NATURE OF THE RIBOSOMAL MESSENGER-RNA TRACK - ANALYSIS OF RIBOSOME-BINDING SITES CONTAINING DIFFERENT SEQUENCES AND SECONDARY STRUCTURES

The ribosomal mRNA track was investigated by toeprinting 30S ribosomes, in the presence or absence of tRNA, using a variety of different ribosome-binding sites. We found that: (1) the ribosome, by itself, recognizes the mRNA translational initiation site; (2) the ribosomal mRNA track makes extensive contact with mRNA independent of tRNA and the start codon; (3) ribosome-mRNA complexes are less stable than complexes containing tRNA; and (4) toeprinting can be used to analyze the contour of the ribosomal mRNA track, yielding information on its ''height'' as well as its ''length'' dimension. Examination of several ribosome-binding sites, including those containing very stable secondary structure, indicated that the ''height' of the mRNA track is quite roomy, while the nucleotide distance between the site of Shine-Dalgarno annealing, the P site, and the 3'-edge of the mRNA track is fixed. The data suggest a mechanism for tethering regulatory elements to the ribosome during translation.