Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins

Abstract

Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.

Inhibition of mitochondrial protein import and proteostasis by a pro-apoptotic lipid

“…This cellular response to mitochondrial dysfunction is also known as the unfolded protein response activated by mistargeting of proteins (UPRam). The heat shock transcription factor Hsf1 plays a central role in this response, as it is activated not only by heat stress but also during the transition from fermentation to respiration and in the presence of mitochondrial import impairment, all of which result in the accumulation of mitochondrial precursors in the cytosol (Boos et al, 2019; Groh et al, 2023; Hahn and Thiele, 2004). The sequestration of cytosolic chaperones by these precursor proteins leads to the release and activation of Hsf1.…”

DeepSTABp: A Deep Learning Approach for the Prediction of Thermal Protein Stability

“…The vast majority (21,885 ids) of protein T m s was derived from the meltome atlas [ 9 ], which not only provides a collection of TPP datasets derived from a multitude of different organisms but also consists of TPP studies involving the heat treatment of cells and proteins lysates. Since the originally available dataset lacked the preparation of S. cerevisiae cells and Homo sapiens lysates, we extended the atlas with data from recently published studies [ 23 , 36 ]. The final dataset consisted of 35,112 proteins originating from Escherichia coli , Saccharomyces cerevisiae , Oleispira antarctica , Arabidopsis thaliana , Drosophila melanogaster , Caenorhabditis elegans , Mus musculus , Homo sapiens , Thermus thermophilius and Picrophilus torridus .…”

The role of the proteasome in mitochondrial protein quality control

“…33,34,46 The heat shock transcription factor Hsf1 plays a central role in this context: it is not only activated upon heat stress, but also during the shift from fermentation to respiration and upon mitochondrial import impairment, thus at conditions at which mitochondrial precursors accumulate in the cytosol. 34,61,62 Such precursor proteins can sequester cytosolic chaperones which leads to the release and activation of Hsf1. This triggers a multi-level cascade of gene inductions, including expression of the transcription factor Rpn4 that, in turn, induces proteasomal genes to increase UPS capacity.…”