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

Abstract

Acute protein folding stress in the mitochondrial matrix activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition. The mitochondrial unfolded protein response (UPRmt) pathway has been studied in detail in the Caenorhabditis elegans roundworm, where it has been shown to sense protein misfolding within the mitochondrial matrix and to induce a program of nuclear gene expression to counteract this stress. How mammalian cells respond to unfolded matrix proteins has remained much less clear. Christian Münch and Wade Harper used pharmacological inhibitors to induce acute protein folding stress in the mitochondrial matrix, and performed transcriptional and quantitative proteomic analysis to examine the response of mammalian cells. They observed widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. This was accompanied by a rapid reduction in the matrix-localized protein synthesis through translational inhibition. The work could spur further investigation of the mammalian UPRmt. 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.