Nucleotide sequences of Acanthamoeba castellanii 5S and 5.8S ribosomal ribonucleic acids: phylogenetic and comparative structural analyses

Abstract

Sequences of 5S and 5.8S rRNAs of the amoeboid protist Acanthamoeba castellanii have been determined by gel sequencing of terminally-labelled RNAs which were partially degraded with chemical reagents or ribonucleases. The sequence of the 5S rRNA is GGAUACGGCC*10AUACUGCA*20GAAAGCACCG*30CUUCCCAUCC*40GAACAGCG AA*50GUUAAGCUGC*60GCCAGGCGGU*70GUUAGUACUG*80GGGUGGGCGA*90CCACCCGGGA*100AUCCACCGUG*110CCGUAUCCU0H. This sequence is compared to eukaryotic 5S rRNA sequences previously published and fitted to a secondary structure model which incorporates features of several previously proposed models. All reported eukaryotic 5S rRNAs fit this model. The sequence of the 5.8S rRNA is AACφCCUAAC*10AACmGGAφAUC*20UUGGUUCUCG*30CGAG GAUGAA*40GAmACGCAGCG*50AAAUGCGAUA*60CGUAGUGUGA*70AUCGCAGGGA*80UCAGUGAAmUC*90AφCGAAUCUSφ*100UGAACGCA AG*110UUGCGCUCUC*120GUGGUUUAAC*130CCCCCGGGAG*140CACGUUCGCU*150UGAGUGCCGC*160U(U)0H. This sequence does not fit parts of existing secondary structure models for 5.8S rRNA, and we question the significance of such models.