Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways

Accumulation of stalled ribosomes at the 3' end of mRNA without a stop codon (non-stop mRNA) is supposed to be toxic to bacterial cells. Escherichia coli has at least two distinct systems to rescue such stalled ribosomes: SsrA-dependent trans-translation and ArfA-dependent ribosome rescue. Combination of the ssrA and arfA mutations is synthetically lethal, suggesting the significance of ribosome rescue. In this study, we identified the E. coli yaeJ gene, encoding a peptide-release factor homologue with GGQ motif, as a multicopy suppressor of the lethal phenotype of ssrA arfA double mutant. The YaeJ protein was shown to bind to ribosomes. Both in vivo and in vitro, YaeJ showed the ribosome-rescue activity and promoted the hydrolysis of peptidyl-tRNA residing in the stalled ribosome. Missense mutation in the GGQ motif or deletion of the C-terminal unstructured tail abolished both the suppressor activity for ssrA arfA synthetic lethality and the ribosome-rescue activity, suggesting the importance of these structural features. On the basis of these observations, we propose that YaeJ acts as a stop codon-independent peptidyl-tRNA hydrolysing factor through binding to ribosomes stalled at the 3' end of non-stop mRNAs. It was also suggested that ArfA and YaeJ rescue the stalled ribosomes by distinct mechanisms.