An irregular satellite sequence is found at the termini of the linear extrachromosomal rDNA in Dictyostelium discoideum.

IN Dictyostelium discoideum most of the rRNA genes are known to be present as linear, extrachromosomal palindromic molecules. Here we report the identification, molecular cloning and partial DNA sequence analysis of the terminal Eco RI restriction fragment (Eco RI 1) of the rDNA. We identify a length heterogeneity confined to the most distal region of uncloned Eco RI 1, and demonstrate, by DNA sequence analysis of five independently isolated recombinant plasmids containing the Eco RI 1 fragment, that the heterogeneity can be accounted for by variable tracts of an unprecedented irregular satellite sequence with the general formula [CnT]m; n varies from 1 to 8 and accounts for the irregularity, while m varies from 18 to 34 and accounts for the length heterogeneity. The proximal [CnT]m pattern is identical (albeit irregular) in all five clones of Eco RI 1, while the distal [CnT]m sequence appears to vary between clones. Immediately proximal to the CnT satellite are found four nearly perfect tandem repeats of a 29 bp sequence. We discuss the evolution of these simple sequences at the rDNA termini and speculate about possible functions for the CnT satellite. Using the cloned terminal restriction fragment as probe, we also show that virtually all the rDNA in Dictyostelium exists in the linear palindromic form.