Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site.

The ribosomal RNA binding site of Bacillus stearothermophilus ribosomal protein S15 (BS15) was analyzed using synthetic RNA oligonucleotides derived from the 16 S rRNA central domain. Native gel electrophoresis mobility shift assays demonstrate that BS15 can specifically interact with an RNA oligonucleotide containing nucleotides 585 to 756 (helices 20 to 23) of 16 S rRNA with an apparent dissociation constant of 35 nM. A series of deletion mutants of the rRNA fragment that contains the BS15 specific binding site was tested for their capacity to bind protein using a competition binding assay. The major determinant of the BS15-rRNA interaction is a three-way junction between helices 20, 21, and 22, while helix 23 (nucleotides 673 to 733 of 16 S rRNA) was dispensable for high affinity binding. Helix 22 contains BS15 binding determinants in an internal loop containing two phylogenetically conserved purine-purine base-pairs. In contrast, only small segments of helices 20 and 21 are required to maintain the integrity of the junction. Kinetic measurements of the dissociation and association rate of the bimolecular complex between BS15 and various minimal rRNA binding sites demonstrate that the basic properties of this interaction were not altered as a result of the deletions. The minimal binding site is a 61 nucleotide RNA that is a good model for the wild-type BS15-16 S rRNA interaction.