RIOK3 mediates the degradation of 40S ribosomes

  • Mol Cell. 2025 Feb 20;85(4):802-814.e12. doi: 10.1016/j.molcel.2025.01.013.
Zixuan Huang  1 ,  Frances F Diehl  2 ,  Mengjiao Wang  1 ,  Yi Li  1 ,  Aixia Song  1 ,  Fei Xavier Chen  1 ,  Nicolle A Rosa-Mercado  2 ,  Roland Beckmann  3 ,  Rachel Green  4 ,  Jingdong Cheng  5
Affiliations
  • 1. Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University Shanghai, China.
  • 2. Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • 3. Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
  • 4. Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address: [email protected].
  • 5. Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University Shanghai, China. Electronic address: [email protected].
PMID: 39947183 DOI: 10.1016/j.molcel.2025.01.013
Abstract

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.

Keywords
40S; RIOK3; RNA degradation; cryo-EM; homeostasis; ribosome; starvation; stress response; translation; ubiquitin.