Xenopus laevis28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications

• DOI: 10.1093/nar/12.15.6197
• Publication Date: 2007-01-04T17:15:07Z
• Authors: C.Graham Clark; Brian W. Tague; Vassie C. Ware; Susan A. Gerbi
• Keywords: Ribosomal Proteins; 0301 basic medicine; Binding Sites; Base Sequence; Biological Evolution; GTP Phosphohydrolases; Structure-Activity Relationship; Xenopus laevis; 03 medical and health sciences; RNA, Ribosomal; Peptidyl Transferases; Animals; Nucleic Acid Conformation; Ribosomes

Based upon the three experimentally derived models of E. coli 23S rRNA (1-3) and the partial model for yeast 26S rRNA (4), which was deduced by homology to E. coli, we derived a secondary structure model for Xenopus laevis 28S rRNA. This is the first complete model presented for eukaryotic 28S rRNA. Compensatory base changes support the general validity of our model and offer help to resolve which of the three E. coli models is correct in regions where they are different from one another. Eukaryotic rDNA is longer than prokaryotic rDNA by virtue of introns, expansion segments and transcribed spacers, all of which are discussed relative to our secondary structure model. Comments are made on the evolutionary origins of these three categories and the processing fates of their transcripts. Functionally important sites on our 28S rRNA secondary structure model are suggested by analogy for ribosomal protein binding, the GTPase center, the peptidyl transferase center, and for rRNA interaction with tRNA and 5S RNA. We discuss how RNA-RNA interactions may play a vital role in translocation.