Abstract
A general paucity of knowledge about the metabolic state of Mycobacterium tuberculosis within the host environment is a major factor impeding development of novel drugs against tuberculosis. Current experimental methods do not allow direct determination of the global metabolic state of a bacterial pathogen in vivo, but the transcriptional activity of all encoded genes has been investigated in numerous microarray studies. We describe a novel algorithm, Differential Producibility Analysis (DPA) that uses a metabolic network to extract metabolic signals from transcriptome data. The method utilizes Flux Balance Analysis (FBA) to identify the set of genes that affect the ability to produce each metabolite in the network. Subsequently, Rank Product Analysis is used to identify those metabolites predicted to be most affected by a transcriptional signal. We first apply DPA to investigate the metabolic response of E. coli to both anaerobic growth and inactivation of the FNR global regulator. DPA successfully extracts metabolic signals that correspond to experimental data and provides novel metabolic insights. We next apply DPA to investigate the metabolic response of M. tuberculosis to the macrophage environment, human sputum and a range of in vitro environmental perturbations. The analysis revealed a previously unrecognized feature of the response of M. tuberculosis to the macrophage environment: a down-regulation of genes influencing metabolites in central metabolism and concomitant up-regulation of genes that influence synthesis of cell wall components and virulence factors. DPA suggests that a significant feature of the response of the tubercle bacillus to the intracellular environment is a channeling of resources towards remodeling of its cell envelope, possibly in preparation for attack by host defenses. DPA may be used to unravel the mechanisms of virulence and persistence of M. tuberculosis and other pathogens and may have general application for extracting metabolic signals from other “-omics” data.
Highlights
The M. tuberculosis complex includes the human pathogen M. tuberculosis, the bovine tubercle bacillus, M. bovis and the attenuated vaccine strain derived from M. bovis
There is growing evidence of a shift to anaerobic respiration during dormant/latent/persistent infection [11] [12] [13]. These findings have been useful in directing rational drug development [14] but a more complete understanding of M. tuberculosis metabolism in vivo remains a major goal of TB drug research
We focused our studies on attempting to define metabolic changes associated with the adaptation of M. tuberculosis to the in vivo environment, as represented by macrophage-grown M. tuberculosis and human sputum-derived M. tuberculosis
Summary
The M. tuberculosis complex includes the human pathogen M. tuberculosis, the bovine tubercle bacillus, M. bovis and the attenuated vaccine strain derived from M. bovis. Control of TB is compromised by the fact that successful treatment takes 6 months or more, leading to lack of patient compliance and subsequent emergence of drug-resistance. These lengthy drug treatment regimes are necessary to kill slowly growing or non-growing cells, known as persisters, in lesions that are refractory to drug treatment [4]. There is growing evidence of a shift to anaerobic respiration during dormant/latent/persistent infection [11] [12] [13] These findings have been useful in directing rational drug development [14] but a more complete understanding of M. tuberculosis metabolism in vivo remains a major goal of TB drug research
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