Complete DNA sequence of yeast chromosome II.

Abstract

In the framework of the EU genome‐sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37‐45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT‐rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT‐rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Identification of a Yeast Peroxisomal Member of the Family of AMP‐Binding Proteins

“…The sequences obtained for the 40-kDa protein (Fig. 1 Feldmann et al, 1994) which was sequenced as part of the yeast genome project.…”

Patterns of Base Composition Within the Genes of Drosophila melanogaster

“…Most attention has focused on large-scale variation along chromosomes, thought until recently to be restricted to mammals. With the sequencing of yeast chromosomes (Oliver et al 1992;Dujon et al 1994;Feldmann et al 1994) and the rapid accumulation of other DNA sequence data, it now appears that variation in base composition along chromosomes is widespread; it has been documented in mammals (Bernardi et al 1985;Bernardi 1989), Drosophila (Carulli et al 1993;Kliman and Hey 1994), yeast (Sharp and Lloyd 1992;Dujon et al 1994;Feldmann et al 1994), and bacteria (Deschavanne and Filipski 1995).…”

“…In mammals, G+C content varies over megabases of DNA (Gardiner et al 1990;Pilia et al 1993), whereas in Saccharomyces cerevisiae, the variation is over a scale of about 50 to 100 kilobases (kb) (Sharp and Lloyd 1992;Dujon et al 1994;Feldmann et al 1994), similar to that found in Escherichia coli (Deschavanne and Filipski 1995). The scale in Drosophila melanogaster remains unclear.…”

Inverted repeat of a large segment unveiled on the right arm of Saccharomyces cerevisiae chromosome II

“…For this purpose, we needed a reference point against the two ATP3 loci. Our choice was YBR030W, an ORF proximal to ATP3 by a distance of 17.3 kbp (Feldmann et al, 1994; see Figure 1), and we decided to introduce TPR1 into this ORF. So, we transformed strain Y1-7A (atp3::HIS3 ATP3 ) with plasmid p030::TRP1 (see Figure 2B) after digestion with PvuII.…”