional changes that correspond with the change in DNA binding. In summary, PknB controls Mtb growth and adaptations to the changing host environment by phosphorylating the global transcriptional regulator Lsr2.
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Affiliation(s)
- Kawther Alqaseer
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,Department of Basic Science, Faculty of Nursing, University of Kufa, Najaf Governorate, P.O. Box 21, Kufa, Najaf, Iraq
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Heena Jagatia
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Angélique De Visch
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Malgorzata Wegrzyn
- Core Biotechnology Services, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Iona L Bartek
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,LISCB, Department of Molecular and Cell Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Paul Ajuh
- Gemini Biosciences Ltd, Liverpool Science Park, Liverpool, L7 8TX, UK
| | - Andrew R Bottrill
- Protein Nucleic Acid Laboratory, University of Leicester, Leicester, LE1 7RH, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Simon J Waddell
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
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26
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Analysis of the microRNA Expression Profile of Bovine Monocyte-derived Macrophages Infected with Mycobacterium avium subsp. Paratuberculosis Reveals that miR-150 Suppresses Cell Apoptosis by Targeting PDCD4. Int J Mol Sci 2019; 20:ijms20112708. [PMID: 31159463 PMCID: PMC6600136 DOI: 10.3390/ijms20112708] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
M. avium subsp. paratuberculosis (MAP) is the causative pathogen of Johne’s disease, a chronic granulomatous enteritis that principally affects ruminants and can survive, proliferate and disseminate in macrophages. MicroRNAs (miRNAs) are important regulators of gene expression and can impact the processes of cells. To investigate the role of miRNAs in monocyte-derived macrophages (MDMs) during MAP infection, we used high-throughput sequencing technology to analyze small RNA libraries of MAP-infected and control MDMs. The results showed that a total of 21 miRNAs were differentially expressed in MDMs after MAP infection, and 8864 target genes were predicted. A functional analysis showed that the target genes were mainly involved in the MAPK signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and apoptosis. In addition, using a dual-luciferase reporter assay, flow cytometry, and a small interfering (si)RNA knockdown assay, the role of miR-150 in regulating macrophage apoptosis by targeting the programmed cell death protein-4 (PDCD4) was demonstrated. These results provide an experimental basis to reveal the regulatory mechanism of MAP infection and suggest the potential of miRNAs as biomarkers for the diagnosis of Johne’s disease in bovines.
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27
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Song N, Li Z, Cui Z, Chen L, Cui Y, Dang G, Li Z, Li H, Liu S. The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B 1. BMC Microbiol 2019; 19:104. [PMID: 31117936 PMCID: PMC6530141 DOI: 10.1186/s12866-019-1492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Vitamin B1 (VB1) is a crucial dietary nutrient and essential cofactor for several key enzymes in the regulation of cellular and metabolic processes, and more importantly in the activation of immune system. To date, the precise role of VB1 in Mycobacterium tuberculosis remains to be fully understood. RESULTS In this study, the transcriptional and metabolic profiles of VB1-treated Mycobacterium. bovis BCG were analyzed by RNA-sequencing and LC-MS (Liquid chromatography coupled to mass spectrometry). The selection of BCG strain was based on its common physiological features shared with M. tuberculosis. The results of cell growth assays demonstrated that VB1 inhibited the BCG growth rate in vitro. Transcriptomic analysis revealed that the expression levels of genes related to fatty acid metabolism, cholesterol metabolism, glycolipid catabolism, DNA replication, protein translation, cell division and cell wall formation were significantly downregulated in M. bovis BCG treated with VB1. In addition, the metabolomics LC-MS data indicated that most of the amino acids and adenosine diphosphate (ADP) were decreased in M. bovis BCG strain after VB1 treatment. CONCLUSIONS This study provides the molecular and metabolic bases to understand the impacts of VB1 on M.bovis BCG.
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Affiliation(s)
- Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhaoli Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liping Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yingying Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhe Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - He Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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28
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Structural insights into chaperone addiction of toxin-antitoxin systems. Nat Commun 2019; 10:782. [PMID: 30770830 PMCID: PMC6377645 DOI: 10.1038/s41467-019-08747-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
SecB chaperones assist protein export by binding both unfolded proteins and the SecA motor. Certain SecB homologs can also control toxin-antitoxin (TA) systems known to modulate bacterial growth in response to stress. In such TA-chaperone (TAC) systems, SecB assists the folding and prevents degradation of the antitoxin, thus facilitating toxin inhibition. Chaperone dependency is conferred by a C-terminal extension in the antitoxin known as chaperone addiction (ChAD) sequence, which makes the antitoxin aggregation-prone and prevents toxin inhibition. Using TAC of Mycobacterium tuberculosis, we present the structure of a SecB-like chaperone bound to its ChAD peptide. We find differences in the binding interfaces when compared to SecB–SecA or SecB-preprotein complexes, and show that the antitoxin can reach a functional form while bound to the chaperone. This work reveals how chaperones can use discrete surface binding regions to accommodate different clients or partners and thereby expand their substrate repertoire and functions. SecB homologs can be associated with stress-responsive type II toxin–antitoxin (TA) systems and form tripartite toxin-antitoxin-chaperone systems (TAC). Here the authors provide structural insights into TACs by presenting the crystal structure of the M. tuberculosis TA-associated SecB chaperone in complex with the C-terminal ChAD (chaperone addiction) extension of the antitoxin HigA1.
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29
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Nazarova EV, Montague CR, Huang L, La T, Russell D, VanderVen BC. The genetic requirements of fatty acid import by Mycobacterium tuberculosis within macrophages. eLife 2019; 8:e43621. [PMID: 30735132 PMCID: PMC6368401 DOI: 10.7554/elife.43621] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) imports and metabolizes fatty acids to maintain infection within human macrophages. Although this is a well-established paradigm, the bacterial factors required for fatty acid import are poorly understood. Previously, we found that LucA and Mce1 are required for fatty acid import in Mtb (Nazarova et al., 2017). Here, we identified additional Mtb mutants that have a reduced ability to import a fluorescent fatty acid substrate during infection within macrophages. This screen identified the novel genes as rv2799 and rv0966c as be necessary for fatty acid import and confirmed the central role for Rv3723/LucA and putative components of the Mce1 fatty acid transporter (Rv0200/OmamB, Rv0172/Mce1D, and Rv0655/MceG) in this process.
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Affiliation(s)
- Evgeniya V Nazarova
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
| | - Christine R Montague
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
| | - Lu Huang
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
| | - Thuy La
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
| | - David Russell
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary MedicineCornell UniversityIthacaUnited States
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30
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Mubin N, Pahari S, Owais M, Zubair S. Mycobacterium tuberculosis host cell interaction: Role of latency associated protein Acr-1 in differential modulation of macrophages. PLoS One 2018; 13:e0206459. [PMID: 30395609 PMCID: PMC6218195 DOI: 10.1371/journal.pone.0206459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/13/2018] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb) contrives intracellular abode as a strategy to combat antibody onslaught. Additionally, to thrive against hostile ambiance inside host macrophages, the pathogen inhibits phago-lysosomal fusion. Finally, to further defy host cell offensives, M.tb opts for dormant phase, where it turns off or slows down most of its metabolic process as an added stratagem. While M.tb restrains most of its metabolic activities during dormancy, surprisingly latency-associated alpha-crystallin protein (Acr-1) is expressed most prominently during this phase. Interestingly, several previous studies described the potential of Acr-1 to induce the robust immuno-prophylactic response in the immunized host. It is intriguing to comprehend the apparent discrepancy that the microbe M.tb overexpresses a protein that has the potential to prime host immune system against the pathogen itself. Keeping this apparent ambiguity into consideration, it is imperative to unravel intricacies involved in the exploitation of Acr-1 by M.tb during its interaction with host immune cells. The present study suggests that Acr-1 exhibits diverse role in the maturation of macrophages (MΦs) and related immunological responses. The early encounter of bone marrow derived immune cells (pre-exposure during differentiation to MΦs) with Acr-1 (AcrMΦpre), results in hampering of their function. The pre-exposure of naïve MΦs with Acr-1 induces the expression of TIM-3 and IL-10. In contrast, exposure of fully differentiated MΦs to Acr-1 results in their down-modulation and induces the phosphorylation of STAT-1 and STAT-4 in host MΦs. Furthermore, Acr-1 mediated activation of MΦs results in the induction of Th1 and Th17 phenotype by activated T lymphocyte.
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Affiliation(s)
- Nida Mubin
- Molecular Immunology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Susanta Pahari
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Mohammad Owais
- Molecular Immunology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
- * E-mail: (SZ); (MO)
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh, India
- * E-mail: (SZ); (MO)
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31
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Agarwal S, Ghosh S, Sharma S, Kaur K, Verma I. Mycobacterium tuberculosis H37Rv expresses differential proteome during intracellular survival within alveolar epithelial cells compared with macrophages. Pathog Dis 2018; 76:5052203. [DOI: 10.1093/femspd/fty058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/28/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- S Agarwal
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - S Ghosh
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - S Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - K Kaur
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - I Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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32
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Katiyar A, Singh H, Azad KK. Identification of Missing Carbon Fixation Enzymes as Potential Drug Targets in Mycobacterium Tuberculosis. J Integr Bioinform 2018; 15:/j/jib.2018.15.issue-3/jib-2017-0041/jib-2017-0041.xml. [PMID: 30218604 PMCID: PMC6340126 DOI: 10.1515/jib-2017-0041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 02/08/2018] [Indexed: 01/22/2023] Open
Abstract
Metabolic adaptation to the host environment has been recognized as an essential mechanism of pathogenicity and the growth of Mycobacterium tuberculosis (Mtb) in the lungs for decades. The Mtb uses CO2 as a source of carbon during the dormant or non-replicative state. However, there is a lack of biochemical knowledge of its metabolic networks. In this study, we investigated the CO2 fixation pathways (such as ko00710 and ko00720) most likely involved in the energy production and conversion of CO2 in Mtb. Extensive pathway evaluation of 23 completely sequenced strains of Mtb confirmed the existence of a complete list of genes encoding the relevant enzymes of the reductive tricarboxylic acid (rTCA) cycle. This provides the evidence that an rTCA cycle may function to fix CO2 in this bacterium. We also proposed that as CO2 is plentiful in the lungs, inhibition of CO2 fixation pathways (by targeting the relevant CO2 fixation enzymes) could be used in the expansion of new drugs against the dormant Mtb. In support of the suggested hypothesis, the CO2 fixation enzymes were confirmed as a potential drug target by analyzing a number of attributes necessary to be a good bacterial target.
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Affiliation(s)
- Amit Katiyar
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Harpreet Singh
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India.,Division of Informatics Systems and Research Management, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India, Phone: +91-11-26589556, Fax: +91-11-26588662
| | - Krishna Kant Azad
- Division of Informatics Systems and Research Management, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
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33
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Papp AC, Azad AK, Pietrzak M, Williams A, Handelman SK, Igo RP, Stein CM, Hartmann K, Schlesinger LS, Sadee W. AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection. PLoS One 2018; 13:e0198221. [PMID: 29847580 PMCID: PMC5976201 DOI: 10.1371/journal.pone.0198221] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022] Open
Abstract
Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq's reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways that differ in part between MDM and HAM. A similar number of expressed genes are detected at all time-points between uninfected MDM and HAM, in common pathways including inflammatory and immune functions, but canonical pathway differences also exist. In particular, at 2 h, multiple genes relevant to the immune response are preferentially expressed in either uninfected HAM or MDM, while the HAM RNA profiles approximate MDM profiles over time in culture, highlighting the unique RNA expression profile of freshly obtained HAM. MDM demonstrate a greater transcriptional response than HAM upon M.tb infection, with 2 to >10 times more genes up- or down-regulated. The results identify key genes involved in cellular responses to M.tb in two different human macrophage types. Follow-up bioinformatics analysis indicates that approximately 30% of response genes have expression quantitative trait loci (eQTLs in GTEx), common DNA variants that can influence host gene expression susceptibility or resistance to M.tb, illustrated with the TREM1 gene cluster and IL-10.
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Affiliation(s)
- Audrey C. Papp
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Abul K. Azad
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Maciej Pietrzak
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Samuel K. Handelman
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert P. Igo
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Proteomics & Bioinformatics, Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Katherine Hartmann
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- European Organization for the Research and Treatment of Cancer, Brussels, Belgium
| | - Larry S. Schlesinger
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- * E-mail: (LSS); (WS)
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (LSS); (WS)
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34
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Parvati Sai Arun PV, Miryala SK, Rana A, Kurukuti S, Akhter Y, Yellaboina S. System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection. Sci Rep 2018; 8:5079. [PMID: 29567998 PMCID: PMC5864717 DOI: 10.1038/s41598-018-22884-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/28/2018] [Indexed: 01/16/2023] Open
Abstract
Molecular signatures and their interactions behind the successful establishment of infection of Mycobacterium tuberculosis (Mtb) inside macrophage are largely unknown. In this work, we present an inter-system scale atlas of the gene expression signatures, their interactions and higher order gene functions of macrophage-Mtb environment at the time of infection. We have carried out large-scale meta-analysis of previously published gene expression microarray studies andhave identified a ranked list of differentially expressed genes and their higher order functions in intracellular Mtb as well as the infected macrophage. Comparative analysis of gene expression signatures of intracellular Mtb with the in vitro dormant Mtb at different hypoxic and oxidative stress conditions led to the identification of the large number of Mtb functional groups, namely operons, regulons and pathways that were common and unique to the intracellular environment and dormancy state. Some of the functions that are specific to intracellular Mtb are cholesterol degradation and biosynthesis of immunomodulatory phenolic compounds. The molecular signatures we have identified to be involved in adaptation to different stress conditions in macrophage environment may be critical for designing therapeutic interventions against tuberculosis. And, our approach may be broadly applicable for investigating other host-pathogen interactions.
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Affiliation(s)
| | - Sravan Kumar Miryala
- IOB-YU Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre Yenepoya University, Mangalore, Karnataka, India
| | - Aarti Rana
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Sailu Yellaboina
- IOB-YU Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre Yenepoya University, Mangalore, Karnataka, India.
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35
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Nazarova EV, Podinovskaia M, Russell DG, VanderVen BC. Flow Cytometric Quantification of Fatty Acid Uptake by Mycobacterium tuberculosis in Macrophages. Bio Protoc 2018; 8:e2734. [PMID: 32368567 DOI: 10.21769/bioprotoc.2734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved to assimilate fatty acids from its host. However, until recently, there was no reliable way to quantify fatty acid uptake by the bacteria during host cell infection. Here we describe a new method to quantify fatty acid uptake by intracellular bacilli. We infect macrophages with Mtb constitutively expressing mCherry and then metabolically label them with Bodipy-palmitate. Following the labeling procedure, we isolate Mtb-containing phagosomes on a sucrose cushion and disrupt the phagosomes with detergent. After extensive washes, the isolated bacteria are analyzed by flow cytometry to determine the level of Bodipy-palmitate signal associated with the bacteria. Using a Mtb mutant strain defective in fatty acid uptake in liquid culture we determined that this mutant assimilated 10-fold less Bodipy-palmitate than the wild type strain during infection in macrophages. This quantitative method of fatty acid uptake can be used to further identify pathways involved in lipid uptake by intracellular Mtb and possibly other bacteria.
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Affiliation(s)
| | | | - David G Russell
- Microbiology & Immunology Department, Cornell University, Ithaca, USA
| | - Brian C VanderVen
- Microbiology & Immunology Department, Cornell University, Ithaca, USA
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36
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Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival. Sci Rep 2018; 8:661. [PMID: 29330469 PMCID: PMC5766484 DOI: 10.1038/s41598-017-18528-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 12/11/2017] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) survives and multiplies inside human macrophages by subversion of immune mechanisms. Although these immune evasion strategies are well characterised functionally, the underlying molecular mechanisms are poorly understood. Here we show that during infection of human whole blood with M. tuberculosis, host gene transcriptional suppression, rather than activation, is the predominant response. Spatial, temporal and functional characterisation of repressed genes revealed their involvement in pathogen sensing and phagocytosis, degradation within the phagolysosome and antigen processing and presentation. To identify mechanisms underlying suppression of multiple immune genes we undertook epigenetic analyses. We identified significantly differentially expressed microRNAs with known targets in suppressed genes. In addition, after searching regions upstream of the start of transcription of suppressed genes for common sequence motifs, we discovered novel enriched composite sequence patterns, which corresponded to Alu repeat elements, transposable elements known to have wide ranging influences on gene expression. Our findings suggest that to survive within infected cells, mycobacteria exploit a complex immune “molecular off switch” controlled by both microRNAs and Alu regulatory elements.
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37
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Wildner LM, Gould KA, Waddell SJ. Transcriptional Profiling Mycobacterium tuberculosis from Patient Sputa. Methods Mol Biol 2018; 1736:117-128. [PMID: 29322464 DOI: 10.1007/978-1-4939-7638-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of drug resistance threatens to destroy tuberculosis control programs worldwide, with resistance to all first-line drugs and most second-line drugs detected. Drug tolerance (or phenotypic drug resistance) is also likely to be clinically relevant over the 6-month long standard treatment for drug-sensitive tuberculosis. Transcriptional profiling the response of Mycobacterium tuberculosis to antimicrobial drugs offers a novel interpretation of drug efficacy and mycobacterial drug-susceptibility that likely varies in dynamic microenvironments, such as the lung. This chapter describes the noninvasive sampling of tuberculous sputa and techniques for mRNA profiling M. tb bacilli during patient therapy to characterize real-world drug actions.
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Affiliation(s)
- Leticia Muraro Wildner
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.,Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Katherine A Gould
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
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38
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Perrone F, De Siena B, Muscariello L, Kendall SL, Waddell SJ, Sacco M. A Novel TetR-Like Transcriptional Regulator Is Induced in Acid-Nitrosative Stress and Controls Expression of an Efflux Pump in Mycobacteria. Front Microbiol 2017; 8:2039. [PMID: 29109706 PMCID: PMC5660060 DOI: 10.3389/fmicb.2017.02039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis has the ability to survive inside macrophages under acid-nitrosative stress. M. tuberculosis Rv1685c and its ortholog in M. smegmatis, MSMEG_3765, are induced on exposure to acid-nitrosative stress. Both genes are annotated as TetR transcriptional regulators, a family of proteins that regulate a wide range of cellular activities, including multidrug resistance, carbon catabolism and virulence. Here, we demonstrate that MSMEG_3765 is co-transcribed with the upstream genes MSMEG_3762 and MSMEG_3763, encoding efflux pump components. RTq-PCR and GFP-reporter assays showed that the MSMEG_3762/63/65 gene cluster, and the orthologous region in M. tuberculosis (Rv1687c/86c/85c), was up-regulated in a MSMEG_3765 null mutant, suggesting that MSMEG_3765 acts as a repressor, typical of this family of regulators. We further defined the MSMEG_3765 regulon using genome-wide transcriptional profiling and used reporter assays to confirm that the MSMEG_3762/63/65 promoter was induced under acid-nitrosative stress. A putative 36 bp regulatory motif was identified upstream of the gene clusters in both M. smegmatis and M. tuberculosis and purified recombinant MSMEG_3765 protein was found to bind to DNA fragments containing this motif from both M. smegmatis and M. tuberculosis upstream regulatory regions. These results suggest that the TetR repressor MSMEG_3765/Rv1685c controls expression of an efflux pump with an, as yet, undefined role in the mycobacterial response to acid-nitrosative stress.
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Affiliation(s)
- Filomena Perrone
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Barbara De Siena
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Lidia Muscariello
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Sharon L Kendall
- Department of Pathobiology and Population Science, Royal Veterinary College, London, United Kingdom
| | - Simon J Waddell
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Margherita Sacco
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
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39
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Prashar A, Schnettger L, Bernard EM, Gutierrez MG. Rab GTPases in Immunity and Inflammation. Front Cell Infect Microbiol 2017; 7:435. [PMID: 29034219 PMCID: PMC5627064 DOI: 10.3389/fcimb.2017.00435] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
Strict spatiotemporal control of trafficking events between organelles is critical for maintaining homeostasis and directing cellular responses. This regulation is particularly important in immune cells for mounting specialized immune defenses. By controlling the formation, transport and fusion of intracellular organelles, Rab GTPases serve as master regulators of membrane trafficking. In this review, we discuss the cellular and molecular mechanisms by which Rab GTPases regulate immunity and inflammation.
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Affiliation(s)
| | | | | | - Maximiliano G. Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, Francis Crick Institute, London, United Kingdom
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40
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Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann JL, Brosch R, Barreiro LB, Gilad Y. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep 2017; 7:5702. [PMID: 28720766 PMCID: PMC5516010 DOI: 10.1038/s41598-017-05878-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023] Open
Abstract
Tuberculosis (TB) is a deadly infectious disease, which kills millions of people every year. The causative pathogen, Mycobacterium tuberculosis (MTB), is estimated to have infected up to a third of the world's population; however, only approximately 10% of infected healthy individuals progress to active TB. Despite evidence for heritability, it is not currently possible to predict who may develop TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from active TB. We measured gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms nearby the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated reasonable performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.
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Affiliation(s)
- John D Blischak
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Ludovic Tailleux
- Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France.
| | - Marsha Myrthil
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Cécile Charlois
- Centre de Lutte Antituberculeuse de Paris, DASES Mairie de Paris, 75013, Paris, France
| | - Emmanuel Bergot
- Service de pneumologie et oncologie thoracique, CHU Côte de Nacre, 14033, Caen, France
| | - Aurélien Dinh
- Maladies Infectieuses, AP-HP, Hôpital Universitaire Raymond-Poincaré, Garches, 92380, France
| | - Gloria Morizot
- Clinical Investigation & Access Biological Resources (ICAReB), Institut Pasteur, Paris, France
| | - Olivia Chény
- Clinical Core, Centre for Translational Science, Institut Pasteur, Paris, France
| | - Cassandre Von Platen
- Clinical Core, Centre for Translational Science, Institut Pasteur, Paris, France
| | - Jean-Louis Herrmann
- INSERM, U1173, UFR Simone Veil, Université de Versailles Saint Quentin, Saint Quentin en Yvelines, France
- APHP, Groupe Hospitalo-Universitaire Paris Île-de-France Ouest, Garches et Boulogne-Billancourt, France
| | - Roland Brosch
- Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Québec, Canada.
- Department of Pediatrics, University of Montreal, Montreal, Québec, Canada.
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.
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41
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Rastogi S, Singh AK, Chandra G, Kushwaha P, Pant G, Singh K, Mitra K, Sashidhara KV, Krishnan MY. The diacylglycerol acyltransferase Rv3371 of Mycobacterium tuberculosis is required for growth arrest and involved in stress-induced cell wall alterations. Tuberculosis (Edinb) 2017; 104:8-19. [DOI: 10.1016/j.tube.2017.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/09/2017] [Accepted: 02/11/2017] [Indexed: 11/25/2022]
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42
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Moores A, Riesco AB, Schwenk S, Arnvig KB. Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis. PLoS One 2017; 12:e0174079. [PMID: 28323872 PMCID: PMC5360333 DOI: 10.1371/journal.pone.0174079] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/02/2017] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis depends on the ability to adjust to stresses encountered in a range of host environments, adjustments that require significant changes in gene expression. Small RNAs (sRNAs) play an important role as post-transcriptional regulators of prokaryotic gene expression, where they are associated with stress responses and, in the case of pathogens, adaptation to the host environment. In spite of this, the understanding of M. tuberculosis RNA biology remains limited. Here we have used a DosR-associated sRNA as an example to investigate multiple aspects of mycobacterial RNA biology that are likely to apply to other M. tuberculosis sRNAs and mRNAs. We have found that accumulation of this particular sRNA is slow but robust as cells enter stationary phase. Using reporter gene assays, we find that the sRNA core promoter is activated by DosR, and we have renamed the sRNA DrrS for DosR Regulated sRNA. Moreover, we show that DrrS is transcribed as a longer precursor, DrrS+, which is rapidly processed to the mature and highly stable DrrS. We characterise, for the first time in mycobacteria, an RNA structural determinant involved in this extraordinary stability and we show how the addition of a few nucleotides can lead to acute destabilisation. Finally, we show how this RNA element can enhance expression of a heterologous gene. Thus, the element, as well as its destabilising derivatives may be employed to post-transcriptionally regulate gene expression in mycobacteria in combination with different promoter variants. Moreover, our findings will facilitate further investigations into the severely understudied topic of mycobacterial RNA biology and into the role that regulatory RNA plays in M. tuberculosis pathogenesis.
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Affiliation(s)
- Alexandra Moores
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Ana B. Riesco
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Stefan Schwenk
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Kristine B. Arnvig
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
- * E-mail:
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43
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Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1. Biochemistry 2017; 56:1559-1572. [PMID: 28169518 DOI: 10.1021/acs.biochem.6b00954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Similarity between the ligand binding profiles of enzymes may aid functional characterization and be of greater relevance to inhibitor development than sequence similarity or structural homology. Fragment screening is an efficient approach for characterization of the ligand binding profile of an enzyme and has been applied here to study the family of cytochrome P450 enzymes (P450s) expressed by Mycobacterium tuberculosis (Mtb). The Mtb P450s have important roles in bacterial virulence, survival, and pathogenicity. Comparing the fragment profiles of seven of these enzymes revealed that P450s which share a similar biological function have significantly similar fragment profiles, whereas functionally unrelated or orphan P450s exhibit distinct ligand binding properties, despite overall high structural homology. Chemical structures that exhibit promiscuous binding between enzymes have been identified, as have selective fragments that could provide leads for inhibitor development. The similarity between the fragment binding profiles of the orphan enzyme CYP144A1 and CYP121A1, a characterized enzyme that is important for Mtb viability, provides a case study illustrating the subsequent identification of novel CYP144A1 ligands. The different binding modes of these compounds to CYP144A1 provide insight into structural and dynamic aspects of the enzyme, possible biological function, and provide the opportunity to develop inhibitors. Expanding this fragment profiling approach to include a greater number of functionally characterized and orphan proteins may provide a valuable resource for understanding enzyme-ligand interactions.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jude Chenge
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Azedine Zoufir
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. Sci Rep 2017; 7:42225. [PMID: 28176867 PMCID: PMC5296737 DOI: 10.1038/srep42225] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/05/2017] [Indexed: 12/11/2022] Open
Abstract
Macrophages play an essential role in the early immune response to Mycobacterium tuberculosis and are the cell type preferentially infected in vivo. Primary macrophages and macrophage-like cell lines are commonly used as infection models, although the physiological relevance of cell lines, particularly for host-pathogen interaction studies, is debatable. Here we use high-throughput RNA-sequencing to analyse transcriptome dynamics of two macrophage models in response to M. tuberculosis infection. Specifically, we study the early response of bone marrow-derived mouse macrophages and cell line J774 to infection with live and γ-irradiated (killed) M. tuberculosis. We show that infection with live bacilli specifically alters the expression of host genes such as Rsad2, Ifit1/2/3 and Rig-I, whose potential roles in resistance to M. tuberculosis infection have not yet been investigated. In addition, the response of primary macrophages is faster and more intense than that of J774 cells in terms of number of differentially expressed genes and magnitude of induction/repression. Our results point to potentially novel processes leading to immune containment early during M. tuberculosis infection, and support the idea that important differences exist between primary macrophages and cell lines, which should be taken into account when choosing a macrophage model to study host-pathogen interactions.
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45
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Bespyatykh JA, Shitikov EA, Ilina EN. Proteomics for the Investigation of Mycobacteria. Acta Naturae 2017; 9:15-25. [PMID: 28461970 PMCID: PMC5406656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 10/25/2022] Open
Abstract
The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
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Affiliation(s)
- J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
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Mvubu NE, Pillay B, Gamieldien J, Bishai W, Pillay M. Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:321-329. [PMID: 27497873 DOI: 10.1016/j.dci.2016.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/31/2016] [Accepted: 07/31/2016] [Indexed: 06/06/2023]
Abstract
Although pulmonary epithelial cells are integral to innate and adaptive immune responses during Mycobacterium tuberculosis infection, global transcriptomic changes in these cells remain largely unknown. Changes in gene expression induced in pulmonary epithelial cells infected with M. tuberculosis F15/LAM4/KZN, F11, F28, Beijing and Unique genotypes were investigated by RNA sequencing (RNA-Seq). The Illumina HiSeq 2000 platform generated 50 bp reads that were mapped to the human genome (Hg19) using Tophat (2.0.10). Differential gene expression induced by the different strains in infected relative to the uninfected cells was quantified and compared using Cufflinks (2.1.0) and MeV (4.0.9), respectively. Gene expression varied among the strains with the total number of genes as follows: F15/LAM4/KZN (1187), Beijing (1252), F11 (1639), F28 (870), Unique (886) and H37Rv (1179). A subset of 292 genes was commonly induced by all strains, where 52 genes were down-regulated while 240 genes were up-regulated. Differentially expressed genes were compared among the strains and the number of induced strain-specific gene signatures were as follows: F15/LAM4/KZN (138), Beijing (52), F11 (255), F28 (55), Unique (186) and H37Rv (125). Strain-specific molecular gene signatures associated with functional pathways were observed only for the Unique and H37Rv strains while certain biological functions may be associated with other strain signatures. This study demonstrated that strains of M. tuberculosis induce differential gene expression and strain-specific molecular signatures in pulmonary epithelial cells. Specific signatures induced by clinical strains of M. tuberculosis can be further explored for novel host-associated biomarkers and adjunctive immunotherapies.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
| | - Balakrishna Pillay
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
| | - Junaid Gamieldien
- South African National Bioinformatics Institute/MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, South Africa.
| | - William Bishai
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, United States.
| | - Manormoney Pillay
- Medical Microbiology and Infection Control, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa.
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47
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Li CW, Lee YL, Chen BS. Genetic-and-Epigenetic Interspecies Networks for Cross-Talk Mechanisms in Human Macrophages and Dendritic Cells during MTB Infection. Front Cell Infect Microbiol 2016; 6:124. [PMID: 27803888 PMCID: PMC5067469 DOI: 10.3389/fcimb.2016.00124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/22/2016] [Indexed: 12/29/2022] Open
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (Mtb) infection. Mtb is one of the oldest human pathogens, and evolves mechanisms implied in human evolution. The lungs are the first organ exposed to aerosol-transmitted Mtb during gaseous exchange. Therefore, the guards of the immune system in the lungs, such as macrophages (Mϕs) and dendritic cells (DCs), are the most important defense against Mtb infection. There have been several studies discussing the functions of Mϕs and DCs during Mtb infection, but the genome-wide pathways and networks are still incomplete. Furthermore, the immune response induced by Mϕs and DCs varies. Therefore, we analyzed the cross-talk genome-wide genetic-and-epigenetic interspecies networks (GWGEINs) between Mϕs vs. Mtb and DCs vs. Mtb to determine the varying mechanisms of both the host and pathogen as it relates to Mϕs and DCs during early Mtb infection. First, we performed database mining to construct candidate cross-talk GWGEIN between human cells and Mtb. Then we constructed dynamic models to characterize the molecular mechanisms, including intraspecies gene/microRNA (miRNA) regulation networks (GRNs), intraspecies protein-protein interaction networks (PPINs), and the interspecies PPIN of the cross-talk GWGEIN. We applied a system identification method and a system order detection scheme to dynamic models to identify the real cross-talk GWGEINs using the microarray data of Mϕs, DCs and Mtb. After identifying the real cross-talk GWGEINs, the principal network projection (PNP) method was employed to construct host-pathogen core networks (HPCNs) between Mϕs vs. Mtb and DCs vs. Mtb during infection process. Thus, we investigated the underlying cross-talk mechanisms between the host and the pathogen to determine how the pathogen counteracts host defense mechanisms in Mϕs and DCs during Mtb H37Rv early infection. Based on our findings, we propose Rv1675c as a potential drug target because of its important defensive role in Mϕs. Furthermore, the membrane essential proteins v1098c, and Rv1696 (or cytoplasm for Rv0667), in Mtb could also be potential drug targets because of their important roles in Mtb survival in both cell types. We also propose the drugs Lopinavir, TMC207, ATSM, and GTSM as potential therapeutic treatments for Mtb infection since they target the above potential drug targets.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
| | - Yun-Lin Lee
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, National Tsing Hua University Hsinchu, Taiwan
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48
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Polena H, Boudou F, Tilleul S, Dubois-Colas N, Lecointe C, Rakotosamimanana N, Pelizzola M, Andriamandimby SF, Raharimanga V, Charles P, Herrmann JL, Ricciardi-Castagnoli P, Rasolofo V, Gicquel B, Tailleux L. Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination. Sci Rep 2016; 6:33162. [PMID: 27616470 PMCID: PMC5018821 DOI: 10.1038/srep33162] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/17/2016] [Indexed: 02/08/2023] Open
Abstract
The mechanisms by which the airborne pathogen Mycobacterium tuberculosis spreads within the lung and leaves its primary niche to colonize other organs, thus inducing extrapulmonary forms of tuberculosis (TB) in humans, remains poorly understood. Herein, we used a transcriptomic approach to investigate the host cell gene expression profile in M. tuberculosis-infected human macrophages (ΜΦ). We identified 33 genes, encoding proteins involved in angiogenesis, for which the expression was significantly modified during infection, and we show that the potent angiogenic factor VEGF is secreted by M. tuberculosis-infected ΜΦ, in an RD1-dependent manner. In vivo these factors promote the formation of blood vessels in murine models of the disease. Inhibiting angiogenesis, via VEGF inactivation, abolished mycobacterial spread from the infection site. In accordance with our in vitro and in vivo results, we show that the level of VEGF in TB patients is elevated and that endothelial progenitor cells are mobilized from the bone marrow. These results strongly strengthen the most recent data suggesting that mycobacteria take advantage of the formation of new blood vessels to disseminate.
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Affiliation(s)
- Helena Polena
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr. Roux, F-75015 Paris, France
| | - Frédéric Boudou
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
| | - Sylvain Tilleul
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
| | - Nicolas Dubois-Colas
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr. Roux, F-75015 Paris, France
| | - Cécile Lecointe
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
| | - Niaina Rakotosamimanana
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France.,Institut Pasteur de Madagascar, Unité des Mycobactéries, Antananarivo, Madagascar
| | - Mattia Pelizzola
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | | | | | - Patricia Charles
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
| | - Jean-Louis Herrmann
- INSERM U1173, UFR Sciences de la Santé Simone Veil, Université Versailles-Saint-Quentin, 78180 Saint-Quentin en Yvelines, France.,Service de Microbiologie, Hôpital Raymond Poincaré, Assistance Publique Hôpitaux de Paris, 92380 Garches, France
| | - Paola Ricciardi-Castagnoli
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Voahangy Rasolofo
- Institut Pasteur de Madagascar, Unité des Mycobactéries, Antananarivo, Madagascar
| | - Brigitte Gicquel
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
| | - Ludovic Tailleux
- Institut Pasteur, Unité de Génétique Mycobactérienne, Paris, France
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49
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Pires D, Marques J, Pombo JP, Carmo N, Bettencourt P, Neyrolles O, Lugo-Villarino G, Anes E. Role of Cathepsins in Mycobacterium tuberculosis Survival in Human Macrophages. Sci Rep 2016; 6:32247. [PMID: 27572605 PMCID: PMC5004184 DOI: 10.1038/srep32247] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/04/2016] [Indexed: 02/07/2023] Open
Abstract
Cathepsins are proteolytic enzymes that function in the endocytic pathway, especially in lysosomes, where they contribute directly to pathogen killing or indirectly, by their involvement in the antigen presentation pathways. Mycobacterium tuberculosis (MTB) is a facultative intracellular pathogen that survives inside the macrophage phagosomes by inhibiting their maturation to phagolysosomes and thus avoiding a low pH and protease-rich environment. We previously showed that mycobacterial inhibition of the proinflammatory transcription factor NF-κB results in impaired delivery of lysosomal enzymes to phagosomes and reduced pathogen killing. Here, we elucidate how MTB also controls cathepsins and their inhibitors, cystatins, at the level of gene expression and proteolytic activity. MTB induced a general down-regulation of cathepsin expression in infected cells, and inhibited IFNγ-mediated increase of cathepsin mRNA. We further show that a decrease in cathepsins B, S and L favours bacterial survival within human primary macrophages. A siRNA knockdown screen of a large set of cathepsins revealed that almost half of these enzymes have a role in pathogen killing, while only cathepsin F coincided with MTB resilience. Overall, we show that cathepsins are important for the control of MTB infection, and as a response, it manipulates their expression and activity to favour its intracellular survival.
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Affiliation(s)
- David Pires
- Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Portugal
| | - Joana Marques
- Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - João Palma Pombo
- Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Nuno Carmo
- Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Portugal
| | - Paulo Bettencourt
- Research Institute for Medicines, iMed-ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Portugal
| | - Olivier Neyrolles
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Geanncarlo Lugo-Villarino
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Elsa Anes
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Portugal
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50
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Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress. Infect Immun 2016; 84:2505-23. [PMID: 27324481 DOI: 10.1128/iai.00072-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/10/2016] [Indexed: 12/27/2022] Open
Abstract
Increasing experimental evidence supports the idea that Mycobacterium tuberculosis has evolved strategies to survive within lysosomes of activated macrophages. To further our knowledge of M. tuberculosis response to the hostile lysosomal environment, we profiled the global transcriptional activity of M. tuberculosis when exposed to the lysosomal soluble fraction (SF) prepared from activated macrophages. Transcriptome sequencing (RNA-seq) analysis was performed using various incubation conditions, ranging from noninhibitory to cidal based on the mycobacterial replication or killing profile. Under inhibitory conditions that led to the absence of apparent mycobacterial replication, M. tuberculosis expressed a unique transcriptome with modulation of genes involved in general stress response, metabolic reprogramming, respiration, oxidative stress, dormancy response, and virulence. The transcription pattern also indicates characteristic cell wall remodeling with the possible outcomes of increased infectivity, intrinsic resistance to antibiotics, and subversion of the host immune system. Among the lysosome-specific responses, we identified the glgE-mediated 1,4 α-glucan synthesis pathway and a defined group of VapBC toxin/anti-toxin systems, both of which represent toxicity mechanisms that potentially can be exploited for killing intracellular mycobacteria. A meta-analysis including previously reported transcriptomic studies in macrophage infection and in vitro stress models was conducted to identify overlapping and nonoverlapping pathways. Finally, the Tap efflux pump-encoding gene Rv1258c was selected for validation. An M. tuberculosis ΔRv1258c mutant was constructed and displayed increased susceptibility to killing by lysosomal SF and the antimicrobial peptide LL-37, as well as attenuated survival in primary murine macrophages and human macrophage cell line THP-1.
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