Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

Commun Biol. 2020 Feb 6;3(1):58. doi: 10.1038/s42003-020-0780-0.

Abstract

Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNAiMet. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNAiMet complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N4-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics*
  • Archaea / metabolism*
  • Biological Evolution*
  • Cryoelectron Microscopy*
  • Models, Molecular
  • Molecular Conformation
  • Peptide Chain Initiation, Translational*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics
  • RNA, Transfer, Met / chemistry
  • RNA, Transfer, Met / genetics
  • Ribosome Subunits, Small, Archaeal / chemistry
  • Ribosome Subunits, Small, Archaeal / metabolism
  • Ribosome Subunits, Small, Archaeal / ultrastructure*
  • Structure-Activity Relationship

Substances

  • RNA, Messenger
  • RNA, Transfer, Met
  • RNA, Transfer