Detection of archaeal- and prokaryotic-like ribosome exit tunnels within eukaryotic kingdoms
Yu, S.; Kushner, A.; Srebnik, S.; Duc, K. D.
Show abstract
The ribosome exit tunnel is a critical sub-compartment that actively regulates the folding and dynamics of nascent polypeptide chains during protein translation. In this study, we systematically examined tunnel structures of 725 ribosome models obtained through cryo-EM and X-ray crystallography, to quantify structural variations across different species and biological domains. Hierarchical clustering revealed significant geometric differences between prokaryotic and eukaryotic ribosomes, with a surprising discovery: six eukaryotic protist species display tunnel structures remarkably similar to those of archaea and bacteria. By analyzing the sequences and structures of ribosomal components forming the tunnel walls, we identified four specific sequence modifications in ribosomal proteins and ribosomal RNAs (rRNA) responsible for these unique geometric variations, and detected these modifications in additional protist species lacking existing 3D structural data. Overall, our findings highlights some complex evolutionary mechanisms governing ribosomal protein and large subunit rRNA, providing novel insights into the tunnels regulatory role in protein translation.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Transcripts’ evolutionary history and structural dynamics give mechanistic insights into the functional diversity of the JNK family 93%
- Mycobacterial methionine aminopeptidase type 1c moonlights as an anti-association factor on the 30S ribosomal subunit 93%
- High-resolution cryo-EM analysis of the therapeutic Pseudomonas phage Pa223 93%
Similar papers in this journal
- Structural comparison of protein-RNA homologous interfaces reveals widespread overall conservation contrasted with versatility in polar contacts 93%
- ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM 93%
- Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome 93%
Similar papers in this journal
Similar papers in this journal
- The origin and evolution of loqs2: a gene encoding an antiviral dsRNA binding protein in Aedes mosquitoes 92%
- Temperature-Dependent Regulation of Upstream Open Reading Frame Translation in S. Cerevisiae 92%
- Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection 91%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.