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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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102
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Petruccioli E, Scriba TJ, Petrone L, Hatherill M, Cirillo DM, Joosten SA, Ottenhoff TH, Denkinger CM, Goletti D. Correlates of tuberculosis risk: predictive biomarkers for progression to active tuberculosis. Eur Respir J 2016; 48:1751-1763. [PMID: 27836953 PMCID: PMC5898936 DOI: 10.1183/13993003.01012-2016] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/08/2016] [Indexed: 02/06/2023]
Abstract
New approaches to control the spread of tuberculosis (TB) are needed, including tools to predict development of active TB from latent TB infection (LTBI). Recent studies have described potential correlates of risk, in order to inform the development of prognostic tests for TB disease progression. These efforts have included unbiased approaches employing “omics” technologies, as well as more directed, hypothesis-driven approaches assessing a small set or even individual selected markers as candidate correlates of TB risk. Unbiased high-throughput screening of blood RNAseq profiles identified signatures of active TB risk in individuals with LTBI, ≥1 year before diagnosis. A recent infant vaccination study identified enhanced expression of T-cell activation markers as a correlate of risk prior to developing TB; conversely, high levels of Ag85A antibodies and high frequencies of interferon (IFN)-γ specific T-cells were associated with reduced risk of disease. Others have described CD27−IFN-γ+CD4+ T-cells as possibly predictive markers of TB disease. T-cell responses to TB latency antigens, including heparin-binding haemagglutinin and DosR-regulon-encoded antigens have also been correlated with protection. Further studies are needed to determine whether correlates of risk can be used to prevent active TB through targeted prophylactic treatment, or to allow targeted enrolment into efficacy trials of new TB vaccines and therapeutic drugs. Promising biomarkers may allow accurate prediction of progression from infection to active TB diseasehttp://ow.ly/OzCL304ezfk
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Affiliation(s)
- Elisa Petruccioli
- Dept of Epidemiology and Preclinical Research, Translational Research Unit, National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa.,Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
| | - Linda Petrone
- Dept of Epidemiology and Preclinical Research, Translational Research Unit, National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa.,Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology and Infectious Diseases, San Raffaele Scientific Institute, HSR, Milan, Italy
| | | | | | | | - Delia Goletti
- Dept of Epidemiology and Preclinical Research, Translational Research Unit, National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
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103
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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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104
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Chen Z, Hu Y, Cumming BM, Lu P, Feng L, Deng J, Steyn AJC, Chen S. Mycobacterial WhiB6 Differentially Regulates ESX-1 and the Dos Regulon to Modulate Granuloma Formation and Virulence in Zebrafish. Cell Rep 2016; 16:2512-24. [PMID: 27545883 DOI: 10.1016/j.celrep.2016.07.080] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/06/2016] [Accepted: 07/27/2016] [Indexed: 01/21/2023] Open
Abstract
During the course of infection, Mycobacterium tuberculosis (Mtb) is exposed to diverse redox stresses that trigger metabolic and physiological changes. How these stressors are sensed and relayed to the Mtb transcriptional apparatus remains unclear. Here, we provide evidence that WhiB6 differentially regulates the ESX-1 and DosR regulons through its Fe-S cluster. When challenged with NO, WhiB6 continually activates expression of the DosR regulons but regulates ESX-1 expression through initial activation followed by gradual inhibition. Comparative transcriptomic analysis of the holo- and reduced apo-WhiB6 complemented strains confirms these results and also reveals that WhiB6 controls aerobic and anaerobic metabolism, cell division, and virulence. Using the Mycobacterium marinum zebrafish infection model, we find that holo- and apo-WhiB6 modulate levels of mycobacterial infection, granuloma formation, and dissemination. These findings provide fresh insight into the role of WhiB6 in mycobacterial infection, dissemination, and disease development.
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Affiliation(s)
- Zhenkang Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 10086, China
| | - Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bridgette M Cumming
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban 4001, South Africa
| | - Pei Lu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lipeng Feng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Adrie J C Steyn
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban 4001, South Africa; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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105
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Ofori-Anyinam B, Kanuteh F, Agbla SC, Adetifa I, Okoi C, Dolganov G, Schoolnik G, Secka O, Antonio M, de Jong BC, Gehre F. Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia. PLoS Negl Trop Dis 2016; 10:e0004801. [PMID: 27387550 PMCID: PMC4936735 DOI: 10.1371/journal.pntd.0004801] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/02/2016] [Indexed: 01/19/2023] Open
Abstract
Background MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis (TB). Mycobacterium africanum West Africa 2 (Maf 2) remains an important cause of TB in West Africa and causes one third of disease in The Gambia. Since the introduction of MPT64 antigen tests, a higher than expected rate of suspected non-tuberculous mycobacteria (NTM) was seen among AFB smear positive TB suspects, which led us to prospectively assess sensitivity of the MPT64 antigen test in our setting. Methodology/Principal Findings We compared the abundance of mRNA encoded by the mpt64 gene in sputa of patients with untreated pulmonary TB caused by Maf 2 and Mycobacterium tuberculosis (Mtb). Subsequently, prospectively collected sputum samples from presumptive TB patients were inoculated in the BACTEC MGIT 960 System. One hundred and seventy-three acid fast bacilli (AFB)-positive and blood agar negative MGIT cultures were included in the study. Cultures were tested on the day of MGIT positivity with the BD MGIT TBc Identification Test. A random set of positives and all negatives were additionally tested with the SD Bioline Ag MPT64 Rapid. MPT64 negative cultures were further incubated at 37°C and retested until positive. Bacteria were spoligotyped and assigned to different lineages. Maf 2 isolates were 2.52-fold less likely to produce a positive test result and sensitivity ranged from 78.4% to 84.3% at the beginning and end of the recommended 10 day testing window, respectively. There was no significant difference between the tests. We further showed that the decreased rapid test sensitivity was attributable to variations in mycobacterial growth behavior and the smear grades of the patient. Conclusions/Significance In areas where Maf 2 is endemic MPT64 tests should be cautiously used and MPT64 negative results confirmed by a second technique, such as nucleic acid amplification tests, to avoid their misclassification as NTMs. Diagnostics for rapid confirmation of positive liquid cultures presumptive of Mycobacterium tuberculosis bacteria, based on the detection of the MPT64 antigen, are being used in many TB diagnostic laboratories worldwide. Of note, diagnostic performance of these tests in West Africa, where TB is uniquely caused by the geographically restricted Mycobacterium africanum (Maf 1 and 2) and Mycobacterium tuberculosis lineages, has not been properly assessed. Although M. tuberculosis and M. africanum are genetically related, they differ in various aspects. Amongst several differences, Maf 2 grows significantly slower than Mtb bacteria. Because secretion of the MTP64 protein is dependent on the bacterial growth rate, we found that the MPT64 rapid test performance for detecting Maf 2 was lower in our setting in The Gambia. These findings might be relevant for other West African Maf 2 endemic countries where this rapid test is commonly used, as Maf 2 infected patients might have been missed in the past. Our finding emphasizes the need to thoroughly consider the presence of bacterial variants specific to certain regions during product development and implementation of novel diagnostic tests.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Fatoumatta Kanuteh
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Schadrac C. Agbla
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Ifedayo Adetifa
- Disease Control and Elimination Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Catherine Okoi
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ousman Secka
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Infectious Diseases, New York University, New York, New York, United States of America
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- * E-mail:
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106
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Liu Y, Tan S, Huang L, Abramovitch RB, Rohde KH, Zimmerman MD, Chen C, Dartois V, VanderVen BC, Russell DG. Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. J Exp Med 2016; 213:809-25. [PMID: 27114608 PMCID: PMC4854729 DOI: 10.1084/jem.20151248] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 03/03/2016] [Indexed: 11/04/2022] Open
Abstract
Successful chemotherapy against Mycobacterium tuberculosis (Mtb) must eradicate the bacterium within the context of its host cell. However, our understanding of the impact of this environment on antimycobacterial drug action remains incomplete. Intriguingly, we find that Mtb in myeloid cells isolated from the lungs of experimentally infected mice exhibit tolerance to both isoniazid and rifampin to a degree proportional to the activation status of the host cells. These data are confirmed by in vitro infections of resting versus activated macrophages where cytokine-mediated activation renders Mtb tolerant to four frontline drugs. Transcriptional analysis of intracellular Mtb exposed to drugs identified a set of genes common to all four drugs. The data imply a causal linkage between a loss of fitness caused by drug action and Mtb's sensitivity to host-derived stresses. Interestingly, the environmental context exerts a more dominant impact on Mtb gene expression than the pressure on the drugs' primary targets. Mtb's stress responses to drugs resemble those mobilized after cytokine activation of the host cell. Although host-derived stresses are antimicrobial in nature, they negatively affect drug efficacy. Together, our findings demonstrate that the macrophage environment dominates Mtb's response to drug pressure and suggest novel routes for future drug discovery programs.
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Affiliation(s)
- Yancheng Liu
- Department of Microbiology and Immunology, Veterinary Medical Center, Cornell University, Ithaca, NY 14853
| | - Shumin Tan
- Department of Microbiology and Immunology, Veterinary Medical Center, Cornell University, Ithaca, NY 14853
| | - Lu Huang
- Department of Microbiology and Immunology, Veterinary Medical Center, Cornell University, Ithaca, NY 14853
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
| | - Kyle H Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827
| | | | - Chao Chen
- Public Health Research Institute, Newark, NJ 07103
| | | | - Brian C VanderVen
- Department of Microbiology and Immunology, Veterinary Medical Center, Cornell University, Ithaca, NY 14853
| | - David G Russell
- Department of Microbiology and Immunology, Veterinary Medical Center, Cornell University, Ithaca, NY 14853
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107
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Molecular characterization of novel immunodominant molybdenum cofactor biosynthesis protein C1 (Rv3111) from Mycobacterium tuberculosis H37Rv. Biochim Biophys Acta Gen Subj 2016; 1860:694-707. [DOI: 10.1016/j.bbagen.2016.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 12/19/2015] [Accepted: 01/06/2016] [Indexed: 11/23/2022]
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108
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Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. Sci Rep 2016; 6:23440. [PMID: 27000948 PMCID: PMC4802306 DOI: 10.1038/srep23440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/07/2016] [Indexed: 12/25/2022] Open
Abstract
Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness.
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109
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Benjak A, Uplekar S, Zhang M, Piton J, Cole ST, Sala C. Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b. BMC Genomics 2016; 17:190. [PMID: 26944551 PMCID: PMC4779234 DOI: 10.1186/s12864-016-2528-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/24/2016] [Indexed: 12/05/2022] Open
Abstract
Background The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models. Results The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses. Conclusion The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2528-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Swapna Uplekar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Current addresses: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Ming Zhang
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Current addresses: Department of Biochemistry, University of Lausanne, Quartier UNIL-Epalinges, Ch. des Boveresses 155, CH-1066, Epalinges, Switzerland.
| | - Jérémie Piton
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
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110
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The MarR family transcription factor Rv1404 coordinates adaptation of Mycobacterium tuberculosis to acid stress via controlled expression of Rv1405c, a virulence-associated methyltransferase. Tuberculosis (Edinb) 2016; 97:154-62. [DOI: 10.1016/j.tube.2015.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 11/20/2022]
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111
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Abstract
Mycobacterium tuberculosis is an incredibly successful pathogen with an extraordinary penetrance of its target host population. The ability to infect many yet cause disease in few is undoubtedly central to this success. This ability relies on sensing and responding to the changing environments encountered during the course of disease in the human host. This chapter discusses these environmental cues and stresses, and explores how the genome of Mtb has evolved under the purifying selections that they exert. In analyzing the response of Mtb to a broad range of intracellular pressures it is clear that, despite genome down-sizing, Mtb has retained an extraordinary flexibility in central carbon metabolism. We believe that it is this metabolic plasticity, more than any of the virulence factors, that is the foundation for Mtb's qualities of endurance.
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112
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Figueiredo HCP, Soares SC, Pereira FL, Dorella FA, Carvalho AF, Teixeira JP, Azevedo VAC, Leal CAG. Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout. BMC Genomics 2015; 16:1095. [PMID: 26694728 PMCID: PMC4687380 DOI: 10.1186/s12864-015-2324-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The genus Weissella belongs to the lactic acid bacteria and includes 18 currently identified species, predominantly isolated from fermented food but rarely from cases of bacteremia in animals. Recently, a new species, designated Weissella ceti, has been correlated with hemorrhagic illness in farm-raised rainbow trout in China, Brazil, and the USA, with high transmission and mortality rates during outbreaks. Although W. ceti is an important emerging veterinary pathogen, little is known about its genomic features or virulence mechanisms. To better understand these and to characterize the species, we have previously sequenced the genomes of W. ceti strains WS08, WS74, and WS105, isolated from different rainbow trout farms in Brazil and displaying different pulsed-field gel electrophoresis patterns. Here, we present a comparative analysis of the three previously sequenced genomes of W. ceti strains from Brazil along with W. ceti NC36 from the USA and those of other Weissella species. Results Phylogenomic and orthology-based analyses both showed a high-similarity in the genetic structure of these W. ceti strains. This structure is corroborated by the highly syntenic order of their genes and the neutral evolution inferred from Tajima’s D. A whole-genome multilocus sequence typing analysis distinguished strains WS08 and NC36 from strains WS74 and WS105. We predicted 10 putative genomic islands (GEI), among which PAIs 3a and 3b are phage sequences that occur only in WS105 and WS74, respectively, whereas PAI 1 is species specific. Conclusions We identified several genes putatively involved in the basic processes of bacterial physiology and pathogenesis, including survival in aquatic environment, adherence in the host, spread inside the host, resistance to immune-system-mediated stresses, and antibiotic resistance. These data provide new insights in the molecular epidemiology and host adaptation for this emerging pathogen in aquaculture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2324-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henrique C P Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Veterinary School, Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, 30161-970, MG, Brazil.
| | - Siomar C Soares
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Felipe L Pereira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Fernanda A Dorella
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Alex F Carvalho
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Júnia P Teixeira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute for Biological Science, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Carlos A G Leal
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y. Mycobacterial infection induces a specific human innate immune response. Sci Rep 2015; 5:16882. [PMID: 26586179 PMCID: PMC4653619 DOI: 10.1038/srep16882] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/21/2015] [Indexed: 12/30/2022] Open
Abstract
The innate immune system provides the first response to infection and is now recognized to be partially pathogen-specific. Mycobacterium tuberculosis (MTB) is able to subvert the innate immune response and survive inside macrophages. Curiously, only 5-10% of otherwise healthy individuals infected with MTB develop active tuberculosis (TB). We do not yet understand the genetic basis underlying this individual-specific susceptibility. Moreover, we still do not know which properties of the innate immune response are specific to MTB infection. To identify immune responses that are specific to MTB, we infected macrophages with eight different bacteria, including different MTB strains and related mycobacteria, and studied their transcriptional response. We identified a novel subset of genes whose regulation was affected specifically by infection with mycobacteria. This subset includes genes involved in phagosome maturation, superoxide production, response to vitamin D, macrophage chemotaxis, and sialic acid synthesis. We suggest that genetic variants that affect the function or regulation of these genes should be considered candidate loci for explaining TB susceptibility.
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Affiliation(s)
- John D Blischak
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.,Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | | | - Amy Mitrano
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Québec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Québec, Canada
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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114
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Tan S, Russell DG. Trans-species communication in the Mycobacterium tuberculosis-infected macrophage. Immunol Rev 2015; 264:233-48. [PMID: 25703563 DOI: 10.1111/imr.12254] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Much of the infection cycle of Mycobacterium tuberculosis (Mtb) is spent within its host cell, the macrophage. As a consequence of the chronic, enduring nature of the infection, this cell-cell interaction has become highly intimate, and the bacterium has evolved to detect, react to, and manipulate the evolving, immune-modulated phenotype of its host. In this review, we discuss the nature of the endosomal/lysosomal continuum, the characterization of the bacterium's transcriptional responses during the infection cycle, and the dominant environmental cues that shape this response. We also discuss how the metabolism of both cells is modulated by the infection and the impact that this has on the progression of the granuloma. Finally, we detail how these transcriptional responses can be exploited to construct reporter bacterial strains to probe the temporal and spatial environmental shifts experienced by Mtb during the course of experimental infections. These reporter strains provide new insights into the fitness of Mtb under immune- and drug-mediated pressure.
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Affiliation(s)
- Shumin Tan
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
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115
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Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients. INFECTION GENETICS AND EVOLUTION 2015; 36:517-523. [PMID: 26319998 DOI: 10.1016/j.meegid.2015.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/01/2015] [Accepted: 08/23/2015] [Indexed: 11/24/2022]
Abstract
We conducted a prospective study to establish factors associated with survival in tuberculosis patients in Russia including social, clinical and pathogen-related genetic parameters. Specifically we wished to determine whether different strains/clades of the Beijing lineage exerted a differential effect of survival. HIV-negative culture-confirmed cases were recruited during 2008-2010 across Samara Oblast and censored in December 2011. Molecular characterization was performed by a combination of spoligotyping, multilocus VNTR typing and whole genome sequencing (WGS). We analyzed 2602 strains and detected a high prevalence of Beijing family (n=1933; 74%) represented largely by two highly homogenous dominant clades A (n=794) and B (n=402) and non-A/non-B (n=737). Multivariable analysis of 1366 patients with full clinical and genotyping data showed that multi- and extensive drug resistance (HR=1.86; 95%CI: 1.52, 2.28 and HR=2.19; 95%CI: 1.55, 3.11) had the largest impact on survival. In addition older age, extensive lung damage, shortness of breath, treatment in the past and alcohol abuse reduced survival time. After adjustment for clinical and demographic predictors there was evidence that clades A and B combined were associated with poorer survival than other Beijing strains (HR=0.48; 95%CI 0.34, 0.67). All other pathogen-related factors (polymorphisms in genes plcA, plcB, plcC, lipR, dosT and pks15/1) had no effect on survival. In conclusion, drug resistance exerted the greatest effect on survival of TB patients. Nevertheless we provide evidence for the independent biological effect on survival of different Beijing family strains even within the same defined geographical population. Better understanding of the role of different strain factors in active disease and their influence on outcome is essential.
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Yasugi M, Sugahara Y, Hoshi H, Kondo K, Talukdar PK, Sarker MR, Yamamoto S, Kamata Y, Miyake M. In vitro cytotoxicity induced by Clostridium perfringens isolate carrying a chromosomal cpe gene is exclusively dependent on sporulation and enterotoxin production. Microb Pathog 2015; 85:1-10. [DOI: 10.1016/j.micpath.2015.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/07/2015] [Accepted: 04/21/2015] [Indexed: 12/31/2022]
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Nelson KM, Viswanathan K, Dawadi S, Duckworth BP, Boshoff HI, Barry CE, Aldrich CC. Synthesis and Pharmacokinetic Evaluation of Siderophore Biosynthesis Inhibitors for Mycobacterium tuberculosis. J Med Chem 2015; 58:5459-75. [PMID: 26110337 DOI: 10.1021/acs.jmedchem.5b00391] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MbtA catalyzes the first committed biosynthetic step of the mycobactins, which are important virulence factors associated with iron acquisition in Mycobacterium tuberculosis. MbtA is a validated therapeutic target for antitubercular drug development. 5'-O-[N-(Salicyl)sulfamoyl]adenosine (1) is a bisubstrate inhibitor of MbtA and exhibits exceptionally potent biochemical and antitubercular activity. However, 1 suffers from suboptimal drug disposition properties resulting in a short half-life (t(1/2)), low exposure (AUC), and low bioavailability (F). Four strategies were pursued to address these liabilities including the synthesis of prodrugs, increasing the pK(a) of the acyl-sulfonyl moiety, modulation of the lipophilicity, and strategic introduction of fluorine into 1. Complete pharmacokinetic (PK) analysis of all compounds was performed. The most successful modifications involved fluorination of the nucleoside that provided substantial improvements in t(1/2) and AUC. Increasing the pK(a) of the acyl-sulfonyl linker yielded incremental enhancements, while modulation of the lipophilicity and prodrug approaches led to substantially poorer PK parameters.
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Affiliation(s)
- Kathryn M Nelson
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kishore Viswanathan
- ‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Surendra Dawadi
- ‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Benjamin P Duckworth
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Helena I Boshoff
- §Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Clifton E Barry
- §Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Courtney C Aldrich
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains. PLoS Negl Trop Dis 2015; 9:e0003918. [PMID: 26147869 PMCID: PMC4492979 DOI: 10.1371/journal.pntd.0003918] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/16/2015] [Indexed: 12/20/2022] Open
Abstract
Background Although cutaneous ulcers (CU) in the tropics is frequently attributed to Treponema pallidum subspecies pertenue, the causative agent of yaws, Haemophilus ducreyi has emerged as a major cause of CU in yaws-endemic regions of the South Pacific islands and Africa. H. ducreyi is generally susceptible to macrolides, but CU strains persist after mass drug administration of azithromycin for yaws or trachoma. H. ducreyi also causes genital ulcers (GU) and was thought to be exclusively transmitted by microabrasions that occur during sex. In human volunteers, the GU strain 35000HP does not infect intact skin; wounds are required to initiate infection. These data led to several questions: Are CU strains a new variant of H. ducreyi or did they evolve from GU strains? Do CU strains contain additional genes that could allow them to infect intact skin? Are CU strains susceptible to azithromycin? Methodology/Principal Findings To address these questions, we performed whole-genome sequencing and antibiotic susceptibility testing of 5 CU strains obtained from Samoa and Vanuatu and 9 archived class I and class II GU strains. Except for single nucleotide polymorphisms, the CU strains were genetically almost identical to the class I strain 35000HP and had no additional genetic content. Phylogenetic analysis showed that class I and class II strains formed two separate clusters and CU strains evolved from class I strains. Class I strains diverged from class II strains ~1.95 million years ago (mya) and CU strains diverged from the class I strain 35000HP ~0.18 mya. CU and GU strains evolved under similar selection pressures. Like 35000HP, the CU strains were highly susceptible to antibiotics, including azithromycin. Conclusions/Significance These data suggest that CU strains are derivatives of class I strains that were not recognized until recently. These findings require confirmation by analysis of CU strains from other regions. Cutaneous ulcers (CU) in children living in equatorial Africa and the South Pacific islands have long been attributed to yaws, which is caused by Treponema pallidum subsp. pertenue. However, PCR-based cross sectional surveys done in yaws-endemic regions show that Haemophilus ducreyi is the leading cause of CU in these regions. H. ducreyi classically causes the genital ulcer (GU) disease chancroid and was once thought to be exclusively sexually transmitted. We show that CU strains obtained from Samoa and Vanuatu are genetically nearly identical to class 1 GU strains and contain no additional genetic content. The CU strains are highly susceptible to antibiotics, including azithromycin. The data suggest an urgent need to obtain and analyze CU isolates from Africa and other countries in the South Pacific and to search for environmental sources of the organism.
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Liu Z, Liu F, Aldrich CC. Stereocontrolled Synthesis of a Potential Transition-State Inhibitor of the Salicylate Synthase MbtI from Mycobacterium tuberculosis. J Org Chem 2015; 80:6545-52. [PMID: 26035083 DOI: 10.1021/acs.joc.5b00455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobactins are small-molecule iron chelators (siderophores) produced by Mycobacterium tuberculosis (Mtb) for iron mobilization. The bifunctional salicylate synthase MbtI catalyzes the first step of mycobactin biosynthesis through the conversion of the primary metabolite chorismate into salicylic acid via isochorismate. We report the design, synthesis, and biochemical evaluation of an inhibitor based on the putative transition state (TS) for the isochorismatase partial reaction of MbtI. The inhibitor mimics the hypothesized charge buildup at C-4 of chorismate in the TS as well as C-O bond formation at C-6. Another important design element of the inhibitor is replacement of the labile pyruvate side chain in chorismate with a stable C-linked propionate isostere. We developed a stereocontrolled synthesis of the highly functionalized cyclohexene inhibitor that features an asymmetric aldol reaction using a titanium enolate, diastereoselective Grignard addition to a tert-butanesulfinyl aldimine, and ring closing olefin metathesis as key steps.
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Affiliation(s)
- Zheng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Feng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
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120
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Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 2015; 4. [PMID: 25732036 PMCID: PMC4384740 DOI: 10.7554/elife.05166] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
To improve understanding of the factors influencing tuberculosis transmission and the
role of pathogen variation, we sequenced all available specimens from patients
diagnosed over 15 years in a whole district in Malawi. Mycobacterium
tuberculosis lineages were assigned and transmission networks
constructed, allowing ≤10 single nucleotide polymorphisms (SNPs) difference.
We defined disease as due to recent infection if the network-determined source was
within 5 years, and assessed transmissibility from forward transmissions resulting in
disease. High-quality sequences were available for 1687 disease episodes (72% of all
culture-positive episodes): 66% of patients linked to at least one other patient. The
between-patient mutation rate was 0.26 SNPs/year (95% CI 0.21–0.31). We showed
striking differences by lineage in the proportion of disease due to recent
transmission and in transmissibility (highest for lineage-2 and lowest for lineage-1)
that were not confounded by immigration, HIV status or drug resistance. Transmissions
resulting in disease decreased markedly over time. DOI:http://dx.doi.org/10.7554/eLife.05166.001 Tuberculosis is an important public health threat around the globe and is
particularly common in developing countries. It is difficult to control the spread of
the disease because the bacteria that cause it can spread when an infected individual
coughs or sneezes. It may take years for an infected individual to develop symptoms
of tuberculosis so it can be hard to trace the source of an outbreak, and people
infected with HIV are particularly susceptible to the disease. The bacterium that causes the majority of cases of tuberculosis is called
Mycobacterium tuberculosis. There are several different varieties
or ‘lineages’ of M. tuberculosis, and it is thought
that they may vary in their ability to spread and cause disease. However, the results
of previous studies have been inconsistent and there also seems to be a lot of
variation between strains within the same lineage. In this study, Guerra-Assunção et al. used an approach called whole
genome sequencing alongside more traditional methods to study the spread of
tuberculosis in Malawi. They sequenced the genomes of every available sample of
M. tuberculosis collected from patients in the Karonga district
of Malawi over a 15-year period. This produced high-quality DNA sequence data about
the bacteria responsible for almost 1700 cases of disease. Using this massive amount of data, Guerra-Assunção et al. constructed
networks that showed how the bacteria had spread in the community. This revealed that
there were differences between the ability of the various M.
tuberculosis lineages to cause disease and to spread in communities. For
example, lineage 1 was less likely than the other lineages to cause disease soon
after infecting an individual and was less able to spread. The data also show that the proportion of cases of disease due to recent infection
declined substantially during the 15-year period. This indicates that the
tuberculosis and HIV control programmes in the area have been successful. Guerra-Assunção et al.'s findings show that it is possible to
understand how tuberculosis is transmitted on a large scale. The next challenge is to
understand why the lineages differ in their ability to cause disease and spread
between individuals. DOI:http://dx.doi.org/10.7554/eLife.05166.002
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Affiliation(s)
- J A Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T Mzembe
- Karonga Prevention Study, Malawi, Malawi
| | - K Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - F Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - L Banda
- Karonga Prevention Study, Malawi, Malawi
| | - A Chiwaya
- Karonga Prevention Study, Malawi, Malawi
| | - R P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P E M Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J Parkhill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - T G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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121
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Li W, Fan X, Long Q, Xie L, Xie J. Mycobacterium tuberculosis effectors involved in host-pathogen interaction revealed by a multiple scales integrative pipeline. INFECTION GENETICS AND EVOLUTION 2015; 32:1-11. [PMID: 25709069 DOI: 10.1016/j.meegid.2015.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter host immunity. Proteins are one important player in the host-pathogen interaction. A comprehensive list of such proteins will benefit our understanding of pathogenesis of Mtb. METHODS A genome-scale dataset was created from different sources of published data: global gene expression studies in disease models; genome-wide insertional mutagenesis defining gene essentiality under different conditions; genes lost in clinical isolates; subcellular localization analysis and non-homology analysis. Using data mining and meta-analysis, expressed proteins critical for intracellular survival of Mtb are first identified, followed by subcellular localization analysis, finally filtering a series of subtractive channel of analysis to find out promising drug target candidates. RESULTS The analysis found 54 potential candidates essential for the intracellular survival of the pathogen and non-homologous to host or gut flora, and might be promising drug targets. CONCLUSION Based on our meta-analysis and bioinformatics analysis, 54 hits were found from Mtb around 4000 open reading frames. These hits can be good candidates for further experimental investigation.
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Affiliation(s)
- Wu Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Shandong 250022, China
| | - Quanxin Long
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases of the Ministry of Education, Chongqing Medical University, 1 Medical Road, Yuzhong District, Chongqing 400016, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Novel inhibitors of cholesterol degradation in Mycobacterium tuberculosis reveal how the bacterium's metabolism is constrained by the intracellular environment. PLoS Pathog 2015; 11:e1004679. [PMID: 25675247 PMCID: PMC4335503 DOI: 10.1371/journal.ppat.1004679] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) relies on a specialized set of metabolic pathways to support growth in macrophages. By conducting an extensive, unbiased chemical screen to identify small molecules that inhibit Mtb metabolism within macrophages, we identified a significant number of novel compounds that limit Mtb growth in macrophages and in medium containing cholesterol as the principle carbon source. Based on this observation, we developed a chemical-rescue strategy to identify compounds that target metabolic enzymes involved in cholesterol metabolism. This approach identified two compounds that inhibit the HsaAB enzyme complex, which is required for complete degradation of the cholesterol A/B rings. The strategy also identified an inhibitor of PrpC, the 2-methylcitrate synthase, which is required for assimilation of cholesterol-derived propionyl-CoA into the TCA cycle. These chemical probes represent new classes of inhibitors with novel modes of action, and target metabolic pathways required to support growth of Mtb in its host cell. The screen also revealed a structurally-diverse set of compounds that target additional stage(s) of cholesterol utilization. Mutants resistant to this class of compounds are defective in the bacterial adenylate cyclase Rv1625/Cya. These data implicate cyclic-AMP (cAMP) in regulating cholesterol utilization in Mtb, and are consistent with published reports indicating that propionate metabolism is regulated by cAMP levels. Intriguingly, reversal of the cholesterol-dependent growth inhibition caused by this subset of compounds could be achieved by supplementing the media with acetate, but not with glucose, indicating that Mtb is subject to a unique form of metabolic constraint induced by the presence of cholesterol. Human beings are the sole ecological niche for M. tuberculosis (Mtb), and it is estimated that 1.8 billion people are currently infected with Mtb. An important aspect of this infection is Mtb’s ability to maintain infection by replicating within macrophages. Within macrophages, Mtb exploits a specialized set of metabolic pathways to utilize host-derived nutrients, such as fatty acids and/or cholesterol, for energy production. Many details regarding Mtb metabolism during infection remain unknown. Here we took a chemical approach to identify small molecule probes, which target Mtb metabolism during infection in macrophages. We found that many of the small molecule inhibitors that we identified require cholesterol for activity. Here we report a novel chemical rescue approach to identify the metabolic targets of three novel inhibitors, and discovered that cAMP signaling is linked to cholesterol utilization in Mtb. Together, these data demonstrate that cholesterol exerts a dominant effect on Mtb metabolism within macrophages. Additionally, the novel inhibitors identified in this study will facilitate evaluation of cholesterol metabolism as a target for chemotherapeutic intervention.
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Singh A, Gopinath K, Sharma P, Bisht D, Sharma P, Singh N, Singh S. Comparative proteomic analysis of sequential isolates of Mycobacterium tuberculosis from a patient with pulmonary tuberculosis turning from drug sensitive to multidrug resistant. Indian J Med Res 2015; 141:27-45. [PMID: 25857493 PMCID: PMC4405938 DOI: 10.4103/0971-5916.154492] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND & OBJECTIVES Tuberculosis is a major health problem in India, and the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) has further complicated the situation. Though several studies characterizing drug sensitive and drug resistant strains are available in literature, almost all studies are done on unrelated strains. Therefore, the objective of this study was to compare the proteomic data of four sequential isolates of Mtb from a single patient who developed MDR-TB during the course of anti-tuberculosis therapy (ATT). METHODS In this study, using two-dimensional (2D) gel electrophoresis and MALDI-TOF mass spectrometry, we compared and analyzed the cell lysate proteins of Mtb sequential clinical isolates from a patient undergoing anti-TB treatment. The mRNA expression levels of selected identified proteins were determined by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The genotypes of all four isolates remained homologous, indicating no re-infection. The initial isolate (before treatment) was sensitive to all first-line drugs, but the consecutive isolates were found to be resistant to isoniazid (INH) and rifampicin (RIF) and developed mutations in the katG, inhA and rpoB. the intensities of 27 protein spots were found to be consistently overexpressed in INH and RIF resistant isolates. The most prominent and overexpressed proteins found during the development of drug resistance were GarA (Rv1827), wag31 (Rv2145c), Rv1437 and Rv2970c. INTERPRETATION & CONCLUSIONS This preliminary proteomic study provides an insight about the proteins that are upregulated during drug resistance development. These upregulated proteins, identified here, could prove useful as immunodiagnostic and possibly drug resistant markers in future. However, more studies are required to confirm these findings.
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Affiliation(s)
- Amit Singh
- Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Krishnamoorthy Gopinath
- Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prashant Sharma
- National JALMA Institute for Leprosy & other Mycobacterial Diseases (ICMR), Agra, India
| | - Deepa Bisht
- National JALMA Institute for Leprosy & other Mycobacterial Diseases (ICMR), Agra, India
| | - Pawan Sharma
- Immunology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi; North-East Region-BPMC, Department of Biotechnology, Govt. of India, New Delhi, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis & Respiratory Diseases, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
- Reprint requests: Dr Sarman Singh, Division of Clinical Microbiology & Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India e-mail: ,
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Warner DF, Koch A, Mizrahi V. Diversity and disease pathogenesis in Mycobacterium tuberculosis. Trends Microbiol 2015; 23:14-21. [DOI: 10.1016/j.tim.2014.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022]
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Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014; 26:431-44. [PMID: 25453224 PMCID: PMC4314449 DOI: 10.1016/j.smim.2014.09.012] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions.
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Affiliation(s)
- Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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126
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bis-Molybdopterin guanine dinucleotide is required for persistence of Mycobacterium tuberculosis in guinea pigs. Infect Immun 2014; 83:544-50. [PMID: 25404027 DOI: 10.1128/iai.02722-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis is able to synthesize molybdopterin cofactor (MoCo), which is utilized by numerous enzymes that catalyze redox reactions in carbon, nitrogen, and sulfur metabolism. In bacteria, MoCo is further modified through the activity of a guanylyltransferase, MobA, which converts MoCo to bis-molybdopterin guanine dinucleotide (bis-MGD), a form of the cofactor that is required by the dimethylsulfoxide (DMSO) reductase family of enzymes, which includes the nitrate reductase NarGHI. In this study, the functionality of the mobA homolog in M. tuberculosis was confirmed by demonstrating the loss of assimilatory and respiratory nitrate reductase activity in a mobA deletion mutant. This mutant displayed no survival defects in human monocytes or mouse lungs but failed to persist in the lungs of guinea pigs. These results implicate one or more bis-MGD-dependent enzymes in the persistence of M. tuberculosis in guinea pig lungs and underscore the applicability of this animal model for assessing the role of molybdoenzymes in this pathogen.
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127
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Behr MA. Comparative genomics of mycobacteria: some answers, yet more new questions. Cold Spring Harb Perspect Med 2014; 5:a021204. [PMID: 25395374 DOI: 10.1101/cshperspect.a021204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Comparative genomic studies permit a genus-level perspective on the distinction between environmental mycobacteria and Mycobacterium tuberculosis, as well as a species-level assessment of genetic variability within M. tuberculosis. Both of these strata of evolutionary analysis serve to generate hypotheses regarding the genomic basis of M. tuberculosis virulence. In contrasting lessons from macroevolutionary study and microevolutionary study, one can form predictions about which segments of the genome are likely to be essential for or dispensable for the pathogenesis of tuberculosis. Although some of these predictions have been experimentally verified, notable exceptions challenge the direct link between these virulence factors and the capacity of M. tuberculosis to successfully cause disease and propagate between human hosts. These unexpected findings serve as the stimulus for further studies, using genomic comparisons and other approaches, to better define the remarkable success of this recalcitrant pathogen.
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Affiliation(s)
- Marcel A Behr
- McGill International Tuberculosis Centre, McGill University, Montreal, Quebec H3G 1A4, Canada Research Institute of the McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
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128
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Abstract
Genomics research has enabled crucial insights into the adaptive evolution of Mycobacterium tuberculosis as an obligate human pathogen. Here, we highlight major recent advances and evaluate the potential for genomics approaches to inform tuberculosis control efforts in high-burden settings.
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129
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Serra-Vidal MM, Latorre I, Franken KLCM, Díaz J, de Souza-Galvão ML, Casas I, Maldonado J, Milà C, Solsona J, Jimenez-Fuentes MÁ, Altet N, Lacoma A, Ruiz-Manzano J, Ausina V, Prat C, Ottenhoff THM, Domínguez J. Immunogenicity of 60 novel latency-related antigens of Mycobacterium tuberculosis. Front Microbiol 2014; 5:517. [PMID: 25339944 PMCID: PMC4189613 DOI: 10.3389/fmicb.2014.00517] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/15/2014] [Indexed: 01/29/2023] Open
Abstract
The aim of our work here was to evaluate the immunogenicity of 60 mycobacterial antigens, some of which have not been previously assessed, notably a novel series of in vivo-expressed Mycobacterium tuberculosis (IVE-TB) antigens. We enrolled 505 subjects and separated them in individuals with and without latent tuberculosis infection (LTBI) vs. patients with active tuberculosis (TB). Following an overnight and 7 days stimulation of whole blood with purified recombinant M. tuberculosis antigens, interferon-γ (IFN-γ) levels were determined by ELISA. Several antigens could statistically significantly differentiate the groups of individuals. We obtained promising antigens from all studied antigen groups [dormancy survival regulon (DosR regulon) encoded antigens; resuscitation-promoting factors (Rpf) antigens; IVE-TB antigens; reactivation associated antigens]. Rv1733, which is a probable conserved transmembrane protein encoded in DosR regulon, turned out to be very immunogenic and able to discriminate between the three defined TB status, thus considered a candidate biomarker. Rv2389 and Rv2435n, belonging to Rpf family and IVE-TB group of antigens, respectively, also stood out as LTBI biomarkers. Although more studies are needed to support our findings, the combined use of these antigens would be an interesting approach to TB immunodiagnosis candidates.
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Affiliation(s)
- Mᵃdel Mar Serra-Vidal
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Irene Latorre
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Kees L. C. M. Franken
- Department of Immunohematology and Blood Transfusion/Department of Infectious Diseases, Leiden University Medical CenterLeiden, Netherlands
| | - Jéssica Díaz
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Maria Luiza de Souza-Galvão
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- Unitat de Tuberculosi de Drassanes, Hospital Universitari Vall d'HebronBarcelona, Spain
| | - Irma Casas
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- Department of Preventive Medicine, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
| | | | - Cèlia Milà
- Unitat de Tuberculosi de Drassanes, Hospital Universitari Vall d'HebronBarcelona, Spain
| | - Jordi Solsona
- Unitat de Tuberculosi de Drassanes, Hospital Universitari Vall d'HebronBarcelona, Spain
| | | | - Neus Altet
- Unitat de Tuberculosi de Drassanes, Hospital Universitari Vall d'HebronBarcelona, Spain
| | - Alícia Lacoma
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Juan Ruiz-Manzano
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
- Department of Pneumology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
| | - Vicente Ausina
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Cristina Prat
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
| | - Tom H. M. Ottenhoff
- Department of Immunohematology and Blood Transfusion/Department of Infectious Diseases, Leiden University Medical CenterLeiden, Netherlands
| | - José Domínguez
- Department of Microbiology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i PujolBadalona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de BarcelonaBellaterra, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos IIIBadalona, Spain
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130
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Peterson EJR, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJR, Sherman DR, Baliga NS. A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Nucleic Acids Res 2014; 42:11291-303. [PMID: 25232098 PMCID: PMC4191388 DOI: 10.1093/nar/gku777] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments of a host. In order to accelerate the discovery and characterization of these adaptive mechanisms, we have mined a compendium of 2325 publicly available transcriptome profiles of MTB to decipher a predictive, systems-scale gene regulatory network model. The resulting modular organization of 98% of all MTB genes within this regulatory network was rigorously tested using two independently generated datasets: a genome-wide map of 7248 DNA-binding locations for 143 transcription factors (TFs) and global transcriptional consequences of overexpressing 206 TFs. This analysis has discovered specific TFs that mediate conditional co-regulation of genes within 240 modules across 14 distinct environmental contexts. In addition to recapitulating previously characterized regulons, we discovered 454 novel mechanisms for gene regulation during stress, cholesterol utilization and dormancy. Significantly, 183 of these mechanisms act uniquely under conditions experienced during the infection cycle to regulate diverse functions including 23 genes that are essential to host-pathogen interactions. These and other insights underscore the power of a rational, model-driven approach to unearth novel MTB biology that operates under some but not all phases of infection.
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Affiliation(s)
| | - David J Reiss
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Serdar Turkarslan
- Seattle Biomed Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Kyle J Minch
- Seattle Biomed Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Tige Rustad
- Seattle Biomed Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | | | | | - David R Sherman
- Seattle Biomed Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
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131
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Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med 2014; 4:a021188. [PMID: 25190252 DOI: 10.1101/cshperspect.a021188] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.
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132
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Boritsch EC, Supply P, Honoré N, Seeman T, Stinear TP, Brosch R. A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent. Mol Microbiol 2014; 93:835-52. [DOI: 10.1111/mmi.12720] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Eva C. Boritsch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Philip Supply
- INSERM U1019; Lille France
- CNRS UMR 8204; Lille France
- University of Lille Nord de France; Lille France
- Institut Pasteur de Lille; Center for Infection and Immunity of Lille; Lille France
| | - Nadine Honoré
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Torsten Seeman
- Victorian Bioinformatics Consortium; Monash University; Clayton Victoria Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology; University of Melbourne; Parkville Victoria Australia
| | - Roland Brosch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
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133
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Baker JJ, Johnson BK, Abramovitch RB. Slow growth of Mycobacterium tuberculosis at acidic pH is regulated by phoPR and host-associated carbon sources. Mol Microbiol 2014; 94:56-69. [PMID: 24975990 DOI: 10.1111/mmi.12688] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2014] [Indexed: 01/07/2023]
Abstract
During pathogenesis, Mycobacterium tuberculosis (Mtb) colonizes environments, such as the macrophage or necrotic granuloma, that are acidic and rich in cholesterol and fatty acids. The goal of this study was to examine how acidic pH and available carbon sources interact to regulate Mtb physiology. Here we report that Mtb growth at acidic pH requires host-associated carbon sources that function at the intersection of glycolysis and the TCA cycle, such as pyruvate, acetate, oxaloacetate and cholesterol. In contrast, in other tested carbon sources, Mtb fully arrests its growth at acidic pH and establishes a state of non-replicating persistence. Growth-arrested Mtb is resuscitated by the addition of pyruvate suggesting that growth arrest is due to a pH-dependent checkpoint on metabolism. Additionally, we demonstrate that the phoPR two-component regulatory system is required to slow Mtb growth at acidic pH and functions to maintain redox homeostasis. Transcriptional profiling and functional metabolic studies demonstrate that signals from acidic pH and carbon source are integrated to remodel pathways associated with anaplerotic central metabolism, lipid anabolism and the regeneration of oxidized cofactors. Because phoPR is required for Mtb virulence in animals, we suggest that pH-driven adaptation may be critical to Mtb pathogenesis.
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Affiliation(s)
- Jacob J Baker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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134
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Rose G, Cortes T, Comas I, Coscolla M, Gagneux S, Young DB. Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome Biol Evol 2014; 5:1849-62. [PMID: 24115728 PMCID: PMC3814196 DOI: 10.1093/gbe/evt138] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genome sequencing has identified an extensive repertoire of single nucleotide polymorphisms among clinical isolates of Mycobacterium tuberculosis, but the extent to which these differences influence phenotypic properties of the bacteria remains to be elucidated. To determine whether these polymorphisms give rise to phenotypic diversity, we have integrated genome data sets with RNA sequencing to assess their impact on the comparative transcriptome profiles of strains belonging to M. tuberculosis Lineages 1 and 2. We observed clear correlations between genotype and transcriptional phenotype. These arose by three mechanisms. First, lineage-specific changes in amino acid sequence of transcriptional regulators were associated with alterations in their ability to control gene expression. Second, changes in nucleotide sequence were associated with alteration of promoter activity and generation of novel transcriptional start sites in intergenic regions and within coding sequences. We show that in some cases this mechanism is expected to generate functionally active truncated proteins involved in innate immune recognition. Finally, genes showing lineage-specific patterns of differential expression not linked directly to primary mutations were characterized by a striking overrepresentation of toxin–antitoxin pairs. Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.
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Affiliation(s)
- Graham Rose
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
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135
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Black PA, Warren RM, Louw GE, van Helden PD, Victor TC, Kana BD. Energy metabolism and drug efflux in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2014; 58:2491-503. [PMID: 24614376 PMCID: PMC3993223 DOI: 10.1128/aac.02293-13] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inherent drug susceptibility of microorganisms is determined by multiple factors, including growth state, the rate of drug diffusion into and out of the cell, and the intrinsic vulnerability of drug targets with regard to the corresponding antimicrobial agent. Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant source of global morbidity and mortality, further exacerbated by its ability to readily evolve drug resistance. It is well accepted that drug resistance in M. tuberculosis is driven by the acquisition of chromosomal mutations in genes encoding drug targets/promoter regions; however, a comprehensive description of the molecular mechanisms that fuel drug resistance in the clinical setting is currently lacking. In this context, there is a growing body of evidence suggesting that active extrusion of drugs from the cell is critical for drug tolerance. M. tuberculosis encodes representatives of a diverse range of multidrug transporters, many of which are dependent on the proton motive force (PMF) or the availability of ATP. This suggests that energy metabolism and ATP production through the PMF, which is established by the electron transport chain (ETC), are critical in determining the drug susceptibility of M. tuberculosis. In this review, we detail advances in the study of the mycobacterial ETC and highlight drugs that target various components of the ETC. We provide an overview of some of the efflux pumps present in M. tuberculosis and their association, if any, with drug transport and concomitant effects on drug resistance. The implications of inhibiting drug extrusion, through the use of efflux pump inhibitors, are also discussed.
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Affiliation(s)
- Philippa A. Black
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Gail E. Louw
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Thomas C. Victor
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Bavesh D. Kana
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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136
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An outer membrane channel protein of Mycobacterium tuberculosis with exotoxin activity. Proc Natl Acad Sci U S A 2014; 111:6750-5. [PMID: 24753609 DOI: 10.1073/pnas.1400136111] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The ability to control the timing and mode of host cell death plays a pivotal role in microbial infections. Many bacteria use toxins to kill host cells and evade immune responses. Such toxins are unknown in Mycobacterium tuberculosis. Virulent M. tuberculosis strains induce necrotic cell death in macrophages by an obscure molecular mechanism. Here we show that the M. tuberculosis protein Rv3903c (channel protein with necrosis-inducing toxin, CpnT) consists of an N-terminal channel domain that is used for uptake of nutrients across the outer membrane and a secreted toxic C-terminal domain. Infection experiments revealed that CpnT is required for survival and cytotoxicity of M. tuberculosis in macrophages. Furthermore, we demonstrate that the C-terminal domain of CpnT causes necrotic cell death in eukaryotic cells. Thus, CpnT has a dual function in uptake of nutrients and induction of host cell death by M. tuberculosis.
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137
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Liu B, Zhang X, Huang H, Zhang Y, Zhou F, Wang G. A novel molecular typing method of Mycobacteria based on DNA barcoding visualization. J Clin Bioinforma 2014; 4:4. [PMID: 24555538 PMCID: PMC3931916 DOI: 10.1186/2043-9113-4-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 02/10/2014] [Indexed: 11/10/2022] Open
Abstract
Different subtypes of Mycobacterium tuberculosis (MTB) may induce diverse severe human infections, and some of their symptoms are similar to other pathogenes, e.g. Nontuberculosis mycobacteria (NTM). So determination of mycobacterium subtypes facilitates the effective control of MTB infection and proliferation. This study exploits a novel DNA barcoding visualization method for molecular typing of 17 mycobacteria genomes published in the NCBI prokaryotic genome database. Three mycobacterium genes (Rv0279c, Rv3508 and Rv3514) from the PE/PPE family of MT Band were detected to best represent the inter-strain pathogenetic variations. An accurate and fast MTB substrain typing method was proposed based on the combination of the aforementioned three biomarker genes and the 16S rRNA gene. The protocol of establishing a bacterial substrain typing system used in this study may also be applied to the other pathogenes.
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Affiliation(s)
| | | | | | | | - Fengfeng Zhou
- Department of Pathogenobiology, Basic Medical College of Jilin University, Changchun, Jilin, China.
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138
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Gouzy A, Larrouy-Maumus G, Bottai D, Levillain F, Dumas A, Wallach JB, Caire-Brandli I, de Chastellier C, Wu TD, Poincloux R, Brosch R, Guerquin-Kern JL, Schnappinger D, Sório de Carvalho LP, Poquet Y, Neyrolles O. Mycobacterium tuberculosis exploits asparagine to assimilate nitrogen and resist acid stress during infection. PLoS Pathog 2014; 10:e1003928. [PMID: 24586151 PMCID: PMC3930563 DOI: 10.1371/journal.ppat.1003928] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/31/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis is an intracellular pathogen. Within macrophages, M. tuberculosis thrives in a specialized membrane-bound vacuole, the phagosome, whose pH is slightly acidic, and where access to nutrients is limited. Understanding how the bacillus extracts and incorporates nutrients from its host may help develop novel strategies to combat tuberculosis. Here we show that M. tuberculosis employs the asparagine transporter AnsP2 and the secreted asparaginase AnsA to assimilate nitrogen and resist acid stress through asparagine hydrolysis and ammonia release. While the role of AnsP2 is partially spared by yet to be identified transporter(s), that of AnsA is crucial in both phagosome acidification arrest and intracellular replication, as an M. tuberculosis mutant lacking this asparaginase is ultimately attenuated in macrophages and in mice. Our study provides yet another example of the intimate link between physiology and virulence in the tubercle bacillus, and identifies a novel pathway to be targeted for therapeutic purposes.
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Affiliation(s)
- Alexandre Gouzy
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Gérald Larrouy-Maumus
- Mycobacterial Research Division, MRC National Institute for Medical Research, London, United Kingdom
| | - Daria Bottai
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Florence Levillain
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Alexia Dumas
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Joshua B. Wallach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Irène Caire-Brandli
- Centre d'Immunologie de Marseille-Luminy (CIML), Inserm UMR 1104, CNRS UMR 7280, Aix-Marseille University UM 2, Marseille, France
| | - Chantal de Chastellier
- Centre d'Immunologie de Marseille-Luminy (CIML), Inserm UMR 1104, CNRS UMR 7280, Aix-Marseille University UM 2, Marseille, France
| | - Ting-Di Wu
- Institut Curie, Laboratoire de Microscopie Ionique, Orsay, France
- INSERM U759, Orsay, France
| | - Renaud Poincloux
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Roland Brosch
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, Paris, France
| | - Jean-Luc Guerquin-Kern
- Institut Curie, Laboratoire de Microscopie Ionique, Orsay, France
- INSERM U759, Orsay, France
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | | | - Yannick Poquet
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
| | - Olivier Neyrolles
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
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139
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Reengineering redox sensitive GFP to measure mycothiol redox potential of Mycobacterium tuberculosis during infection. PLoS Pathog 2014; 10:e1003902. [PMID: 24497832 PMCID: PMC3907381 DOI: 10.1371/journal.ppat.1003902] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/10/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) survives under oxidatively hostile environments encountered inside host phagocytes. To protect itself from oxidative stress, Mtb produces millimolar concentrations of mycothiol (MSH), which functions as a major cytoplasmic redox buffer. Here, we introduce a novel system for real-time imaging of mycothiol redox potential (EMSH ) within Mtb cells during infection. We demonstrate that coupling of Mtb MSH-dependent oxidoreductase (mycoredoxin-1; Mrx1) to redox-sensitive GFP (roGFP2; Mrx1-roGFP2) allowed measurement of dynamic changes in intramycobacterial EMSH with unprecedented sensitivity and specificity. Using Mrx1-roGFP2, we report the first quantitative measurements of EMSH in diverse mycobacterial species, genetic mutants, and drug-resistant patient isolates. These cellular studies reveal, for the first time, that the environment inside macrophages and sub-vacuolar compartments induces heterogeneity in EMSH of the Mtb population. Further application of this new biosensor demonstrates that treatment of Mtb infected macrophage with anti-tuberculosis (TB) drugs induces oxidative shift in EMSH , suggesting that the intramacrophage milieu and antibiotics cooperatively disrupt the MSH homeostasis to exert efficient Mtb killing. Lastly, we analyze the membrane integrity of Mtb cells with varied EMSH during infection and show that subpopulation with higher EMSH are susceptible to clinically relevant antibiotics, whereas lower EMSH promotes antibiotic tolerance. Together, these data suggest the importance of MSH redox signaling in modulating mycobacterial survival following treatment with anti-TB drugs. We anticipate that Mrx1-roGFP2 will be a major contributor to our understanding of redox biology of Mtb and will lead to novel strategies to target redox metabolism for controlling Mtb persistence.
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140
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Burian J, Ramón-García S, Howes CG, Thompson CJ. WhiB7, a transcriptional activator that coordinates physiology with intrinsic drug resistance inMycobacterium tuberculosis. Expert Rev Anti Infect Ther 2014; 10:1037-47. [DOI: 10.1586/eri.12.90] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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141
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Pandey R, Rodriguez GM. IdeR is required for iron homeostasis and virulence in Mycobacterium tuberculosis. Mol Microbiol 2013; 91:98-109. [PMID: 24205844 DOI: 10.1111/mmi.12441] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 01/07/2023]
Abstract
Iron is an essential but potentially harmful nutrient, poorly soluble in aerobic conditions, and not freely available in the human host. To acquire iron, bacteria have evolved high affinity iron acquisition systems that are expressed under iron limitation often in conjunction with virulence determinants. Because excess iron can be dangerous, intracellular iron must be tightly controlled. In mycobacteria, IdeR functions as a global iron dependent transcriptional regulator, but because inactivation of ideR is lethal for Mycobacterium tuberculosis, it has not been possible to use genetics to fully characterize this protein's function or examine the requirement of iron regulation during tuberculosis infection. In this work, a conditional M. tuberculosis ideR mutant was generated and used to study the basis of IdeR's essentiality. This investigation uncovered positive regulation of iron storage as a critical aspect of IdeR's function in regular culture and a prominent factor for survival under stresses associated with life in macrophages. Moreover, this study demonstrates that IdeR is indispensable in the mouse model of tuberculosis, thereby linking iron homeostasis to virulence in M. tuberculosis.
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Affiliation(s)
- Ruchi Pandey
- Public Health Research Institute at New Jersey Medical School, Rutgers State University of New Jersey, 225 Warren Street, Newark, NJ, 07103, USA
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142
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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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143
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Ramirez MV, Dawson CC, Crew R, England K, Slayden RA. MazF6 toxin of Mycobacterium tuberculosis demonstrates antitoxin specificity and is coupled to regulation of cell growth by a Soj-like protein. BMC Microbiol 2013; 13:240. [PMID: 24172039 PMCID: PMC3834876 DOI: 10.1186/1471-2180-13-240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/24/2013] [Indexed: 09/03/2023] Open
Abstract
Background Molecular programs employed by Mycobacterium tuberculosis (Mtb) for the establishment of non-replicating persistence (NRP) are poorly understood. In order to investigate mechanisms regulating entry into NRP, we asked how cell cycle regulation is linked to downstream adaptations that ultimately result in NRP. Based on previous reports and our recent studies, we reason that, in order to establish NRP, cells are halted in the cell cycle at the point of septum formation by coupled regulatory mechanisms. Results Using bioinformatic consensus modeling, we identified an alternative cell cycle regulatory element, SojMtb encoded by rv1708. SojMtb coordinates a regulatory mechanism involving cell cycle control at the point of septum formation and elicits the induction of the MazF6 toxin. MazF6 functions as an mRNA interferase leading to bacteriostasis that can be prevented by interaction with its cognate antitoxin, MazE6. Further, MazEF6 acts independently of other Maz family toxin:antitoxin pairs. Notably, sojMtb and mazEF6 transcripts where identified at 20, 40 and 100 days post-infection in increasing abundance indicating a role in adaption during chronic infection. Conclusions Here we present the first evidence of a coupled regulatory system in which cell cycle regulation via SojMtb is linked to downstream adaptations that are facilitated through the activity of the MazEF6 TA pair.
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Affiliation(s)
| | | | | | | | - Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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144
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Ramón-García S, Ng C, Jensen PR, Dosanjh M, Burian J, Morris RP, Folcher M, Eltis LD, Grzesiek S, Nguyen L, Thompson CJ. WhiB7, an Fe-S-dependent transcription factor that activates species-specific repertoires of drug resistance determinants in actinobacteria. J Biol Chem 2013; 288:34514-28. [PMID: 24126912 DOI: 10.1074/jbc.m113.516385] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WhiB-like (Wbl) proteins are well known for their diverse roles in actinobacterial morphogenesis, cell division, virulence, primary and secondary metabolism, and intrinsic antibiotic resistance. Gene disruption experiments showed that three different Actinobacteria (Mycobacterium smegmatis, Streptomyces lividans, and Rhodococcus jostii) each exhibited a different whiB7-dependent resistance profile. Heterologous expression of whiB7 genes showed these resistance profiles reflected the host's repertoire of endogenous whiB7-dependent genes. Transcriptional activation of two resistance genes in the whiB7 regulon, tap (a multidrug transporter) and erm(37) (a ribosomal methyltransferase), required interaction of WhiB7 with their promoters. Furthermore, heterologous expression of tap genes isolated from Mycobacterium species demonstrated that divergencies in drug specificity of homologous structural proteins contribute to the variation of WhiB7-dependent drug resistance. WhiB7 has a specific tryptophan/glycine-rich region and four conserved cysteine residues; it also has a peptide sequence (AT-hook) at its C terminus that binds AT-rich DNA sequence motifs upstream of the promoters it activates. Targeted mutagenesis showed that these motifs were required to provide antibiotic resistance in vivo. Anaerobically purified WhiB7 from S. lividans was dimeric and contained 2.1 ± 0.3 and 2.2 ± 0.3 mol of iron and sulfur, respectively, per protomer (consistent with the presence of a 2Fe-2S cluster). However, the properties of the dimer's absorption spectrum were most consistent with the presence of an oxygen-labile 4Fe-4S cluster, suggesting 50% occupancy. These data provide the first insights into WhiB7 iron-sulfur clusters as they exist in vivo, a major unresolved issue in studies of Wbl proteins.
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Affiliation(s)
- Santiago Ramón-García
- From the Department of Microbiology and Immunology, Centre for Tuberculosis Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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145
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Burian J, Yim G, Hsing M, Axerio-Cilies P, Cherkasov A, Spiegelman GB, Thompson CJ. The mycobacterial antibiotic resistance determinant WhiB7 acts as a transcriptional activator by binding the primary sigma factor SigA (RpoV). Nucleic Acids Res 2013; 41:10062-76. [PMID: 23990327 PMCID: PMC3905903 DOI: 10.1093/nar/gkt751] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Tuberculosis therapeutic options are limited by the high intrinsic antibiotic resistance of Mycobacterium tuberculosis. The putative transcriptional regulator WhiB7 is crucial for the activation of systems that provide resistance to diverse antibiotic classes. Here, we used in vitro run-off, two-hybrid assays, as well as mutagenic, complementation and protein pull-down experiments, to characterize WhiB7 as an auto-regulatory, redox-sensitive transcriptional activator in Mycobacterium smegmatis. We provide the first direct biochemical proof that a WhiB protein promotes transcription and also demonstrate that this activity is sensitive to oxidation (diamide). Its partner protein for transcriptional activation was identified as SigA, the primary sigma factor subunit of RNA polymerase. Residues required for the interaction mapped to region 4 of SigA (including R515H) or adjacent domains of WhiB7 (including E63D). WhiB7's ability to provide a specific spectrum of antibiotic-resistance was dependent on these residues as well as its C-terminal AT-hook module that binds to an AT-rich motif immediately upstream of the -35 hexamer recognized by SigA. These experimentally established constrains, combined with protein structure predictions, were used to generate a working model of the WhiB7-SigA-promoter complex. Inhibitors preventing WhiB7 interactions could allow the use of previously ineffective antibiotics for treatment of mycobacterial diseases.
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Affiliation(s)
- Ján Burian
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, Centre for Tuberculosis Research, University of British Columbia, Vancouver, Canada V6T 1Z3 and Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada V6T 1Z3
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146
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Arya S, Sethi D, Singh S, Hade MD, Singh V, Raju P, Chodisetti SB, Verma D, Varshney GC, Agrewala JN, Dikshit KL. Truncated hemoglobin, HbN, is post-translationally modified in Mycobacterium tuberculosis and modulates host-pathogen interactions during intracellular infection. J Biol Chem 2013; 288:29987-99. [PMID: 23983123 DOI: 10.1074/jbc.m113.507301] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a phenomenally successful human pathogen having evolved mechanisms that allow it to survive within the hazardous environment of macrophages and establish long term, persistent infection in the host against the control of cell-mediated immunity. One such mechanism is mediated by the truncated hemoglobin, HbN, of Mtb that displays a potent O2-dependent nitric oxide dioxygenase activity and protects its host from the toxicity of macrophage-generated nitric oxide (NO). Here we demonstrate for the first time that HbN is post-translationally modified by glycosylation in Mtb and remains localized on the cell membrane and the cell wall. The glycan linkage in the HbN was identified as mannose. The elevated expression of HbN in Mtb and M. smegmatis facilitated their entry within the macrophages as compared with isogenic control cells, and mutation in the glycan linkage of HbN disrupted this effect. Additionally, HbN-expressing cells exhibited higher survival within the THP-1 and mouse peritoneal macrophages, simultaneously increasing the intracellular level of proinflammatory cytokines IL-6 and TNF-α and suppressing the expression of co-stimulatory surface markers CD80 and CD86. These results, thus, suggest the involvement of HbN in modulating the host-pathogen interactions and immune system of the host apart from protecting the bacilli from nitrosative stress inside the activated macrophages, consequently driving cells toward increased infectivity and intracellular survival.
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Affiliation(s)
- Swati Arya
- From the Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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147
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Schuessler DL, Cortes T, Fivian-Hughes AS, Lougheed KEA, Harvey E, Buxton RS, Davis EO, Young DB. Induced ectopic expression of HigB toxin in Mycobacterium tuberculosis results in growth inhibition, reduced abundance of a subset of mRNAs and cleavage of tmRNA. Mol Microbiol 2013; 90:195-207. [PMID: 23927792 PMCID: PMC3912914 DOI: 10.1111/mmi.12358] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2013] [Indexed: 01/20/2023]
Abstract
In Mycobacterium tuberculosis, the genes Rv1954A-Rv1957 form an operon that includes Rv1955 and Rv1956 which encode the HigB toxin and the HigA antitoxin respectively. We are interested in the role and regulation of this operon, since toxin-antitoxin systems have been suggested to play a part in the formation of persister cells in mycobacteria. To investigate the function of the higBA locus, effects of toxin expression on mycobacterial growth and transcript levels were assessed in M. tuberculosis H37Rv wild type and in an operon deletion background. We show that expression of HigB toxin in the absence of HigA antitoxin arrests growth and causes cell death in M. tuberculosis. We demonstrate HigB expression to reduce the abundance of IdeR and Zur regulated mRNAs and to cleave tmRNA in M. tuberculosis, Escherichia coli and Mycobacterium smegmatis. This study provides the first identification of possible target transcripts of HigB in M. tuberculosis.
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Affiliation(s)
- Dorothée L Schuessler
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
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148
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Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00541-13. [PMID: 23908284 PMCID: PMC3731838 DOI: 10.1128/genomea.00541-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium tuberculosis East African Indian (EAI) strain OSDD271 from India.
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149
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Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice. mBio 2013; 4:mBio.00250-13. [PMID: 23900170 PMCID: PMC3735190 DOI: 10.1128/mbio.00250-13] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In infection experiments with genetically distinct Mycobacterium tuberculosis complex (MTBC) strains, we identified clade-specific virulence patterns in human primary macrophages and in mice infected by the aerosol route, both reflecting relevant model systems. Exclusively human-adapted M. tuberculosis lineages, also termed clade I, comprising “modern” lineages, such as Beijing and Euro-American Haarlem strains, showed a significantly enhanced capability to grow compared to that of clade II strains, which include “ancient” lineages, such as, e.g., East African Indian or M. africanum strains. However, a simple correlation of inflammatory response profiles with strain virulence was not apparent. Overall, our data reveal three different pathogenic profiles: (i) strains of the Beijing lineage are characterized by low uptake, low cytokine induction, and a high replicative potential, (ii) strains of the Haarlem lineage by high uptake, high cytokine induction, and high growth rates, and (iii) EAI strains by low uptake, low cytokine induction, and a low replicative potential. Our findings have significant implications for our understanding of host-pathogen interaction and factors that modulate the outcomes of infections. Future studies addressing the underlying mechanisms and clinical implications need to take into account the diversity of both the pathogen and the host. Clinical strains of the Mycobacterium tuberculosis complex (MTBC) are genetically more diverse than previously anticipated. Our analysis of mycobacterial growth characteristics in primary human macrophages and aerogenically infected mice shows that the MTBC genetic differences translate into pathogenic differences in the interaction with the host. Our study reveals for the first time that “TB is not TB,” if put in plain terms. We are convinced that it is very unlikely that a single molecular mechanism may explain the observed effects. Our study refutes the hypothesis that there is a simple correlation between cytokine induction as a single functional parameter of host interaction and mycobacterial virulence. Instead, careful consideration of strain- and lineage-specific characteristics must guide our attempts to decipher what determines the pathological potential and thus the outcomes of infection with MTBC, one of the most important human pathogens.
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150
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Macrophages in tuberculosis: friend or foe. Semin Immunopathol 2013; 35:563-83. [PMID: 23864058 DOI: 10.1007/s00281-013-0388-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/20/2013] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains one of the greatest threats to human health. The causative bacterium, Mycobacterium tuberculosis (Mtb), is acquired by the respiratory route. It is exquisitely human adapted and a prototypic intracellular pathogen of macrophages, with alveolar macrophages (AMs) being the primary conduit of infection and disease. The outcome of primary infection is most often a latently infected healthy human host, in whom the bacteria are held in check by the host immune response. Such individuals can develop active TB later in life with impairment in the immune system. In contrast, in a minority of infected individuals, the host immune response fails to control the growth of bacilli, and progressive granulomatous disease develops, facilitating spread of the bacilli via infectious aerosols coughed out into the environment and inhaled by new hosts. The molecular details of the Mtb-macrophage interaction continue to be elucidated. However, it is clear that a number of complex processes are involved at the different stages of infection that may benefit either the bacterium or the host. Macrophages demonstrate tremendous phenotypic heterogeneity and functional plasticity which, depending on the site and stage of infection, facilitate the diverse outcomes. Moreover, host responses vary depending on the specific characteristics of the infecting Mtb strain. In this chapter, we describe a contemporary view of the behavior of AMs and their interaction with various Mtb strains in generating unique immunologic lung-specific responses.
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