Gene expression response to mitochondrial DNA depletion

Mitochondrial defects are associated with a spectrum of human disorders, ranging from rare, inborn errors of metabolism to common, age-associated diseases such as diabetes and neurodegeneration. In lower organisms, genetic “retrograde” signaling programs have been identified that promote cellular and organism survival in the face of mitochondrial dysfunction. Here, we characterized the transcriptional component of the human mitochondrial retrograde response in an inducible model of mitochondrial dysfunction. We used an HEK293-derived cell line that expresses a dominant negative DNA polymerase gamma (PolGdn) under tet repressor control. Upon induction with doxycycline, PolGdn inhibits replication of mitochondrial DNA (mtDNA), so that existing copies of mtDNA are progressively diluted as cells continue to divide. Upon removal of doxycycline, repression of PolGdn is re-established, and mtDNA copy number, as well as mitochondrial protein expression and oxidative phosphorylation complex abundance, recovers. We used microarrays to study transcriptional changes arising from mtDNA depletion. We found a robust transcriptional response that is partially mediated by ATF4, which appears to effect an adaptive rewiring of serine and one-carbon metabolism.