Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis

Abstract

Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that can adapt to the various nutrients available during its life cycle. However, in the nutritionally stringent environment of the macrophage phagolysosome, Mtb relies mainly on cholesterol. In previous studies, we demonstrated that Mtb can accumulate and utilize cholesterol as the sole carbon source. However, a growing body of evidence suggests that a lipid-rich environment may have a much broader impact on the pathogenesis of Mtb infection than previously thought. Therefore, we applied high-resolution transcriptome profiling and the construction of various mutants to explore in detail the global effect of cholesterol on the tubercle bacillus metabolism. The results allow re-establishing the complete list of genes potentially involved in cholesterol breakdown. Moreover, we identified the modulatory effect of vitamin B12 on Mtb transcriptome and the novel function of cobalamin in cholesterol metabolite dissipation which explains the probable role of B12 in Mtb virulence. Finally, we demonstrate that a key role of cholesterol in mycobacterial metabolism is not only providing carbon and energy but involves also a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment far before specific stress-inducing phagosomal signals occur.

Using a Whole Genome Co-expression Network to Inform the Functional Characterisation of Predicted Genomic Elements fromMycobacterium tuberculosisTranscriptomic Data

“…Restricting iron availability to growing cells is meant to replicate a host response to infection and will stimulate a cascade of pathways to enable the pathogen to survive in a slow-growing, or latent state. The co-expression of genes involved in metal ion homeostasis and genes known to be involved in adaptation to cholesterol and lipids is supported by observations in a recent study that the presence of cholesterol causes changes in metal ion metabolism (Pawełczyk et al, 2021) and closer inspection may uncover gene interactions related to the metabolic changes made in anticipation of re-entry from hypoxic environments when bacteria are particularly vulnerable to oxidative stress (Eoh et al, 2017; Gerrick et al, 2018).…”

“…One condition that causes a major shift in the transcriptome is the adaptation of Mtb to a cholesterol or lipid-rich environment, a process that involves a multitude of gene pathways to facilitate the pathogen's survival and persistence in the infected macrophage (Del Portillo et al, 2019;Pandey Amit K. & Sassetti Christopher M., 2008;Pawełczyk et al, 2021). In fact, a recent study, published after this analysis, observes differential expression of over 500 protein-coding genes with a switch from glycerol to cholesterol as the carbon source (Pawełczyk et al, 2021).…”

“…One condition that causes a major shift in the transcriptome is the adaptation of Mtb to a cholesterol or lipid-rich environment, a process that involves a multitude of gene pathways to facilitate the pathogen's survival and persistence in the infected macrophage (Del Portillo et al, 2019;Pandey Amit K. & Sassetti Christopher M., 2008;Pawełczyk et al, 2021). In fact, a recent study, published after this analysis, observes differential expression of over 500 protein-coding genes with a switch from glycerol to cholesterol as the carbon source (Pawełczyk et al, 2021). Our network includes transcriptomes from several samples that utilise cholesterol and fatty-acid containing media over a range of growth conditions including hypoxia (SRA project: PRJNA390669) (Aguilar-Ayala et al, 2017) and although several modules have a significant correlation with the cholesterol media trait, other modules with clusters of genes related to cholesterol catabolism are correlated to hypoxia or extended hypoxia conditions.…”

“…The 5' UTR for Rv0677c and 3' UTRs for Rv0676c and Rv0677c are also hubs. This operon is involved in siderophore transport and expressed in cholesterol and lipid-rich environments (Aguilar-Ayala, et al, 2017;Pawełczyk et al, 2021). Other detoxification-linked genes in the module, such as the ABCfamily transporter efflux system, Rv1216c-1219c and the operon including PPE53 (Rv3159c), Rv3160c and Rv3161c, have also been implicated in transcriptomic remodelling in response to cholesterol (Aguilar-Ayala et al, 2017;Pawełczyk et al, 2021).…”

Macrophage global metabolomics identifies cholestenone as host/pathogen cometabolite present in human Mycobacterium tuberculosis infection

“…Interestingly, Mycobacterium leprae has lost the genes for cholesterol catabolism, but retains hsd and the ability to make cholestenone ( 50 , 51 ). In addition, in M. tuberculosis Rv1106c/ hsd is not transcriptionally regulated with other genes required for cholesterol metabolism ( 52 ). Combined, these observations suggest that cholestenone or other 3β-Hsd–generated host-pathogen cometabolites might be involved in pathogenesis.…”