ArticleNucleic acids research2019
Differences in the path to exit the ribosome across the three domains of life.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 95 citations in OpenAlex.
- High Throughput Characterization of Eukaryotic 2A-Like Peptides Identifies Novel Leucine-Associated Reduction in Protein Abundance.bioRxiv : the preprint server for biology · 2026Article
- Evolution of the ribosomal exit tunnel through the eyes of the nascent chain.Nucleic acids research · 2026Article
- RiboScreenBiomedicines · 2026Review
- Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel.PLoS computational biology · 2026Article
- Mechanical forces regulate the composition and fate of stalled nascent chains.Molecular cell · 2026Article
- The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking.Nature structural & molecular biology · 2025Article
- Evolution of ribosome X-ray crystallography: from first crystals to atomic resolution.Biophysical reviews · 2025Review
- The assembly factor Reh1 is released from the ribosome during its initial round of translation.Nature communications · 2025Article
- Resolving chaperone-assisted protein folding on the ribosome at the peptide level.Nature structural & molecular biology · 2024Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.Nucleic acids research · 2024Article
- Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.Journal of chemical information and modeling · 2024Article
- Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.bioRxiv : the preprint server for biology · 2024Article
- How the ribosome shapes cotranslational protein folding.Current opinion in structural biology · 2024Review
- 2'-O-ribose methylation levels of ribosomal RNA distinguish different types of growth arrest in human dermal fibroblasts.Journal of cell science · 2024Article
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- RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures.Nucleic acids research · 2023Article
- Geometric differences in the ribosome exit tunnel impact the escape of small nascent proteins.Biophysical journal · 2023Article
- Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.Computational and structural biotechnology journal · 2023Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, 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 the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.