A 23S ribosomal RNA gene of Pseudomonas cepacia has been cloned and sequenced. A general higher-order structure model based on earlier published models has been derived from comparative analysis of 23S-like rRNAs of eubacteria, archaebacteria, organelles and eukaryotes. Differences between the previous models were carefully analyzed and controversial regions evaluated. Moderately large insertions and deletions have been found at new points in the secondary structure. The analysis of 50 published as well as unpublished 23S rRNA sequences provide additional proof for six of the seven previously suggested tertiary interactions within the 23S rRNA. P. cepacia is the first representative of the β subgroup of the Proteobacteria phylum whose 23S rRNA has been sequenced. A tree reflecting evolutionary relationships of prokaryotes was constructed. The topology of this tree is in good agreement with the 16S rRNA tree.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1989.tb15123.x

The 23S ribosomal RNA higher‐order structure of Pseudomonas cepacia and other prokaryotes

HOW many primary lineages of life exist and what are their evolutionary relationships? These are fundamental but highly controversial issues1. Woese and co-workers2–4 propose that archaebacteria, eubacteria and eukaryotes are the three primary lines of descent and their relationships can be represented by Fig. 1a (the 'archaebacterial tree') if one neglects the root of the tree. In contrast, Lake5,6 claims that archaebacteria are paraphyletic, and he groups eocytes (extremely thermophilic, sulphur-dependent bacteria) with eukaryotes, and halobacteria with eubacteria (the 'eocyte tree', Fig. 1b). Lake's view has gained considerable support as a result of an analysis6 of small subunit ribosomal RNA sequence data by a new approach, the evolutionary parsimony method7. Here we report that analysis of small subunit data by the neighbour-joining and maximum parasimony methods8,9 favours the archaebacterial tree and that computer simulations using either the archaebacterial or the eocyte tree as a model tree show that the probability of recovering the model tree is very high (>90 per cent) for both the neighbour-joining and maximum parsimony methods but is relatively low for the evolutionary parsimony method. Moreover, analysis of large subunit rRNA sequences by all three methods strongly favours the archaebacterial tree.

Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree.

During evolution, the potential for sequence (and length) variation of large-subunit rRNA has been mostly restricted over 12 divergent domains (termed D1–D12) interspersed along the molecule. Here, we have focused our attention onto the D3 divergent domain, through a detailed analysis of its pattern of variation in the phylogeny, both in terms of primary and secondary structures. We have systematically compared all the procaryotic and eucaryotic sequences published so far (i.e. 36 species), together with a series of 10 additional eucaryotic specimens, which were determined by direct RNA sequencing. Secondary structures supported by comparative evidence have been derived for archaebacteria, eubacteria and eucaryotes respectively, which shows that the D3 domain contains a subset of universally conserved structural features interspersed with four variable subdomains. Within the four portions where a structural diversification has taken place, elementary structures specific of large phylogenetic groups can be identified. Remarkably such diversified structures appear to be preserved despite sequence divergence, suggesting they correspond to functionally important structures. Accordingly, the mode of sequence variation of the D3 domain suggests this region of the molecule may encode elementary functions of rRNA which could have significantly diversified during the evolution of the major groups of organisms.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1990.tb15393.x

Evolution of large-subunit rRNA structure. The diversification of divergent D3 domain among major phylogenetic groups.

Modifications in Thermus thermophilus 23 S Ribosomal RNA Are Centered in Regions of RNA-RNA Contact

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2891%2980372-A

Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnostic oligonucleotide probes

Norbert Ulrich

Papers

Complete nucleotide sequence of a 23S ribosomal RNA gene from Thermus thermophilus HB8