The mitochondrial matrix is unique in that it must integrate the folding and assembly of proteins derived from the nuclear and mitochondrial genomes. In Caenorhabditis elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis1,2,3. While misfolded mitochondrial-matrix-localized ornithine transcarbamylase induces chaperonin expression4,5,6, our understanding of mammalian UPRmt is rudimentary7, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 (ref. 8) or LON protease9, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response encompasses 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 caused by transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3 (ref. 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 UPRmt.
Gene Expression Omnibus
RNA sequencing data have been deposited in the Gene Expression Omnibus under accession number GSE75411.
We thank D. C. Altieri for GTPP, J. Paulo and S. P. Gygi for assistance with mass spectrometry, and L. Pontano and S. H. Sui for assistance with RNA-seq. This work was supported by National Institutes of Health grant R37NS083524 and Biogen, Inc. (J.W.H.), and an EMBO Fellowship (C.M.).
Extended data figures
This file contains Supplementary Tables 1-4.