Nucleotide sequence of theSchizosaccharomyces pombe25S ribosomal RNA and its phylogenetic implications

Schizosaccharomyces pombe is a fission yeast which is only distantly related to the budding yeast Saccharomyces cerevisiae. While its cell cycle has been studied extensively, ribosome biogenesis is still poorly documented in this important organism. We have thus begun to characterize the components of the nucleolus of 5.pombe, including nucleolar proteins (1, 2), small nucleolar RNAs and the rDNA genes. We constructed a subgenomic library with the DNA prepared from the widely used strain 972, and isolated a recombinant plasmid (pBL1263) which contains a Hindm fragment of 11 kb that corresponds to the entire rDNA repeated unit. We report here the primary structure of the 25S rRNA coding region, which has been sequenced on both strands. Its 5' and 3' termini have not been determined directly but have been unambiguously inferred from comparison with S. cerevisiae (3). The sequence is in perfect agreement with three partial determinations already available, i.e., for 45 5' terminal nucleotides sequenced from a rDNA clone (4) and for two segments, 3-362 and 674-833 directly analyzed by RNA sequencing (5,6). S.pombe 25S rRNA is 3497 nucleotides long, which is 105 nucleotides longer than its S. cerevisiae homologue. The two yeast sequences exhibit a 84.5% overall homology and their comparison confirms the mosaic pattern of structural evolution of the rRNA molecule, with the majority of nucleotide differences mapping within the divergent domains, or expansion segments of the molecule (7). Boundaries of these variable domains have the following positions along the S.pombe sequence: 106-274 (Dl), 441-651 (D2), 703-816 (D3), 1010-1017 (D4), 1097-1134 (D5), 1379-1390 (D6), 1573-1884 (D7), 2004-2183 (D8), 2549-2558 (D9), 2614-2682 (D10), 3089-3091 (Dll) and 3247-3387 (D12). The divergent domains are generally larger in S.pombe than in S.cerevisiae, with the largest expansions observed in the D2, D7 and D8 domains (17, 21 and 33 nucleotides, respectively). The interspersed conserved regions of 25S rRNA, which encompass 2240 nucleotides, exhibit a 93.4% sequence identity with S.cerevisiae. The S.pombe sequence further supports the universally conserved core of secondary structure (7). Over its paired portions, all the nucleotides differences wim the other eukaryotes correspond to compensatory changes at opposite stem positions (8).