Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution

Abstract

In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, only molecular models of large 50S subunits have been reported for archaea. Here, we present a complete molecular model for the Pyrococcus furiosus 70S ribosome based on a 6.6 Å cryo-electron microscopy map. Moreover, we have determined cryo-electron microscopy reconstructions of the Euryarchaeota Methanococcus igneus and Thermococcus kodakaraensis 70S ribosomes and Crenarchaeota Staphylothermus marinus 50S subunit. Examination of these structures reveals a surprising promiscuous behavior of archaeal ribosomal proteins: We observe intersubunit promiscuity of S24e and L8e (L7ae), the latter binding to the head of the small subunit, analogous to S12e in eukaryotes. Moreover, L8e and L14e exhibit intrasubunit promiscuity, being present in two copies per archaeal 50S subunit, with the additional binding site of L14e analogous to the related eukaryotic r-protein L27e. Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity.

The Functional Role of eL19 and eB12 Intersubunit Bridge in the Eukaryotic Ribosome

“…In mutant eL19 1–154 , the C-terminal 35 amino acid residues were removed, eliminating the bridge forming region in which eL19 interacts with 18S RNA ES6S and ribosomal proteins eS7 and uS17. Mutant eL19 1–146 , harbouring a deletion of 43 amino acid residues, mimicked the archaeal version of eL19 12 . In mutant eL19 1–133 , the entire C-terminal α-helix (56 amino acid residues) was deleted.…”

The L7Ae protein binds to two kink-turns in the Pyrococcus furiosus RNase P RNA

“…Cryo-electron microscopy-based studies recently reported that L7Ae, first identified as a large rRNA-associated subunit, has a second binding site on the small rRNA subunit and even a third site on the large rRNA (59). However, this third site appears to be missing in ribosomes of late branches of euryarchaea (e.g.…”

Cryo-EM study of start codon selection during archaeal translation initiation

“…An initial data set of ∼192,000 particles was sorted using several rounds of classical two-dimensional classification protocols implemented in RELION. Then, a 3D-classification in RELION using a 70 Å filtered map of the archaeal 30S (extracted from the Pyrococcus furiosus 70S structure48) helped to isolate several well-resolved classes that were used for further 3D classification. The following sorting procedure allowed us to discard classes without or with poorly resolved aIF1, aIF1A or tRNA.…”

“…The structures of the head and body parts of the 30S subunits were extracted from the P. furiosus 70S coordinates48 (PDB entry 4V6U). The head and body were manually placed independently into the electron density map using Chimera, before automatically refining the position in the same programme.…”

“…The models used to account for the electron density correspond to the structures of Pyrococcus furiosus 30S (PDB entry 4V6U; ref. 48), of Sulfolobus solfataricus TC (PDB entry 3V11; ref. 23), of Pa-aIF1A (PDB entry 4MNO) and of Methanocaldococcus jannaschii aIF1 (PDB entry 4MO0; Supplementary Fig.…”