28. The Nucleotide Sequence of Schizosaccha- romyces pombe Chromosome III
Mitsuoki Morimyo, Etsuko Hongo, Go Kenu, Tomoyasu Higashi, Yukari Ito, Yumiko Yoshida, Masahiro Ajimura, Etsuko Shiroma, Kazuei Mita, Kimihiko Sugaya, Shunichi Sasanuma and Izumi Matsumoto
Keywords: S. pombe cDNA, BAC clone, shotgun sequencing, gene expression map
In a study of the structure and function of the housekeeping genes of eukaryote, we chose Schizosaccharomyces pombe (S. pombe) as a model organism. It is assumed to have 6,000 genes and the genome size of 14 megabases (Mb) compared to 40,000 genes and 3,000 Mb for humans. In spite of the greater numbers for humans, S. pombe can be used as a model organism for humans, because its genes are similar to human genes which can be normally expressed in yeast, its housekeeping genes are conserved through eukaryotic evolution, and many of its genes have introns which make cDNA sequences essential to determine physical organization of genes from the genomic DNA sequence. Moreover, the functions of S. pombe genes are easily identified by disrupting them with homologous recombination.
We have analyzed 12,000 cDNA clones made by mRNA prepared from late log phase cells of S. pombe and identified over 2,500 genes (900 similar clones with known genes and 1800 newly found clones). Among the cDNA clones, 8,118 were deposited with the DDBJ and put on the ftp site of NIRS. By using these cDNA clones mapped on the chromosome III of S. pombe, we made a BAC contig map of chromosome III. A minimum set of 20 BAC clones covering the whole chromosome III was selected for the shotgun sequencing. The BAC DNA was partially digested by an endonuclease, followed by the fractionation in a sucrose gradient sedimentation and DNA fragments ranging from 1 to 3 kbp were recovered for sequencing at a redundancy of 6-10. Except for the tandem repeats of rDNA regions at both ends, we determined the DNA sequence of chromosome III which was 2,482,668 bp without interruption. The centromere contained 10 repeats of 6.6 kbp unit length fragments. We identified an ORF found in the assembled DNA sequence as a gene by using the gene-finding program developed for S. pombe and a homology search in protein databases and our S. pombe cDNA database (http://220.127.116.11). In all, we found 1162 protein-coding genes on chromosome III. Therefore, average gene length was estimated to be 2137 bp. Combining the information about gene location on the chromosome obtained from genome sequencing and its relative gene expression got from cDNA analysis with the genetic map, we made the gene expression map of S. pombe chromosome III.
1) Morimyo, M., Mita, K., Hongo, E., Ajimura, M., Higashi, T., Sugaya, K., Inoue, H., Yamauchi, M., Tsuji, S., Saito, T., Ito, H., Sasanuma, S., Nohata, J., Kimura, T., Ishihara, Y., Hattori, A., Hayashi, A., Koike, Y., Shiroma, E.: Mol. Bio. Cell, 11 suppl., 1572 (2000).
2) Morimyo, M.: UNESCO-EOLSS (in press).
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