Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components

BMC Evol Biol. 2008 Oct 23;8:290. doi: 10.1186/1471-2148-8-290.

Abstract

Background: Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis.

Results: Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea.

Conclusion: We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain [PSI+] mediated eRF3 precipitation.

MeSH terms

  • Amino Acid Sequence
  • Archaea / classification*
  • Archaea / genetics
  • Endoribonucleases / chemistry
  • Endoribonucleases / genetics
  • Eukaryotic Cells / classification*
  • Evolution, Molecular*
  • GTP-Binding Proteins / genetics
  • Peptide Termination Factors / chemistry
  • Peptide Termination Factors / genetics*
  • Phylogeny
  • Protein Structure, Tertiary
  • RNA Stability / genetics*
  • Sequence Alignment

Substances

  • Peptide Termination Factors
  • Endoribonucleases
  • GTP-Binding Proteins