The U3 snoRNA coding sequences from the genomic
DNAs of Kluyveromyces delphensis and four variants
of the Kluyveromyces marxianus species were cloned
by PCR amplification. Nucleotide sequence analysis of the
amplification products revealed a unique U3 snoRNA gene
sequence in all the strains studied, except for K.
marxianus var. fragilis. The K.
marxianus U3 genes were intronless, whereas an
intron similar to those of the Saccharomyces cerevisiae
U3 genes was found in K. delphensis. Hence, U3
genes with and without intron are found in yeasts of the
Saccharomycetoideae subfamily. The secondary structure
of the K. delphensis pre-U3 snoRNA and of the
K. marxianus mature snoRNAs were studied experimentally.
They revealed a strong conservation in yeasts of (1) the
architecture of U3 snoRNA introns, (2) the 5′-terminal
domain of the mature snoRNA, and (3) the protein-anchoring
regions of the U3 snoRNA 3′ domain. In contrast,
stem-loop structures 2, 3, and 4 of the 3′ domain
showed great variations in size, sequence, and structure.
Using a genetic test, we show that, in spite of these variations,
the Kluyveromyces U3 snoRNAs are functional in
S. cerevisiae. We also show that S. cerevisiae
U3A snoRNAs lacking the stem-loop structure 2 or 4 are
functional. Hence, U3 snoRNA function can accommodate great
variations of the RNA 3′-terminal domain.