Terminal-Sequence Analysis of Bacterial Ribosomal RNA. Correlation between the 3'-Terminal-Polypyrimidine Sequence of 16-S RNA and Translational Specificity of the Ribosome

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Abstract
The 3′-terminal sequences of 16-S ribosomal RNA from a number of bacteria have been determined by a stepwise degradation and 3′-terminal labelling procedure. The sequences obtained were: Bacillus stearothermophilas, -G(Z)≅5 Y-U-C-C-U-U-U-C-U (A); B. subtilis, -G(Z)≅7 Y-C-U-U-U-C-U; Caulobacter crescentus, -G(Z)3, Y-U-C-C-U-U-U-C-U; Pseudomonas aeruginosa, -G-Z-Z-Y-C-U-C-U-C-C-U-U(A), where Z is any nucleotide other than G. Thus, as previously found in Escherichia coli, all bacterial 16-S rRNAs contain a pyrimidine-rich tract at the 3′-terminus. In B. stearothermophilus and Ps. aeruginosa this region shows substantial heterogeneity involving the 3′-terminal adenylic acid. A low level of 3′-terminal heterogeneity cannot be excluded for the other bacterial 16-S rRNAs examined. The 3′-termini of bacterial 16-S rRNA can be divided into two groups on the basis of sequence homology. The first group comprises E. coli and Ps. aeruginosa; the second, B. stearo-thermophilus, B. subtilis and C. crescentus. This division correlates with a previous separation of bacterial ribosomes into two categories based on ability to translate different mRNA preparations [Stallcup, Sharrock & Rabinowitz (1974) Biochem. Biophys. Res. Commun. 58, 92–98]. We have previously proposed that the precise base sequence at the 3′-terminus of 16-S rRNA determines the intrinsic capacity of bacterial ribosomes to translate a particular cistron [Shine & Dalgarno (1975) Nature (Lond.) 254, 34–38]. No difference was found in the 3′-terminal heptanucleotide sequence of 16-S rRNA from bacteriophage T7-infected E. coli, as compared to that in uninfected cells. Thus, the T7-induced alteration in translational specificity of E. coli ribosomes is probably not mediated by modification of the terminal seven nucleotides of the smaller rRNA. The 3′-terminal sequences of the 23-S rRNA species were also determined. The sequences obtained were: B. stearothermophilus and B. subtilis, -Y-C; C. crescentus, -Y-C-U; Ps. aeruginosa, -Y-C-A; E. coli, -G-Y-U-U-A-A-C-C-U-U. No evidence for 3′-terminal heterogeneity was found. The results obtained are discussed in relation to possible base-pairing roles for the 3′-end of 16-S rRNA in bacterial protein synthesis.

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