Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding

Abstract

The ribosome is a molecular machine that converts genetic information in the form of RNA, into protein. Recent structural studies reveal a complex set of interactions between the ribosome and its ligands, mRNA and tRNA, that indicate ways in which the ribosome could avoid costly translational errors. Ribosomes must decode each successive codon accurately, and structural data provide a clear indication of how ribosomes limit recruitment of the wrong tRNA (sense errors). In a triplet-based genetic code there are three potential forward reading frames, only one of which encodes the correct protein. Errors in which the ribosome reads a codon out of the normal reading frame (frameshift errors) occur less frequently than sense errors, although it is not clear from structural data how these errors are avoided. Some mRNA sequences, termed programmed-frameshift sites, cause the ribosome to change reading frame. Based on recent work on these sites, this article proposes that the ribosome uses the structure of the codon-anticodon complex formed by the peptidyl-tRNA, especially its wobble interaction, to constrain the incoming aminoacyl-tRNA to the correct reading frame.

Fig. 1

Interactions between the ribosome and mRNA–tRNA complexes. The nucleotides of the rRNA (red), mRNA (blue) and tRNA (purple) are numbered to represent their position in the RNA chain; the mRNA is numbered 5′–3′ starting at the beginning of the A-site codon. A Mg²⁺ ion (orange) mediates an interaction between the mRNA, C518 of the 16S rRNA and Pro44 of rpS12 (amino acids represented as green squares). Filled circles represent the phosphoribose backbone. Arrows indicate direct contacts without distinguishing between types of interactions. G1401 is shown as blocking further extension of the P-site codon helix.

Fig. 2

The structure of the decoding center imposes a three-nucleotide codon. The P-site (pale blue) and A-site (green) codons are connected through a kink in the phosphoribose backbone. The kink constrains the position of the first nucleotide of the A-site codon (top). The anticodon of tRNA entering the A site (orange) must begin pairing with that first base. Nucleotide C1054 (red) of the 16S rRNA inserts immediately below the third, or wobble, nucleotide of the tRNA. This blocks formation of a fourth base-pair. The combination of the kink and C1054 imposes a maximum size of three base-pairs on the codon–anticodon complex. The figure was created in RasMol using coordinates downloaded from the RCSB Protein Data Bank (http://www.rcsb.org/pdb/); the identification for the PDB coordinate file is 1IBM.

Fig. 3

Unconventional P-site wobble pairs increase the probability of out-of-frame decoding; the possible effect of base mismatches on frame maintenance. The eight nucleotides accessible on the inner surface of the ribosome at the decoding center are shown interacting with P- and A-site tRNAs. Rectangles represent nucleotides; circles represent the phosphoribose backbone; mRNA is shown in blue; tRNAs in purple; A and P represent the two decoding sites; nucleotides that cannot form normal interactions with the ribosome, and that are expected to have an energetic cost, are red. (a) Normal Watson–Crick pairing in both A- and P sites. (b) Out-of-frame binding in the A site. This requires bypassing one nucleotide between the A- and P sites, which could disrupt normal ribosomal interactions with the P-site wobble pair. The cartoon does not indicate a specific structure for the complex. (c) A clash caused by pairing of G–I nucleotides at the wobble position in the P site would, at the minimum, disrupt interaction of an in-frame tRNA at the first nucleotide in the A site, possibly reducing the efficiency of translation. (d) An unconventional P-site wobble pair would reduce the energetic cost of out-of-frame binding relative to in-frame binding.