Abstract
Biochemical studies suggested 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. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.
Highlights
The ribosome translates mRNA into protein and represents one of the main antibiotic targets in the bacterial cell
Incubation of E. coli (BL21) cultures for 1 min with increasing concentrations of Api resulted in a severe inhibition of protein synthesis (Figure 1-figure supplement 1A)
We proceeded to the Ribo-seq experiments in order to obtain an unbiased view of how treatment with Api alters the global distribution of translating ribosomes in cellular mRNAs (Ingolia et al, 2009; Oh et al, 2011)
Summary
The ribosome translates mRNA into protein and represents one of the main antibiotic targets in the bacterial cell. A number of antibiotics impede initiation of translation by preventing mRNA binding or departure of the ribosome from the start codon (Lin et al, 2018; Polikanov et al, 2018; Wilson, 2009). It was only recently that apidaecin, an antimicrobial peptide from honeybees (Casteels et al, 1989), was described as the first antibiotic targeting translation termination (Florin et al, 2017). The action of apidaecin is principally different Even though this PrAMP binds in the exit tunnel and closely approaches the PTC, it does not directly obstruct the catalytic site (Florin et al, 2017; Krizsan et al, 2015). Biochemical analyses carried out with the synthetic peptide Api137 (Berthold et al, 2013) (referred to, throughout, as Api) showed that Api traps deacyl-
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