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Abedi V, Yeasin M, Zand R. Empirical study using network of semantically related associations in bridging the knowledge gap. J Transl Med 2014; 12:324. [PMID: 25428570 PMCID: PMC4252998 DOI: 10.1186/s12967-014-0324-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/11/2014] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The data overload has created a new set of challenges in finding meaningful and relevant information with minimal cognitive effort. However designing robust and scalable knowledge discovery systems remains a challenge. Recent innovations in the (biological) literature mining tools have opened new avenues to understand the confluence of various diseases, genes, risk factors as well as biological processes in bridging the gaps between the massive amounts of scientific data and harvesting useful knowledge. METHODS In this paper, we highlight some of the findings using a text analytics tool, called ARIANA--Adaptive Robust and Integrative Analysis for finding Novel Associations. RESULTS Empirical study using ARIANA reveals knowledge discovery instances that illustrate the efficacy of such tool. For example, ARIANA can capture the connection between the drug hexamethonium and pulmonary inflammation and fibrosis that caused the tragic death of a healthy volunteer in a 2001 John Hopkins asthma study, even though the abstract of the study was not part of the semantic model. CONCLUSION An integrated system, such as ARIANA, could assist the human expert in exploratory literature search by bringing forward hidden associations, promoting data reuse and knowledge discovery as well as stimulating interdisciplinary projects by connecting information across the disciplines.
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Affiliation(s)
- Vida Abedi
- The Center for Modeling Immunity to Entering Pathogens, Nutritional Immunology and Molecular Medicine Laboratory, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA.
| | - Mohammed Yeasin
- Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA.
- College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, TN, 38152, USA.
| | - Ramin Zand
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Motswaledi MS, Sekgwama R, Kasvosve I. Tuberculosis alters pancreatic enzymes in the absence of pancreatitis. Afr J Lab Med 2014; 3:129. [PMID: 29043180 PMCID: PMC5637765 DOI: 10.4102/ajlm.v3i1.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 07/17/2014] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Lipases and phospholipases are thought to contribute to the pathogenesis of Mycobacterium tuberculosis (MTB) infection. Genes coding for lipases, phospholipases and amylase are present in MTB, enabling the bacteria to produce these enzymes. OBJECTIVE To compare serum lipase and amylase activity levels in patients with tuberculosis (TB) against those of healthy controls. METHODS Serum lipase and amylase activity levels were measured in 99 patients and 143 healthy controls using the Vitros 250 Chemistry analyser. Reference ranges for serum lipase and amylase were 23-300 U/L and 30-110 U/L, respectively. RESULTS Lipase was higher in patients with MTB than in controls (81.5 IU/L versus 66.5 IU/L, p = 0.006). Similarly, amylase was higher in the MTB patient group (76 IU/L versus 60 IU/L, p < 0.001). The Pearson correlation coefficient for lipase versus amylase (R) was higher in the controls (R = 0.351, p < 0.0001) compared with MTB patients (R = 0.217, p = 0.035). Amongst MTB patients, lipase activity correlated positively with erythrocyte sedimentation rate (ESR) (R = 0.263, p = 0.013), but not with haemoglobin concentration or treatment duration. A weak inverse correlation was noted between ESR and treatment duration (R = -0.222, p = 0.028). CONCLUSION Pancreatic enzyme levels differ between MTB patients and normal controls; however, this difference still lies within the normal range. The concomitant increase of lipase with ESR, an inflammatory marker, could conceivably suggest a causal relationship. Further research is necessary to characterise MTB-derived enzymes for diagnostic and therapeutic utility.
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Affiliation(s)
- Modisa S Motswaledi
- Faculty of Health Sciences, Department of Medical Laboratory Sciences, University of Botswana, Botswana
| | | | - Ishmael Kasvosve
- Faculty of Health Sciences, Department of Medical Laboratory Sciences, University of Botswana, Botswana
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103
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Yamashiro LH, Oliveira SC, Báfica A. Innate immune sensing of nucleic acids from mycobacteria. Microbes Infect 2014; 16:991-7. [PMID: 25284681 DOI: 10.1016/j.micinf.2014.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/16/2023]
Abstract
Endosomal and cytosolic receptors engage recognition of mycobacterial-derived nucleic acids (MyNAs). In contrast, virulent mycobacteria may utilize nucleic acid recognition pathways to escape the host immune system. This short review will summarize the mechanisms by which MyNAs are sensed and how they influence host protective responses.
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Affiliation(s)
- Lívia Harumi Yamashiro
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Brazil; Pharmacology Graduate Program, Federal University of Santa Catarina, Brazil
| | - Sérgio Costa Oliveira
- Laboratory of Immunology and Infectious Diseases, Federal University of Minas Gerais, Brazil
| | - André Báfica
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Brazil; Pharmacology Graduate Program, Federal University of Santa Catarina, Brazil.
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104
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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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105
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Meißner T, Eckelt E, Basler T, Meens J, Heinzmann J, Suwandi A, Oelemann WMR, Trenkamp S, Holst O, Weiss S, Bunk B, Spröer C, Gerlach GF, Goethe R. The Mycobacterium avium ssp. paratuberculosis specific mptD gene is required for maintenance of the metabolic homeostasis necessary for full virulence in mouse infections. Front Cell Infect Microbiol 2014; 4:110. [PMID: 25177550 PMCID: PMC4132290 DOI: 10.3389/fcimb.2014.00110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/25/2014] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease, a chronic granulomatous enteritis in ruminants. Furthermore, infections of humans with MAP have been reported and a possible association with Crohn's disease and diabetes type I is currently discussed. MAP owns large sequence polymorphisms (LSPs) that were exclusively found in this mycobacteria species. The relevance of these LSPs in the pathobiology of MAP is still unclear. The mptD gene (MAP3733c) of MAP belongs to a small group of functionally uncharacterized genes, which are not present in any other sequenced mycobacteria species. mptD is part of a predicted operon (mptABCDEF), encoding a putative ATP binding cassette-transporter, located on the MAP-specific LSP14. In the present study, we generated an mptD knockout strain (MAPΔmptD) by specialized transduction. In order to investigate the potential role of mptD in the host, we performed infection experiments with macrophages. By this, we observed a significantly reduced cell number of MAPΔmptD early after infection, indicating that the mutant was hampered with respect to adaptation to the early macrophage environment. This important role of mptD was supported in mouse infection experiments where MAPΔmptD was significantly attenuated after peritoneal challenge. Metabolic profiling was performed to determine the cause for the reduced virulence and identified profound metabolic disorders especially in the lipid metabolism of MAPΔmptD. Overall our data revealed the mptD gene to be an important factor for the metabolic adaptation of MAP required for persistence in the host.
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Affiliation(s)
- Thorsten Meißner
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Elke Eckelt
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Tina Basler
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Jochen Meens
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Julia Heinzmann
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Abdulhadi Suwandi
- Helmholtz Centre for Infection Research, Molecular Immunology Braunschweig, Germany
| | - Walter M R Oelemann
- Departamento de Imunologia, Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro (UFRJ) Rio de Janeiro, Brazil ; Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences Borstel, Germany
| | | | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences Borstel, Germany
| | - Siegfried Weiss
- Helmholtz Centre for Infection Research, Molecular Immunology Braunschweig, Germany
| | - Boyke Bunk
- Bioinformatics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; German Centre of Infection Research, Partner Site Hannover-Braunschweig Braunschweig, Germany
| | - Cathrin Spröer
- Bioinformatics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; German Centre of Infection Research, Partner Site Hannover-Braunschweig Braunschweig, Germany
| | - Gerald-F Gerlach
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Ralph Goethe
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany
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106
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Mehrotra P, Jamwal SV, Saquib N, Sinha N, Siddiqui Z, Manivel V, Chatterjee S, Rao KVS. Pathogenicity of Mycobacterium tuberculosis is expressed by regulating metabolic thresholds of the host macrophage. PLoS Pathog 2014; 10:e1004265. [PMID: 25058590 PMCID: PMC4110042 DOI: 10.1371/journal.ppat.1004265] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 06/06/2014] [Indexed: 11/18/2022] Open
Abstract
The success of Mycobacterium tuberculosis as a pathogen derives from its facile adaptation to the intracellular milieu of human macrophages. To explore this process, we asked whether adaptation also required interference with the metabolic machinery of the host cell. Temporal profiling of the metabolic flux, in cells infected with differently virulent mycobacterial strains, confirmed that this was indeed the case. Subsequent analysis identified the core subset of host reactions that were targeted. It also elucidated that the goal of regulation was to integrate pathways facilitating macrophage survival, with those promoting mycobacterial sustenance. Intriguingly, this synthesis then provided an axis where both host- and pathogen-derived factors converged to define determinants of pathogenicity. Consequently, whereas the requirement for macrophage survival sensitized TB susceptibility to the glycemic status of the individual, mediation by pathogen ensured that the virulence properties of the infecting strain also contributed towards the resulting pathology. Mycobacterium tuberculosis (Mtb) is a highly successful human pathogen, representing the leading bacterial cause of death worldwide. Mtb infects macrophages and it adapts to the hostile intracellular milieu of this cell by exploiting the plasticity of its central carbon metabolism machinery. While several studies have detailed the bacterial adaptations that accompany infection, it is still unclear whether this process also involves engagement with host metabolic pathways. We therefore profiled the kinetic flux of host cell metabolites in macrophages that were infected with differently virulent Mtb strains. Interestingly, we found that Mtb pathogenicity was indeed intimately linked to its capacity to regulate host cell metabolism. A unique subset of host pathways was targeted so as to integrate the glycolytic threshold governing macrophage viability with mechanisms ensuring intracellular bacterial survival. Perturbation of macrophage glycolytic flux was enforced through pathogen-induced enhancement in glucose uptake, which in turn was also influenced by the extracellular glucose concentration. This observation rationalizes the increased susceptibility of diabetic individuals to TB infection Interestingly, Mtb strains also differed in their capacities to stimulate macrophage glucose uptake. Consequently, the resulting pathology is likely dictated both by the individual's glycemic status, and the nature of the infecting strain.
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Affiliation(s)
- Parul Mehrotra
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shilpa V. Jamwal
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Najmuddin Saquib
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Neeraj Sinha
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Zaved Siddiqui
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Venkatasamy Manivel
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Samrat Chatterjee
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kanury V. S. Rao
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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107
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Mycobacterial gene cuvA is required for optimal nutrient utilization and virulence. Infect Immun 2014; 82:4104-17. [PMID: 25047842 DOI: 10.1128/iai.02207-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To persist and cause disease in the host, Mycobacterium tuberculosis must adapt to its environment during infection. Adaptations include changes in nutrient utilization and alterations in growth rate. M. tuberculosis Rv1422 is a conserved gene of unknown function that was found in a genetic screen to interact with the mce4 cholesterol uptake locus. The Rv1422 protein is phosphorylated by the M. tuberculosis Ser/Thr kinases PknA and PknB, which regulate cell growth and cell wall synthesis. Bacillus subtilis strains lacking the Rv1422 homologue yvcK grow poorly on several carbon sources, and yvcK is required for proper localization of peptidoglycan synthesis. Here we show that Mycobacterium smegmatis and M. tuberculosis strains lacking Rv1422 have growth defects in minimal medium containing limiting amounts of several different carbon sources. These strains also have morphological abnormalities, including shortened and bulging cells, suggesting a cell wall defect. In both mycobacterial species, the Rv1422 protein localizes uniquely to the growing cell pole, the site of peptidoglycan synthesis in mycobacteria. An M. tuberculosis ΔRv1422 strain is markedly attenuated for virulence in a mouse infection model, where it elicits decreased inflammation in the lungs and shows impaired bacterial persistence. These findings led us to name this gene cuvA (carbon utilization and virulence protein A) and to suggest a model in which deletion of cuvA leads to changes in nutrient uptake and/or metabolism that affect cell wall structure, morphology, and virulence. Its role in virulence suggests that CuvA may be a useful target for novel inhibitors of M. tuberculosis during infection.
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108
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Parameswaran S, Saudagar P, Dubey VK, Patra S. Discovery of novel anti-leishmanial agents targeting LdLip3 lipase. J Mol Graph Model 2014; 49:68-79. [DOI: 10.1016/j.jmgm.2014.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/19/2014] [Accepted: 01/20/2014] [Indexed: 10/27/2022]
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110
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111
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Non-replicating Mycobacterium tuberculosis elicits a reduced infectivity profile with corresponding modifications to the cell wall and extracellular matrix. PLoS One 2014; 9:e87329. [PMID: 24516549 PMCID: PMC3916317 DOI: 10.1371/journal.pone.0087329] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 12/20/2013] [Indexed: 12/21/2022] Open
Abstract
A key feature of Mycobacterium tuberculosis is its ability to become dormant in the host. Little is known of the mechanisms by which these bacilli are able to persist in this state. Therefore, the focus of this study was to emulate environmental conditions encountered by M. tuberculosis in the granuloma, and determine the effect of such conditions on the physiology and infectivity of the organism. Non-replicating persistent (NRP) M. tuberculosis was established by the gradual depletion of nutrients in an oxygen-replete and controlled environment. In contrast to rapidly dividing bacilli, NRP bacteria exhibited a distinct phenotype by accumulating an extracellular matrix rich in free mycolate and lipoglycans, with increased arabinosylation. Microarray studies demonstrated a substantial down-regulation of genes involved in energy metabolism in NRP bacteria. Despite this reduction in metabolic activity, cells were still able to infect guinea pigs, but with a delay in the development of disease when compared to exponential phase bacilli. Using these approaches to investigate the interplay between the changing environment of the host and altered physiology of NRP bacteria, this study sheds new light on the conditions that are pertinent to M. tuberculosis dormancy and how this organism could be establishing latent disease.
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112
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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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113
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Shleeva M, Goncharenko A, Kudykina Y, Young D, Young M, Kaprelyants A. Cyclic AMP-dependent resuscitation of dormant Mycobacteria by exogenous free fatty acids. PLoS One 2013; 8:e82914. [PMID: 24376605 PMCID: PMC3871856 DOI: 10.1371/journal.pone.0082914] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/29/2013] [Indexed: 12/26/2022] Open
Abstract
One third of the world population carries a latent tuberculosis (TB) infection, which may reactivate leading to active disease. Although TB latency has been known for many years it remains poorly understood. In particular, substances of host origin, which may induce the resuscitation of dormant mycobacteria, have not yet been described. In vitro models of dormant ("non-culturable") cells of Mycobacterium smegmatis (mc(2)155) and Mycobacterium tuberculosis H37Rv were used. We found that the resuscitation of dormant M. smegmatis and M. tuberculosis cells in liquid medium was stimulated by adding free unsaturated fatty acids (FA), including arachidonic acid, at concentrations of 1.6-10 µM. FA addition enhanced cAMP levels in reactivating M. smegmatis cells and exogenously added cAMP (3-10 mM) or dibutyryl-cAMP (0.5-1 mM) substituted for FA, causing resuscitation of M. smegmatis and M. tuberculosis dormant cells. A M. smegmatis null-mutant lacking MSMEG_4279, which encodes a FA-activated adenylyl cyclase (AC), could not be resuscitated by FA but it was resuscitated by cAMP. M. smegmatis and M. tuberculosis cells hyper-expressing AC were unable to form non-culturable cells and a specific inhibitor of AC (8-bromo-cAMP) prevented FA-dependent resuscitation. RT-PCR analysis revealed that rpfA (coding for resuscitation promoting factor A) is up-regulated in M. smegmatis in the beginning of exponential growth following the cAMP increase in lag phase caused by FA-induced cell activation. A specific Rpf inhibitor (4-benzoyl-2-nitrophenylthiocyanate) suppressed FA-induced resuscitation. We propose a novel pathway for the resuscitation of dormant mycobacteria involving the activation of adenylyl cyclase MSMEG_4279 by FAs resulted in activation of cellular metabolism followed later by increase of RpfA activity which stimulates cell multiplication in exponential phase. The study reveals a probable role for lipids of host origin in the resuscitation of dormant mycobacteria, which may function during the reactivation of latent TB.
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Affiliation(s)
- Margarita Shleeva
- Bach Institute of Biochemistry Russian Academy of Sciences, Moscow, Russia
| | - Anna Goncharenko
- Bach Institute of Biochemistry Russian Academy of Sciences, Moscow, Russia
| | - Yuliya Kudykina
- Bach Institute of Biochemistry Russian Academy of Sciences, Moscow, Russia
| | - Danielle Young
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Michael Young
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Arseny Kaprelyants
- Bach Institute of Biochemistry Russian Academy of Sciences, Moscow, Russia
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114
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Zimmermann M, Thormann V, Sauer U, Zamboni N. Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry. Anal Chem 2013; 85:8284-90. [PMID: 23895734 DOI: 10.1021/ac401555n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coenzyme A (CoA) thioesters are ubiquitously present in metabolic networks and play a pivotal role in enzymatic formation and cleavage of carbon-carbon bonds. We present a method allowing nontargeted profiling of CoA-thioesters in biological samples. The reported UHPLC-MS/MS approach employes ion-pairing chromatography to separate CoA-metabolites carrying different chemical functionalities such as hydroxyl or multiple carboxyl groups and to distinguish between isomers. Selective detection of CoA-thioesters is accomplished by precursor ion scanning on a triple quadrupole mass spectrometer and takes advantage of the abundant fragment with m/z = -408 that originates from the CoA-moiety. We used a mixture of 19 commercially available CoA-derivatives to develop and optimize our method. As a proof of concept we demonstrated detection of the major CoA-intermediates of branched chain amino acid degradation in biological samples. We then applied our method to investigate degradation of lipids in the microorganism Mycobacterium smegmatis. Profiling of CoA-thioesters led to the discovery of a novel intermediate of cholesterol degradation. This demonstrates the power of our method for untargeted profiling of CoA-thioesters and adds a missing link in mycobacterial cholesterol catabolism.
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Affiliation(s)
- Michael Zimmermann
- Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland
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115
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O'Garra A, Redford PS, McNab FW, Bloom CI, Wilkinson RJ, Berry MPR. The immune response in tuberculosis. Annu Rev Immunol 2013; 31:475-527. [PMID: 23516984 DOI: 10.1146/annurev-immunol-032712-095939] [Citation(s) in RCA: 898] [Impact Index Per Article: 81.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There are 9 million cases of active tuberculosis reported annually; however, an estimated one-third of the world's population is infected with Mycobacterium tuberculosis and remains asymptomatic. Of these latent individuals, only 5-10% will develop active tuberculosis disease in their lifetime. CD4(+) T cells, as well as the cytokines IL-12, IFN-γ, and TNF, are critical in the control of Mycobacterium tuberculosis infection, but the host factors that determine why some individuals are protected from infection while others go on to develop disease are unclear. Genetic factors of the host and of the pathogen itself may be associated with an increased risk of patients developing active tuberculosis. This review aims to summarize what we know about the immune response in tuberculosis, in human disease, and in a range of experimental models, all of which are essential to advancing our mechanistic knowledge base of the host-pathogen interactions that influence disease outcome.
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Affiliation(s)
- Anne O'Garra
- Division of Immunoregulation, MRC National Institute for Medical Research, London NW7 1AA, UK.
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116
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Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. Proc Natl Acad Sci U S A 2013; 110:7820-5. [PMID: 23610393 DOI: 10.1073/pnas.1218599110] [Citation(s) in RCA: 720] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Immunoresponsive gene 1 (Irg1) is highly expressed in mammalian macrophages during inflammation, but its biological function has not yet been elucidated. Here, we identify Irg1 as the gene coding for an enzyme producing itaconic acid (also known as methylenesuccinic acid) through the decarboxylation of cis-aconitate, a tricarboxylic acid cycle intermediate. Using a gain-and-loss-of-function approach in both mouse and human immune cells, we found Irg1 expression levels correlating with the amounts of itaconic acid, a metabolite previously proposed to have an antimicrobial effect. We purified IRG1 protein and identified its cis-aconitate decarboxylating activity in an enzymatic assay. Itaconic acid is an organic compound that inhibits isocitrate lyase, the key enzyme of the glyoxylate shunt, a pathway essential for bacterial growth under specific conditions. Here we show that itaconic acid inhibits the growth of bacteria expressing isocitrate lyase, such as Salmonella enterica and Mycobacterium tuberculosis. Furthermore, Irg1 gene silencing in macrophages resulted in significantly decreased intracellular itaconic acid levels as well as significantly reduced antimicrobial activity during bacterial infections. Taken together, our results demonstrate that IRG1 links cellular metabolism with immune defense by catalyzing itaconic acid production.
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117
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Nambi S, Gupta K, Bhattacharyya M, Ramakrishnan P, Ravikumar V, Siddiqui N, Thomas AT, Visweswariah SS. Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism. J Biol Chem 2013; 288:14114-14124. [PMID: 23553634 DOI: 10.1074/jbc.m113.463992] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetylation of lysine residues is a posttranslational modification that is used by both eukaryotes and prokaryotes to regulate a variety of biological processes. Here we identify multiple substrates for the cAMP-dependent protein lysine acetyltransferase from Mycobacterium tuberculosis (KATmt). We demonstrate that a catalytically important lysine residue in a number of FadD (fatty acyl CoA synthetase) enzymes is acetylated by KATmt in a cAMP-dependent manner and that acetylation inhibits the activity of FadD enzymes. A sirtuin-like enzyme can deacetylate multiple FadDs, thus completing the regulatory cycle. Using a strain deleted for the KATmt ortholog in Mycobacterium bovis Bacillus Calmette-Guérin (BCG), we show for the first time that acetylation is dependent on intracellular cAMP levels. KATmt can utilize propionyl CoA as a substrate and, therefore, plays a critical role in alleviating propionyl CoA toxicity in mycobacteria by inactivating acyl CoA synthetase (ACS). The precision by which mycobacteria can regulate the metabolism of fatty acids in a cAMP-dependent manner appears to be unparalleled in other biological organisms and is ideally suited to adapt to the complex environment that pathogenic mycobacteria experience in the host.
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Affiliation(s)
- Subhalaxmi Nambi
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Parvathy Ramakrishnan
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Vaishnavi Ravikumar
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Nida Siddiqui
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Ann Terene Thomas
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India.
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118
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Morris D, Guerra C, Khurasany M, Guilford F, Saviola B, Huang Y, Venketaraman V. Glutathione supplementation improves macrophage functions in HIV. J Interferon Cytokine Res 2013; 33:270-9. [PMID: 23409922 DOI: 10.1089/jir.2012.0103] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this study, we determined the effects of glutathione (GSH)-enhancing agents in restoring the levels of GSH in isolated macrophages from individuals with HIV infection thereby resulting in improved control of Mycobacterium tuberculosis. Our results indicate that treatment with N-acetyl cysteine or a liposomal formulation of glutathione (lGSH) resulted in replenishment of reduced also known as free GSH (rGSH), and correlated with a decrease in the intracellular growth of M. tuberculosis. Finally, we observed differences in the amount of the catalytic subunit of glutamine-cysteine ligase (GCLC), glutathione synthase, and glutathione reductase present in macrophages derived from healthy and HIV-infected individuals. These changes correlated with changes in free radicals as well as rGSH levels. Our results indicate that HIV infection leads to increased production of free radicals and decreased production of GCLC resulting in depletion of rGSH and this may lead, in part, to the loss of innate immune function observed in HIV patients. These findings represent a novel mechanism for control of M. tuberculosis infection, and a possible supplement to current HIV treatments.
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Affiliation(s)
- Devin Morris
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
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119
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Weigoldt M, Meens J, Bange FC, Pich A, Gerlach GF, Goethe R. Metabolic adaptation of Mycobacterium avium subsp. paratuberculosis to the gut environment. Microbiology (Reading) 2013; 159:380-391. [DOI: 10.1099/mic.0.062737-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mathias Weigoldt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Medical School Hannover, Hannover, Germany
| | - Gerald F. Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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120
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Lee W, VanderVen BC, Fahey RJ, Russell DG. Intracellular Mycobacterium tuberculosis exploits host-derived fatty acids to limit metabolic stress. J Biol Chem 2013; 288:6788-800. [PMID: 23306194 DOI: 10.1074/jbc.m112.445056] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent data indicate that the nutrients available to Mycobacterium tuberculosis (Mtb) inside its host cell are restricted in their diversity. Fatty acids and cholesterol appear more favored; however, their degradation can result in certain metabolic stresses. Their breakdown can generate propionyl-CoA, which gives rise to potentially toxic intermediates. Detoxification of propionyl-CoA relies on the activity of the methylcitrate cycle, the methylmalonyl pathway, or incorporation of the propionyl-CoA into methyl-branched lipids in the cell wall. The current work explores carbon flux through these pathways, focusing primarily on those pathways responsible for the incorporation of propionyl-CoA into virulence-associated cell wall lipids. Exploiting both genetic and biochemical rescue, we demonstrate that these metabolic pressures are experienced by Mtb inside its host macrophage and that the bacterium accesses host fatty acid stores. The metabolism of these host lipids expands the acetyl-CoA pool and alleviates the pressure from propionyl-CoA. These data have major implications for our appreciation of central metabolism of Mtb during the course of infection.
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Affiliation(s)
- Wonsik Lee
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
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121
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Podinovskaia M, Lee W, Caldwell S, Russell DG. Infection of macrophages with Mycobacterium tuberculosis induces global modifications to phagosomal function. Cell Microbiol 2013; 15:843-59. [PMID: 23253353 DOI: 10.1111/cmi.12092] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 01/01/2023]
Abstract
The phagosome is a central mediator of both the homeostatic and microbicidal functions of a macrophage. Following phagocytosis, Mycobacterium tuberculosis (Mtb) is able to establish infection through arresting phagosome maturation and avoiding the consequences of delivery to the lysosome. The infection of a macrophage by Mtb leads to marked changes in the behaviour of both the macrophage and the surrounding tissue as the bacterium modulates its environment to promote its survival. In this study, we use functional physiological assays to probe the biology of the phagosomal network in Mtb-infected macrophages. The resulting data demonstrate that Mtb modifies phagosomal function in a TLR2/TLR4-dependent manner, and that most of these modifications are consistent with an increase in the activation status of the cell. Specifically, superoxide burst is enhanced and lipolytic activity is decreased upon infection. There are some species- or cell type-specific differences between human and murine macrophages in the rates of acidification and the degree of proteolysis. However, the most significant modification is the marked reduction in intra-phagosomal lipolysis because this correlates with the marked increase in the retention of host lipids in the infected macrophage, which provides a potential source of nutrients that can be accessed by Mtb.
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Affiliation(s)
- Maria Podinovskaia
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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122
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Russell DG. The evolutionary pressures that have molded Mycobacterium tuberculosis into an infectious adjuvant. Curr Opin Microbiol 2013; 16:78-84. [PMID: 23290190 DOI: 10.1016/j.mib.2012.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is highly immunogenic and appears to have evolved to preserve its antigenicity. The retention of antigenicity is important to the maintenance of a robust immune response that contributes greatly to the late-stage tissue damage required for transmission and completion of the pathogen's life cycle. Bacterial persistence is achieved through the remodeling of the tissue at site of infection and maintaining the lymphocytes at a distance from the infected macrophages in the granuloma core. The tissue metabolism within the granuloma leads to lipid sequestration that supports bacterial growth. However, growth on host lipids places metabolic stresses on Mtb, which has evolved to incorporate potentially harmful metabolic intermediates into the very cell wall lipids that induce the remodeling of the host tissue response.
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Affiliation(s)
- David G Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
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123
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Pitt JM, Blankley S, McShane H, O'Garra A. Vaccination against tuberculosis: how can we better BCG? Microb Pathog 2012; 58:2-16. [PMID: 23257069 DOI: 10.1016/j.micpath.2012.12.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/05/2012] [Accepted: 12/06/2012] [Indexed: 01/01/2023]
Abstract
Tuberculosis remains one of the most significant human diseases of the developing world, accounting for 3800 worldwide deaths per day. Although we currently have a vaccine for tuberculosis, BCG, this is insufficient at protecting from adult pulmonary tuberculosis in the parts of the world where a good vaccine is most needed. This has prompted the search for new vaccination strategies that can protect better than BCG, or can boost BCG-induced immunity. We discuss these subjects in line with what is known of the immune responses to BCG and Mycobacterium tuberculosis - the etiological agent of the disease, as well as the particular difficulties facing development of new vaccines against tuberculosis. A greater understanding of the factors constituting optimal protection against Mycobacterium tuberculosis infection, as well as which pathogenic factors facilitate active disease, will accelerate the delivery of safe vaccines able to restrict active tuberculosis and thus impede contagion.
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Affiliation(s)
- Jonathan M Pitt
- Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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124
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Zhang L, Li W, He ZG. DarR, a TetR-like transcriptional factor, is a cyclic di-AMP-responsive repressor in Mycobacterium smegmatis. J Biol Chem 2012; 288:3085-96. [PMID: 23250743 DOI: 10.1074/jbc.m112.428110] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclic dinucleotides, including cyclic di-AMP (c-di-AMP), are known to be ubiquitous second messengers involved in bacterial signal transduction. However, no transcriptional regulator has been characterized as a c-di-AMP receptor/effector to date. In the present study, using a c-di-AMP/transcription factor binding screen, we identified Ms5346, a TetR family regulator in Mycobacterium smegmatis, as a c-di-AMP receptor in bacteria. Ms5346 could specifically bind c-di-AMP with K(d) of 2.3 ± 0.5 μM. Using EMSA and DNase I footprinting assays, c-di-AMP was found to stimulate the DNA binding activity of Ms5346 and to enhance its ability to protect its target DNA sequence. A conserved 14-bp palindromic motif was identified as the DNA-binding site for Ms5346. Further, Ms5346 was found to negatively regulate expression of three target genes including Ms5347 (encoding a major facilitator family transporter), Ms5348 (encoding a medium chain fatty acyl-CoA ligase), and Ms5696 (encoding a cold shock protein, CspA). Ms5346 is the first cyclic di-AMP receptor regulator to be identified in bacteria, and we have designated it as DarR. Our findings enhance our understanding of the function and regulatory mechanism of the second messenger c-di-AMP in bacteria.
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Affiliation(s)
- Lei Zhang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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125
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Casabon I, Crowe AM, Liu J, Eltis LD. FadD3 is an acyl-CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria. Mol Microbiol 2012; 87:269-83. [PMID: 23146019 DOI: 10.1111/mmi.12095] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2012] [Indexed: 01/28/2023]
Abstract
The cholesterol catabolic pathway occurs in most mycolic acid-containing actinobacteria, such as Rhodococcus jostii RHA1, and is critical for Mycobacterium tuberculosis (Mtb) during infection. FadD3 is one of four predicted acyl-CoA synthetases potentially involved in cholesterol catabolism. A ΔfadD3 mutant of RHA1 grew on cholesterol to half the yield of wild-type and accumulated 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), consistent with the catabolism of half the steroid molecule. This phenotype was rescued by fadD3 of Mtb. Moreover, RHA1 but not ΔfadD3 grew on HIP. Purified FadD3(Mtb) catalysed the ATP-dependent CoA thioesterification of HIP and its hydroxylated analogues, 5α-OH HIP and 1β-OH HIP. The apparent specificity constant (k(cat) /K(m) ) of FadD3(Mtb) for HIP was 7.3 ± 0.3 × 10(5) M(-1) s(-1) , 165 times higher than for 5α-OH HIP, while the apparent K(m) for CoASH was 110 ± 10 μM. In contrast to enzymes involved in the catabolism of rings A and B, FadD3(Mtb) did not detectably transform a metabolite with a partially degraded C17 side-chain. Overall, these results indicate that FadD3 is a HIP-CoA synthetase that initiates catabolism of steroid rings C and D after side-chain degradation is complete. These findings are consistent with the actinobacterial kstR2 regulon encoding ring C/D degradation enzymes.
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Affiliation(s)
- Israël Casabon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
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126
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Uplekar S, Rougemont J, Cole ST, Sala C. High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Res 2012; 41:961-77. [PMID: 23222129 PMCID: PMC3553938 DOI: 10.1093/nar/gks1260] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dynamics of RNA polymerase (RNAP) and the anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the data sets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.
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Affiliation(s)
- Swapna Uplekar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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127
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Skvortsov TA, Azhikina TL. [Adaptive changes of Mycobacterium tuberculosis gene expression during the infectious process]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [PMID: 23189553 DOI: 10.1134/s1068162012040139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mycobacterium tuberculosis causes an infection in humans with clinical manifestations varying from asymptomatic carriage of bacteria to rapidly progressing tuberculosis. Infection outcomes depend on complex and still not fully understood interactions between the pathogenic bacteria and their host organism. Gene expression changes in response to host defense mechanisms are needed for M. tuberculosis survival and functioning. This review focuses on the analysis of dynamic changes in the M. tuberculosis transcriptome taking place during infection processes in host tissues. Presently available data on mycobacterial transcriptome changes obtained from different infection models are discussed. A major part of this review is devoted to the description of biochemical changes occurring in M. tuberculosis infection process, from the primary through latent infection to pathogen reactivation. At each stage of the infection, gene expression changes and induced bacterial metabolic variations are discussed.
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128
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Singh V, Jamwal S, Jain R, Verma P, Gokhale R, Rao KVS. Mycobacterium tuberculosis-driven targeted recalibration of macrophage lipid homeostasis promotes the foamy phenotype. Cell Host Microbe 2012; 12:669-81. [PMID: 23159056 DOI: 10.1016/j.chom.2012.09.012] [Citation(s) in RCA: 203] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/27/2012] [Accepted: 09/17/2012] [Indexed: 11/28/2022]
Abstract
Upon infection, Mycobacterium tuberculosis (Mtb) metabolically alters the macrophage to create a niche that is ideally suited to its persistent lifestyle. Infected macrophages acquire a "foamy" phenotype characterized by the accumulation of lipid bodies (LBs), which serve as both a source of nutrients and a secure niche for the bacterium. While the functional significance of the foamy phenotype is appreciated, the biochemical pathways mediating this process are understudied. We found that Mtb induces the foamy phenotype via targeted manipulation of host cellular metabolism to divert the glycolytic pathway toward ketone body synthesis. This dysregulation enabled feedback activation of the anti-lipolytic G protein-coupled receptor GPR109A, leading to perturbations in lipid homeostasis and consequent accumulation of LBs in the macrophage. ESAT-6, a secreted Mtb virulence factor, mediates the enforcement of this feedback loop. Finally, we demonstrate that pharmacological targeting of pathways mediating this host-pathogen metabolic crosstalk provides a potential strategy for developing tuberculosis chemotherapy.
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Affiliation(s)
- Varshneya Singh
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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129
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Khare S, Lawhon SD, Drake KL, Nunes JES, Figueiredo JF, Rossetti CA, Gull T, Everts RE, Lewin HA, Galindo CL, Garner HR, Adams LG. Systems biology analysis of gene expression during in vivo Mycobacterium avium paratuberculosis enteric colonization reveals role for immune tolerance. PLoS One 2012; 7:e42127. [PMID: 22912686 PMCID: PMC3422314 DOI: 10.1371/journal.pone.0042127] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 07/03/2012] [Indexed: 12/31/2022] Open
Abstract
Survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP) in the intestinal mucosa is associated with host immune tolerance. However, the initial events during MAP interaction with its host that lead to pathogen survival, granulomatous inflammation, and clinical disease progression are poorly defined. We hypothesize that immune tolerance is initiated upon initial contact of MAP with the intestinal Peyer's patch. To test our hypothesis, ligated ileal loops in neonatal calves were infected with MAP. Intestinal tissue RNAs were collected (0.5, 1, 2, 4, 8 and 12 hrs post-infection), processed, and hybridized to bovine gene expression microarrays. By comparing the gene transcription responses of calves infected with the MAP, informative complex patterns of expression were clearly visible. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis, and genes were grouped into the specific pathways and gene ontology categories to create a holistic model. This model revealed three different phases of responses: i) early (30 min and 1 hr post-infection), ii) intermediate (2, 4 and 8 hrs post-infection), and iii) late (12 hrs post-infection). We describe here the data that include expression profiles for perturbed pathways, as well as, mechanistic genes (genes predicted to have regulatory influence) that are associated with immune tolerance. In the Early Phase of MAP infection, multiple pathways were initiated in response to MAP invasion via receptor mediated endocytosis and changes in intestinal permeability. During the Intermediate Phase, perturbed pathways involved the inflammatory responses, cytokine-cytokine receptor interaction, and cell-cell signaling. During the Late Phase of infection, gene responses associated with immune tolerance were initiated at the level of T-cell signaling. Our study provides evidence that MAP infection resulted in differentially regulated genes, perturbed pathways and specifically modified mechanistic genes contributing to the colonization of Peyer's patch.
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Affiliation(s)
- Sangeeta Khare
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kenneth L. Drake
- Seralogix, Limited Liability Company, Austin, Texas, United States of America
| | - Jairo E. S. Nunes
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Josely F. Figueiredo
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Carlos A. Rossetti
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tamara Gull
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Robin E. Everts
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Harris A. Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Cristi L. Galindo
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Harold R. Garner
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Leslie Garry Adams
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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130
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Behler F, Steinwede K, Balboa L, Ueberberg B, Maus R, Kirchhof G, Yamasaki S, Welte T, Maus UA. Role of Mincle in alveolar macrophage-dependent innate immunity against mycobacterial infections in mice. THE JOURNAL OF IMMUNOLOGY 2012; 189:3121-9. [PMID: 22869905 DOI: 10.4049/jimmunol.1201399] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The role of macrophage-inducible C-type lectin Mincle in lung innate immunity against mycobacterial infection is incompletely defined. In this study, we show that wild-type (WT) mice responded with a delayed Mincle induction on resident alveolar macrophages and newly immigrating exudate macrophages to infection with Mycobacterium bovis bacillus Calmette-Guérin (BCG), peaking by days 14-21 posttreatment. As compared with WT mice, Mincle knockout (KO) mice exhibited decreased proinflammatory mediator responses and leukocyte recruitment upon M. bovis BCG challenge, and they demonstrated increased mycobacterial loads in pulmonary and extrapulmonary organ systems. Secondary mycobacterial infection on day 14 after primary BCG challenge led to increased cytokine gene expression in sorted alveolar macrophages of WT mice, but not Mincle KO mice, resulting in substantially reduced alveolar neutrophil recruitment and increased mycobacterial loads in the lungs of Mincle KO mice. Collectively, these data show that WT mice respond with a relatively late Mincle expression on lung sentinel cells to M. bovis BCG infection. Moreover, M. bovis BCG-induced upregulation of C-type lectin Mincle on professional phagocytes critically shapes antimycobacterial responses in both pulmonary and extrapulmonary organ systems of mice, which may be important for elucidating the role of Mincle in the control of mycobacterial dissemination in mice.
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Affiliation(s)
- Friederike Behler
- Department of Experimental Pneumology, Hannover Medical School, Hannover 30625, Germany
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131
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Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PLoS Pathog 2012; 8:e1002769. [PMID: 22737072 PMCID: PMC3380936 DOI: 10.1371/journal.ppat.1002769] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 05/07/2012] [Indexed: 12/27/2022] Open
Abstract
Intracellular pathogens such as Mycobacterium tuberculosis have evolved strategies for coping with the pressures encountered inside host cells. The ability to coordinate global gene expression in response to environmental and internal cues is one key to their success. Prolonged survival and replication within macrophages, a key virulence trait of M. tuberculosis, requires dynamic adaptation to diverse and changing conditions within its phagosomal niche. However, the physiological adaptations during the different phases of this infection process remain poorly understood. To address this knowledge gap, we have developed a multi-tiered approach to define the temporal patterns of gene expression in M. tuberculosis in a macrophage infection model that extends from infection, through intracellular adaptation, to the establishment of a productive infection. Using a clock plasmid to measure intracellular replication and death rates over a 14-day infection and electron microscopy to define bacterial integrity, we observed an initial period of rapid replication coupled with a high death rate. This was followed by period of slowed growth and enhanced intracellular survival, leading finally to an extended period of net growth. The transcriptional profiles of M. tuberculosis reflect these physiological transitions as the bacterium adapts to conditions within its host cell. Finally, analysis with a Transcriptional Regulatory Network model revealed linked genetic networks whereby M. tuberculosis coordinates global gene expression during intracellular survival. The integration of molecular and cellular biology together with transcriptional profiling and systems analysis offers unique insights into the host-driven responses of intracellular pathogens such as M. tuberculosis. The impact of Mycobacterium tuberculosis on global health is undeniable, with ∼2 million deaths and ∼9 million new cases of tuberculosis each year. A key to the success of M. tuberculosis as a persistent, intracellular pathogen is its ability to survive for extended periods within professional phagocytes. Sustained growth within macrophage phagosomes requires avoiding or resisting antimicrobial mechanisms and adapting to replicate in a stressful, nutrient-restricted environment. Our understanding of the survival strategies, metabolism, and physiology of M. tuberculosis during intracellular growth remains incomplete. We employed multi-disciplinary approaches to gain new insights into adaptive responses that M. tuberculosis mobilizes to secure a productive infection. We simultaneously quantified replication and death rates, used electron microscopy to evaluate bacterial integrity, and determined the temporal changes in bacterial gene expression during a 14-day infection. By overlaying this temporal transcriptome dataset onto an extended Transcriptional Regulatory Network model, we identified regulatory pathways, stress responses, and metabolic adaptations activated during key physiological transitions over the 14 days of infection.
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132
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Cossu A, Sechi LA, Zanetti S, Rosu V. Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour. BMC Microbiol 2012; 12:87. [PMID: 22646160 PMCID: PMC3416667 DOI: 10.1186/1471-2180-12-87] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have identified in Mycobacterium avium subsp. paratuberculosis (MAP), already known as a pathogen in ruminants, a potential zoonotic agent of some autoimmune diseases in humans. Therefore, considering the possible risk for public health, it is necessary a thorough understanding of MAP's gene expression during infection of human host as well as the identification of its immunogenic and/or virulence factors for the development of appropriate diagnostic and therapeutic tools. RESULTS In order to characterize MAP's transcriptome during macrophage infection, we analyzed for the first time the whole gene expression of a human derived strain of MAP in simulated intraphagosomal conditions and after intracellular infection of the human macrophage cell line THP-1 by using the DNA-microarray technology. Results showed that MAP shifts its transcriptome to an adaptive metabolism for an anoxic environment and nutrient starvation. It up-regulates several response factors to oxidative stress or intracellular conditions and allows, in terms of transcription, a passive surface peptidoglycan spoliation within the macrophage along with an intensification of the anabolic activity for lipidic membrane structures. CONCLUSIONS These results indicate a possible interactive system between MAP and its host cell based on the internal mimicry unlike other intracellular pathogens, bringing new hypothesis in the virulence and pathogenicity of MAP and its importance in human health.
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Affiliation(s)
- Andrea Cossu
- Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, Sassari, Italy.
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133
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Abstract
Heterogeneity within a clonal population of cells can increase survival in the face of environmental stress. In a recent issue of Science, Aldridge et al. (2012) demonstrate that cell division in mycobacteria is asymmetric, producing daughter cells that differ in size, growth rate, and susceptibility to antibiotics.
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Affiliation(s)
- Christopher D Aakre
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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134
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Saravanan P, Dubey VK, Patra S. Potential selective inhibitors against Rv0183 of Mycobacterium tuberculosis targeting host lipid metabolism. Chem Biol Drug Des 2012; 79:1056-62. [PMID: 22405030 DOI: 10.1111/j.1747-0285.2012.01373.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tuberculosis is the second leading infectious killer with 9 million new cases in 2009. Extensive use of pathogen's lipid metabolism especially in utilizing the host lipids and virulence highlights the importance of exported lipid-catabolizing enzymes. Current study aims to emphasize the importance of Rv0183, an exported monoacylglycerol lipase, involved in metabolizing the host cell membrane lipids. Sequence analysis and homology modeling shows Rv0183 is highly conserved throughout mycobacterial species even in Mycobacterium leprae and also significantly divergent from mammalian lipases. Additionally, employing virtual screening using NCI diversity set and ZINC database with criteria of molecules with higher predicted free energy of binding toward Rv0183 than human lipase, potential inhibitors have been identified for Rv0183. A tautomer of ZINC13451138, known inhibitor for HIV-1 integrase is the best hit with difference in free energy of binding of 8.72 kcal/mol. The sequence and structure analysis were helpful in identifying the ligand binding sites and molecular function of the mycobacterial specific monoacylglycerol lipase. Rv0183 represents a suitable and promising drug target and is also a step towards understanding dormancy development and reactivation, thereby addressing pathogen's drug resistance. Experimental studies on the discovered potential inhibitors in this virtual screen should further validate the therapeutic utility of Rv0183.
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135
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Griffin JE, Pandey AK, Gilmore SA, Mizrahi V, McKinney JD, Bertozzi CR, Sassetti CM. Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations. CHEMISTRY & BIOLOGY 2012; 19:218-27. [PMID: 22365605 PMCID: PMC3292763 DOI: 10.1016/j.chembiol.2011.12.016] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 12/10/2011] [Accepted: 12/13/2011] [Indexed: 12/22/2022]
Abstract
To understand the adaptation of Mycobacterium tuberculosis to the intracellular environment, we used comprehensive metabolite profiling to identify the biochemical pathways utilized during growth on cholesterol, a critical carbon source during chronic infection. Metabolic alterations observed during cholesterol catabolism centered on propionyl-CoA and pyruvate pools. Consequently, growth on this substrate required the transcriptional induction of the propionyl-CoA-assimilating methylcitrate cycle (MCC) enzymes, via the Rv1129c regulatory protein. We show that both Rv1129c and the MCC enzymes are required for intracellular growth in macrophages and that the growth defect of MCC mutants is largely attributable to the degradation of host-derived cholesterol. Together, these observations define a coordinated transcriptional and metabolic adaptation that is required for scavenging carbon during intracellular growth.
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Affiliation(s)
- Jennifer E Griffin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
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136
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Morris D, Guerra C, Donohue C, Oh H, Khurasany M, Venketaraman V. Unveiling the mechanisms for decreased glutathione in individuals with HIV infection. Clin Dev Immunol 2011; 2012:734125. [PMID: 22242038 PMCID: PMC3254057 DOI: 10.1155/2012/734125] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 02/07/2023]
Abstract
We examined the causes for decreased glutathione (GSH) in individuals with HIV infection. We observed lower levels of intracellular GSH in macrophages from individuals with HIV compared to healthy subjects. Further, the GSH composition found in macrophages from HIV(+) subjects heavily favors oxidized glutathione (GSSG) which lacks antioxidant activity, over free GSH which is responsible for GSH's antioxidant activity. This decrease correlated with an increase in the growth of Mycobacterium tuberculosis (M. tb) in macrophages from HIV(+) individuals. In addition, we observed increased levels of free radicals, interleukin-1 (IL-1), interleukin-17 (IL-17) and transforming growth factor-β (TGF-β) in plasma samples derived from HIV(+) individuals compared to healthy subjects. We observed decreased expression of the genes coding for enzymes responsible for de novo synthesis of GSH in macrophages derived from HIV(+) subjects using quantitative PCR (qPCR). Our results indicate that overproduction of proinflammatory cytokines in HIV(+) individuals lead to increased production of free radicals. This combined with the decreased expression of GSH synthesis enzymes leads to a depletion of free GSH and may lead in part to the loss of immune function observed in HIV patients.
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Affiliation(s)
- Devin Morris
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Carlos Guerra
- Science Department, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Clare Donohue
- Pitzer College, 1050 N Mills Avenue, Claremont, CA 91711, USA
| | - Hyoung Oh
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Melissa Khurasany
- College of Dental Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Vishwanath Venketaraman
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
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137
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Khan A, Sarkar D. Nitrate reduction pathways in mycobacteria and their implications during latency. MICROBIOLOGY-SGM 2011; 158:301-307. [PMID: 22174380 DOI: 10.1099/mic.0.054759-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mycobacterial persistence has gained a lot of attention with respect to developing novel antitubercular drugs, which could drastically reduce the duration of tuberculosis (TB) therapy. A better understanding of the physiology of Mycobacterium tuberculosis, and of the metabolic state of the bacillus during the latent period, is a primary need in finding drug targets against persistent TB. Recent biochemical and genetic studies of nitrate reduction in mycobacteria have revealed the roles of distinct proteins and enzymes involved in the pathway. The differential degree of nitrate reduction among pathogenic and non-pathogenic mycobacterial species, and its regulation during oxygen and nutrient limitation, suggest a link between nitrate reduction pathways and latency. The respiratory and assimilatory reduction of nitrate in mycobacteria may be interconnected to facilitate rapid adaptation to changing oxygen and/or nitrogen conditions, increasing metabolic flexibility for survival in the hostile host environment. This review summarizes the nitrate metabolic pathways operative in mycobacteria to provide an insight into the mechanisms that M. tuberculosis has evolved to adapt successfully to the host environment.
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Affiliation(s)
- Arshad Khan
- Department of Pathology and Laboratory Medicine, University of Texas, Health Science Center at Houston, Medical School, Houston, TX 77030, USA
| | - Dhiman Sarkar
- Combi Chem-Bio Resource Center, National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
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138
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Capyk JK, Casabon I, Gruninger R, Strynadka NC, Eltis LD. Activity of 3-ketosteroid 9α-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. J Biol Chem 2011; 286:40717-24. [PMID: 21987574 DOI: 10.1074/jbc.m111.289975] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (k(cat)/K(m)) of KshAB for the CoA thioester substrates was 20-30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent K(m)(O(2)) was 90 ± 10 μM in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ(1) ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism.
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Affiliation(s)
- Jenna K Capyk
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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139
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Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog 2011; 7:e1002251. [PMID: 21980284 PMCID: PMC3182942 DOI: 10.1371/journal.ppat.1002251] [Citation(s) in RCA: 783] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 07/18/2011] [Indexed: 11/17/2022] Open
Abstract
The pathways that comprise cellular metabolism are highly interconnected, and alterations in individual enzymes can have far-reaching effects. As a result, global profiling methods that measure gene expression are of limited value in predicting how the loss of an individual function will affect the cell. In this work, we employed a new method of global phenotypic profiling to directly define the genes required for the growth of Mycobacterium tuberculosis. A combination of high-density mutagenesis and deep-sequencing was used to characterize the composition of complex mutant libraries exposed to different conditions. This allowed the unambiguous identification of the genes that are essential for Mtb to grow in vitro, and proved to be a significant improvement over previous approaches. To further explore functions that are required for persistence in the host, we defined the pathways necessary for the utilization of cholesterol, a critical carbon source during infection. Few of the genes we identified had previously been implicated in this adaptation by transcriptional profiling, and only a fraction were encoded in the chromosomal region known to encode sterol catabolic functions. These genes comprise an unexpectedly large percentage of those previously shown to be required for bacterial growth in mouse tissue. Thus, this single nutritional change accounts for a significant fraction of the adaption to the host. This work provides the most comprehensive genetic characterization of a sterol catabolic pathway to date, suggests putative roles for uncharacterized virulence genes, and precisely maps genes encoding potential drug targets.
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Affiliation(s)
- Jennifer E Griffin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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140
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Abstract
Tuberculosis results in an estimated 1·7 million deaths each year and the worldwide number of new cases (more than 9 million) is higher than at any other time in history. 22 low-income and middle-income countries account for more than 80% of the active cases in the world. Due to the devastating effect of HIV on susceptibility to tuberculosis, sub-Saharan Africa has been disproportionately affected and accounts for four of every five cases of HIV-associated tuberculosis. In many regions highly endemic for tuberculosis, diagnosis continues to rely on century-old sputum microscopy; there is no vaccine with adequate effectiveness and tuberculosis treatment regimens are protracted and have a risk of toxic effects. Increasing rates of drug-resistant tuberculosis in eastern Europe, Asia, and sub-Saharan Africa now threaten to undermine the gains made by worldwide tuberculosis control programmes. Moreover, our fundamental understanding of the pathogenesis of this disease is inadequate. However, increased investment has allowed basic science and translational and applied research to produce new data, leading to promising progress in the development of improved tuberculosis diagnostics, biomarkers of disease activity, drugs, and vaccines. The growing scientific momentum must be accompanied by much greater investment and political commitment to meet this huge persisting challenge to public health. Our Seminar presents current perspectives on the scale of the epidemic, the pathogen and the host response, present and emerging methods for disease control (including diagnostics, drugs, biomarkers, and vaccines), and the ongoing challenge of tuberculosis control in adults in the 21st century.
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Affiliation(s)
- Stephen D Lawn
- The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
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141
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Abstract
Mycobacterium tuberculosis is an extremely successful pathogen that demonstrates the capacity to modulate its host both at the cellular and tissue levels. At the cellular level, the bacterium enters its host macrophage and arrests phagosome maturation, thus avoiding many of the microbicidal responses associated with this phagocyte. Nonetheless, the intracellular environment places certain demands on the pathogen, which, in response, senses the environmental shifts and upregulates specific metabolic programs to allow access to nutrients, minimize the consequences of stress, and sustain infection. Despite its intracellular niche, Mycobacterium tuberculosis demonstrates a marked capacity to modulate the tissues surrounding infected cells through the release of potent, bioactive cell wall constituents. These cell wall lipids are released from the host cell by an exocytic process and induce physiological changes in neighboring phagocytes, which drives formation of a granuloma. This tissue response leads to the generation and accumulation of caseous debris and the progression of the human tuberculosis granuloma. Completion of the life cycle of tuberculosis requires damaging the host to release infectious bacteria into the airways to spread the infection. This damage reflects the pathogen's ability to subvert the host's innate and acquired immune responses to its own nefarious ends.
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Affiliation(s)
- David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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142
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Abramovitch RB, Rohde KH, Hsu FF, Russell DG. aprABC: a Mycobacterium tuberculosis complex-specific locus that modulates pH-driven adaptation to the macrophage phagosome. Mol Microbiol 2011; 80:678-94. [PMID: 21401735 DOI: 10.1111/j.1365-2958.2011.07601.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following phagocytosis by macrophages, Mycobacterium tuberculosis (Mtb) senses the intracellular environment and remodels its gene expression for growth in the phagosome. We have identified an acid and phagosome regulated (aprABC) locus that is unique to the Mtb complex and whose gene expression is induced during growth in acidic environments in vitro and in macrophages. Using the aprA promoter, we generated a strain that exhibits high levels of inducible fluorescence in response to growth in acidic medium in vitro and in macrophages. aprABC expression is dependent on the two-component regulator phoPR, linking phoPR signalling to pH sensing. Deletion of the aprABC locus causes defects in gene expression that impact aggregation, intracellular growth, and the relative levels of storage and cell wall lipids. We propose a model where phoPR senses the acidic pH of the phagosome and induces aprABC expression to fine-tune processes unique for intracellular adaptation of Mtb complex bacteria.
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Affiliation(s)
- Robert B Abramovitch
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14583, USA
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143
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Elkington PT, D'Armiento JM, Friedland JS. Tuberculosis immunopathology: the neglected role of extracellular matrix destruction. Sci Transl Med 2011; 3:71ps6. [PMID: 21346167 PMCID: PMC3717269 DOI: 10.1126/scitranslmed.3001847] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The extracellular matrix in the lung must be destroyed for Mycobacterium tuberculosis--the agent that causes tuberculosis (TB)--to spread. The current paradigm proposes that this destruction occurs as a result of the action of proinflammatory cytokines, chemokines, immune cells, and lipids that mediate TB-associated necrosis in the lung. However, this view neglects the fact that lung matrix can only be degraded by proteases. We propose an original conceptual framework of TB immunopathology that may lead directly to treatments that involve inhibition of matrix metalloproteinase activity to hinder matrix destruction and reduce the morbidity and mortality associated with TB.
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Affiliation(s)
- Paul T Elkington
- Department of Infectious Diseases and Immunity, Imperial College London, London W6 0DT, UK.
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144
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Regulation between survival, persistence, and elimination of intracellular mycobacteria: a nested equilibrium of delicate balances. Microbes Infect 2010; 13:121-33. [PMID: 20971210 DOI: 10.1016/j.micinf.2010.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 10/14/2010] [Indexed: 02/07/2023]
Abstract
This review elaborates on recent insights gained on the dynamic aspects of interactions between pathogen and the host intracellular machinery in tuberculosis infection. In addition we will also discuss the utility of adopting a systems biology approach, both for a better understanding of TB biology, and for the development of more effective ways for disease management.
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