The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E. coli

The DNA sequence of the 23S-5S rRNA intergenic region has been determined for two ribosomal RNA operons in E. coli. The spacer in both rrnX and rrnD^* is 92 bp long; the sequences are identical except for two heterogeneities. 130 bp at the 3′ end of the 23S rRNA gene have also been sequenced. We observe that a region surrounding the 3′ end of 23S is complementary to sequences surrounding the 5′ end of the gene. This complementarity predicts a giant stem and loop structure closed by an almost perfectly double-stranded helix of 28 bp that includes both termini of mature 23S rRNA. Moreover, we find that this helix can be extended after a brief interruption to include a substantial number of additional residues from the two spacer regions flanking the 23S gene; interestingly, the extended structure involves sequences that are conserved in the distal portion of the two different types of 16S-23S spacer region-those containing tRNA_1B^Ala and tRNA₁^Ile, and those with tRNA₂^Glu. We have also analyzed the ends of the precursor 23S RNA (23S_III) produced by in vitro RNAase III cleavage of the 30S pre-rRNA. The terminal sequences of 23S_III appear in the 28 bp helical region, several nucleotides beyond the 23S mature ends. Thus we propose that residues separated by the 2900 nucleotides of 23S rRNA come together to form a processing site for RNAase III in the ribosomal RNA precursor molecule.