Characterization of transcripts from the Var1 region on mitochondrial DNA of Saccharomyces cerevisiae

We have identified transcripts with sequence homology to the var1 region on yeast mtDNA. In wild type, and in cytoplasmic petite strains retaining the var1 region, we detect four RNA species, 19 S, 16 S, 14 S, and 13 S, which hybridize to var1 DNA probes. The 16 S RNA is by far the most abundant of these RNAs in wild type cells. We also observe hybridization of the 15 S rRNA and a 10 S RNA species to var1 DNA probes. This hybridization is most likely due to the presence in these RNAs of a GC-rich cluster which has near perfect sequence homology to a GC-rich cluster in the var1 region. We find that the 16 S RNA, estimated to be 2000 to 2100 nucleotides long, varies in size in direct correspondence with the size of var1 polypeptide; it is about 100 nucleotides longer in strains with the var1 (44,000) allele than in strains with var1 (40,000). The amount of the 16 S RNA also varies in correspondence with the amount of var1 polypeptide made; it is increased in an oxi-3 mit- strain (CAD245) which makes about 10 times more var1 protein than wild type, and is barely detected in PZ200, a strain with very low levels of mitochondrial protein synthesis harboring two mutations within var1. We have purified the 16 S RNA following chromatography over oligo(dT) cellulose columns. When the RNA is end-labeled and hybridized to a HincII digest of wild type mtDNA, we observe hybridization only to the fragment containing the entire var1 region, HincII fragment 10.