The Enigmatic Ribosome Tunnel. Despite over 40 years of intensive research on the ribosome, the function of the ribosome tunnel has been a long-standing mystery. In recent years, a growing body of evidence has challenged the idea that the tunnel is simply a passive water-filled conduit through which all polypeptides transit uniformly. The rate of translation, for example, can be influenced by the electrostatic potential that variably distributes along the tunnelThe recognition of specific peptide sequences inside the tunnel of bacterial, fungal, and higher eukaryotic ribosomes has been shown to arrest translation at either the elongation or termination phase. Certain nascent chains can also adopt α-helical or more compacted structures that might influence protein folding and targeting . In all these cases, polypeptide “discrimination” appears to be monitored by ribosomal components that line the tunnel wall, including the L4 and L22 proteins and segments of 23S rRNA, which subsequently transmits a signal to the distal segments of the ribosome. We seek to address: 1) How do mutations in the ribosomal proteins that line the tunnel wall attenuate translation?  2) Are the attenuations linked to specific changes in intraribosomal structure and electrostatic potential?

AZ_tunnelRibosome Inhibiting Factors. Macrolide antibiotics inhibit protein synthesis by binding inside the ribosome tunnel, presumably by blocking the elongation of newly synthesized polypeptide chains. The inability of macrolides to fully arrest the synthesis of every protein has been observed for more than two decades, but the possible mechanisms of incomplete inhibition have only begun to emerge in more recent studies. To determine how particular protein sequences are more sensitive to macrolide inhibition than others, we recently performed genome-wide ribosome profiling to map the position of stalled-ribosome in macrolide-treated cells. We found that the antibiotic-bound ribosomes only stall at specific sites that are highly enriched in proline and charged residues. Surprisingly, these residues are also the preferred amino acids of ribosome stalling among other ligand-dependent and independent arrest peptides. We are investigating how the drug-bound ribosome recognizes specific protein sequence to induce translation arrest.

← ↑Nascent polypeptide (orange) traverses through the ribosome tunnel. 23S rRNA residues critical for peptide-depedent translation arrest are colored in magenta and yellow. PTC, peptidyltransferase center; AZ, azithromycin; ERY, erythromycin; L22, ribosomal protein L22.