ARCHITECTURE OF THE U5 SMALL NUCLEAR-RNA

We have used comparative sequence analysis and deletion analysis to ex amine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phy logenetic analysis. Our results indicate that fungal U5 snRNAs, like t heir counterparts from other taxa, can be folded into a secondary stru cture characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved internal loop (internal loop 1). In addition, several of the fungal U5 snRNAs include a novel stem-loo p structure (ca. 30 nucleotides) that is adjacent to stem-loop 1. By d eletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (i ii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site. Remarkably, all essential, U5-specific primary sequence elements are encoded by a 39-nucleotide domain consisting of stem-loop 1 and internal loop 1. This domain must, therefore, contain all US-sp ecific sequences that are essential for splicing activity, including b inding sites for U5-specific proteins.