Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

Abstract

The nutrients consumed by intracellular pathogens are mostly unknown. This is mainly due to the challenge of disentangling host and pathogen metabolism sharing the majority of metabolic pathways and hence metabolites. Here, we investigated the metabolic changes of Mycobacterium tuberculosis, the causative agent of tuberculosis, and its human host cell during early infection. To this aim, we combined gene expression data of both organisms and metabolite changes during the course of infection through integration into a genome-wide metabolic network. This led to the identification of infection-specific metabolic alterations, which we further exploited to model host-pathogen interactions quantitatively by flux balance analysis. These in silico data suggested that tubercle bacilli consume up to 33 different nutrients during early macrophage infection, which the bacteria utilize to generate energy and biomass to establish intracellular growth. Such multisubstrate fueling strategy renders the pathogen’s metabolism robust toward perturbations, such as innate immune responses or antibiotic treatments.

Loving the poison: the methylcitrate cycle and bacterial pathogenesis

“…Blocking this pathway in several notable pathogens results in extreme sensitivity to propionate and reduced virulence. For example, several studies have indicated that the primary carbon source for M. tuberculosis is fatty acids/cholesterol when residing within host macrophages [56][57][58]. In support of this, PrpC was found to be required for intracellular growth in macrophages, indicating that propionyl-CoA metabolism is critical for maintaining the intracellular lifestyle [34,58,59].…”

Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria

“…Mtb resides within the hostile and ever-changing environment of the host phagosome, which is naturally poor in nutrients. Recent evidence suggests that the intracellular bacteria likely feed on substrates containing two or three carbon atoms [5], the end products of fatty acid and cholesterol catabolism [29,45,49].In Mtb, two parallel pathways are responsible for the catabolism of such compounds, the methylcitrate (MCIT) and the methylmalonyl CoA (MMCO) pathway ( Figure 1). The two seemingly redundant pathways can both fulfill the task of fueling the central carbon metabolism from three-carbon compounds.…”

Dual RNAseq of human leprosy lesions identifies bacterial determinants linked to host immune response

“…The advent of a "dual-RNAseq" approach has recently been applied to simultaneously sequence the transcriptomes of both the host and pathogen organisms in vitro, with subsequent isolation of each transcriptome in silico through alignment of the respective genomes of the organisms (Damron et al, 2016;Niemiec et al, 2017;Nuss et al, 2017;Thanert et al, 2017;Wesolowska-Andersen et al, 2017;Westermann et al, 2016;Zimmermann et al, 2017). The transcriptomes, which can lead to poor coverage of bacterial pathogens.…”

“…The transcriptomes, which can lead to poor coverage of bacterial pathogens. This challenge has been addressed by molecular enrichment of bacterial RNA or by investigating cell cultures and animal models in which the multiplicity of infection is high (Damron et al, 2016;Niemiec et al, 2017;Nuss et al, 2017;Thanert et al, 2017;Wesolowska-Andersen et al, 2017;Westermann et al, 2016;Zimmermann et al, 2017). However, dual-RNA-seq has yet to be carried out in lesions of a human disease.…”