Evidence for tertiary structural RNA-RNA interactions within the protein S4 binding site at the 5′-end of 16S ribosomal RNA of Escherichia coli.+

Abstract

Evidence is presented for tertiary structural interaction(s) (interactions(s)) between two regions of an RNA molecule that are widely separated in the RNA sequence) within the 5′-one third of the 16S ribosomal RNA of Escherichia coli that constitutes the binding site of protein S ⁴ . The two main interacting RNA regions were separated by about 120 nucleotides (sections Q to M) of the 16S RNA sequence. A second, smaller gap, of 13 nucleotides, occurred within section C″. The two main interacting regions contain about 150 nucleotides (sections H″ to Q) and 160 nucleotides-(sections M to C″). They are folded back on one another and, especially in the presence of protein S ⁴ , are strongly protected against ribonuclease digestion. The intermediate region (sections Q to M), however, is relatively accessible to ribonucleases in the s4-RNF. By partial removal of subfragments from the RNA complex it was possible to localise the two main interacting sites within sections H″ - H and sections I″ - C″. Three main criteria for the specificity of the RNA-RNA interactions were invoked and satisfied. The possibility of other tertiary structural RNA-RNA interactions occurring in other regions of the 16S RNA is discussed. Finally, all the structural information on the S4-RNP is summarised and a tentative model is proposed.