Modification of 30 S ribosomal subunits with kethoxal causes loss of their ability to associate with 50 S subunits under tight couple conditions. To identify those 16 S RNA sequences important for the association. 32P-labeled 30 S subunits were partially inactivated by reaction with kethoxal. The remaining association-competent 30 S subunits were selected from the modified population by their ability to form 70 S ribosomes. Comparison of kethoxal diagonal maps of the association-competent subunits with those of the total population of modified subunits reveals nine sites in 16 S RNA whose modification leads to loss of association activity. Eight of these sites were previously found to be protected from kethoxal attack and one was shown to have enhanced reactivity in 70 S ribosomes (Chapman & Noller, 1977). As before, these sites are not distributed thoughout the molecule, but are found to be clustered in two regions, at the middle and at the 3′ terminus of the 16 S RNA chain.
We interpret these findings in terms of a simple preliminary model for the functional organization of 16 S RNA, supported by the observations of other investigators, in which we divide the molecule into four domains. (1) Residues 1 to 600 are involved mainly in structural organization and assembly. (2) Residues 600 to 850 include sites which make contact with the 50 S subunit and are essential for subunit association. (3) Sites from the domain comprising residues 850 to 1350 line a pocket at the interface between the two ribosomal subunits. and contribute to the binding site(s) for transfer RNA. (4) Residues 1350 to 1541 also contain sequences which bind the 50 S subunit, but some sites in this domain alternatively participate in the initiation of protein synthesis.