Mitochondria are essential constituents of a eukaryotic cell by supplying ATP and contributing to many mayor metabolic processes. As endosymbiotic organelles, they represent a cellular subcompartment exhibiting many autonomous functions, most importantly containing a complete endogenous machinery responsible for protein expression, folding and degradation. This article summarizes the biochemical processes and the enzymatic components that are responsible for maintaining mitochondrial protein homoeostasis. As mitochondria lack a large part of the required genetic information, most proteins are synthesized in the cytosol and imported into the organelle. After reaching their destination, polypeptides must fold and assemble into active proteins. Under pathological conditions, mitochondrial proteins become misfolded or damaged and need to be repaired with the help of molecular chaperones or eventually removed by specific proteases. Failure of these protein quality control mechanisms results in loss of mitochondrial function and structural integrity. Recently, novel mechanisms have been identified that support mitochondrial quality on the organellar level. A mitochondrial unfolded protein response allows the adaptation of chaperone and protease activities. Terminally damaged mitochondria may be removed by a variation of autophagy, termed mitophagy. An understanding of the role of protein quality control in mitochondria is highly relevant for many human pathologies, in particular neurodegenerative diseases.

Aggregated polypeptides accumulating inside mitochondria are sequestered in a single cellular quality compartment, called IMiQ. Its formation retains proteotoxic aggregates in a distinct cellular localization, increasing mitochondrial fitness by relieving the protein quality control system of misfolded polypeptides.

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Proteins of the Hsp100 chaperone family support protein homeostasis, the maintenance of protein activity under stress, by refolding aggregated proteins or targeting them for degradation. Hsp78, the ClpB-type mitochondrial member of the Hsp100 family, can be found in lower eukaryotes like yeast. Although Hsp78 has been shown to contribute to protection against elevated temperatures in yeast, the biochemical mechanisms underlying this mitochondria- specific thermotolerance are still largely unclear. To identify endogenous chaperone substrate proteins, we generated an Hsp78- ATPase mutant with a stabilized substrate binding behaviour. We used two SILAC- based quantitative mass spectrometry approaches to analyze the role of Hsp78 during heat stress-induced mitochondrial protein aggregation and disaggregation processes on a proteomic level. In the first setup, Hsp78-interacting polypeptides were identified to reveal the endogenous substrate spectrum of the chaperone. Our analysis revealed that Hsp78 is interacting with a wide variety of proteins related to metabolic functions including energy production and protein synthesis, as well as other chaperones, thus maintaining crucial functions for mitochondrial stress resistance. We compared these interaction data with a second experimental setup that focussed on the on overall aggregation and disaggregation processes in mitochondria under heat stress on a proteomic level. This revealed specific aggregation-prone protein populations and demonstrated the direct quantitative impact of Hsp78 on stress-dependent protein solubility different conditions and. We conclude that Hsp78 together with its cofactors represents a recovery system that protects major mitochondrial metabolic functions during heat stress as well restores protein biogenesis capacity after return to normal conditions.

Aggregation processes can cause severe perturbations of cellular homeostasis and are frequently associated with diseases. We performed a comprehensive analysis of mitochondrial quality and function in presence of misfolded, aggregation-prone polypeptides. Although we observed significant aggregate formation inside mitochondria, we observed only a minor impairment of mitochondrial function. We could show that detoxification of misfolded reporter polypeptides as well as endogenous proteins inside mitochondria takes place via their sequestration into the specific organellar deposit site Intra-Mitochondrial Protein Quality Control Compartment (IMiQC). Only minor amounts of co-aggregated proteins were associated with IMiQC and neither resolubilization nor degradation by the mitochondrial PQC system were observed. The single IMiQC aggregate deposit was not transferred to daughter cells during cell division. Detoxification of misfolded polypeptides via IMiQC formation was highly dependent on a functional mitochondrial fission machinery. We conclude that the formation of the aggregate deposit is an important mechanism to maintain full functionality of mitochondria under proteotoxic stress conditions.