Nucleotide sequence of cytoplasmic 5S rRNA from a eukaryotic thermophilic unicellular alga, Cyanidium caldarium.

From a total RNA extract of Cyanidium caldarium (Cca) cells we isolated, by the use of polyacrylamide gel electrophoresis under denaturing conditions, cytoplasmic 5S rRNA and determined its primary and possible secondary structure (Figure 1). The Cca 5S rRNA (i) is 124 nt long, (ii) harbors, at the expected positions, both internal transcription signals characteristic of this class of RNA polymerase El-transcripts: the A Box [consensus sequence: R^YsN^yi^YgGgGjo (1)] with a single mismatch (G/o— C61), and the C Box [consensus sequence: RIR2T3G4G5G6W7G8A9C10C11 (1)] with three mismatches (W-^G^ as well as the compensatory changes Gj—Agg and C/o—U93), and (iii) contains all those secondary structural elements that are characteristic of all known 5S rRNAs: stems A to E, internal loops b and d, hairpin loops c and e and the three-stem junction a (2). With regard to the debated phylogenetic position of the genus Cyanidium [cf. (3)] we argue, on the basis of the following data, that Cca is a true red alga (Rhodophyta): (1) when the nucleotide sequence of the Cca 5S rRNA is aligned with those of the 5S rRNAs from various species representing very different evolutionary levels according to the multiple alignment program MULTALIN v. 3.0 (4) using a special symbol comparison score (53 for identical bases, 23 for transitions, 0 for transversions and —29 for gaps) table developed by us, Cca unequivocally falls into a cluster containing bonafide red algae (not shown). (2) The Cca 5S rRNA exhibits all those secondary structural features which are characteristic of red algae, as reported by Van den Eynde et al. (5): (i) presence of a bulge (U18) on the 5' strand of helix B, (ii) twenty seven nucleotide residues in helix C plus loop c, (iii) asymmetry of internal loop b and (iv) presence of a bulged G residue (G^) on helix E. We note that the thermophilicity of Cca is not reflected in an expected thermostability of the structure of its 5S rRNA because Cca 5S rRNA has (i) neither an exceptionally high GC content (53%) similarly to Cca 5.8S rRNA (49%) (6), (ii) nor an extended secondary structure, in contrast to Cca 5.8S rRNA (6).