The three copies of the ATP1 gene are arranged in tandem on chromosome II of Saccharomyces cerevisiae S288C.

In the yeast Saccharomyces cerevisiae there are three copies of the F(1)F(0)-ATPase alpha-subunit gene ATP1 on chromosome II (Takeda et al., 1995). However, after genome analysis using S. cerevisiae strain S288C, only one ATP1 gene sequence was observed (Feldman et al., 1994; Obermaier et al., 1995). To check whether the number of copies of ATP1 is strain-dependent or not, we carried out three different experiments: (a) long-PCR analyses of total DNAs isolated from several reference strains, carried out by preparing 29-mer oligonucleotides based on the 5'- and 3'- up- and downstream regions of the ATP1 nucleotide sequence using the data from the genome project to synthesize primers; (b) restriction analyses of chromosome II from the reference strains with SplI; and (c) long-PCR analyses of prime clones 70113 and 70804, both of which contained two ATP1 gene copies, ATP1a and ATP1b, and ATP1b and ATP1c, respectively, using 30 nucleotides just inside the 3'-end (sense) and 5'-end (antisense) of the ATP1-coding region as primers. In the case of the long-PCR experiments, the reference strains DC5, SEY2102, W303-1A, W303-1B, LL20 and DBY746, as well as strain S288C, generated a DNA fragment of approximately 32 kb, which hybridized with ATP1. During SplI digestion, a DNA fragment of more than 50 kb which hybridized with ATP1, was obtained from all reference strains. In the case of prime clone analyses using the long-PCR experiments, the distance between ATP1a and ATP1b or ATP1b and ATP1c was approximately 10 kb or 7 kb, respectively. The S288C strain generated these two DNA fragments, as do the other strains. These results showed that all these strains contained three copies of ATP1 on chromosome II.