Primary structures of four novel small ribosomal RNAs from Crithidia fasciculata

We report here the complete primary structures of four novel small RNA species (designated e, f, g, and j) found in the large ribosomal subunit of Crithidia fasciculata, a trypanosomatid protozoan. These RNAs, which are distinct from Crithidia 5S (species h) and 5.8S (species i) rRNAs, do not have counterparts in the more conventional eukaryotic ribosomes characterized to date. The small RNAs are 212 (e), 183 (f), 135-136 (g), and 72-73 (j) nucleotides long, with g and j displaying 5'-terminal heterogeneity. All have unique sequences and all contain 5'-monophosphorylated and 3'-unphosphorylated termini. In their basic structural features, therefore, species e, f, g, and j are indistinguishable from other RNAs (including 5S and 5.8S) that are recognized components of eukaryotic ribosomes, although they are unrelated to 5S or 5.8S rRNA in sequence. Since previous work from this laboratory has ruled out the possibility that these small RNAs are generated by quantitative and highly specific (albeit artifactual) RNase cleavage of large rRNAs during isolation, we conclude that species e, f, g, and j are native components of the Crithidia ribosome. With the exception of e, which appears to contain a single pseudouridine residue, all of these novel RNA species are devoid of modified nucleosides. In connection with primary sequence analysis, we present a simple modification of the standard G-specific chemical sequencing reaction which in our hands yields reproducible and unambiguous results using commercially available dimethyl sulfate.