Evolution of Eukaryotic rRNA: Constraints Imposed by RNA Interactions

In this chapter we will discuss the effects of alter-ations within the ribosomal DNA (rDNA) genes. RNA interactions that are important for regions within rRNA impose selective constraints upon propagation of mutations within the gene. As a consequence, there are functionally important regions in rRNA that are highly conserved in primary sequence, even between different kingdoms, rRNA also has an evolutionarily conserved core secondary st ucture. Finally, in this chapter we will examine U3 small nuclear RNA (snRNA), and discuss whether its structure can support models of its putative interaction with the rRNA pre-cursor. Structure of Xenopus rDNA Transcription Unit The rDNA of Xenopus laevis, the South African clawed toad, was the first eukaryotic gene to be cloned (Morrow et al. 1974), and we have used this model system to study its evolution. Figure 1 depicts a typical repeat unit of X. laevis rDNA; there are about 450 tandem copies of this rDNA repeat in the nucleolus organizer region (Brown and Weber 1968a,b). The stretch coding for the 40S RNA precursor alternates with the so-called nontranscribed spacer (NTS). Re-cent evidence suggests that the NTS is, in fact, also transcribed as part of a larger precursor that must be