ArfB can displace mRNA to rescue stalled ribosomes

Nat Commun. 2020 Nov 3;11(1):5552. doi: 10.1038/s41467-020-19370-z.


Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biocatalysis
  • Dimerization
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / ultrastructure
  • Models, Biological
  • Protein Conformation
  • RNA Stability
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA, Messenger / ultrastructure
  • Ribosome Subunits / metabolism
  • Ribosomes / metabolism*
  • Ribosomes / ultrastructure


  • Escherichia coli Proteins
  • RNA, Messenger