Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

Abstract

The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. In this study, we determined that the second-generation oxazolidinone radezolid also induces stalling with alanine at the penultimate position. However, the molecular basis for context-specificity of these inhibitors has not been elucidated. In this study, we determined high-resolution cryo-EM structures of both linezolid and radezolid-stalled ribosome complexes. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling by forcing the antibiotic to adopt a conformation that narrows the hydrophobic alanine pocket. Together, the structural and biochemical findings presented in this work provide molecular understanding of context-specific inhibition of translation by clinically important oxazolidinone antibiotics.

Signal peptide mimicry primes Sec61 for client-selective inhibition

“…5B), where they are stabilized in a nonproductive configuration, possibly via direct interactions with a composite surface defined by Sec61 and R-5 of the bound cotransin. This mechanism is reminiscent of nascent chain-selective ribosome inhibitors, which bind to a composite surface defined by the ribosome exit tunnel and specific nascent polypeptide sequences that traverse the exit tunnel [38][39][40] . Cotransin-resistant signal peptides, on the other hand, can apparently displace the bound inhibitor, intercalate between the lateral gate helices, insert into the lipid bilayer, and ultimately promote opening of the lumenal plug domain.…”