LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis

The Mycobacterium tuberculosis complex (MTBC) includes ten human-adapted lineages with varying geography and pathogenicity. Lineage 1 (L1) shows low virulence while Lineage 2 (L2) is hyper-virulent, more transmissible, and associated with drug-resistance. We performed comparative analyses integrating whole-genome sequencing with transcriptomic and proteomic profiling of L1 and L2 clinical strains under two in vitro growth conditions. Transcript-protein correlations varied by strain and gene category, suggesting lineage-specific post-translational regulation. Expression differences scaled with phylogenetic distance, one in three SNPs affected gene expression. A new transcriptional regulatory model identified master transcription factors, linked to the sigma factor network, whose targets were differentially expressed between L1 and L2. For instance, DosR regulon proteins had higher basal levels and exhibited a stronger nitric oxide response in L2. Time-course experiments involving LysG (Rv1985c) induction and wild-type H37Rv under hypoxia and subsequent reaeration confirmed that LysG contributes to reduced metabolic activity, thereby promoting increased tolerance to the novel tuberculosis drug bedaquiline in L2 strains relative to L1. Overall, our findings show how limited genetic variation in the MTBC can yield major phenotypic differences through differential regulation of key transcriptional networks. Lineages within the Mycobacterium tuberculosis complex display differences in virulence and drug susceptibility patterns. Here, Banaei-Esfahani et al. compare strains from two lineages and show that small genetic variations are associated with lineage-specific differences in gene expression networks, metabolism, and tolerance to bedaquiline.