Genome-wide effects of the antimicrobial peptide apidaecin on translation termination

Biochemical studies had shown that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Genome-wide analysis revealed that Api leads to pronounced ribosome arrest at stop codons and ribosome queuing. In addition, Api causes a dramatic increase of stop codon bypass by ribosomes paused in a pre-release state, resulting in accumulation of proteins with C-terminal extensions. Stop codon bypass occurs in 0-frame, by misincorporating near-cognate aminoacyl-tRNAs, or via frameshifting. Api-mediated pervasive stalling of pre-release ribosomes futilely activates the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may contribute to development of new treatments for infections and genetic diseases, and research tools for genome exploration.