Sequence of the 23S rRNA gene from the archaebacterium Methanococcus vannielii: evolutionary and functional implications

Abstract

The nucleotide sequence was determined of the genes coding for 23S and 5S rRNA within a putative 16S-23S-5S rRNA transcriptional unit from Methanococcus vannielii. The 23S rRNA gene is 2958 bases in length (compared to 2904 for the E. coli sequence). Determination of the homology of the primary structure with the Escherichia coli sequence gives a value similar to that previously found for the 16S rRNA sequences, indicating an identical phylogenetic drift for the two genes. The putative transcript of the 16S, 23S, and 5S rRNA genes plus flanking regions has been folded into a secondary structure following the comparative approach. The model provides evidence for processing signals of the putative primary transcript into pre-16S and pre-23S rRNA molecules. The 23S secondary structure when compared to those for eubacterial and eukaryotic large ribosomal rRNA's reveals a mosaic architecture: It shows insertions at positions where they are also present in eukaryotic large ribosomal RNA's; other parts of the molecule, however, are almost identical to eubacterial structures (e.g. the equivalent of the E. coli ribosomal protein L11 binding region). — The 5S rRNA coding region is separated from the 23S rRNA gene by a spacer of 59 base pairs. This rRNA-operon-linked 5S gene differs by a total of 13 base substitutions from that of the tRNA-operon-linked 5S gene previously described. — A correlation seems to exist between 23S rRNA structural domains and sensitivity or resistance to some 70S and 80S ribosome-targeted inhibitors: (i) The degree of sensitivity to the 80S ribosome inactivating RNase α-sarcin is correlated with the presence of the eukaryotic type cleavage site; (ii) inactivity of erythromycin as an inhibitor of Methanococcus protein synthesis may be a consequence of the presence of a G residue (instead of an “A” found in sensitive organisms) in position 2127 (the “peptidyl-transferase loop”) of the sequence; (iii) sensitivity of Methanococcus ribosomes to thiostrepton, on the other hand, is correlated with a highly conserved (compared to E. coli) binding domain for an L11 equivalent protein.