An additional ribosome-binding site on mRNA of highly expressed genes and a bifunctional site on the colicin fragment of 16S rRNA fromEscherichia coli: important determinants of the efficiency of translation-initiation

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Abstract
For various genes of E.coli, three regions (−55 to −1; −35 to −1; −21 to −1)5' to AUG codon on mRNA were searched for sites of interaction with colicin fragment of 16S rRNA. The detailed sequence comparison points out that apart from Shine-Dalgarno base pairing, an additional ribosome binding site, a subsequence of 5′-UGAUCC-3′ invariably exists in mRNA for highly expressed genes. Poorly expressed genes appear to be controlled by only Shine-Dalgarno base pairing. The analysis indicates that in the initiator region, the −55 to −1 region contains the signal which decides the efficiency of the translation-initiation. The site on 16S rRNA, 5′-GGAUCA-3′ at position 1529, that can base pair to the above site, has a recognition site on 23S rRNA at position 2390. In the light of the conserved nature and accessibility of these sites, it is proposed that the site on 16S rRNA plays a bifunctional role-initially it binds to mRNA from highly expressed genes to form a stable 30S initiation complex, and upon association with 505 subunit it exchanges base pairing with 23S rRNA, thus leaving the site on mRNA free.