Conserved arrangements of repeated DNA sequences in nontranscribed spacers of ciliate ribosomal RNA genes: evidence for molecular coevolution.

We have analyzed the nucleotide sequences of the nontranscribed spacer (NTS) and transcription initiation and termination regions of the extrachromosomal rDNAs of the ciliated protozoans Tetrahymena thermophila and Glaucoma chattoni. The sequences surrounding the sites of transcription initiation and termination are highly conserved. The only extensive homologies of the NTS regions occur in five sets of dispersed repetitive sequences. Type I, II and III repeats in the 5' NTS are strongly conserved in sequence between Tetrahymena and Glaucoma in the case of the type I and III repeats, and in location relative to the transcription initiation site in the case of type I and II repeats. We identify two new repeat types, designated IV and V, in the 3' NTS. The sequence of type IV repeats, and the location relative to the transcription termination site of type IV and V repeats, are conserved. All five types of repeats are interspersed with nonconserved DNA sequences. These results suggest that the five repeat types in the 5' and 3' NTSs are important in rRNA gene function; the sequence organization, and the differing rates of divergence between species of the repeat types, provide strong evidence for their functional selection through the process of molecular coevolution.