Differences in the path to exit the ribosome across the three domains of life

Abstract

Recent advances in biological imaging have led to a surge of fine-resolution structures of the ribosome from diverse organisms. Comparing these structures, especially the exit tunnel, to characterize the key similarities and differences across species is essential for various important applications, such as designing antibiotic drugs and understanding the intricate details of translation dynamics. Here, we compile and compare 20 fine-resolution cryo-EM and X-ray crystallography structures of the ribosome recently obtained from all three domains of life (bacteria, archaea and eukarya). We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins localized near the tunnel, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure, and sequence. We find that the tunnel is more conserved in its upper part, from the polypeptide transferase center to the constriction site. In the lower part, tunnels are significantly narrower in eukaryotes than in bacteria, and we provide evidence for the existence of a second constriction site in eukaryotic tunnels. We also show that ribosomal RNA and protein sequences are more likely to be conserved closer to the tunnel, as is the presence of positively charged amino acids. Overall, our comparative analysis shows how the geometric and biophysical properties of the exit tunnel play an important role in ensuring proper transit of the nascent polypeptide chain, and may explain the differences observed in several co-translational processes across species.

Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes

“…Since the translation elongation mechanism is generally well conserved among all kingdoms of life, the conservation of this noncanonical ribosome dynamics is not surprising. In particular, the ribosome tunnel and the PTC region are well conserved 2 . We thus conclude that IRD is a conserved property of the ribosomes from E. coli to eukaryotes.…”

“…Essentially, the ribosomes decode any codon on ORFs. The lengthening nascent polypeptides pass through the ribosomal exit tunnel 1 , which encloses 30–40 amino acids of the growing nascent polypeptidyl-tRNA 2 , 3 .…”

PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress

“…The cryo-EM structure of the human 80S ribosome (Natchiar et al, 2017) (PDB 6QZP) was accessed in PyMOL (Molecular Graphics System, Version 2.0 Schrödinger, LLC). The peptide exit tunnel was visualized with the coordinates previously reported for this structure (Duc et al, 2019).…”

Ribosome profiling reveals multiple roles of SecA in cotranslational protein export

“…The first SecA binding peak ends at residue 105 of the first periplasmic loop. Considering that over 20 amino acids at the N-terminus of the loop are inserted into SecYEG for a TMD in type II topology 34 , and at least 30 amino acids 36 at the C-terminus of the loop are still in the ribosomal exit tunnel, we reasoned that the emergence of residues 20–75 in this loop determined SecA association. If SecA engagement is sequence-dependent, it would be abolished with AcrB-Δ71aa, in which residues 20–90 of this loop is deleted.…”