Biochemical Genetics of the Mitochondrial Replicase: Clustering of Pathogenic Mutations into Five Functional Modules in Human DNA Polymerase γ

Abstract

Mutations in Pol γ represent a major cause of human mitochondrial diseases, especially those affecting the nervous system in adults and in children. More than 160 POLG1 disease mutations have been identified, which are nearly uniformly distributed along the length of the POLG1 sequence. We have assessed structure‐function relationships for these mutations by evaluating biochemical data on site‐directed mutagenesis of the human, Drosophila and yeast Pol γs, and their close homologues from the family A DNA polymerase group. We have done so in the context of a molecular model of Pol γ in complex with primer‐template DNA that we developed based upon the crystal structure of the apoenzyme form. We present evidence that 130 pathogenic mutations cluster within five distinct functional modules in the catalytic core of Pol γ. Among these is a novel structural module found only in the Pol γ subfamily of the family A DNA polymerases, which we propose affects the interplay between pol and exo function to achieve the high fidelity of DNA synthesis that is characteristic of Pol γ. Our results suggest that cluster prediction can be used to evaluate both the likely biochemical defects and the relative pathogenicity of new Pol γ variants.