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

• 成果类型: Article
• 署名作者: Eckartt, Kathryn A.; Delbeau, Madeleine; Munsamy-Govender, Vanisha; DeJesus, Michael A.; Azadian, Zachary A.; Reddy, Abhijna K.; Chandanani, Joshua; Poulton, Nicholas C.; Quinones-Garcia, Stefany; Bosch, Barbara; Landick, Robert; Campbell, Elizabeth A.; Rock, Jeremy M.
• 署名单位: Rockefeller University; Rockefeller University; University of Wisconsin System; University of Wisconsin Madison; University of Wisconsin System; University of Wisconsin Madison
• 刊物名称: Nature
• ISSN/ISSBN: 0028-6505
• DOI: 10.1038/s41586-024-07206-5
• 发表日期: 2024-04-04
• 页码: 186-+
• 关键词: initiation-factor 2; antibiotic-resistance; mycobacterium-tuberculosis; rifampin resistance; biological cost; transcription termination; gene-expression; rpob mutations; rna-polymerase; ribosomal-rna

摘要

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.