Nucleotides in 23 S rRNA protected by the association of 30 S and 50 S ribosomal subunits

We have studied the effect of subunit association on the accessibility of nucleotides in 23 S and 5 S rRNA. Escherichia coli 50 S subunits and 70 S ribosomes were subjected to a combination of chemical probes and the sites of attack identified by primer extension. Since the ribose groups and all of the bases were probed, the present study provides a comprehensive map of the nucleotides that are likely to be involved in subunit-subunit interactions. Upon subunit association, the bases of 22 nucleotides and the ribose groups of more than 60 nucleotides are protected in 23 S rRNA; no changes are seen in 5S rRNA. interestingly, the bases of nucleotides A1866, A1891 and A1896, and G2505 become more reactive to chemical probes, indicating localized rearrangement of the structure of the 50 S subunit upon association with the 30 S subunit. Most of the protected nucleotides are located in four stem-loop structures around positions 715, 890, 1700, and 1920. In free 50 S subunits, virtually all of the ribose groups in these four regions are strongly cleaved by hydroxyl radicals, suggesting that these stems protrude from the 50 S subunit. When the 30 S subunit is bound, most of the ribose groups in the 715, 890, 1700 and 1920 stemloops are protected, as are many bases in and around the corresponding apical loops. Intriguingly, three of the protected regions of 23 S rRNA are known to be linked via tertiary interactions to features of the peptidyl transferase center. Together with the juxtaposition of the subunit-protected regions of 16 S rRNA with the small subunit tRNA binding sites, our findings suggest the existence of a communication pathway between the codon-anticodon binding sites of the 30 S subunit with the peptidyl transferase center of the 50 S subunit via rRNA-rRNA interactions. (C) 1999 Academic Press.