Madhura N. Paranjpe, V. Marina, Aleksandr A. Grachev
Sep 16, 2022
Nucleic Acids Research
Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site. HIGHLIGHTS Thermorubin is a potent inhibitor of protein synthesis both in vivo and in vitro; Thermorubin does not prevent the binding of P- and A-site tRNAs; Thermorubin affects multiple steps of translation elongation with a major impact on binding stability of the A-site tRNA; Thermorubin can act as an inhibitor of translation termination on some ORFs.