Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance

Abstract

The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a mechanism of genetically encoded but rapidly reversible drug tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of 7 cytosines (7C) in the glpK gene. Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multidrug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis-infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug tolerance, treatment failure, and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates.

Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis

“…When infected animals were treated with antibiotics, we found only a small number of genes that broadly alter drug efficacy. These included glpK, which is necessary for glycerol metabolism and has been shown to alter the effect of HRZE in vivo (36) and several drugs in vitro (55). Similarly, mutation of a putative fatty-acyl-CoA reductase encoded by rv1543 broadly sensitizes the bacterium to different drugs.…”

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence

“…The GlpK enzyme catalyzes the first step in the glycerolipid pathway converting glycerol into glycerol-3-phosphate, a modification that ensures the entrance of this carbon source in the catabolic pathways and promotes the formation of glycerolipids. Mutations of glpK have been also found in Mycobacterium tuberculosis in response to long antibiotic treatments, however, these are transient and the mechanism behind the antibiotic tolerance remains unexplained52,53 . Others have speculated that GlpK may have an alternative role as a transcriptional regulator52 .…”

Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases

“…A homopolymeric tract in glpK of M. tuberculosis has garnered recent attention for undergoing frequent, reversible, frameshifts [53, 54]. Variants with such rapid emergence and reversal could theoretically pass our phylogenetic filtering method, yet none of the positions comprising the phase-variable glpK homopolymeric tract were identified as blind spots (Table S7).…”