RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

• Published in: Nature communications Vol. 15; no. 1; pp. 6579 - 15
• Main Authors: Zheng, Yayun, Chai, Ruochen, Wang, Tianmin, Xu, Zeqi, He, Yihui, Shen, Ping, Liu, Jintao
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.08.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 13/31; 13/44; 38/15; 38/70; 38/71; 38/90; 45/22; 45/23; 45/77; 45/91; 631/326/22/1434; 631/326/41/2482; 631/337/1427; 631/337/572; 631/553/1833; 82/58; Aminoglycoside antibiotics; Aminoglycosides; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; Biological evolution; Coliforms; Coupling (molecular); Disruption; DNA repair; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; Drug resistance; Drug Resistance, Bacterial - genetics; E coli; Effectiveness; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - metabolism; Genomes; Genomic Instability; Genotoxicity; Gentamicin; Gentamicins - pharmacology; Humanities and Social Sciences; multidisciplinary; Mutagenesis; Mutation; Protein Biosynthesis - drug effects; Ribonucleic acid; Ribosomes - drug effects; Ribosomes - metabolism; RNA; RNA polymerase; rRNA; Science; Science (multidisciplinary); Stalling; Transcription, Genetic - drug effects; Transcription-coupled repair; Translation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50917-6

Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here, we find that a broad range of ribosome-targeting antibiotics cause mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we find that the translation inhibitor causes genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis shows that the stalling is caused by the disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induce lesions to the DNA via transcription-coupled repair. While most of the bacteria are killed by genotoxicity, a small subpopulation acquires mutations via SOS-induced mutagenesis. Given that these processes are triggered shortly after antibiotic addition, resistance rapidly emerges in the population. Our work reveals a mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance. Bacteria evolve antibiotic resistance via genetic mutations, but the process remains somewhat unclear. This work finds that the disruption of transcription-translation coupling is crucial for mutagenesis caused by ribosome-targeting antibiotics in Escherichia coli .