Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

Abstract

We have derived a secondary structure model for 16S ribosomal RNA on the basis of comparative sequence analysis, chemical modification studies and nuclease susceptibility data. Nucleotide sequences of the E. coli and B. brevis 16S rRNA chains, and of RNAse T1 oligomer catalogs from 16S rRNAs of over 100 species of eubacteria were used for phylogenetic comparison. Chemical modification of G by glyoxal, A by m-chloroperbenzoic acid and C by bisulfite in naked 16S rRNA, and G by kethoxal in active and inactive 30S ribosomal subunits was taken as an indication of single stranded structure. Further support for the structure was obtained from susceptibility to RNases A and T1. These three approaches are in excellent agreement. The structure contains fifty helical elements organized into four major domains, in which 46 percent of the nucleotides of 16S rRNA are involved in base pairing. Phylogenetic comparison shows that highly conserved sequences are found principally in unpaired regions of the molecule. No knots are created by the structure.

Sequence of the 3′‐terminal domain of mouse 18 S rRNA

“…The first complete sequence of this domain of a mammalian 18 S rRNA shows a striking homology (97%) with the other vertebrate sequence available, Xenopus laevis [19]. The comparison of the mouse sequence with other prokaryotic [21] or eukaryotic [22,23] sequences reinforces the view of a critical functional role of this 3'-terminal domain of small subunit rRNA molecule; this is again indicated by the conservation of a common basic RNA folding pattern from prokaryotes [ 15,16] to mouse, as reported earlier for yeast and Xenopus [20].…”

“…This conclusion has been substantiated more directly by the finding that very detailed restriction maps established for chromosomal mouse rDNA through Southern blot hybridizations (in preparation) did not reveal any difference with the present cloned rDNA fragment. Model for mouse RNA was built by reference to E. coli 16 S rRNA secondary structure model [ 15,16]. Boxes show phylogenetically conserved sequences, either in both pro-and eukaryotes (unshaded) or only in eukaryotes (shaded).…”

“…tion of large stretches within this region both in prokaryotes [ 15,31 ] and in a series of eukaryotes, ranging from yeast [18] to insects [22,23] and amphibia [ 19]. The mouse sequence was compared with its published counterparts in prokaryotic or eukaryotic systems, after alignment for maximum homology ( fig.2).…”

“…Secondary structure models for prokaryotic 16 S rRNA have been proposed on the combined basis of comparative sequence analysis and from direct experimental evidence [ 15,16]. A large number of secondary structure features appear to be conserved from E. coli to yeast and Xenopus 18 S rRNA [20].…”

“…Due both to its known location at subunit interface and to direct experimental evidence [6,13,14], the 3'-te rminal domain of small subunit rRNA appears to be more directly involved in these functions. A more precise knowledge of its role should be gained from comparative RNA sequence analysis which has proved valuable for establishing secondary structure models for prokaryotic rRNAs [15][16][17]. Among eukaryotes, yeast [ 18] and Xenopus [ 19] are the only complete 18 S rRNA sequences published so far; their comparison has revealed extensive stretches of high homology interspersed with heterologous tracts while conserved sequences with prokaryotes are clearly restricted to the 3'-terminal region of the molecule.…”