Sequence and secondary structure of 5.8S rRNA in the tick, Ixodes scapularis

While sequence homology among eukaryotic 5.8S rRNAs is relatively high, even among distantly related organisms (1), the secondary structure of this region, although similarly conserved, does not rely completely on sequence integrity. That is, the functional folding pattern remains the same while utilizing different rRNA base pairs achieved through compensatory mutation. Ticks in the genus Ixodes share 5.8S rDNA sequence homology with other arthropods from which this region has been described (2,3) (Figure 1). Parsimony analysis of bases 1 -122 and 131-157 from Figure 1 (first consensus base at 5'and 3'-end of Drosophila 5.8S spacer), places the Ixodes outgroup squarely between clusters of Culex, Drosophila and Bombyx, Acyrthosiphon. The secondary structure of the complex of 5.8S, 2S and the 5' end of the 28S rRNAs has been described for Drosophila (4). Figure 2 illustrates the probable secondary structure of this region for Ixodes. While the structures predicted for the Dipteran and Ixodes complexes are similar, three major differences in nucleotide composition are evident. The Ixodes bases 28-31 are involved in the first stem (A) in Figure 2; in the proposed Drosophila secondary structure, these bases pair externally with a portion of the 28S region. Ixodes bases 61—88, composing a stem (B) of nine consecutive bases, compare with a seven base stem in Drosophila, while the loop size is identical for the two species. Bases 114—123 in the Ixodes complex form an eight base stem (Q with a single missmatch ending in a four base loop. The Drosophila stem, of similar length with one missmatch, results in a 30 base loop which is spliced out during rRNA processing to form the Dipteran 2S fragment (5). These features of the Ixodes 5.8S/28S complex serve to reinforce previous observations of general conservation of secondary structure regardless of overall sequence homology.