Identification of a cAMP-dependent protein-DNA interaction at a sequence near the yeast mitochondrial rRNA genes

We have shown that expression of yeast mitochondrial (mt) rRNA genes (S. cerevisiae) is controlled in a cAMP-dependent manner via PKA, suggesting a trans-activation process involving phosphorylation-dependent protein-mt DNA interaction. We used filter-binding assays, mt protein extracts, and mt DNA from a rho-mutant strain retaining the 21S rRNA gene to demonstrate such an interaction. Competition assays with the cloned 21S-related mt DNA fragment undergoing interaction showed that a sequence in that fragment is present in mt DNA from a rho-strain retaining the 16S mt rRNA gene, but not in a VAR1-retaining rho-strain that lacks cAMP-mediated mt transcription. The sequence of the 21S-related mt DNA fragment undergoing protein interaction includes a GC cluster; that GC cluster sequence is also present near the 16S gene but not near VAR1. These and other data are consistent with a role for the GC cluster in cAMP-mediated expression of mt rRNA genes.