Interplay between the Ribosomal Tunnel, Nascent Chain, and Macrolides Influences Drug Inhibition

Abstract

Accumulating evidence suggests that, during translation, nascent chains can form specific interactions with ribosomal exit tunnel to regulate translation and promote initial folding events. The clinically important macrolide antibiotics bind within the exit tunnel and inhibit translation by preventing progression of the nascent chain and inducing peptidyl-tRNA drop-off. Here, we have synthesized amino acid- and peptide-containing macrolides, which are used to demonstrate that distinct amino acids and peptides can establish interaction with components of the ribosomal tunnel and enhance the ribosome-binding and inhibitory properties of the macrolide drugs, consistent with the concept that the exit tunnel is not simply a Teflon-like channel. Surprisingly, we find that macrolide antibiotics do not inhibit translation of all nascent chains similarly, but rather exhibit polypeptide-specific inhibitory effects, providing a change to our general mechanistic understanding of macrolide inhibition.

Binding and Action of CEM-101, a New Fluoroketolide Antibiotic That Inhibits Protein Synthesis

“…Several recent findings indicate that macrolides may inhibit translation in a polypeptide-specific manner (24,25,29,40,42). In this regard, it is noteworthy that although the affinity of CEM-101 for the ribosome in vitro is similar to that of the older macrolides, the drug has a clearly improved potency in inhibiting cell growth (26,34).…”

Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center

“…As a result, PTC inhibitors halt translation at multiple locations along the gene, whereas macrolides arrest ribosome only at a limited number of codons within the ORF, and synthesis of the proteins lacking the "problematic" sequences may not be inhibited at all (32,39). For this reason, cells treated with excess of macrolide antibiotics continue to synthesize a limited subset of polypeptides (32), whereas protein translation in cells exposed to CHL or LZD is essentially abolished (Fig.…”

Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation

“…However, a growing body of evidence suggests that the synthesis of the very first 4 amino acids possesses special features. In prokaryotes, the presence of macrolides allows synthesis of at least 4 amino acids before peptidyl-tRNA release even though the macrolide binding sites is far below the PTC [26]. It has also been reported that overexpression of very short minigenes triggers ribosome drop-off.…”