The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA

Cytoplasmic degradation of eukaryotic mRNAs in 3’ to 5’ direction is catalyzed by the exosome complex together with the Ski complex and, in the yeast Saccharomyces cerevisiae, the Ski7 protein. This exosome-Ski-system also degrades ribosome-associated aberrant mRNAs lacking a stop codon, a pathway called non-stop-mRNA decay (NSD). However, the interplay between the Ski components and the ribosome is unknown. Here, we report that the Ski complex can associate with ribosomes in vitro and in vivo independently of Ski7. Ribosome profiling suggests that this association is important for NSD but also for general mRNA turnover. A cryo-electron microscopy structure reveals that the Ski complex binds near the mRNA entry site of the 40S subunit, facilitating the threading of the mRNA into the Ski2 helicase. Collectively, these results demonstrate an unanticipated role for the Ski complex in mRNA decay of ribosome-associated mRNAs, mediated by a direct interaction with the translation machinery. Overall design: Ribosome profiling of 80S monosomes and in vivo pullouts of Ski complex associated 80S ribosomes. In vivo pullouts were performed using a yeast strain expressing C-terminally TAP (tandem affinity purification) tagged Ski3. Control mRNA from the total cell lysate and pull-down mRNA from the pullouts were also sequenced respectively.