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

Iskander Khusainov, Natalie Romanov, Camille Goemans, Beata Turoňová, Christian E. Zimmerli, Sonja Welsch, Julian D. Langer, Athanasios Typas and Martin Beck ()
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Iskander Khusainov: Max Planck Institute of Biophysics
Natalie Romanov: Max Planck Institute of Biophysics
Camille Goemans: Genome Biology Unit
Beata Turoňová: Max Planck Institute of Biophysics
Christian E. Zimmerli: Max Planck Institute of Biophysics
Sonja Welsch: Max Planck Institute of Biophysics
Julian D. Langer: Max Planck Institute of Biophysics
Athanasios Typas: Genome Biology Unit
Martin Beck: Max Planck Institute of Biophysics

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-49084-5

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