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

Journal Article · 25 February 2019 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkz106 · OSTI ID:1625576

Dao Duc, Khanh ^[1]; Batra, Sanjit S. ^[2]; Bhattacharya, Nicholas ^[3]; Cate, Jamie H D. ^[4]; Song, Yun S ^[5]

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1. Computer Science Division, University of California, Berkeley, CA 94720, USA; DOE/OSTI
2. Computer Science Division, University of California, Berkeley, CA 94720, USA
3. Department of Mathematics, University of California, Berkeley, CA 94720, USA
4. Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
5. Computer Science Division, University of California, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA

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.

• Research Organization: Lawrence Berkeley National Lab (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: Chan Zuckerburg Biohub; National Institutes of Health (NIH); Packard Fellowship; USDOE Office of Science (SC)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1625576
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 8 Vol. 47; ISSN 0305-1048
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United States
• Language: English