Conservation of ribosomal protein binding sites in prokaryotic 16S RNAs

The Escherichia coli 30S ribosomal subunit proteins S4, S7, S8, S15, S17, and S20 that interact independently with 16S RNA from E. coli formed specific heterologous complexes with 16S RNAs extracted from 11 different prokaryotes covering a broad phylogenetic range. Complex formation was shown to be specific by saturation of binding in the presence of excess protein. Binding stoichiometries and the apparent affinities for a given protein varied depending on which 16S RNA was used, although the pattern of binding was not strictly correlated with phylogenetic relationships. The size-distribution of fragments resulting from limited hydrolysis of free prokaryotic 16S RNAs with T1 and pancreatic ribonucleases indicated that the structural organization of 16S RNA from E. coli is similar to that of 16S RNAs from closely related species, but differs, although to an unknown extent, from that of 16S RNAs from other prokaryotes tested. Digestions of RNA-protein complexes under similar conditions indicated that the proteins remain bound to specific RNA fragments. For those 16S RNAs isolated from species closely related to E. coli, the fragments were comparable to those generated by hydrolysis of the homologous complex.