Mycobacterium Abscessus HelR Interacts with RNA Polymerase to Confer Intrinsic Rifamycin Resistance

Abstract

Bacterial RNA polymerase is a target of the potent and broad-spectrum rifamycin group of antibiotics. Mutations within rpoB and inactivation by a diverse group of enzymes constitute the most widespread mechanisms of resistance. Rifampicin (RIF) constitutes the frontline therapy against M. tuberculosis as well as most slow-growing non-tuberculous mycobacteria (NTM) but is completely ineffective against M. abscessus. This high level of RIF resistance is despite the absence of mutations in the rifampicin resistance determining region of Mab_rpoB and is partially attributed to the presence of an ADP-ribosyltransferase (Arr) activity that inactivates RIF. Rifabutin (RBT), a close analogue of RIF, has recently been shown to be effective against M. abscessus in vitro and in a mouse model and comprises a promising therapeutic against M. abscessus infections. Using RNA sequencing we show that exposure of M. abscessus to sublethal doses of RIF and RBT results in ~25-fold upregulation of Mab_ helR in laboratory and clinical isolates; an isogenic deletion mutant of Mab_ helR is hypersensitive to RIF and RBT, and over-expression of Mab_ helR confers RIF tolerance in M. tuberculosis implying that Mab_helR constitutes a significant determinant of inducible RIF and RBT resistance. We demonstrate a preferential association of MabHelR with RNA polymerase in vivo in bacteria exposed to RIF and show that purified MabHelR can rescue transcription inhibition in the presence of RIF in in vitro transcription assays. Furthermore, MabHelR can dissociate RNAP from RIF-stalled initiation complexes in vitro, a species we envisage accumulates upon RIF exposure. Lastly, we show that the tip of the PCh-loop of Mab_ helR, in particular residues E496 and D497 that are in proximity to RIF, is critical for conferring RIF resistance without being required for dissociation of antibiotic-stalled RNAP complexes. This suggests that HelR may be additionally involved in displacing RIF bound to RNAP and function as an RNAP protection protein.