Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA

Nat Commun. 2021 Jan 12;12(1):328. doi: 10.1038/s41467-020-20373-z.

Abstract

While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acids / metabolism
  • Aminoacylation
  • Anticodon / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Codon / genetics
  • Escherichia coli / metabolism
  • Fluorescence Resonance Energy Transfer
  • Frameshifting, Ribosomal / genetics*
  • Genome, Bacterial*
  • Guanosine Triphosphate / metabolism
  • Hydrolysis
  • Methylation
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleotide Motifs / genetics
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics*
  • RNA, Transfer / metabolism
  • Ribosomes / metabolism
  • Salmonella typhimurium / genetics*

Substances

  • Amino Acids
  • Anticodon
  • Bacterial Proteins
  • Codon
  • Guanosine Triphosphate
  • RNA, Transfer