Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis

• Published in: Nature (London) 2024-04, Vol.628 (8006), p.186-194
• Main Authors: Eckartt, Kathryn A., Delbeau, Madeleine, Munsamy-Govender, Vanisha, DeJesus, Michael A., Azadian, Zachary A., Reddy, Abhijna K., Chandanani, Joshua, Poulton, Nicholas C., Quiñones-Garcia, Stefany, Bosch, Barbara, Landick, Robert, Campbell, Elizabeth A., Rock, Jeremy M.
• Format: Article
• Language: English
• Subjects: 38/43; 631/326/325/2482; 631/326/41/2531; 631/326/421; Antimicrobial agents; Bacteria; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Conserved Sequence; CRISPR; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - antagonists & inhibitors; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; Drug resistance; Drug Resistance, Bacterial - drug effects; Drug Resistance, Bacterial - genetics; E coli; Escherichia coli - genetics; Escherichia coli - metabolism; Evolution; Evolution, Molecular; Fitness; Genes; Genetic Fitness; Genomes; Genomics; Humanities and Social Sciences; Humans; Molecular modelling; multidisciplinary; Mutation; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - enzymology; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - metabolism; Pathogens; Peptide Elongation Factors - genetics; Peptide Elongation Factors - metabolism; Physiology; Positive selection; Rifampin; Rifampin - pharmacology; Rifampin - therapeutic use; RNA polymerase; Science; Science (multidisciplinary); Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Tuberculosis; Tuberculosis, Multidrug-Resistant - drug therapy; Tuberculosis, Multidrug-Resistant - microbiology
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-024-07206-5

Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors 1 – 8 . Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy 9 , 10 . However, RifR Mtb accounts for one-quarter of all deaths due to drug-resistant bacteria 11 , 12 . We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli , Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA 13 . We find this pro-pausing NusG–RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG–RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb. In Mycobacterium tuberculosis , the fitness cost of rifampicin resistance is partially due to excessive RNA polymerase pausing and is rescued by mutations in the pro-pausing transcription factor NusG.