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ABSTRACT: Candidate transmission survival genome of Mycobacterium tuberculosis - RNAseq data

PROVIDER: PRJNA1140188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29995334_1.fastq.gz	Fastqsanger.gz
	SRR29995334_2.fastq.gz	Fastqsanger.gz
	SRR29995335_1.fastq.gz	Fastqsanger.gz
	SRR29995335_2.fastq.gz	Fastqsanger.gz
	SRR29995336_1.fastq.gz	Fastqsanger.gz

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Project description:Beste2007 - Genome-scale metabolic network of Mycobacterium tuberculosis (GSMN_TB) This model is described in the article: GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Beste DJ, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell ME, Wheeler P, Klamt S, Kierzek AM, McFadden J. Genome Biol. 2007; 8(5): R89 Abstract: BACKGROUND: An impediment to the rational development of novel drugs against tuberculosis (TB) is a general paucity of knowledge concerning the metabolism of Mycobacterium tuberculosis, particularly during infection. Constraint-based modeling provides a novel approach to investigating microbial metabolism but has not yet been applied to genome-scale modeling of M. tuberculosis. RESULTS: GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed, consisting of 849 unique reactions and 739 metabolites, and involving 726 genes. The model was calibrated by growing Mycobacterium bovis bacille Calmette Guérin in continuous culture and steady-state growth parameters were measured. Flux balance analysis was used to calculate substrate consumption rates, which were shown to correspond closely to experimentally determined values. Predictions of gene essentiality were also made by flux balance analysis simulation and were compared with global mutagenesis data for M. tuberculosis grown in vitro. A prediction accuracy of 78% was achieved. Known drug targets were predicted to be essential by the model. The model demonstrated a potential role for the enzyme isocitrate lyase during the slow growth of mycobacteria, and this hypothesis was experimentally verified. An interactive web-based version of the model is available. CONCLUSION: The GSMN-TB model successfully simulated many of the growth properties of M. tuberculosis. The model provides a means to examine the metabolic flexibility of bacteria and predict the phenotype of mutants, and it highlights previously unexplored features of M. tuberculosis metabolism. This model is hosted on BioModels Database and identified by: MODEL1507180021. 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.

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