Unusual base pairing during the decoding of a stop codon by the ribosome

Abstract

During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.

FIGURE 1. Chemical differences between uridine and pseudouride and experimental set-up

(a) Uridine (U, 1-ß-D-ribofuranosyluracil) and pseudouridine (Ψ, 5-ß-D-ribofuranosyluracil). (b) Top, diagram of the three synthetic mRNA constructs designed for the in vitro nonsense suppression experiment in bacteria. Bottom, anti-His and anti-Flag immunoblot analysis of the in-vitro translation assays in E. coli. (c) The tRNA^Ser anticodon stem loop (ASL) and mRNA used in this study.

FIGURE 2. Overall and detailed view of the base pairs involved in the codon/anticodon interaction

(a) Overview of the 30S subunit and detail of the 30S decoding site with the ΨAG/ASL-tRNA^Ser. The ASL-tRNA^Ser is depicted in red, the ΨAG codon in yellow, the 16S rRNA in gray and protein S12 in blue. Right, unbiased difference Fourier density for the ASL and codon. (b) The base pairs for the codon-anticodon interaction are shown with boxes over the first (left), second (middle) and third (right) positions; the actual structures of the base pair is shown below in unbiased difference Fourier maps contoured at 1.5σ.

FIGURE 3. Interaction of ribosomal bases with the codon-anticodon base pairs

Details of base pairing for the first, second and third positions of the ΨAG/ASL-tRNA^Ser structure with the ribosomal bases involved in minor groove recognition are shown on the left. For comparison, the corresponding positions of the codon-anticodon base pairs of a phenylalanine UUU codon with its cognate ASL anticodon from a previous study are shown on the right.