Specific interaction between ribosomal protein S4 and the alpha operon messenger RNA

The Escherichia coli ribosomal protein S4 is known to repress translation of its own gene and several other ribosomal protein (r-protein) genes in the alpha operon as part of a general mechanism coordinating the levels of rRNA and r-protein synthesis. Using a filter binding assay and RNA transcripts prepared in vitro, we have detected and quantitated specific interactions between S4 and alpha mRNA fragments. The main results are the following: Only the alpha mRNA leader is required for specific recognition, with a small fraction of the binding free energy derived from sequences at the ribosome initiation site. 16S rRNA and alpha mRNA compete for binding to S4 with about the same affinity (approximately equal to 2 X 10(7) M-1), suggesting that S4 utilizes the same recognition features in each RNA. Nonspecific binding of S4 to tRNA or other mRNA sequences is strongly salt dependent, while the specific S4-alpha mRNA affinity is nearly independent of salt. At physiological salt concentrations the nonspecific S4-RNA affinity (10(5)-10(6) M-1) is large enough to strongly buffer the free S4 concentration in vivo.