COMPREHENSIVE COMPARISON OF STRUCTURAL CHARACTERISTICS IN EUKARYOTIC CYTOPLASMIC LARGE SUBUNIT (23 S-LIKE) RIBOSOMAL-RNA

Comparative modeling of secondary structure is a proven approach to pr edicting higher order structural elements in homologous RNA molecules. Here we present the results of a comprehensive comparison of newly mo deled or refined secondary structures for the cytoplasmic large subuni t (23 S-like) rRNA of eukaryotes. This analysis, which covers a broad phylogenetic spectrum within the eukaryotic lineage, has defined regio ns that differ widely in their degree of structural conservation, rang ing from a core of primary sequence and secondary structure that is vi rtually invariant, to highly variable regions. New comparative informa tion allows us to propose structures for many of the variable regions that had not been modeled before, and rigorously to confirm or refine variable region structures previously proposed by us or others. The pr esent analysis also serves to identify phylogenetically informative fe atures of primary and secondary structure that characterize these mode ls of eukaryotic cytoplasmic 23 S-like rRNA. Finally, the work summari zed here provides a basis for experimental studies designed both to te st further the validity of the proposed secondary structures and to ex plore structure-function relationships. (C) 1996 Academic Press Limite d