Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Petr Tesina, Laura N. Lessen, Robert Buschauer, Jingdong Cheng, Colin Chih Chien Wu, Otto Berninghausen, Allen R. Buskirk, Thomas Becker, Roland Beckmann, Rachel Green

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.

Original languageEnglish (US)
Article numbere103365
JournalEMBO Journal
Issue number3
StatePublished - Feb 3 2020


  • disome
  • frameshift
  • ribosome collision
  • stalling
  • translation

ASJC Scopus subject areas

  • General Neuroscience
  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


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