Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction

• Published in: Nature communications Vol. 15; no. 1; pp. 4783 - 15
• Main Authors: Khusainov, Iskander, Romanov, Natalie, Goemans, Camille, Turoňová, Beata, Zimmerli, Christian E., Welsch, Sonja, Langer, Julian D., Typas, Athanasios, Beck, Martin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 05.06.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 101/58; 631/337/574/1789; 631/535/1258/1260; Anti-Bacterial Agents - pharmacology; Antibiotics; Antimicrobial agents; Bacteria; Bacteriostats; Binding Sites; Cryoelectron Microscopy; E coli; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli K12 - drug effects; Escherichia coli K12 - genetics; Escherichia coli K12 - metabolism; Genetic code; Gram-negative bacteria; Humanities and Social Sciences; Humans; Mode of action; multidisciplinary; Protein biosynthesis; Protein Biosynthesis - drug effects; Protein synthesis; Proteins; Proteomes; Ribonucleic acid; Ribosomes; Ribosomes - drug effects; Ribosomes - metabolism; RNA; RNA, Transfer - genetics; RNA, Transfer - metabolism; Sample preparation; Science; Science (multidisciplinary); Strains (organisms); Tetracycline - pharmacology; Therapeutic targets; Thermal stability
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49084-5

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. Using our approach for close-to-native E. coli sample preparation, we assess the two strains by cryo-ET and visualize their ribosomes at high resolution in situ. Upon tetracycline treatment, these exhibit virtually identical drug binding sites, yet the conformation distribution of ribosomal complexes differs. While K-12 retains ribosomes in a translation-competent state, tRNAs are lost in the vast majority of ED1a ribosomes. These structural findings together with the proteome-wide abundance and thermal stability assessments indicate that antibiotic responses are complex in cells and can differ between different strains of a single species, thus arguing that all relevant bacterial strains should be analyzed in situ when addressing antibiotic mode of action. The human gut contains diverse bacterial strains that are beneficial/critical for health. Here, the authors compare the response of human gut and laboratory E. coli strains to the antibiotic tetracycline in molecular detail and find a severe dysfunction of protein synthesis only in the gut strain.