The Context Theory as Applied to the Decoding of the Initiator tRNA by Escherichia coli Ribosomes

Abstract

The involvement of nucleotides adjacent to the termination codons in tRNA during the suppression of termination has been formulated as the ‘context theory’ by Bossi and Roth (1980) [Nature (Lond.) 286, 123–127], The finding that U‐U‐G functions as an initiator codon has revived the discussion on the participation of the nucleotides flanking the initiator triplet in the decoding of initiator tRNA (context theory of initiation by the ribosome). We compared the capacity of oligonucleotides cognate to the anticodon loop of formylmethionine tRNA, such as A‐U‐G, A‐U‐G‐A and U‐A‐U‐G‐A, to enhance the formation of the 30‐S and 70‐S ribosomal initiation complexes. Three different methods were used to determine the apparent binding constants and the stoichiometries of the respective complexes : adsorption of the complexes to nitrocellulose filters, equilibrium dialysis, and velocity sedimentation. We found that in the 30‐S ribosomal initiation complex and in the presence of initiation factor 2 and GTP, formylmethionyl‐tRNA is preferentially decoded by more than three mRNA bases. With the 70‐S ribosome, however, once initiation factor 2 had been released, A‐U‐G represented the most effective codon to direct the formylmethionyl‐tRNA to the peptidyl site. An extended initiator sequence may either give additional stability to the 30‐S initiation complex or may allow for an ambiguity by one base pair in the decoding of the initiator tRNA.

Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles.

“…(a) Ribosome binding studies carried out with synthetic AUG-containing oligonucleotides suggest involvement of the nucleotide immediately preceding the initiator codon (position -1) and the nucleotide immediately following the initiator codon (position +4). A pyrimidine in position -1 promotes the highest level of oligonucleotide binding (102,125), whereas a purine is most effective in position +4 (403,404). (The latter effect was not observed in all experiments, however [125].)…”

Biased Codon Usage: An Exploration of Its Role in Optimization of Translation

“…Schmitt et al (1982) compared the binding efficiency of synthetic oligonucleotides with the sequences AUG and AUGA to 30S ribosomal suppressor tRNA and the 3' adjacent tRNA determines the efficiency of suppression. Schmitt et al (1982) compared the binding efficiency of synthetic oligonucleotides with the sequences AUG and AUGA to 30S ribosomal suppressor tRNA and the 3' adjacent tRNA determines the efficiency of suppression.…”