Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum

Abstract

Mycobacterium africanum lineage (L) 6 is an important pathogen in West Africa, causing up to 40% of pulmonary tuberculosis (TB). The biology underlying the clinical differences between M. africanum and M. tuberculosis sensu stricto remains poorly understood. We performed ex vivo expression of 2179 genes of the most geographically dispersed cause of human TB, M. tuberculosis L4 and the geographically restricted, M. africanum L6 directly from sputa of 11 HIV-negative TB patients from The Gambia who had not started treatment. The DosR regulon was the most significantly decreased category in L6 relative to L4. Further, we identified nonsynonymous mutations in major DosR regulon genes of 44 L6 genomes of TB patients from The Gambia and Ghana. Using Lebek's test, we assessed differences in oxygen requirements for growth. L4 grew only at the aerobic surface while L6 grew throughout the medium. In the host, the DosR regulon is critical for M. tuberculosis in adaptation to oxygen limitation. However, M. africanum L6 appears to have adapted to growth under hypoxic conditions or to different biological niches. The observed under expression of DosR in L6 fits with the genomic changes in DosR genes, microaerobic growth and the association with extrapulmonary disease.

Comparative Genomics Shows Differences in the Electron Transport and Carbon Metabolic Pathways ofMycobacterium africanumrelative toMycobacterium tuberculosisand suggests an adaptation to low oxygen tension

“…M. smegmatis strains that had mutations in the bc1-aa3 complex were significantly growth impaired, confirming the essentiality of the bc1-aa3 respiratory pathway for mycobacterial growth. Taken together, our analysis provides further support for the view that MAF is adapted to a distinct niche, less dependent on aerobic respiration and more adapted to a microaerobic lifestyle (15). Furthermore, mutations in bc1-aa3 complex genes likely contribute to the slow growth phenotype of the MAF lineages.…”

“…To the best of our knowledge, this is the first work demonstrating that the critical bc1-aa3 complex is mutated in MAF lineages. We submit that this finding is crucial to understanding the difference in energy metabolism, particularly oxidative phosphorylation, between the MTB and MAF lineages, especially because MAF lineages preferentially grow microaerobically (15, 92–95) and significantly underexpress the dormancy regulon required for adaptation to oxygen limitation (15). Notably, the Imidazopyridine amide in Phase 2 clinical trials, Telacebec (Q203), inhibits qcrB of Cytochrome bc1, further emphasizing the importance of this complex for the survival of MTB.…”

“…Significant genomic differences between MTB and MAF lineages presented in this analysis warrant further studies in order to properly characterize the regulatory network of MAF. Recently, the regulatory network of H37Rv (MTB L4) was characterized yet what pertains to MAF lineages is not clearly defined, even though it has been shown that master regulators like PhoPR and Rv0081 as well as the DosR regulon are underexpressed and/or mutated in MAF (15, 114–116). A single mutation in PhoP, which abrogates ESX1 secretion, explains the complete loss of virulence of H37Ra.…”

“…MAF lineages are associated with extrapulmonary disease and MAF L6 more commonly causes disease in immunocompromised persons and those with lower Body Mass Index, implying a more opportunistic pathogen (10, 12). Furthermore, MAF L5 and L6 grow markedly slower than MTB and prefer microaerobic growth conditions (13–15). Reasons for these differences are not completely known, although ours and other’s previous studies have attempted to explain some of the observations.…”

“…A study documented non-synonymous SNPs or frameshift mutations in some genes associated with growth attenuation in MAF and higher mutation frequency in genes necessary for transport of sulphur, ions and lipids/fatty acids across the cell membrane (14). Another reported under-expression of, and MAF L6 specific mutations in, dormancy regulon genes, a network of genes crucial for the survival of MTB during hypoxia or anaerobiosis (15, 16).…”