RIOK3 mediates the degradation of ubiquitylated 40S ribosomal subunits

Protein synthesis and ribosome production demand significant cellular resources and are therefore tightly regulated. In response to stress, mammalian cells downregulate synthesis of new ribosomes and induce degradation of existing ribosomes. However, how ribosomes are targeted for degradation in stress conditions remains unclear. Here we show that the atypical protein kinase RIOK3 recognizes and mediates the degradation of ubiquitylated 40S ribosomal subunits. We establish that during starvation, the E3 ligase RNF10 ubiquitylates 40S ribosomal proteins uS3 and uS5, resulting in a striking depletion of 40S subunits relative to 60S subunits. Cryo-EM structures show that these ubiquitylated 40S subunits are subsequently recognized by RIOK3, which directly interacts with ubiquitin moieties on uS3 and uS5 through a unique N-terminal ubiquitin interacting motif. RIOK3 binds both mature and immature ubiquitylated 40S subunits and facilitates their degradation, as RIOK3 knockout prevents 40S subunit depletion during starvation. Cryo-EM structures of RIOK3-40S complexes reveal sequential degradation states of RIOK3-bound 40S subunits undergoing progressive decay of 18S rRNA. Together, these data show how 40S ribosomes are targeted for degradation in response to stress, connecting quality control-mediated ubiquitylation to downstream regulation of ribosome homeostasis.