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.