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Martínez-Pérez A, Estévez O, González-Fernández Á. Contribution and Future of High-Throughput Transcriptomics in Battling Tuberculosis. Front Microbiol 2022; 13:835620. [PMID: 35283833 PMCID: PMC8908424 DOI: 10.3389/fmicb.2022.835620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
While Tuberculosis (TB) infection remains a serious challenge worldwide, big data and “omic” approaches have greatly contributed to the understanding of the disease. Transcriptomics have been used to tackle a wide variety of queries including diagnosis, treatment evolution, latency and reactivation, novel target discovery, vaccine response or biomarkers of protection. Although a powerful tool, the elevated cost and difficulties in data interpretation may hinder transcriptomics complete potential. Technology evolution and collaborative efforts among multidisciplinary groups might be key in its exploitation. Here, we discuss the main fields explored in TB using transcriptomics, and identify the challenges that need to be addressed for a real implementation in TB diagnosis, prevention and therapy.
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Affiliation(s)
- Amparo Martínez-Pérez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - Olivia Estévez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - África González-Fernández
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
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2
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Borah K, Mendum TA, Hawkins ND, Ward JL, Beale MH, Larrouy‐Maumus G, Bhatt A, Moulin M, Haertlein M, Strohmeier G, Pichler H, Forsyth VT, Noack S, Goulding CW, McFadden J, Beste DJV. Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis. Mol Syst Biol 2021; 17:e10280. [PMID: 33943004 PMCID: PMC8094261 DOI: 10.15252/msb.202110280] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
The co-catabolism of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady-state chemostat system. We demonstrate that Mtb efficiently co-metabolises either cholesterol or glycerol, in combination with two-carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.
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Affiliation(s)
- Khushboo Borah
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Tom A Mendum
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Nathaniel D Hawkins
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Jane L Ward
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Michael H Beale
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Gerald Larrouy‐Maumus
- MRC Centre for Molecular Bacteriology and InfectionDepartment of Life SciencesFaculty of Natural SciencesImperial College LondonLondonUK
| | - Apoorva Bhatt
- School of BiosciencesUniversity of BirminghamEdgbastonUK
| | - Martine Moulin
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Michael Haertlein
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Gernot Strohmeier
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
| | - Harald Pichler
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
- Institute of Molecular BiotechnologyNAWI GrazBioTechMed GrazGraz University of TechnologyGrazAustria
| | - V Trevor Forsyth
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
- Faculty of Natural SciencesKeele UniversityStaffordshireUK
| | - Stephan Noack
- Institute of Bio‐ and Geosciences 1: Biotechnology 2Forschungszentrum Jülich GmbHJülichGermany
| | - Celia W Goulding
- Department of Pharmaceutical Sciences & Molecular Biology & BiochemistryUniversity of California IrvineIrvineCAUSA
| | - Johnjoe McFadden
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Dany J V Beste
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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3
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Hamidieh F, Farnia P, Nowroozi J, Farnia P, Velayati AA. An Overview of Genetic Information of Latent Mycobacterium tuberculosis. Tuberc Respir Dis (Seoul) 2020; 84:1-12. [PMID: 33121230 PMCID: PMC7801807 DOI: 10.4046/trd.2020.0116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis has infected more than two billion individuals worldwide, of whom 5%–10% have clinically active disease and 90%–95% remain in the latent stage with a reservoir of viable bacteria in the macrophages for extended periods of time. The tubercle bacilli at this stage are usually called dormant, non-viable, and/or non-culturable microorganisms. The patients with latent bacilli will not have clinical pictures and are not infectious. The infections in about 2%–23% of the patients with latent status become reactivated for various reasons such as cancer, human immunodeficiency virus infection, diabetes, and/or aging. Many studies have examined the mechanisms involved in the latent state of Mycobacterium and showed that latency modified the expression of many genes. Therefore, several mechanisms will change in this bacterium. Hence, this study aimed to briefly examine the genes involved in the latent state as well as the changes that are caused by Mycobacterium tuberculosis. The study also evaluated the relationship between the functions of these genes.
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Affiliation(s)
- Faezeh Hamidieh
- Departement of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamileh Nowroozi
- Departement of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Poopak Farnia
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technology in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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4
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Lee BS, Sviriaeva E, Pethe K. Targeting the cytochrome oxidases for drug development in mycobacteria. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 152:45-54. [PMID: 32081616 DOI: 10.1016/j.pbiomolbio.2020.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/15/2020] [Accepted: 02/06/2020] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis strictly depends on oxygen to multiply, and the terminal oxidases are a vital part of the oxidative phosphorylation pathway. The bacterium possesses two aerobic respiratory branches: a cytochrome bcc-aa3 and a bacteria-specific cytochrome bd oxidase. The identification of small-molecule inhibitors of the cytochrome bcc-aa3 under numerous experimental conditions reflects the essentiality of the pathway for the optimum growth of M. tuberculosis. Recent findings on the biology of the cytochrome bcc-aa3 as well as the report of the first high-resolution structure of a mycobacterial cytochrome bcc-aa3 complex will help in the characterization and further development of potent inhibitors. Although the aerobic cytochrome bd respiratory branch is not strictly essential for growth, the discovery of a strong synthetic lethal interaction with the cytochrome bcc-aa3 placed the cytochrome bd oxidase under the spotlight as an attractive drug target for its synergistic role in potentiating the efficacy of cytochrome bcc-aa3 inhibitors and other drugs targeting oxidative phosphorylation. In this review, we are discussing current knowledge about the two mycobacterial aerobic respiratory branches, their potential as drug targets, as well as potential drawbacks.
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Affiliation(s)
- Bei Shi Lee
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Ekaterina Sviriaeva
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 636921, Singapore.
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5
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Gilbert R, Torres M, Clemens R, Hateley S, Hosamani R, Wade W, Bhattacharya S. Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model. NPJ Microgravity 2020; 6:4. [PMID: 32047838 PMCID: PMC7000411 DOI: 10.1038/s41526-019-0091-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022] Open
Abstract
While it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but the increased virulence phenotype of S. marcescens did not persist after the bacterial cultures were passaged on the ground. Increased virulence was also observed in bacteria that were grown in simulated microgravity conditions on the ground using the rotating wall vessel. Increased virulence of the space-flown bacteria was similar in magnitude between wild-type flies and those that were mutants for the well-characterized immune pathways Imd and Toll, suggesting that changes to the host immune system after infection are likely not a major factor contributing towards increased susceptibility of ground-reared flies infected with space-flown bacteria. Characterization of the bacteria shows that at later timepoints spaceflight bacteria grew at a greater rate than ground controls in vitro, and in the host. These results suggest complex physiological changes occurring in pathogenic bacteria in space environments, and there may be novel mechanisms mediating these physiological effects that need to be characterized.
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Affiliation(s)
- Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - Medaya Torres
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Rachel Clemens
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Shannon Hateley
- 3Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Ravikumar Hosamani
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - William Wade
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
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Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions. Microbiol Spectr 2017; 5. [PMID: 28597820 DOI: 10.1128/microbiolspec.tbtb2-0014-2016] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.
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7
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Mawatwal S, Behura A, Ghosh A, Kidwai S, Mishra A, Deep A, Agarwal S, Saha S, Singh R, Dhiman R. Calcimycin mediates mycobacterial killing by inducing intracellular calcium-regulated autophagy in a P2RX7 dependent manner. Biochim Biophys Acta Gen Subj 2017; 1861:3190-3200. [PMID: 28935606 DOI: 10.1016/j.bbagen.2017.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 12/19/2022]
Abstract
Phenotypic screening led to the identification of calcimycin as a potent inhibitor of Mycobacterium bovis BCG (M. bovis BCG) growth in vitro and in THP-1 cells. In the present study, we aim to decipher the mechanism of antimycobacterial activity of calcimycin. We noticed that treatment with calcimycin led to up-regulation of different autophagy markers like Beclin-1, autophagy-related gene (Atg) 7, Atg 3 and enhanced microtubule-associated protein 1A/1B-light chain 3-I (LC3-I) to LC3-II conversion in macrophages. This calcimycin-mediated killing of intracellular M. smegmatis and M. bovis BCG was abrogated in the presence of 3-methyladenine (3-MA). We also demonstrate that calcimycin binding with purinergic receptor P2X7 (P2RX7) led to increase in intracellular calcium level that regulates the extracellular release of ATP. ATP was able to regulate calcimycin-induced autophagy through P2RX7 in an autocrine fashion. Blocking of either P2RX7 expression by 1-[N,O-bis(5-Isoquinolinesulfonyl)-N-methyl-l-tyrosyl]-4-phenylpiperazine (KN-62) or reducing intracellular calcium levels by 1,2-Bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetra (acetoxy-methyl) ester (BAPTA-AM) abrogated the antimycobacterial activity of calcimycin. Taken together, these results showed that calcimycin exerts its antimycobacterial effect by regulating intracellular calcium-dependent ATP release that induces autophagy in a P2RX7 dependent manner.
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Affiliation(s)
- Shradha Mawatwal
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abhirupa Ghosh
- Bioinformatics Centre, Bose Institute, Kolkata 700054, West Bengal, India
| | - Saqib Kidwai
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 4, Faridabad 121001, Haryana, India
| | - Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Amar Deep
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 4, Faridabad 121001, Haryana, India
| | - Sakshi Agarwal
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 4, Faridabad 121001, Haryana, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata 700054, West Bengal, India
| | - Ramandeep Singh
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 4, Faridabad 121001, Haryana, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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8
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Yan S, Xu M, Wang R, Li Q, Yu Z, Xie J. Overexpression of Rv2788 increases mycobacterium stresses survival. Microbiol Res 2016; 195:51-59. [PMID: 28024526 DOI: 10.1016/j.micres.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis-one of the most devastating infectious diseases, is a successful intracellular pathogen capable of surviving diverse stresses. Unveiling the molecular mechanisms governing this superior adaptation will inspire better control measures against tuberculosis. To define the role of Rv2788, a manganese-dependent transcriptional repressor, M.smegmatis was used as the host strain for heterologous expression Rv2788. Rv2788 can significantly change the colony morphology and fatty acids and permeability of cell wall, enhance the growth of the recombinants and resistance to diverse stresses, such as hydrogen peroxide (H₂O₂), diamide exposure, surface stress, acidic condition, multiple antibiotics treatment including chloramphenicol, vancomycin and amikacin. The dysregulation of the target genes of Rv2788, such as whiB1 and lexA, might underpin such phenotypes. The results implicate important roles of Rv2788 in the survival of Mycobacterium under stresses, and might represent ideal novel antibiotics target candidate.
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Affiliation(s)
- Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengmeng Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
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9
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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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10
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Abstract
Mycobacteria inhabit a wide range of intracellular and extracellular environments. Many of these environments are highly dynamic and therefore mycobacteria are faced with the constant challenge of redirecting their metabolic activity to be commensurate with either replicative growth or a non-replicative quiescence. A fundamental feature in this adaptation is the ability of mycobacteria to respire, regenerate reducing equivalents and generate ATP via oxidative phosphorylation. Mycobacteria harbor multiple primary dehydrogenases to fuel the electron transport chain and two terminal respiratory oxidases, an aa3 -type cytochrome c oxidase and cytochrome bd-type menaquinol oxidase, are present for dioxygen reduction coupled to the generation of a protonmotive force. Hypoxia leads to the downregulation of key respiratory complexes, but the molecular mechanisms regulating this expression are unknown. Despite being obligate aerobes, mycobacteria have the ability to metabolize in the absence of oxygen and a number of reductases are present to facilitate the turnover of reducing equivalents under these conditions (e.g. nitrate reductase, succinate dehydrogenase/fumarate reductase). Hydrogenases and ferredoxins are also present in the genomes of mycobacteria suggesting the ability of these bacteria to adapt to an anaerobic-type of metabolism in the absence of oxygen. ATP synthesis by the membrane-bound F1FO-ATP synthase is essential for growing and non-growing mycobacteria and the enzyme is able to function over a wide range of protonmotive force values (aerobic to hypoxic). The discovery of lead compounds that target respiration and oxidative phosphorylation in Mycobacterium tuberculosis highlights the importance of this area for the generation of new front line drugs to combat tuberculosis.
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11
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Rienksma RA, Suarez-Diez M, Spina L, Schaap PJ, Martins dos Santos VAP. Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets. Semin Immunol 2014; 26:610-22. [PMID: 25453232 DOI: 10.1016/j.smim.2014.09.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 12/28/2022]
Abstract
Systems-level metabolic network reconstructions and the derived constraint-based (CB) mathematical models are efficient tools to explore bacterial metabolism. Approximately one-fourth of the Mycobacterium tuberculosis (Mtb) genome contains genes that encode proteins directly involved in its metabolism. These represent potential drug targets that can be systematically probed with CB models through the prediction of genes essential (or the combination thereof) for the pathogen to grow. However, gene essentiality depends on the growth conditions and, so far, no in vitro model precisely mimics the host at the different stages of mycobacterial infection, limiting model predictions. These limitations can be circumvented by combining expression data from in vivo samples with a validated CB model, creating an accurate description of pathogen metabolism in the host. To this end, we present here a thoroughly curated and extended genome-scale CB metabolic model of Mtb quantitatively validated using 13C measurements. We describe some of the efforts made in integrating CB models and high-throughput data to generate condition specific models, and we will discuss challenges ahead. This knowledge and the framework herein presented will enable to identify potential new drug targets, and will foster the development of optimal therapeutic strategies.
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MESH Headings
- Antitubercular Agents/therapeutic use
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Carbon Isotopes
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Gene Regulatory Networks
- Genome, Bacterial
- Host-Pathogen Interactions
- Humans
- Metabolic Networks and Pathways/genetics
- Models, Statistical
- Molecular Targeted Therapy
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/metabolism
- Systems Biology
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/metabolism
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Multidrug-Resistant/pathology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/metabolism
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
| | - Lucie Spina
- Centre National de la Rescherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (UMR 5089), Department of Tuberculosis and Infection Biology and Université de Toulouse (Université Paul Sabatier, Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
| | - Vitor A P Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; Lifeglimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany.
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12
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Salina EG, Waddell SJ, Hoffmann N, Rosenkrands I, Butcher PD, Kaprelyants AS. Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states. Open Biol 2014; 4:140106. [PMID: 25320096 PMCID: PMC4221891 DOI: 10.1098/rsob.140106] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022] Open
Abstract
Dormancy in non-sporulating bacteria is an interesting and underexplored phenomenon with significant medical implications. In particular, latent tuberculosis may result from the maintenance of Mycobacterium tuberculosis bacilli in non-replicating states in infected individuals. Uniquely, growth of M. tuberculosis in aerobic conditions in potassium-deficient media resulted in the generation of bacilli that were non-culturable (NC) on solid media but detectable in liquid media. These bacilli were morphologically distinct and tolerant to cell-wall-targeting antimicrobials. Bacterial counts on solid media quickly recovered after washing and incubating bacilli in fresh resuscitation media containing potassium. This resuscitation of growth occurred too quickly to be attributed to M. tuberculosis replication. Transcriptomic and proteomic profiling through adaptation to, and resuscitation from, this NC state revealed a switch to anaerobic respiration and a shift to lipid and amino acid metabolism. High concordance with mRNA signatures derived from M. tuberculosis infection models suggests that analogous NC mycobacterial phenotypes may exist during disease and may represent unrecognized populations in vivo. Resuscitation of NC bacilli in potassium-sufficient media was characterized by time-dependent activation of metabolic pathways in a programmed series of processes that probably transit bacilli through challenging microenvironments during infection.
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Affiliation(s)
- Elena G Salina
- Institution of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry RAS, Moscow, Russia
| | - Simon J Waddell
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Nadine Hoffmann
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Philip D Butcher
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Arseny S Kaprelyants
- Institution of the Russian Academy of Sciences A.N. Bach Institute of Biochemistry RAS, Moscow, Russia
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13
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Koul A, Vranckx L, Dhar N, Göhlmann HWH, Özdemir E, Neefs JM, Schulz M, Lu P, Mørtz E, McKinney JD, Andries K, Bald D. Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism. Nat Commun 2014; 5:3369. [PMID: 24569628 PMCID: PMC3948051 DOI: 10.1038/ncomms4369] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/03/2014] [Indexed: 01/07/2023] Open
Abstract
Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multidrug-resistant tuberculosis in decades. Though BDQ has shown excellent efficacy in clinical trials, its early bactericidal activity during the first week of chemotherapy is minimal. Here, using microfluidic devices and time-lapse microscopy of Mycobacterium tuberculosis, we confirm the absence of significant bacteriolytic activity during the first 3-4 days of exposure to BDQ. BDQ-induced inhibition of ATP synthesis leads to bacteriostasis within hours after drug addition. Transcriptional and proteomic analyses reveal that M. tuberculosis responds to BDQ by induction of the dormancy regulon and activation of ATP-generating pathways, thereby maintaining bacterial viability during initial drug exposure. BDQ-induced bacterial killing is significantly enhanced when the mycobacteria are grown on non-fermentable energy sources such as lipids (impeding ATP synthesis via glycolysis). Our results show that BDQ exposure triggers a metabolic remodelling in mycobacteria, thereby enabling transient bacterial survival.
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Affiliation(s)
- Anil Koul
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Luc Vranckx
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Neeraj Dhar
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Hinrich W H Göhlmann
- CREATe, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Emre Özdemir
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Jean-Marc Neefs
- CREATe, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Melanie Schulz
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ping Lu
- Department of Molecular Cell Biology, AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ejvind Mørtz
- Alphalyse A/S, Unsbjergvej 4, DK-5220 Odense SØ, Denmark
| | - John D McKinney
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Koen Andries
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Dirk Bald
- Department of Molecular Cell Biology, AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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14
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Berney M, Cook GM. Respiration and Oxidative Phosphorylation in Mycobacteria. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Cunningham-Bussel A, Zhang T, Nathan CF. Nitrite produced by Mycobacterium tuberculosis in human macrophages in physiologic oxygen impacts bacterial ATP consumption and gene expression. Proc Natl Acad Sci U S A 2013; 110:E4256-65. [PMID: 24145454 PMCID: PMC3831502 DOI: 10.1073/pnas.1316894110] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In high enough concentrations, such as produced by inducible nitric oxide synthase (iNOS), reactive nitrogen species (RNS) can kill Mycobacterium tuberculosis (Mtb). Lesional macrophages in macaques and humans with tuberculosis express iNOS, and mice need iNOS to avoid succumbing rapidly to tuberculosis. However, Mtb's own ability to produce RNS is rarely considered, perhaps because nitrate reduction to nitrite is only prominent in axenic Mtb cultures at oxygen tensions ≤1%. Here we found that cultures of Mtb-infected human macrophages cultured at physiologic oxygen tensions produced copious nitrite. Surprisingly, the nitrite arose from the Mtb, not the macrophages. Mtb responded to nitrite by ceasing growth; elevating levels of ATP through reduced consumption; and altering the expression of 120 genes associated with adaptation to acid, hypoxia, nitric oxide, oxidative stress, and iron deprivation. The transcriptomic effect of endogenous nitrite was distinct from that of nitric oxide. Thus, whether or not Mtb is hypoxic, the host expresses iNOS, or hypoxia impairs the action of iNOS, Mtb in vivo is likely to encounter RNS by producing nitrite. Endogenous nitrite may slow Mtb's growth and prepare it to resist host stresses while the pathogen waits for immunopathology to promote its transmission.
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Affiliation(s)
| | - Tuo Zhang
- Department of Microbiology and Immunology and
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, NY 10065
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16
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Williams KJ, Bryant WA, Jenkins VA, Barton GR, Witney AA, Pinney JW, Robertson BD. Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules. BMC Genomics 2013; 14:436. [PMID: 23819599 PMCID: PMC3706326 DOI: 10.1186/1471-2164-14-436] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/20/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. RESULTS A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. CONCLUSIONS Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments.
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Affiliation(s)
- Kerstin J Williams
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London SW7 2AZ, UK
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17
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Cox RA, Garcia MJ. Adaptation of mycobacteria to growth conditions: a theoretical analysis of changes in gene expression revealed by microarrays. PLoS One 2013; 8:e59883. [PMID: 23593152 PMCID: PMC3625197 DOI: 10.1371/journal.pone.0059883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/19/2013] [Indexed: 11/19/2022] Open
Abstract
Background Microarray analysis is a powerful technique for investigating changes in gene expression. Currently, results (r-values) are interpreted empirically as either unchanged or up- or down-regulated. We now present a mathematical framework, which relates r-values to the macromolecular properties of population-average cells. The theory is illustrated by the analysis of published data for two species; namely, Mycobacterium bovis BCG Pasteur and Mycobacterium smegmatis mc2 155. Each species was grown in a chemostat at two different growth rates. Application of the theory reveals the growth rate dependent changes in the mycobacterial proteomes. Principal Findings The r-value r(i) of any ORF (ORF(i)) encoding protein p(i) was shown to be equal to the ratio of the concentrations of p(i) and so directly proportional to the ratio of the numbers of copies of p(i) per population-average cells of the two cultures. The proportionality constant can be obtained from the ratios DNA: RNA: protein. Several subgroups of ORFs were identified because they shared a particular r-value. Histograms of the number of ORFs versus the expression ratio were simulated by combining the particular r-values of several subgroups of ORFs. The largest subgroup was ORF(j) (r(j) = 1.00± SD) which was estimated to comprise respectively 59% and 49% of ORFs of M. bovis BCG Pasteur and M. smegmatis mc2 155. The standard deviations reflect the properties of the cDNA preparations investigated. Significance The analysis provided a quantitative view of growth rate dependent changes in the proteomes of the mycobacteria studied. The majority of the ORFs were found to be constitutively expressed. In contrast, the protein compositions of the outer permeability barriers and cytoplasmic membranes were found to be dependent on growth rate; thus illustrating the response of bacteria to their environment. The theoretical approach applies to any cultivatable bacterium under a wide range of growth conditions.
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Affiliation(s)
- Robert Ashley Cox
- Division of Mycobacterial Research, National Institute for Medical Research, London, United Kingdom.
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18
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Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PLoS Pathog 2012; 8:e1002769. [PMID: 22737072 PMCID: PMC3380936 DOI: 10.1371/journal.ppat.1002769] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 05/07/2012] [Indexed: 12/27/2022] Open
Abstract
Intracellular pathogens such as Mycobacterium tuberculosis have evolved strategies for coping with the pressures encountered inside host cells. The ability to coordinate global gene expression in response to environmental and internal cues is one key to their success. Prolonged survival and replication within macrophages, a key virulence trait of M. tuberculosis, requires dynamic adaptation to diverse and changing conditions within its phagosomal niche. However, the physiological adaptations during the different phases of this infection process remain poorly understood. To address this knowledge gap, we have developed a multi-tiered approach to define the temporal patterns of gene expression in M. tuberculosis in a macrophage infection model that extends from infection, through intracellular adaptation, to the establishment of a productive infection. Using a clock plasmid to measure intracellular replication and death rates over a 14-day infection and electron microscopy to define bacterial integrity, we observed an initial period of rapid replication coupled with a high death rate. This was followed by period of slowed growth and enhanced intracellular survival, leading finally to an extended period of net growth. The transcriptional profiles of M. tuberculosis reflect these physiological transitions as the bacterium adapts to conditions within its host cell. Finally, analysis with a Transcriptional Regulatory Network model revealed linked genetic networks whereby M. tuberculosis coordinates global gene expression during intracellular survival. The integration of molecular and cellular biology together with transcriptional profiling and systems analysis offers unique insights into the host-driven responses of intracellular pathogens such as M. tuberculosis. The impact of Mycobacterium tuberculosis on global health is undeniable, with ∼2 million deaths and ∼9 million new cases of tuberculosis each year. A key to the success of M. tuberculosis as a persistent, intracellular pathogen is its ability to survive for extended periods within professional phagocytes. Sustained growth within macrophage phagosomes requires avoiding or resisting antimicrobial mechanisms and adapting to replicate in a stressful, nutrient-restricted environment. Our understanding of the survival strategies, metabolism, and physiology of M. tuberculosis during intracellular growth remains incomplete. We employed multi-disciplinary approaches to gain new insights into adaptive responses that M. tuberculosis mobilizes to secure a productive infection. We simultaneously quantified replication and death rates, used electron microscopy to evaluate bacterial integrity, and determined the temporal changes in bacterial gene expression during a 14-day infection. By overlaying this temporal transcriptome dataset onto an extended Transcriptional Regulatory Network model, we identified regulatory pathways, stress responses, and metabolic adaptations activated during key physiological transitions over the 14 days of infection.
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19
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Mycobacterium tuberculosis protein kinase K enables growth adaptation through translation control. J Bacteriol 2012; 194:4184-96. [PMID: 22661693 DOI: 10.1128/jb.00585-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis serine/threonine protein kinases (STPKs) are responsible for orchestrating critical metabolic and physiological changes that dictate mycobacterial growth adaptation. Previously, we established that PknK participates in regulatory pathways that slow the growth of M. tuberculosis in a variety of in vitro stress environments and during persistent infection in mice. In the present study, we have elaborated on the mechanism of PknK-mediated regulation. Through transcription profiling of wild-type H37Rv and a ΔpknK mutant strain during logarithmic and stationary growth phases, we determined that PknK regulates the expression of a large subset of tRNA genes so that regulation is synchronized with growth phase and cellular energy status. Elevated levels of wild-type M. tuberculosis PknK (PknK(Mtb)), but not phosphorylation-defective PknK(Mtb), in Mycobacterium smegmatis cause significant retardation of the growth rate and altered colony morphology. We investigated a role for PknK in translational control and established that PknK directs the inhibition of in vitro transcription and translation processes in a phosphorylation-dependent manner. Increasing concentrations of ATP or PknK exert cooperative effects and enhance the inhibitory function of PknK. Furthermore, truncation and mutational analyses of PknK revealed that PknK is autoregulated via intramolecular interactions with its C-terminal region. Significantly, the invariant lysine 55 residue was only essential for activity in the full-length PknK protein, and the truncated mutant proteins were active. A model for PknK autoregulation is proposed and discussed.
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20
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Berney M, Weimar MR, Heikal A, Cook GM. Regulation of proline metabolism in mycobacteria and its role in carbon metabolism under hypoxia. Mol Microbiol 2012; 84:664-81. [PMID: 22507203 DOI: 10.1111/j.1365-2958.2012.08053.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genes with a role in proline metabolism are strongly expressed when mycobacterial cells are exposed to nutrient starvation and hypoxia. Here we show that proline metabolism in mycobacteria is mediated by the monofunctional enzymes Δ(1) -pyrroline-5-carboxylate dehydrogenase (PruA) and proline dehydrogenase (PruB). Proline metabolism was controlled by a unique membrane-associated DNA-binding protein PruC. Under hypoxia, addition of proline led to higher biomass production than in the absence of proline despite excess carbon and nitrogen. To identify the mechanism responsible for this enhanced growth, microarray analysis of wild-type Mycobacterium smegmatis versus pruC mutant was performed. Expression of the DNA repair machinery and glyoxalases was increased in the pruC mutant. Glyoxalases are proposed to degrade methylglyoxal, a toxic metabolite produced by various bacteria due to an imbalance in intermediary metabolism, suggesting the pruC mutant was under methylglyoxal stress. Consistent with this notion, pruB and pruC mutants were hypersensitive to methylglyoxal. Δ(1) -pyrroline-5-carboxylate is reported to react with methylglyoxal to form non-toxic 2-acetyl-1-pyrroline, thus providing a link between proline metabolism and methylglyoxal detoxification. In support of this mechanism, we show that proline metabolism protects mycobacterial cells from methylglyoxal toxicity and that functional proline dehydrogenase, but not Δ(1) -pyrroline-5-carboxylate dehydrogenase, is essential for this protective effect.
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Affiliation(s)
- Michael Berney
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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21
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Mukhopadhyay S, Nair S, Ghosh S. Pathogenesis in tuberculosis: transcriptomic approaches to unraveling virulence mechanisms and finding new drug targets. FEMS Microbiol Rev 2011; 36:463-85. [PMID: 22092372 DOI: 10.1111/j.1574-6976.2011.00302.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/31/2011] [Accepted: 08/05/2011] [Indexed: 01/12/2023] Open
Abstract
Tuberculosis (TB) remains a major health problem worldwide. Attempts to control this disease have proved difficult owing to our poor understanding of the pathobiology of Mycobacterium tuberculosis and the emergence of strains that are resistant to multiple drugs currently available for treatment. Genome-wide expression profiling has provided new insight into the transcriptome signatures of the bacterium during infection, notably of macrophages and dendritic cells. These data indicate that M. tuberculosis expresses numerous genes to evade the host immune responses, to suit its intracellular life style, and to respond to various antibiotic drugs. Among the intracellularly induced genes, several have functions in lipid metabolism, cell wall synthesis, iron uptake, oxidative stress resistance, protein secretion, or inhibition of apoptosis. Herein we review these findings and discuss possible ways to exploit the data to understand the complex etiology of TB and to find new effective drug targets.
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Affiliation(s)
- Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India.
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22
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The Mycobacterium tuberculosis cytochromes P450: physiology, biochemistry & molecular intervention. Future Med Chem 2011; 2:1339-53. [PMID: 21426022 DOI: 10.4155/fmc.10.216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The human pathogen Mycobacterium tuberculosis (Mtb) encodes 20 cytochrome P450 (P450) enzymes. Gene essentiality for viability or host infection was demonstrated for Mtb P450s CYP128, CYP121 and CYP125. Structure/function studies on Mtb P450s revealed key roles contributing to bacterial virulence and persistence in the host. Various azole-class drugs bind with high affinity to the Mtb P450 heme and are potent Mtb antibiotics. This paper reviews the current understanding of the biochemistry of Mtb P450s, their interactions with azoles and their potential as novel Mtb drug targets. Mtb multidrug resistance is widespread and novel therapeutics are desperately needed. Simultaneous drug targeting of several Mtb P450s crucial to bacterial viability/persistence could offer a new route to effective antibiotics and minimize the development of drug resistance.
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23
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Beste DJV, Bonde B, Hawkins N, Ward JL, Beale MH, Noack S, Nöh K, Kruger NJ, Ratcliffe RG, McFadden J. ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathog 2011; 7:e1002091. [PMID: 21814509 PMCID: PMC3141028 DOI: 10.1371/journal.ppat.1002091] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 04/13/2011] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis requires the enzyme isocitrate lyase (ICL) for growth and virulence in vivo. The demonstration that M. tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme which extends beyond fat metabolism. As isocitrate lyase is a potential drug target elucidating the role of this enzyme is of importance; however, the role of isocitrate lyase has never been investigated at the level of in vivo fluxes. Here we show that deletion of one of the two icl genes impairs the replication of Mycobacterium bovis BCG at slow growth rate in a carbon limited chemostat. In order to further understand the role of isocitrate lyase in the central metabolism of mycobacteria the effect of growth rate on the in vivo fluxes was studied for the first time using ¹³C-metabolic flux analysis (MFA). Tracer experiments were performed with steady state chemostat cultures of BCG or M. tuberculosis supplied with ¹³C labeled glycerol or sodium bicarbonate. Through measurements of the ¹³C isotopomer labeling patterns in protein-derived amino acids and enzymatic activity assays we have identified the activity of a novel pathway for pyruvate dissimilation. We named this the GAS pathway because it utilizes the Glyoxylate shunt and Anapleurotic reactions for oxidation of pyruvate, and Succinyl CoA synthetase for the generation of succinyl CoA combined with a very low flux through the succinate--oxaloacetate segment of the tricarboxylic acid cycle. We confirm that M. tuberculosis can fix carbon from CO₂ into biomass. As the human host is abundant in CO₂ this finding requires further investigation in vivo as CO₂ fixation may provide a point of vulnerability that could be targeted with novel drugs. This study also provides a platform for further studies into the metabolism of M. tuberculosis using ¹³C-MFA.
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Affiliation(s)
- Dany J. V. Beste
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, United Kingdom
| | - Bhushan Bonde
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, United Kingdom
| | - Nathaniel Hawkins
- Rothamsted Research, National Centre for Plant and Microbial Metabolomics, Harpenden, Herts, United Kingdom
| | - Jane L. Ward
- Rothamsted Research, National Centre for Plant and Microbial Metabolomics, Harpenden, Herts, United Kingdom
| | - Michael H. Beale
- Rothamsted Research, National Centre for Plant and Microbial Metabolomics, Harpenden, Herts, United Kingdom
| | - Stephan Noack
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences 1: Biotechnology 2, Jülich, Germany
| | - Katharina Nöh
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences 1: Biotechnology 2, Jülich, Germany
| | - Nicholas J. Kruger
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Johnjoe McFadden
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, United Kingdom
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24
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Bonde BK, Beste DJV, Laing E, Kierzek AM, McFadden J. Differential producibility analysis (DPA) of transcriptomic data with metabolic networks: deconstructing the metabolic response of M. tuberculosis. PLoS Comput Biol 2011; 7:e1002060. [PMID: 21738454 PMCID: PMC3127818 DOI: 10.1371/journal.pcbi.1002060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 04/02/2011] [Indexed: 11/27/2022] Open
Abstract
A general paucity of knowledge about the metabolic state of Mycobacterium tuberculosis within the host environment is a major factor impeding development of novel drugs against tuberculosis. Current experimental methods do not allow direct determination of the global metabolic state of a bacterial pathogen in vivo, but the transcriptional activity of all encoded genes has been investigated in numerous microarray studies. We describe a novel algorithm, Differential Producibility Analysis (DPA) that uses a metabolic network to extract metabolic signals from transcriptome data. The method utilizes Flux Balance Analysis (FBA) to identify the set of genes that affect the ability to produce each metabolite in the network. Subsequently, Rank Product Analysis is used to identify those metabolites predicted to be most affected by a transcriptional signal. We first apply DPA to investigate the metabolic response of E. coli to both anaerobic growth and inactivation of the FNR global regulator. DPA successfully extracts metabolic signals that correspond to experimental data and provides novel metabolic insights. We next apply DPA to investigate the metabolic response of M. tuberculosis to the macrophage environment, human sputum and a range of in vitro environmental perturbations. The analysis revealed a previously unrecognized feature of the response of M. tuberculosis to the macrophage environment: a down-regulation of genes influencing metabolites in central metabolism and concomitant up-regulation of genes that influence synthesis of cell wall components and virulence factors. DPA suggests that a significant feature of the response of the tubercle bacillus to the intracellular environment is a channeling of resources towards remodeling of its cell envelope, possibly in preparation for attack by host defenses. DPA may be used to unravel the mechanisms of virulence and persistence of M. tuberculosis and other pathogens and may have general application for extracting metabolic signals from other “-omics” data. Mycobacterium tuberculosis causes tuberculosis, leading to millions of deaths each year. Treatment takes 6 months or more, leading to lack of patient compliance and emergence of drug resistance. The pathogen takes so long to kill because it is able to enter a state of dormancy/latency/persistence where it is insensitive to drugs. There is an urgent unmet need to develop new antibiotics that target dormant/persistent/latent organisms. Most antibiotics target metabolic processes but it is difficult to examine the metabolism of the pathogen directly inside the host or host cells. It is of course possible to identify which genes are active by transcriptomics but there are no established and validated methods to use transcriptome data to predict metabolism. We here describe the development of such a method, called DPA. We validate the method with E. coli data and then use DPA to predict the metabolism of the TB pathogen growing inside host cells and from TB sputum samples. DPA demonstrates that the TB bacillus remodels its cells in response to the host environment, possibly to increase the pathogen's defenses against the host immune system. Discovering the metabolic details of this remodeling may identify vulnerable metabolic reactions that may be targeted with new TB drugs.
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Affiliation(s)
- Bhushan K. Bonde
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Dany J. V. Beste
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Emma Laing
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Andrzej M. Kierzek
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Johnjoe McFadden
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- * E-mail:
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25
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Abstract
Batch cultures have predominately been used for the study of physiology and gene expression in mycobacteria. This chapter describes the assembly of chemostats and the methodology that is being used for growing Mycobacterium tuberculosis in continuous culture, which provides the greatest control over experimental conditions. It is difficult to determine the underlying genetic changes that enable M. tuberculosis to adapt to the host environment, but in vitro experiments aid the interpretation of gene expression profiles of the bacillus in vivo. Selecting relevant host conditions for study presents a major challenge. Oxygen availability has been identified as an important environmental stimulus and is a simple parameter to adjust and monitor. Described here are continuous culture methods to determine the response of M. tuberculosis to low oxygen environments.
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Affiliation(s)
- Joanna Bacon
- TB Research, Health Protection Agency, CEPR, Porton Down, Salisbury SP4 OJG, UK.
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26
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Bull AT. The renaissance of continuous culture in the post-genomics age. J Ind Microbiol Biotechnol 2010; 37:993-1021. [PMID: 20835748 DOI: 10.1007/s10295-010-0816-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/11/2010] [Indexed: 01/08/2023]
Abstract
The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent CT27NJ, UK.
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Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. J Bacteriol 2010; 192:4348-56. [PMID: 20585061 DOI: 10.1128/jb.00454-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bacterial chromosomally encoded type II toxin-antitoxin (TA) loci may be involved in survival upon exposure to stress and have been linked to persistence and dormancy. Therefore, understanding the role of the numerous predicted TA loci within the human pathogen Mycobacterium tuberculosis has become a topic of great interest. Antitoxin proteins are known to autoregulate TA expression under normal growth conditions, but it is unknown whether they have a more global role in transcriptional regulation. This study focuses on analyzing the regulatory role of the M. tuberculosis HigA antitoxin. We first show that the M. tuberculosis higBA locus is functional within its native organism, as higB, higA, and Rv1957 were successfully deleted from the genome together while the deletion of higA alone was not possible. The effects of higB-Rv1957 deletion on M. tuberculosis global gene expression were investigated, and a number of potential HigA-regulated genes were identified. Transcriptional fusion and protein-DNA-binding assays were utilized to confirm the direct role of HigA in Rv1954A-Rv1957 repression, and the M. tuberculosis HigA DNA-binding motif was defined as ATATAGG(N(6))CCTATAT. As HigA failed to bind to the next-most-closely related motif within the M. tuberculosis genome, HigA may not directly regulate any other genes in addition to its own operon.
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Malhotra V, Arteaga-Cortés LT, Clay G, Clark-Curtiss JE. Mycobacterium tuberculosis protein kinase K confers survival advantage during early infection in mice and regulates growth in culture and during persistent infection: implications for immune modulation. MICROBIOLOGY-SGM 2010; 156:2829-2841. [PMID: 20522497 PMCID: PMC3068690 DOI: 10.1099/mic.0.040675-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis serine/threonine protein kinases (STPKs) are key regulators of growth and metabolism; however, evidence for their roles in virulence is limited. In a preliminary screen based on comparative expression between strains H37Rv and H37Ra, six STPK genes, pknD, pknG, pknH, pknJ, pknK and pknL, showed higher expression in H37Rv. In the second screen, STPK expression was analysed in H37Rv-infected human macrophages. Interestingly, significant expression of pknK was detected only at 18 h post-infection, suggesting its involvement in early infection events. We have investigated the roles of PknK in vitro and in vivo. PknK levels were induced under stationary phase and deletion of pknK resulted in increased resistance of the mutant to acidic pH, hypoxia, oxidative and stationary-phase stresses in vitro. These results, together with the increased survival of the ΔpknK strain during persistent infection in mice, reveal a role for PknK in adaptive mechanisms that slow the growth of mycobacteria. A novel finding of this study was the inhibition of growth of ΔpknK strain during acute infection in mice that correlated with the significant upregulation of tumour necrosis factor as well as the simultaneous downregulation of interleukin-12p40, interferon-γ and induced nitric oxide synthase transcripts. Finally, we provide evidence for the localization of PknK during infection and discuss its implications in pathogenesis.
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Affiliation(s)
- Vandana Malhotra
- Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
| | - Lourdes T Arteaga-Cortés
- Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
| | - Gwendolyn Clay
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Josephine E Clark-Curtiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
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Chowdhury RP, Saraswathi R, Chatterji D. Mycobacterial stress regulation: The Dps "twin sister" defense mechanism and structure-function relationship. IUBMB Life 2010; 62:67-77. [PMID: 20014234 DOI: 10.1002/iub.285] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this work, we have tried to emphasize the connection between mycobacterial growth and regulation of gene expression. Utilization of multiple carbon sources and diauxic growth helps bacteria to regulate gene expression at an optimum level so that the inhospitable conditions encountered during nutrient depletion can be circumvented. These aspects will be discussed with respect to mycobacterial growth in subsequent sections. Identification and characterization of genes induced under such conditions is helpful to understand the physiology of the bacterium. Although it is necessary to compare the total expression profile of proteins as they transit from vegetative growth to stationary phase, at times a lot of insights can be deciphered from the expression pattern of one or two proteins. We have compared the protein expression and sigma factor selectivity of two such proteins in M. smegmatis to understand the differential regulation of genes playing diverse function in the same species. Some newer insights on the structure and function of one of the Dps proteins are also explained.
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Abstract
Transcriptional profiling has revealed that Mycobacterium tuberculosis adapts both its metabolic and respiratory states during infection, utilising lipids as a carbon source and switching to alternative electron acceptors. These global gene expression datasets may be exploited to identify virulence determinants and to screen for new targets for rational drug design. Characterising the changing physiological predicament of distinct M. tb populations during infection will help expose the fundamental biology of M. tb highlighting mechanisms that influence tuberculosis pathogenicity.
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Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS One 2010; 5:e8614. [PMID: 20062806 PMCID: PMC2799521 DOI: 10.1371/journal.pone.0008614] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 12/10/2009] [Indexed: 12/27/2022] Open
Abstract
Mycobacteria are a group of obligate aerobes that require oxygen for growth, but paradoxically have the ability to survive and metabolize under hypoxia. The mechanisms responsible for this metabolic plasticity are unknown. Here, we report on the adaptation of Mycobacterium smegmatis to slow growth rate and hypoxia using carbon-limited continuous culture. When M. smegmatis is switched from a 4.6 h to a 69 h doubling time at a constant oxygen saturation of 50%, the cells respond through the down regulation of respiratory chain components and the F1Fo-ATP synthase, consistent with the cells lower demand for energy at a reduced growth rate. This was paralleled by an up regulation of molecular machinery that allowed more efficient energy generation (i.e. Complex I) and the use of alternative electron donors (e.g. hydrogenases and primary dehydrogenases) to maintain the flow of reducing equivalents to the electron transport chain during conditions of severe energy limitation. A hydrogenase mutant showed a 40% reduction in growth yield highlighting the importance of this enzyme in adaptation to low energy supply. Slow growing cells at 50% oxygen saturation subjected to hypoxia (0.6% oxygen saturation) responded by switching on oxygen scavenging cytochrome bd, proton-translocating cytochrome bc1-aa3 supercomplex, another putative hydrogenase, and by substituting NAD+-dependent enzymes with ferredoxin-dependent enzymes thus highlighting a new pattern of mycobacterial adaptation to hypoxia. The expression of ferredoxins and a hydrogenase provides a potential conduit for disposing of and transferring electrons in the absence of exogenous electron acceptors. The use of ferredoxin-dependent enzymes would allow the cell to maintain a high carbon flux through its central carbon metabolism independent of the NAD+/NADH ratio. These data demonstrate the remarkable metabolic plasticity of the mycobacterial cell and provide a new framework for understanding their ability to survive under low energy conditions and hypoxia.
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Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederweis M. Physiology of mycobacteria. Adv Microb Physiol 2009; 55:81-182, 318-9. [PMID: 19573696 DOI: 10.1016/s0065-2911(09)05502-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis is a prototrophic, metabolically flexible bacterium that has achieved a spread in the human population that is unmatched by any other bacterial pathogen. The success of M. tuberculosis as a pathogen can be attributed to its extraordinary stealth and capacity to adapt to environmental changes throughout the course of infection. These changes include: nutrient deprivation, hypoxia, various exogenous stress conditions and, in the case of the pathogenic species, the intraphagosomal environment. Knowledge of the physiology of M. tuberculosis during this process has been limited by the slow growth of the bacterium in the laboratory and other technical problems such as cell aggregation. Advances in genomics and molecular methods to analyze the M. tuberculosis genome have revealed that adaptive changes are mediated by complex regulatory networks and signals, resulting in temporal gene expression coupled to metabolic and energetic changes. An important goal for bacterial physiologists will be to elucidate the physiology of M. tuberculosis during the transition between the diverse conditions encountered by M. tuberculosis. This review covers the growth of the mycobacterial cell and how environmental stimuli are sensed by this bacterium. Adaptation to different environments is described from the viewpoint of nutrient acquisition, energy generation, and regulation. To gain quantitative understanding of mycobacterial physiology will require a systems biology approach and recent efforts in this area are discussed.
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Affiliation(s)
- Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
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Beste DJV, Espasa M, Bonde B, Kierzek AM, Stewart GR, McFadden J. The genetic requirements for fast and slow growth in mycobacteria. PLoS One 2009; 4:e5349. [PMID: 19479006 PMCID: PMC2685279 DOI: 10.1371/journal.pone.0005349] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/31/2009] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium tuberculosis infects a third of the world's population. Primary tuberculosis involving active fast bacterial replication is often followed by asymptomatic latent tuberculosis, which is characterised by slow or non-replicating bacteria. Reactivation of the latent infection involving a switch back to active bacterial replication can lead to post-primary transmissible tuberculosis. Mycobacterial mechanisms involved in slow growth or switching growth rate provide rational targets for the development of new drugs against persistent mycobacterial infection. Using chemostat culture to control growth rate, we screened a transposon mutant library by Transposon site hybridization (TraSH) selection to define the genetic requirements for slow and fast growth of Mycobacterium bovis (BCG) and for the requirements of switching growth rate. We identified 84 genes that are exclusively required for slow growth (69 hours doubling time) and 256 genes required for switching from slow to fast growth. To validate these findings we performed experiments using individual M. tuberculosis and M. bovis BCG knock out mutants. We have demonstrated that growth rate control is a carefully orchestrated process which requires a distinct set of genes encoding several virulence determinants, gene regulators, and metabolic enzymes. The mce1 locus appears to be a component of the switch to slow growth rate, which is consistent with the proposed role in virulence of M. tuberculosis. These results suggest novel perspectives for unravelling the mechanisms involved in the switch between acute and persistent TB infections and provide a means to study aspects of this important phenomenon in vitro.
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Affiliation(s)
| | - Mateus Espasa
- FHMS, University of Surrey, Guildford, United Kingdom
| | - Bhushan Bonde
- FHMS, University of Surrey, Guildford, United Kingdom
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Bacterial growth and cell division: a mycobacterial perspective. Microbiol Mol Biol Rev 2008; 72:126-56, table of contents. [PMID: 18322037 DOI: 10.1128/mmbr.00028-07] [Citation(s) in RCA: 271] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Mycobacterium is best known for its two major pathogenic species, M. tuberculosis and M. leprae, the causative agents of two of the world's oldest diseases, tuberculosis and leprosy, respectively. M. tuberculosis kills approximately two million people each year and is thought to latently infect one-third of the world's population. One of the most remarkable features of the nonsporulating M. tuberculosis is its ability to remain dormant within an individual for decades before reactivating into active tuberculosis. Thus, control of cell division is a critical part of the disease. The mycobacterial cell wall has unique characteristics and is impermeable to a number of compounds, a feature in part responsible for inherent resistance to numerous drugs. The complexity of the cell wall represents a challenge to the organism, requiring specialized mechanisms to allow cell division to occur. Besides these mycobacterial specializations, all bacteria face some common challenges when they divide. First, they must maintain their normal architecture during and after cell division. In the case of mycobacteria, that means synthesizing the many layers of complex cell wall and maintaining their rod shape. Second, they need to coordinate synthesis and breakdown of cell wall components to maintain integrity throughout division. Finally, they need to regulate cell division in response to environmental stimuli. Here we discuss these challenges and the mechanisms that mycobacteria employ to meet them. Because these organisms are difficult to study, in many cases we extrapolate from information known for gram-negative bacteria or more closely related GC-rich gram-positive organisms.
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Garton NJ, Waddell SJ, Sherratt AL, Lee SM, Smith RJ, Senner C, Hinds J, Rajakumar K, Adegbola RA, Besra GS, Butcher PD, Barer MR. Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Med 2008; 5:e75. [PMID: 18384229 PMCID: PMC2276522 DOI: 10.1371/journal.pmed.0050075] [Citation(s) in RCA: 313] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 02/14/2008] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tuberculous sputum provides a sample of bacilli that must be eliminated by chemotherapy and that may go on to transmit infection. A preliminary observation that Mycobacterium tuberculosis cells contain triacylglycerol lipid bodies in sputum, but not when growing in vitro, led us to investigate the extent of this phenomenon and its physiological basis. METHODS AND FINDINGS Microscopy-positive sputum samples from the UK and The Gambia were investigated for their content of lipid body-positive mycobacteria by combined Nile red and auramine staining. All samples contained a lipid body-positive population varying from 3% to 86% of the acid-fast bacilli present. The recent finding that triacylglycerol synthase is expressed by mycobacteria when they enter in vitro nonreplicating persistence led us to investigate whether this state was also associated with lipid body formation. We found that, when placed in laboratory conditions inducing nonreplicating persistence, two M. tuberculosis strains had lipid body levels comparable to those found in sputum. We investigated these physiological findings further by comparing the M. tuberculosis transcriptome of growing and nonreplicating persistence cultures with that obtained directly from sputum samples. Although sputum has traditionally been thought to contain actively growing tubercle bacilli, our transcript analyses refute the hypothesis that these cells predominate. Rather, they reinforce the results of the lipid body analyses by revealing transcriptional signatures that can be clearly attributed to slowly replicating or nonreplicating mycobacteria. Finally, the lipid body count was highly correlated (R(2) = 0.64, p < 0.03) with time to positivity in diagnostic liquid cultures, thereby establishing a direct link between this cytological feature and the size of a potential nonreplicating population. CONCLUSION As nonreplicating tubercle bacilli are tolerant to the cidal action of antibiotics and resistant to multiple stresses, identification of this persister-like population of tubercle bacilli in sputum presents exciting and tractable new opportunities to investigate both responses to chemotherapy and the transmission of tuberculosis.
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Affiliation(s)
- Natalie J Garton
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
| | - Simon J Waddell
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, London, United Kingdom
| | - Anna L Sherratt
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
| | - Su-Min Lee
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
| | - Rebecca J Smith
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
| | - Claire Senner
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, London, United Kingdom
| | - Jason Hinds
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, London, United Kingdom
| | - Kumar Rajakumar
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
- Department of Clinical Microbiology, University Hospitals of Leicester National Health Service Trust, Leicester, United Kingdom
| | | | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Philip D Butcher
- Medical Microbiology, Division of Cellular and Molecular Medicine, St George's University of London, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (PDB); (MRB)
| | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester Medical School, Leicester, United Kingdom
- Department of Clinical Microbiology, University Hospitals of Leicester National Health Service Trust, Leicester, United Kingdom
- * To whom correspondence should be addressed. E-mail: (PDB); (MRB)
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Quorum sensing influences Vibrio harveyi growth rates in a manner not fully accounted for by the marker effect of bioluminescence. PLoS One 2008; 3:e1671. [PMID: 18301749 PMCID: PMC2249925 DOI: 10.1371/journal.pone.0001671] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 01/13/2008] [Indexed: 11/30/2022] Open
Abstract
Background The light-emitting Vibrios provide excellent material for studying the interaction of cellular communication with growth rate because bioluminescence is a convenient marker for quorum sensing. However, the use of bioluminescence as a marker is complicated because bioluminescence itself may affect growth rate, e.g. by diverting energy. Methodology/Principal Findings The marker effect was explored via growth rate studies in isogenic Vibrio harveyi (Vh) strains altered in quorum sensing on the one hand, and bioluminescence on the other. By hypothesis, growth rate is energy limited: mutants deficient in quorum sensing grow faster because wild type quorum sensing unleashes bioluminescence and bioluminescence diverts energy. Findings reported here confirm a role for bioluminescence in limiting Vh growth rate, at least under the conditions tested. However, the results argue that the bioluminescence is insufficient to explain the relationship of growth rate and quorum sensing in Vh. A Vh mutant null for all genes encoding the bioluminescence pathway grew faster than wild type but not as fast as null mutants in quorum sensing. Vh quorum sensing mutants showed altered growth rates that do not always rank with their relative increase or decrease in bioluminescence. In addition, the cell-free culture fluids of a rapidly growing Vibrio parahaemolyticus (Vp) strain increased the growth rate of wild type Vh without significantly altering Vh's bioluminescence. The same cell-free culture fluid increased the bioluminescence of Vh quorum mutants. Conclusions/Significance The effect of quorum sensing on Vh growth rate can be either positive or negative and includes both bioluminescence-dependent and independent components. Bioluminescence tends to slow growth rate but not enough to account for the effects of quorum sensing on growth rate.
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Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS One 2008; 3:e1403. [PMID: 18167562 PMCID: PMC2151136 DOI: 10.1371/journal.pone.0001403] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 12/06/2007] [Indexed: 11/20/2022] Open
Abstract
Background Transcriptional profiling using microarrays provides a unique opportunity to decipher host pathogen cross-talk on the global level. Here, for the first time, we have been able to investigate gene expression changes in both Mycobacterium tuberculosis, a major human pathogen, and its human host cells, macrophages and dendritic cells. Methodology/Principal Findings In addition to common responses, we could identify eukaryotic and microbial transcriptional signatures that are specific to the cell type involved in the infection process. In particular M. tuberculosis shows a marked stress response when inside dendritic cells, which is in accordance with the low permissivity of these specialized phagocytes to the tubercle bacillus and to other pathogens. In contrast, the mycobacterial transcriptome inside macrophages reflects that of replicating bacteria. On the host cell side, differential responses to infection in macrophages and dendritic cells were identified in genes involved in oxidative stress, intracellular vesicle trafficking and phagosome acidification. Conclusions/Significance This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments.
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