Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure.

The transcription start point (tsp) of a ribosomal RNA (rRNA)-encoding gene (rDNA) from Echinococcus granulosus has been mapped at a position located 1.1 kb upstream from the small subunit (SSU) rRNA coding sequence. As expected from the analysis of the putative promoter sequence (-200 to +50), no homology was found with rDNA promoters from other organisms. Nevertheless, some interesting motifs were found. There is a d(T)11 track flanked by an inverted repeat (IR) centered at position -32, which is analogous to the position of the TATA box in promoters transcribed by RNA polymerase II. Two other IR were observed that are also present in the Trypanosoma cruzi rDNA promoter. We have also determined the SSU rDNA sequence and established a secondary structure model. The analysis of the secondary structure strongly suggests that this gene encodes a functional SSU rRNA. The fact that both the promoter and the rRNA coding sequence are derived from the same rDNA repeat indicates that the promoter is also functional.