The 3′-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3′-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5S rRNA

Abstract

The sequence of the 110 nucleotide fragment located at the 3'-end of E.coli, P.vuZgaiz and A.puncata 23S rRNAs has been determined. The homology between the E.coti and P.vutga&ii6 fragments is 90%, whereas that between the E.coti and A.punctata fragments is only 60%. The three rRNA fragments have sequences compatible with a secondary structure consisting of two hairpins. Using chemical and enzymatic methods recently developed for the study of the secondary structure of RNA, we demonstrated that one of these hairpins and part of the other are actually present in the three 3'-terminal fragments in solution. This supports the existence of these two hairpins in the intact molecule. Indeed, results obtained upon limited digestion of intact 23S RNA with T1 RNasewere in good agreement with the existence of these two hairpins.We observed that the primary structures of the 3'-terminal regions of yea6t 26S rRNA and X.&aeviZ 28S rRNA are both compatible with a secondary structure similar to that found at the 3'-end of bacterial 23S rRNAs. Furthermore, both tobacco and wheW chloroplast 4.5S rRNAs can also be folded in a similar way as the 3'-terminal region of bacterial 23S rRNA , the 3'-end of chloroplast 4.5S rRNAs being complementary to the 5'-end of chloroplast 23S rRNA. This strongly reinforces the hypothesis that chloroplast 4.5S rRNA originates from the 3'-end of bacterial 23S rRNA and suggests that this rRNA may be base-paired with the 5'-end of chloroplast 23S rRNA. Invariant oligonucleotides are present at identical positions in the homologous secondary structures of E.Cofi 23S, yea6t 26S , X.Ztaevi 28S and Whew and tobacco 4.5S rRNAs. Surprisingly, the sequences of these oligonucleotides are not all conserved in the 3'-terminal regions of A.putctata or even P.Vuwga&lZ 23S rRNAs. Results obtained upon mild methylation of E.colL 50S subunits with dimethylsulfate strongly suggest that these invariant oligonucleotides are involved in RNA tertiary structure or in RNA-protein interactions.

Xenopus laevis28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications

“…The RNA 3' to this "spacer" is chloroplast 4.5S RNA (Fig. VII), and corresponds to the 3' terminus of E. coli 23S rRNA (29,(48)(49)(50).…”

Modification of 18 S rRNA in the 40 S ribosomal subunit of yeast with dimethyl sulfate

“…When this work was completed we have learned that the similar approach had been used to study the structural organization of the 3'-end segment of 23 S rRNA in large subunits of prokaryotic ribosomes [ 14].…”

Structure and evolution of the 4.5–5S ribosomal RNA intergenic region fromGlycine max(Soya bean)

“…Sequence studies indicate that all of the chloroplast rRNAs are transcribed as a common larger precursor molecule, the sequences being arranged in the order 5'-16S-23S-4.5S-5S-3' (5-7). As ribosomal RNA from many origins have been sequenced, comparisons have clearly shown (5)(6)(7)(8) that the 4.5S rRNA sequence is not unique to plant chloroplasts; it is actually equivalent to the 3' end of the eubacterial 23S rRNA and is the result of an extra cleavage or processing step in the chlorplast rRNA precursor.…”