RIOK3 mediates the degradation of 40S ribosomes

Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3′ end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis. • Amino acid starvation induces selective degradation of ubiquitylated 40S ribosomes • RIOK3 binds ubiquitylated 40S ribosomes via an unusual ubiquitin-interacting motif • Cryo-EM structures capture 40S ribosome degradation intermediates • RIOK3 binding to 40S ribosomes triggers 18S rRNA decay starting from the 3′ end Huang et al. identify a pathway for stress-induced 40S ribosome degradation: 40S ribosomes ubiquitylated by RNF10 are subsequently bound by the atypical kinase RIOK3, which mediates their degradation by triggering 18S rRNA decay from the 3′ end. Cryo-EM structures capture degradation intermediates, providing insights into the mechanisms of ribosome degradation.