No abstract

The sequences of the 5 S rRNAs isolated from 8 ascomycete species belonging to the genera Aspergillus, Penicillium, Acremonium and Candida are reported. Two of the examined strains each yielded a mixture of 3 slightly different 5 S RNAs, which were individually sequenced after fractionation. A previously published sequence for Aspergillus nidulans 5 S RNA was found to contain errors. Reconstruction of an evolutionary tree based on 5 S RNA sequences showed that the 16 presently examined ascomycetes form three clusters. The same threefold partition can be observed in the secondary structure pattern, each cluster showing a slightly different variant of the general 5-helix model for 5 S rRNA (De Wachter, Chen and Vandenberghe (1982) Biochimie 64, 311-329), and different sets of secondary structure equilibrium forms in helices C and E of the aforementioned model.

The basic assumption in this paper is that the secondary structure of a 5-S ribosomal RNA cannot be represented by a single model. We propose that the molecule can adopt, at least within the ribosome, a series of slightly different structures of nearly equal stability. The different structures arise from the existence of ambiguous base-pairing opportunities in bulged helices and the adjacent interior loops. In eubacterial 5-S RNAs there is one such an area, in eukaryotic 5-S RNAs two such areas that can give rise to structural switches. We explain how a change in secondary structure in these areas may influence the relative orientation of the surrounding helices, in other words how bulges and interior loops may serve as articulations and give rise to a flexible tertiary structure.

The corrected nucleotide sequences of the cytoplasmic 5 S ribosomal RNAs of 6 angiosperms are reported. The previously reported sequences, reconstructed from oligonucleotide catalogs, had been suspected for some time to contain errors. The corrected seqeuences fit in a universal J-helii model for 5 S RNA secondary structure. The model involves the existence of a dynamic ~uilibrium between slightly different base-pairing schemes in two areas of the structure. Reconstruction of a phylogenetic tree from over 200 known 5 S RNA sequences yields a general picture of biological evolution. It confirms the tripartite descent of living species -eubacteria, archaebacteria, eukaryotes -and the endosymbiotic origin of plant mitochondria and chloroplasts.5 S rRNA Secondary ~t~ct~re