Mycobacterium abscessus HelR interacts with RNA polymerase to confer intrinsic rifamycin resistance

• Published in: Molecular cell 2022-09, Vol.82 (17), p.3166-3177.e5
• Main Authors: Hurst-Hess, Kelley R, Saxena, Aavrati, Rudra, Paulami, Yang, Yong, Ghosh, Pallavi
• Format: Article
• Language: English
• Subjects: DNA-Directed RNA Polymerases - genetics; Drug Resistance, Bacterial - genetics; Humans; Microbial Sensitivity Tests; Mycobacterium abscessus; Mycobacterium tuberculosis - genetics; Rifabutin - pharmacology; Rifampin - pharmacology; Rifamycins - pharmacology; Tuberculosis - microbiology
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2022.06.034

Rifampicin (RIF), the frontline drug against M. tuberculosis, is completely ineffective against M. abscessus, partially due to the presence of an ADP-ribosyltransferase (Arr) that inactivates RIF. Using RNA-seq, we show that exposure of M. abscessus to sublethal doses of RIF and Rifabutin (RBT), a close analog of RIF, results in an ∼25-fold upregulation of Mab_helR in laboratory and clinical isolates. An isogenic deletion in Mab_helR results in RIF/RBT hypersensitivity, and overexpression of Mab_helR confers RIF tolerance in M. tuberculosis. We demonstrate an increased HelR-RNAP association in RIF-exposed bacteria and a MabHelR-mediated dissociation of RNAP from stalled initiation complexes in vitro. Finally, we show that the tip of the PCh-loop of Mab_helR, present in proximity to RIF, is critical for conferring RIF resistance but dispensable for dissociation of stalled RNAP complexes, suggesting that HelR-mediated RIF resistance requires a step in addition to displacement of RIF-stalled RNAP.