Dataset Information

Fang2010 - Genome-scale metabolic network of Mycobacterium tuberculosis (iNJ661m)

ABSTRACT: Fang2010 - Genome-scale metabolic network of Mycobacterium tuberculosis (iNJ661m) This model is described in the article: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. Fang X, Wallqvist A, Reifman J. BMC Syst Biol 2010; 4: 160 Abstract: BACKGROUND: During infection, Mycobacterium tuberculosis confronts a generally hostile and nutrient-poor in vivo host environment. Existing models and analyses of M. tuberculosis metabolic networks are able to reproduce experimentally measured cellular growth rates and identify genes required for growth in a range of different in vitro media. However, these models, under in vitro conditions, do not provide an adequate description of the metabolic processes required by the pathogen to infect and persist in a host. RESULTS: To better account for the metabolic activity of M. tuberculosis in the host environment, we developed a set of procedures to systematically modify an existing in vitro metabolic network by enhancing the agreement between calculated and in vivo-measured gene essentiality data. After our modifications, the new in vivo network contained 663 genes, 838 metabolites, and 1,049 reactions and had a significantly increased sensitivity (0.81) in predicted gene essentiality than the in vitro network (0.31). We verified the modifications generated from the purely computational analysis through a review of the literature and found, for example, that, as the analysis suggested, lipids are used as the main source for carbon metabolism and oxygen must be available for the pathogen under in vivo conditions. Moreover, we used the developed in vivo network to predict the effects of double-gene deletions on M. tuberculosis growth in the host environment, explore metabolic adaptations to life in an acidic environment, highlight the importance of different enzymes in the tricarboxylic acid-cycle under different limiting nutrient conditions, investigate the effects of inhibiting multiple reactions, and look at the importance of both aerobic and anaerobic cellular respiration during infection. CONCLUSIONS: The network modifications we implemented suggest a distinctive set of metabolic conditions and requirements faced by M. tuberculosis during host infection compared with in vitro growth. Likewise, the double-gene deletion calculations highlight the importance of specific metabolic pathways used by the pathogen in the host environment. The newly constructed network provides a quantitative model to study the metabolism and associated drug targets of M. tuberculosis under in vivo conditions. This model is hosted on BioModels Database and identified by: MODEL1507180018. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Nicolas Le Novère

PROVIDER: MODEL1507180018 | BioModels | 2015-07-30

REPOSITORIES: BioModels

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	MODEL1507180018?filename=MODEL1507180018-biopax2.owl	Owl
	MODEL1507180018?filename=MODEL1507180018-biopax3.owl	Owl
	MODEL1507180018?filename=MODEL1507180018.m	Other
	MODEL1507180018?filename=MODEL1507180018.pdf	Pdf
	MODEL1507180018?filename=MODEL1507180018.png	Other

Items per page:

1 - 5 of 11

Publications

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis.

Fang Xin X Wallqvist Anders A Reifman Jaques J

BMC systems biology 20101123

<h4>Background</h4>During infection, Mycobacterium tuberculosis confronts a generally hostile and nutrient-poor in vivo host environment. Existing models and analyses of M. tuberculosis metabolic networks are able to reproduce experimentally measured cellular growth rates and identify genes required for growth in a range of different in vitro media. However, these models, under in vitro conditions, do not provide an adequate description of the metabolic processes required by the pathogen to infe ...[more]

PMID: 21092312

Similar Datasets

Project description:Jamshidi2007 - Genome-scale metabolic network of Mycobacterium tuberculosis (iNJ661) This model is described in the article: Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. Jamshidi N, Palsson BØ. BMC Syst Biol 2007; 1: 26 Abstract: BACKGROUND: Mycobacterium tuberculosis continues to be a major pathogen in the third world, killing almost 2 million people a year by the most recent estimates. Even in industrialized countries, the emergence of multi-drug resistant (MDR) strains of tuberculosis hails the need to develop additional medications for treatment. Many of the drugs used for treatment of tuberculosis target metabolic enzymes. Genome-scale models can be used for analysis, discovery, and as hypothesis generating tools, which will hopefully assist the rational drug development process. These models need to be able to assimilate data from large datasets and analyze them. RESULTS: We completed a bottom up reconstruction of the metabolic network of Mycobacterium tuberculosis H37Rv. This functional in silico bacterium, iNJ661, contains 661 genes and 939 reactions and can produce many of the complex compounds characteristic to tuberculosis, such as mycolic acids and mycocerosates. We grew this bacterium in silico on various media, analyzed the model in the context of multiple high-throughput data sets, and finally we analyzed the network in an 'unbiased' manner by calculating the Hard Coupled Reaction (HCR) sets, groups of reactions that are forced to operate in unison due to mass conservation and connectivity constraints. CONCLUSION: Although we observed growth rates comparable to experimental observations (doubling times ranging from about 12 to 24 hours) in different media, comparisons of gene essentiality with experimental data were less encouraging (generally about 55%). The reasons for the often conflicting results were multi-fold, including gene expression variability under different conditions and lack of complete biological knowledge. Some of the inconsistencies between in vitro and in silico or in vivo and in silico results highlight specific loci that are worth further experimental investigations. Finally, by considering the HCR sets in the context of known drug targets for tuberculosis treatment we proposed new alternative, but equivalent drug targets. This model is hosted on BioModels Database and identified by: MODEL1507180001. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:This is the joined genome scale reconstruction of both Mycobacterium tuberculosis and the human alveloar macrophage metabolism, iAB-AMØ-1410-Mt-661, described in the article: Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Mol Syst Biol. 2010 Oct 19;6:422. PMID: 20959820 , DOI: 10.1038/msb.2010.68 Abstract: Metabolic coupling of Mycobacterium tuberculosis to its host is foundational to its pathogenesis. Computational genome-scale metabolic models have shown utility in integrating -omic as well as physiologic data for systemic, mechanistic analysis of metabolism. To date, integrative analysis of host-pathogen interactions using in silico mass-balanced, genome-scale models has not been performed. We, therefore, constructed a cell-specific alveolar macrophage model, iAB-AMØ-1410, from the global human metabolic reconstruction, Recon 1. The model successfully predicted experimentally verified ATP and nitric oxide production rates in macrophages. This model was then integrated with an M. tuberculosis H37Rv model, iNJ661, to build an integrated host-pathogen genome-scale reconstruction, iAB-AMØ-1410-Mt-661. The integrated host-pathogen network enables simulation of the metabolic changes during infection. The resulting reaction activity and gene essentiality targets of the integrated model represent an altered infectious state. High-throughput data from infected macrophages were mapped onto the host-pathogen network and were able to describe three distinct pathological states. Integrated host-pathogen reconstructions thus form a foundation upon which understanding the biology and pathophysiology of infections can be developed. This model was downloaded from the supplementary materials ( link ) to the article. To make this file valid SBML the units of all parameters where changed from mmole per gDW per hour to mmole per hour. The model can be used eg. fpr FBA with the COBRA toolbox , amongst others. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.