EVOLUTION OF SECONDARY STRUCTURE IN THE FAMILY OF 7SL-LIKE RNAS

Primate and rodent genomes are populated with hundreds of thousands co pies of Alu and BI elements dispersed by retroposition, i.e., by genom ic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the ter minal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserv ed from prokaryotes to distant eukaryotic species. Yet only in primate s and rodents did this molecule give rise to retroposing Alu and B1 RN As and to apparently functional BC200 and 4.5S RNAs. To understand thi s transition and the underlying molecular events, we examined, by comp arative analysis, the evolution of RNA structure in this family of mol ecules derived from 7SL RNA. RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats wer e derived from their genomic consensus sequences taken from the litera ture and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data o n 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropos itionally active RNAs are conserved among Alu and B1 subfamilies in di fferent genomes. In RNAs that do not proliferate by retroposition thes e motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by spe cific interactions with proteins; these functions were either useful f or the host or served the selfish propagation of RNA templates within the host genome.