Molecular Cell
Volume 82, Issue 18, 15 September 2022, Pages 3424-3437.e8
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Article
Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover

https://doi.org/10.1016/j.molcel.2022.08.018Get rights and content
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Highlights

  • Decoding-defective ribosomes are stalled as individual 80S at the initiation codon

  • Mag2 flags potentially inactive ribosomes by mono-ubiquitination of uS3

  • Ubiquitin chain extension by Fap1 drives rRNA decay of individual stalled 80S

  • Fap1 senses 80S stalling by probing the mRNA at the entry and exit channels

Summary

Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. Here, focusing on noncolliding stalling exhibited by decoding-defective ribosomes, we identified Fap1 as a stalling sensor triggering 18S nonfunctional rRNA decay via polyubiquitination of uS3. Ribosome profiling revealed an enrichment of Fap1 at the translation initiation site but also an association with elongating individual ribosomes. Cryo-EM structures of Fap1-bound ribosomes elucidated Fap1 probing the mRNA simultaneously at both the entry and exit channels suggesting an mRNA stasis sensing activity, and Fap1 sterically hinders the formation of canonical collided di-ribosomes. Our findings indicate that individual stalled ribosomes are the potential signal for ribosome dysfunction, leading to accelerated turnover of the ribosome itself.

Keywords

individual ribosomes
ribosomal stalling
E3 ubiquitin ligase
mRNA stasis sensing
ubiquitination
rRNA decay
translational quality control
ribosome profiling
cryo-EM

Data and code availability

  • Raw sequencing files and processed data have been deposited at GEO. Cryo-EM structural maps and molecular models have been deposited at the Electron Microscopy Data Bank (EMDB) and at the Protein Data Bank (PDB). Accession numbers are listed in the key resources table and are publicly available as of the date of publication. Original western blot and northern blot images have been deposited at Mendeley and are publicly available as of the date of publication. The DOI is listed in the key resources table.

  • This paper does not report original code.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Cited by (0)

5

These authors contributed equally

6

Lead contact