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 n ucleotides in 23 S and 5 S rRNA. Escherichia coli 50 S subunits and 70 S ri bosomes 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 th e nucleotides that are likely to be involved in subunit-subunit interaction s. Upon subunit association, the bases of 22 nucleotides and the ribose gro ups 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 A 1896, and G2505 become more reactive to chemical probes, indicating localiz ed 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 st em-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 stro ngly cleaved by hydroxyl radicals, suggesting that these stems protrude fro m the 50 S subunit. When the 30 S subunit is bound, most of the ribose grou ps in the 715, 890, 1700 and 1920 stemloops are protected, as are many base s in and around the corresponding apical loops. Intriguingly, three of the protected regions of 23 S rRNA are known to be linked via tertiary interact ions to features of the peptidyl transferase center. Together with the juxt aposition of the subunit-protected regions of 16 S rRNA with the small subu nit tRNA binding sites, our findings suggest the existence of a communicati on pathway between the codon-anticodon binding sites of the 30 S subunit wi th the peptidyl transferase center of the 50 S subunit via rRNA-rRNA intera ctions. (C) 1999 Academic Press.