Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria

Narayan Prasad Parajuli, Andrew Emmerich, Chandra Sekhar Mandava, Michael Y. Pavlov and Suparna Sanyal ()
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Narayan Prasad Parajuli: Uppsala University
Andrew Emmerich: Uppsala University
Chandra Sekhar Mandava: Uppsala University
Michael Y. Pavlov: Uppsala University
Suparna Sanyal: Uppsala University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted Escherichia coli translation system and 1.96 Å resolution cryo-EM structure of THB-bound 70S ribosome with mRNA and initiator tRNA, independently suggest that THB binding at the intersubunit bridge B2a near decoding center of the ribosome interferes with the binding of A-site substrates aminoacyl-tRNAs and class-I release factors, thereby inhibiting elongation and termination steps of bacterial translation. Furthermore, THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. Our results show that THB does not inhibit translation initiation as proposed earlier and provide a complete mechanism of how THB perturbs bacterial protein synthesis. This in-depth characterization will hopefully spur efforts toward the design of THB analogs with improved solubility and effectivity against multidrug-resistant bacteria.

Date: 2023
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DOI: 10.1038/s41467-023-36528-7

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