Lipidomics and genomics of Mycobacterium tuberculosis reveal lineage-specific trends in mycolic acid biosynthesis.
Bottom Line: We found significant variations in the MA patterns between different MTBC strains and lineages.MA patterns of "ancient" lineages contrasted those from "modern" lineages, with a lower representation of alpha-mycolates among Lineage 6 strains and an inversion of the methoxy: keto-mycolates ratio in Lineage 1 strains.By interrogating the whole genome sequences of these MTBC strains, we identified relevant single-nucleotide polymorphisms that may sustain the lineage-specific MA patterns.
Affiliation: Mycobacterial Division Research, NIMR, MRC, NW71AA, London, United Kingdom; Department of Medical Parasitology and Infection Biology, Swiss TPH, 4002, Basel, Switzerland; University of Basel, 4002, Basel, Switzerland.Show MeSH
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Mentions: Nonsynonymous SNPs among the MA pathway were extracted from full genome sequences and listed in Table S2. We identified 97 SNPs across all four lineages, and almost 50% of them were singletons; that is, only detected in one strain. About 30% of these polymorphisms were shared by two strains or more within the same lineage. We identified 17 nsSNPs present exclusively in one of the four MTB lineages, and three nsSNPs shared by the two “modern” lineages. Only one lineage-specific nsSNP was found in each of Lineage 2 and 4, whereas five and 11 nsSNPs were detected in Lineage 1 and 6, respectively. The genes were grouped according to their involvement in the MA metabolism pathway and depicted in Figure 6. We then investigated the predicted functional effect that individual nsSNPs, and therefore amino acid substitution, could bring to the related protein using SIFT prediction algorithm (Sim et al. 2012). When the amino acid substitution was predicted to have a significant effect on protein function (P < 0.05), the respective gene was highlighted (Fig. 6). Interestingly, nine of the 20 nsSNPs that were predicted to affect protein function belonged to “ancient” strains but none to the “modern” lineages.
Affiliation: Mycobacterial Division Research, NIMR, MRC, NW71AA, London, United Kingdom; Department of Medical Parasitology and Infection Biology, Swiss TPH, 4002, Basel, Switzerland; University of Basel, 4002, Basel, Switzerland.