Interaction of proteins S16, S17 and S20 with 16 S ribosomal RNA

Abstract

We have used rapid chemical probing methods to examine the effect of assembly of ribosomal proteins S16, S17 and S20 on the reactivity of individual residues of 16 S rRNA. Protein S17 strongly protects a compact region of the RNA between positions 245 and 281, a site previously assigned to binding of S20. Protein S20 also protects many of these same positions, albeit more weakly than S17. Strong S20-dependent protections are seen elsewhere in the 5′ domain, most notably at positions 108, and in the 160–200 and 330 loop regions. Enenpectedly, S20 also causes protection of several bases in the 1430–1450 region, in the 3′ minor domain. In the presence of the primary binding proteins S4, S8 and S20, we observe a variety of effects that result from assembly of the secondary binding protein S16. Most strongly protected are nucleotides around positions 50, 120, 300 to 330 and 360 in the 5′ domain, and positions 606 to 630 in the central domain. In addition, numerous nucleotides in the 5′ and central domains exhibit enhanced reactivity in response to S16. Interestingly, the strength of the S20-dependent effects in the 1430–1450 region is attenuated in the presence of S4+S8+S20, and restored in the presence of S4+S8+S20+S16. Finally, the previously observed rearrangement of the 300 region stem-loop that occurs during assembly is shown to be an S16-dependent event. We discuss these findings with respect to assignment of RNA binding sites for these proteins, and in regard to the co-operativity of ribosome assembly.