The mitochondrial unfolded protein response in mammalian physiology

Mitochondria, the main site of cellular energy harvesting, are derived from proteobacteria that evolved within our cells in endosymbiosis. Mitochondria retained vestiges of their proteobacterial genome, the circular mitochondrial DNA, which encodes 13 subunits of the oxidative phosphorylation multiprotein complexes in the electron transport chain (ETC), while the remaining similar to 80 ETC components are encoded in the nuclear DNA (nDNA). A further similar to 1,400 proteins, which are essential for mitochondrial function are also encoded in nDNA. Thus, a majority of mitochondrial proteins are translated in the cytoplasm, then imported, processed, and assembled in the mitochondria. An intricate protein quality control (PQC) network, constituted of chaperones and proteases that refold or degrade defective proteins, maintains mitochondrial proteostasis and ensures the cell and organism health. The mitochondrial unfolded protein response is a relatively recently discovered PQC pathway, which senses the proteostatic disturbances specifically in the mitochondria and resolves the stress by retrograde signaling to the nucleus and consequent transcriptional activation of protective genes. This PQC system does not only transiently resolve the local stress but also can have long-lasting effects on whole body metabolism, fitness, and longevity. A delicate tuning of its activation levels might constitute a treatment of various diseases, such as metabolic diseases, cancer, and neurodegenerative disorders.

Mitochondrial stress signalling and its impacts on physiology

Adrienne Joëlle Laurence Mottis

Mitochondria are responsible for respiration and energy harvesting across the eukaryotic kingdom. They also take part in other cellular processes like intermediary metabolism. As a result, mitochondrial function directly impacts organismal features such as metabolic homeostasis, fitness and aging. Moreover, mitochondrial dysfunction is involved in numerous pathologies, such as neurodegenerative disease, obesity, diabetes and cancer. Several surveillance pathways constantly monitor mitochondria to ensure their proper function. Among the pathways triggered by stress, the mitochondrial unfolded protein response (UPRmt) aims to restore proteostasis within this organelle. A better understanding of the cellular response to mitochondrial stress would expand our fundamental knowledge of physiological and pathological processes involving mitochondria, leading to potential new therapeutics that target these organelles. This thesis focuses on the mechanistic and physiological characterization of the mitochondrial stress response in several organisms. I used the model organism Caenorhabtis elegans to screen for novel players of the UPRmt and found the poly(A)-binding protein pab-1. Using transcript profiling, we showed that the induction of immune genes is a common consequence of several mitochondrial stressors. We demonstrated that pab-1 regulates the activation of the mitochondrial stress response and innate immunity as well. On top, pab-1 is required for the survival of C. elegans upon bacterial infection. Transcriptomic data from multiple human tissues suggest that the human pab-1 orthologue, PABPC1, has a conserved role in immunity. In mice, I explored the regulation of the mitochondrial stress response using a combination of bioinformatics and in vivo experimental approaches. Combined transcriptomic and proteomic analyses in the BXD mouse genetic reference population revealed a tight co-regulation of the orthologues of the UPRmt under normal physiological conditions. As a complementary approach, we triggered mitochondrial stress pharmacologically in newly born and adult mice. Due to the bacterial ancestry of mitochondria, the effects of the antibiotic doxycycline (dox) are also deleterious to this organelle. We found that dox impairs mitochondrial proteostasis and oxygen consumption in adult mice. However, mitochondrial stress induced by post-natal dox treatment did not cause long-lasting effects on mouse physiology and longevity, which is very distinct from observations in C. elegans. The mammalian gut flora plays an important role in organismal homeostasis. The use of an antibiotic causes perturbations of the microbiota, with repercussions on metabolism, inflammation, and the nervous system. To eliminate these confounding effects, we also treated germ-free mice with dox to characterize the response of the mouse to a so-called âpureâ mitochondrial stress. Using multi-omics profiling, we found that organs highly dependent on mitochondria display specific transcriptomic and proteomic signatures following dox treatment. In the kidney, we observed an inhibition of translation and of the mTOR pathway, accompanied by an activation of the ATF4 integrated stress response (ISR). In the liver, dox led to a remodelling of lipid metabolism. In both organs, target transcripts of type I interferon anti-viral response were induced. This thesis demonstrates that the response to mitochondrial stress is a multi-faceted process with conserved aspects acr

EPFL2018

Enhancing mitochondrial quality control to fight neuromuscular degeneration in aging and disease

Mario Romani

Loss of mitochondrial function and proteostasis typify aging and age-associated degenerative disorders such as Alzheimer's disease and muscle aging. To date, no cure or preventive measure is available to manage these conditions. Alterations of cellular proteostasis, such as accumulation of misfolded or aggregated proteins, can directly affect mitochondrial homeostasis leading to activation of specific mitochondrial stress pathways capable of maintaining mitochondrial function. However, the contribution of these pathways in age-associated diseases characterized by proteotoxic aggregates is largely unknown. My thesis aims to understand the connection between cellular and mitochondrial proteostasis with a particular focus on mitochondrial stress pathways involved in the response to proteotoxic stress. To this end, I performed 2 studies: Reduction of Amyloid-beta proteotoxicity through activation of mitochondrial quality control: Accumulation of Amyloid-beta (Aß) peptidic aggregates, generated by the miscleavage of amyloid precursor protein (APP), is often associated with mitochondrial dysfunction. However, it is largely unknown how mitochondria react to these proteotoxic insults. We identified a cross-species conserved mitochondrial stress response, from nematodes to humans, activated during Aß proteotoxic stress. This response entails key mitochondrial quality control pathways such as the mitochondrial unfolded protein response (UPRmt) and mitophagy. Importantly, activation of these pathways through administration of mitochondrial regulators Doxycycline and the NAD+ booster nicotinamide riboside (NR), was sufficient to reduce Aß accumulation and proteotoxicity in nematodes and human cell lines. Moreover, boosting mitochondrial quality control in vivo in a mouse model of Alzheimer's disease with the compound NR led to a reduction of brain Aß plaques and preservation of cognitive function. Skeletal muscle aging is characterized by amyloid-like protein aggregates: Skeletal muscle aging is characterized by accumulation of dysfunctional mitochondria and misfolded proteins. However, the connection between these two hallmarks of muscle aging remains elusive. We found that aged skeletal muscles present a similar perturbation of mitochondrial and APP processing pathways when compared to muscles from inclusion body myositis patients (IBM), a disease characterized by intracellular protein deposits containing also Aß aggregates. In line with this, we identified amyloid-like aggregates in aged muscle closely resembling the ones observed during IBM with concomitant mitochondrial dysfunction. Strategies aiming at restoring mitochondrial homeostasis led to activation of the mitochondrial quality control accompanied by a reduction of amyloid-like aggregates in vitro and in vivo in mammalian and nematode systems. In summary, our work demonstrated that amyloidosis characterizes muscle, and possibly brain, aging in a similar fashion to what is observed in muscle and brain tissues from IBM and Alzheimer's patients, respectively. Importantly, restoring mitochondrial homeostasis through activation of mitochondrial quality control is sufficient to alleviate protein aggregation and improve tissue function in aging, IBM and Alzheimer's disease models.

EPFL2021

Mitochondrial unfolded protein response, its molecular mechanism and physiological impact

Virginija Jovaisaite

Mitochondria are the main producers of ATP, the energy currency of the cell, and they perform a wide array of other fundamental functions. These organelles are essential not only for cellular metabolism, but also for organismal physiology and lifespan. A recently discovered mitochondrial unfolded protein response (UPRmt) maintains the mitochondrial proteostasis by managing protein quality control (PQC) network during proteotoxic stress. Recent findings show that activation of this repair pathway improves mitochondrial function and is associated with increased longevity. My thesis aims to expand the knowledge about the UPRmt by exploring its molecular mechanism and impact on mitochondrial stress induced longevity. We performed three studies: Identification of two epigenetic UPRmt regulators (chapter 2). In collaboration with Prof. Dillinâs laboratory (UCB, USA), we identified the conserved histone demethylases jmjd-1.2/PHF8 and jmjd-3.1/JMJD3 as positive regulators of UPRmt and longevity in response to mitochondrial electron transport chain (ETC) dysfunction across species. A systems genetics analysis of data from the BXD mouse genetic reference population (GRP) further indicates conserved roles of the mammalian orthologs of these demethylases in longevity and UPRmt signaling. These findings illustrate an evolutionary conserved epigenetic mechanism that determines the rate of aging, downstream of mitochondrial perturbations. Relation between UPRmt and TCA cycle (chapter 3). We investigated the effects of genetic perturbations of the TCA cycle on the UPRmt and lifespan. We found that downregulation of several TCA cycle enzymes induces UPRmt, but they have divergent effects on lifespan. Restricting the knockdown of these genes to early larval development stages had positive effects on longevity, which was dependent on UPRmt. We analysed the transcriptomes of C. elegans with knockdown of these TCA cycle genes and compared them with those obtained after the knockdown of other mitochondrial genes, which are known to induce the UPRmt. We identified a core set of transcripts, which change in common and which likely represent a signature of mitochondrial dysfunction associated with UPRmt induction. Bioinformatic analysis of UPRmt (chapter 4). In two collaborative studies, we investigated the UPRmt using newly collected data from the BXD mouse GRP. In the first study, we quantified the transcriptome and proteome from 40 strains of the BXD mouse GRP on two different diets. Integrated molecular profiles were used to characterize the UPRmt, which shows strikingly variant responses at the transcript and protein level that are conserved between C.elegans, mice and humans. In the second study, whole genomes of BXD GRP strains were sequenced to detect sequence variants, which were then used to find novel associations within a high coverage phenome of various traits. One of the novel associations included a missense mutation in fumarate hydratase that controls variation in the UPRmt in both mouse and C. elegans. In summary, our work characterized novel epigenetic regulators of UPRmt and associated mitochondrial stress induced longevity, described the connection between the UPRmt and the TCA cycle, and illustrated the conservation of UPRmt in a mouse GRP. These results expand the knowledge about the UPRmt and promote further investigation of its role in longevity and mitochondrial diseases.

EPFL2016