Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

• Published in: Cell 2015-08, Vol.162 (4), p.872-884
• Main Authors: Young, David J., Guydosh, Nicholas R., Zhang, Fan, Hinnebusch, Alan G., Green, Rachel
• Format: Article
• Language: English
• Subjects: 3′UTR; ABCE1; Dom34; reinitiation; ribosome recycling; Rli1; termination
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2015.07.041

To study the function of Rli1/ABCE1 in vivo, we used ribosome profiling and biochemistry to characterize its contribution to ribosome recycling. When Rli1 levels were diminished, 80S ribosomes accumulated both at stop codons and in the adjoining 3′UTRs of most mRNAs. Frequently, these ribosomes reinitiated translation without the need for a canonical start codon, as small peptide products predicted by 3′UTR ribosome occupancy in all three reading frames were confirmed by western analysis and mass spectrometry. Eliminating the ribosome-rescue factor Dom34 dramatically increased 3′UTR ribosome occupancy in Rli1 depleted cells, indicating that Dom34 clears the bulk of unrecycled ribosomes. Thus, Rli1 is crucial for ribosome recycling in vivo and controls ribosome homeostasis. 3′UTR translation occurs in wild-type cells as well, and observations of elevated 3′UTR ribosomes during stress suggest that modulating recycling and reinitiation is involved in responding to environmental changes. [Display omitted] •Rli1/ABCE1 recycles ribosomes throughout the transcriptome in vivo•Unrecycled ribosomes queue at stop codons and reinitiate translation in 3′UTRs•Reinitiation occurs near the canonical stop codon without apparent codon preference•Dom34/PELO rescues 3′UTR-bound ribosomes that escape Rli1-mediated recycling Unrecycled ribosomes enter mRNA 3′UTRs and reinitiate translation without start codon preference to produce small peptides. 80S ribosome levels in 3′UTRs are enhanced when ribosome recycling is compromised and under stress conditions, suggesting that modulation of recycling helps shape the proteome in response to environmental perturbations.