Commonalities of Mycobacterium tuberculosis Transcriptomes in Response to Defined Persisting Macrophage Stresses

Abstract

As the goal of a bacterium is to become bacteria, evolution has imposed continued selections for gene expression. The intracellular pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis, has adopted a fine-tuned response to survive its host’s methods to aggressively eradicate invaders. The development of microarrays and later RNA sequencing has led to a better understanding of biological processes controlling the relationship between host and pathogens. In this study, RNA-seq was performed to detail the transcriptomes of M. tuberculosis grown in various conditions related to stresses endured by M. tuberculosis during host infection and to delineate a general stress response incurring during persisting macrophage stresses. M. tuberculosis was subjected to long-term growth, nutrient starvation, hypoxic and acidic environments. The commonalities between these stresses point to M. tuberculosis maneuvering to exploit propionate metabolism for lipid synthesis or to withstand propionate toxicity whilst in the intracellular environment. While nearly all stresses led to a general shutdown of most biological processes, up-regulation of pathways involved in the synthesis of amino acids, cofactors, and lipids were observed only in hypoxic M. tuberculosis. This data reveals genes and gene cohorts that are specifically or exclusively induced during all of these persisting stresses. Such knowledge could be used to design novel drug targets or to define possible M. tuberculosis vulnerabilities for vaccine development. Furthermore, the disruption of specific functions from this gene set will enhance our understanding of the evolutionary forces that have caused the tubercle bacillus to be a highly successful pathogen.

Mycobacterium abscessus DosRS two-component system controls a species-specific regulon required for adaptation to hypoxia

“…All four MCE loci in Mtb are differentially expressed in response to hypoxia, suggesting an important role for this family of lipid/cholesterol transporters in adaptation to this stress. While mce2 and mce3 were induced in a hypoxia model similar to ours (1% O 2, 5 days), mce1 was repressed, and mce4 expression remained unchanged ( Vilcheze et al., 2022 ). A separate study by Rathor et al.…”

“…The Mab hypoxia response included induction of 1,190 genes (≥ 1 log 2 fold change compared to 20% O 2 ) and downregulation of 1,062 genes (≤ 1 log 2 fold change compared to 20% O 2 ). This represented a larger set of hypoxia-induced genes than observed in Mtb in two studies under similar 1% O 2 hypoxia conditions (induction of ~400 genes detected via microarray and ~682 via RNAseq) ( Rustad et al., 2009 ; Vilcheze et al., 2022 ). These data highlight the functional genomic differences between Mab and Mtb , in particular their distinct patterns of gene regulation in response to hypoxia which are discussed in detail below.…”

“…The only TCS gene displaying substantial downregulation was Mab _ 3520c (log 2 FC = -9.7). The Mtb ortholog of Mab _ 3520c , Rv0260c, is known to be upregulated in hypoxia and to interact with DosS via protein-protein interaction independent of DosR; however, the function of Rv0260c has not been identified ( Gautam et al., 2019 ; Vilcheze et al., 2022 ). The opposite pattern of regulation of Rv0260c (induced) and Mab _3520c (repressed) in hypoxia implies they are utilized differently for adaptation to hypoxia.…”

“…The list of hypoxia-induced genes included loci involved in fatty acid and cholesterol metabolism, components of the NADH-quinone oxidoreductase subunits ( nuoA - N ), 6 epoxide hydrolases ( ephD ), ATP synthase subunits, 5 mammalian cell entry operons (MCE), members of the glycopeptidolipid locus (GPL), and 520 hypothetical genes ( Tables S3, 4 ). Several pathways critical for pathogenesis of Mtb , such as fatty acid and cholesterol metabolism, are also induced in various hypoxia models (Wayne model, 1% O 2 ) and within granulomas ( Wilburn et al., 2018 ; Yang et al., 2021 ; Vilcheze et al., 2022 ). All four MCE loci in Mtb are differentially expressed in response to hypoxia, suggesting an important role for this family of lipid/cholesterol transporters in adaptation to this stress.…”

Mycobacterium tuberculosis transcriptome in intraocular tuberculosis

“…The downregulation of the DosR regulon by M. tb in AIOF and RPE cells seems incongruous with the concurrent slowing of M. tb replication and transcriptional dampening of active processes. The DosR regulon is induced by stresses attributed to the intra-phagosomal environment of macrophages [26,27] and extracellularly within granulomas [28,29] and is important for maintaining M. tb survival during dormancy [30]. It has been proposed that M. tb infection is not binary, i.e.…”