Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure

Abstract

Extensive studies in our laboratory using different ribonucleases resulted in valuable data on the topography of the E.coli 16S ribosomal RNA within the native 30S subunit, within partially unfolded 30S subunits, in the free state, and in association with individual ribosomal proteins. Such studies have precise details on the accessibility of certain residues and delineated highly accessible RNA regions. Furthermore, they provided evidence that the 16S rRNA is organized in its subunit into four distinct domains. A secondary structure model of the E.coli 16S rRNA has been derived from these topographical data. Additional information from comparative sequence analyses of the small ribosomal subunit RNAs from other species sequenced so far has been used.

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).…”

“…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].…”

“…In this regard, structure (II), between nucleotides 48-159, is particularly interesting because it spans the more divergent region of this domain for the previously sequenced eukaryotic rRNAs. Despite extensive variations from prokaryotic sequence, an homologous long helical structure can be built for mouse rRNA, which is much more stable than its E. coli counterpart [ 15,16]. Other eukaryotic sequences in this domain of the molecule can also be arranged in similar structures ( fig.5).…”

“…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.…”