title: Expression of GC clusters in the yeast mitochondrial var 1 gene. Translation and secondary structure implications.
abstract: 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.
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics*; D005796:Genes; D005800:Genes, Fungal; D008715:Methionine / Q000032:analysis; D010446:Peptide Fragments / Q000032:analysis; D011392:Proline / Q000032:analysis; D014176:Protein Biosynthesis; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D010446:Peptide Fragments; D011392:Proline; D008715:Methionine