Expression of GC clusters in the yeast mitochondrial var 1 gene. Translation and secondary structure implications

Alleles of the yeast mitochondrial var 1 gene, which encode a protein (var 1) associated with the small mitochondrial ribosomal subunit, contain one or two identical GC clusters within the coding region that are transcribed and retained in the putative var 1 mRNA (Zassenhaus, H.P., and Butow, R. A. (1984) J. Biol. Chem. 259, 8417-8421). By comparing peptide fragments generated by defined chemical and enzymatic cleavages of the products of these alleles, we show that these GC clusters encode amino acids in the var 1 protein. First, there is a strict correlation between the presence of an optional GC cluster in the var 1 gene and a corresponding increase in size of the peptide that would contain the "extra" amino acids encoded by that GC cluster. Second, we find proline residues in specific peptides of var 1 that, from DNA sequence, would only be present if the GC clusters were translated. Thus, although the yeast mitochondrial genome contains 70-100 GC clusters similar to those in var 1, the var 1 protein is the only mitochondrial translation product now known to contain amino acids encoded by these elements. We have also examined predictions of var 1 secondary structure and find little resemblance to the secondary structures predicted for most other ribosomal proteins. Finally, our analysis suggests a significant conformational difference between the var 1 protein containing amino acids encoded by the optional GC cluster and the form of the protein lacking those amino acids.