Secondary structure conservation of the U3 small nucleolar RNA introns in Saccharomyces

Using a strategy based on PCR amplification of DNA and sequence analysis, we showed that the presence of introns with the characteristic features of introns spliced in a spliceosome, in the U3A and U3B snoRNA genes that code for the U3 small nucleolar RNA, is not a property restricted to Saccharomyces cerevisiae. It is probably an ancient property of yeasts from the genus Saccharomyces. We detected the U3A and U3B snoRNA genes in Saccharomyces bayanus and in a lager brewing yeast strain. The U3A and U3B intronic sequences are highly conserved. Two additional "U3B-like" snoRNA genes were detected in the lager brewing yeast. Their intronic sequences show several differences, when compared to the U3B intronic sequence. However, despite the numerous mutations, the intron secondary structure is conserved, especially, the central structure. This strongly suggests an important role of this central stem/loop structure for spliceosome assembly and efficient splicing.