Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 117; no. 28; pp. 16333 - 16338
• Main Authors: Nguyen, Ha An, Sunita, S., Dunham, Christine M.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 14.07.2020
• Subjects: Ablation; anticodon; Anticodon - chemistry; Anticodon - genetics; Anticodon - metabolism; Base Pairing; BASIC BIOLOGICAL SCIENCES; Binding; Biological Sciences; Codon - genetics; Codon - metabolism; Codons; Correlation; Crystallography, X-Ray; Disruption; miscoding; Misreading; Models, Molecular; Mutation; Nucleic Acid Conformation; Nucleotide sequence; Nucleotides; Protein Biosynthesis - genetics; ribosome; Ribosomes - chemistry; Ribosomes - metabolism; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Ribosomal, 23S - chemistry; RNA, Ribosomal, 23S - genetics; RNA, Ribosomal, 23S - metabolism; RNA, Transfer - chemistry; RNA, Transfer - genetics; RNA, Transfer - metabolism; rRNA; rRNA 23S; structural biology; Thermus thermophilus - genetics; Thermus thermophilus - metabolism; tRNA; ribosome; structural biology; anticodon; tRNA; miscoding
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2004170117

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem−loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. Here, we solved structures of the bacterial ribosome containing either wild-type tRNA GGC Ala or tRNA GGC Ala containing a reversed 32–38 pair on cognate and near-cognate codons. Structures of wild-type tRNA GGC Ala bound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon−anticodon interaction is cognate or near cognate. Further, the 32–38 pair is destabilized in the context of a near-cognate codon−anticodon pair. Reversal of the pairing in tRNA GGC Ala ablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32–38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.