Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation

The mitochondrial matrix is unique in that it must integrate folding and assembly of proteins derived from nuclear and mitochondrial genomes. In C. elegans, the mitochondrial unfolded protein response (UPR(mt)) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis(1–3). While misfolded mitochondrial matrix-localized ornithine trans-carbamylase (OTC) induces chaperonin expression(4–6), our understanding of mammalian UPR(mt) is rudimentary(7), reflecting a lack of acute triggers for UPR(mt) activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPR(mt) on mitochondrial translation to control protein folding loads. Here, we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1(8) or LON protease(9), which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPR(mt). This response involved widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing due to transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3(10). This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPR(mt).