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TitleDoublet decoding of tRNA demonstrates plasticity of ribosomal decoding center.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 5402, Year 2025
Publish dateJun 26, 2025
AuthorsShruthi Krishnaswamy / Shirin Akbar / Daniel S D Larsson / Yang Chen / Maria Selmer /
PubMed AbstractFrameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNA has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to ...Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNA has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. However, it has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. Here, we perform single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNA bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon.
External linksNat Commun / PubMed:40571681 / PubMed Central
MethodsEM (single particle)
Resolution2.49 - 2.61 Å
Structure data

51679

9gxx

EMDB-51679, PDB-9gxx:
70S ribosome with doublet-decoding tRNASer3 bound to A-site GCA codon
Method: EM (single particle) / Resolution: 2.61 Å

51758

9h0l

EMDB-51758, PDB-9h0l:
70S ribosome with cognate tRNASer3 bound to A-site AGC codon
Method: EM (single particle) / Resolution: 2.49 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SPD:
SPERMIDINE

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-SPM:
SPERMINE

ChemComp-ZN:
Unknown entry

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / decoding / frame shift / translation

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