Prof. Dr. Aleksandra Trifunovic

Research Area: Mitochondrial Stress Responses in Disease and Ageing

Branches: GeneticsImmunologyStem Cell Biology

Website: Trifunovic Lab

Prof. Dr. Aleksandra Trifunovic, Ageing Grad School Cologne

1. Research background:

Mitochondria are essential organelles found in every eukaryotic cell, required to convert food into usable energy. The mitochondrial oxidative phosphorylation (OXPHOS), which produces the majority of cellular energy in the form of ATP, is controlled by two distinct genomes: the nuclear and the mitochondrial genome (mtDNA). Mutations in mitochondrial genes encoded by either genome could cause mitochondrial disorders, and have emerged as a key factor in a myriad of “common” diseases, including Parkinson’s and Alzheimer’s Disease, Type 2 Diabetes, and are strongly linked to the aging process. Despite all this, it is surprising that our understanding of the mechanisms governing the mitochondrial gene expression, its reliance on the complex nature of dual genome control and associated pathologies remain superficial, with therapeutic interventions largely unexplored. Remarkably, mitochondria are now also viewed as main regulators of signal transduction. Within a last few years, multiple mitochondria-centric signaling mechanisms have been proposed, including release of multiple metabolites, and the scaffolding of signaling complexes on the outer mitochondrial membrane. It has also been shown that mitochondrial dysfunction causes induction of stress responses, bolstering the idea that mitochondria communicate their fitness to the rest of the cell. Studies in this area are not only of basic scientific interest, but may also provide new avenues towards treatment of mitochondrial dysfunction in a variety of human diseases and ageing.

2. Research questions addresses by the group:

When mitochondria experience stress or when dysfunction occurs, the organelle sends signals to the cell nucleus, which launches different types of adaptive cell responses. Transcription factors are activated and stimulate the expression of specific sets of genes, whose products enable the cell to adapt to the changes. Most recent scientific advances reveal that mitochondria also play a central role in proinflammatory signalling, on one side as a signalling platform, but also as an active producer of potent damage-associated molecular patterns (DAMPs) that control activation of innate immunity and the inflammatory response. We aim to further understand these largely unknown mechanisms that play a central role in determining the extent of tissue specific defect arising from the respiratory deficiency and systemic metabolic and inflammatory changes. The primary focus of our research is in deciphering the precise signaling cascade of the pathogenic mechanisms leading to mitochondrial diseases and ageing, with the ultimate goal of identifying new therapeutic targets and strategies.

Our group has successfully advanced research approaches that focus on the communication between mitochondria and other parts of the cell. We have shown that mitochondrial dysfunction is sensed independently of the respiratory chain deficiency, questioning current view on molecular mechanisms contributing to the development of mitochondrial diseases (1, 2). We reported that the pathway for induction of mtUPR differs between C. elegans and mice (3-5). We also look for novel pathways involved in the adaptation of cells and organisms to mitochondrial dysfunction that could lead to prolongation of lifespan (6), or discovery of novel homeostatic pathways (7, 8). Recently, we reported that mitochondrial stress response is regulated by an intricate interplay between three transcription factors: CHOP, C/EBPβ, and ATF4 and tissues specific cytokines  (9, 10).

3. Possible projects:

a. Regulation of mitochondrial remodelling upon metabolic stress

When cells have an increase in energy demand, they respond by elevating the production of new mitochondria. However, the process of mitochondrial biogenesis is an extremely complex and relies heavily on coordinated regulation of both nuclear and mitochondrial DNA (mtDNA) gene expression, ultimately leading to changes in levels of 1000-1500 proteins. Remarkably we know very little of how this process is regulated especially during stress conditions that promote mitochondrial biogenesis, such as dietary restriction, resveratrol treatment, and physical exercise, but also pathological states as cancer progression and cardiac hypertrophy.

A genome-wide screen for factors that promote mitochondrial biogenesis identified depletion of cytoplasmic ribosomal proteins as a major pathway promoting mitochondrial gene expression. Depletion of individual ribosomal proteins leads to inefficient ribosomal biogenesis resulting in altered translation fidelity. Our further preliminary data showed that this induces synthesis of SPTF-3 transcription factor, that in turn promotes mitochondrial gene expression and increases mito-biogenesis. In C. elegans this pathway is activated upon caloric restriction and heat stress, and is highly conserved in mammalian cells, where is initiated upon nutrient deprivation. Remarkably, this stress pathway seems to be independent of mTOR activation, and the bona-fide mitochondrial biogenesis factor PGC1a. The major goal of the proposed project is to identify the mechanism by which nutrient deprivation and other stresses affects fidelity of cytoplasmic translation and how this leads to increase in mitochondrial OXPHOS biosynthesis.

b. Mitochondrial CLPP protease as a regulator of innate immunity

Due to its bacterial origin mitochondria contain numerous potent immunostimulatory damage-associated molecular patterns (DAMPs), including hypomethylated mtDNA, dsRNA and formylated proteins, that can activate the innate immune system, type I interferon (IFN-I) in particular. The exposure of cells to mtDNA has long been known to be immunostimulatory and the release of mtDNA into the cytosol can activate several pattern recognition receptors (PPRs) to trigger a variety of innate immune responses. In recent years it was increasingly recognized that besides supporting the antiviral response orchestrated by PRRs, uncontrolled and excessive release of mitochondrial DAMPs contributes to the dysregulated process observed in numerous inflammatory and autoimmune conditions, as well as in ischemic heart disease and cancer. Whilst new evidence in recent studies has revealed more about the role of mitochondria in the modulation of innate immunity, we are left with more questions than answers, and this project proposal aims to answer some of them.

Our preliminary data suggest that mtDNA release might be a highly regulated process that does not depend on the level of mitochondrial dysfunction or physical damage. Instead, we show that mitochondrial matrix protease CLPP, part of mitochondrial quality control machinery, guards against the release of mitochondrial DAMPs and the activation of IFN-I response. Furthermore, CLPP deficiency in vivo provides hints for the crosstalk between innate immunity responses and control of systemic metabolism that were previously not investigated. Using a combination of cell and in vivo models we aim to discover molecular mechanisms behind these processes, to precisely map mitochondrial DAMPs and their signaling cascades.

c. Quality control of respiratory chain

Mitochondria are highly dynamic and stress-responsive organelles that are renewed, maintained and removed by a number of different mechanisms. Recent findings bring more evidence for the focused, defined, and regulatory function of the intramitochondrial proteases extending far beyond the traditional concepts of damage control and stress responses. Until recently, the macrodegradation processes, such as mitophagy, were promoted as the major regulator of OXPHOS remodelling and turnover. However, the spatiotemporal dynamics of the OXPHOS system can be greatly modulated by the intrinsic mitochondrial mechanisms acting apart from changes in the global mitochondrial dynamics. This, in turn, may substantially contribute to the shaping of the metabolic status of the cell.

We have recently described the salvage pathway as the mechanism that safeguard against the accumulation of dysfunctional CI arising from the inactivation of the N-module subunits due to attrition caused by its constant activity under physiological conditions (7, 8). Now, we would like to further explore proteolytic control of OXPHOS function by mitochondrial matrix proteases CLPP and LONP1 under physiological and pathophysiological conditions. 

4. Applied methods and model organisms:

The group mainly uses in vivo transgenic mouse models and also the roundworm Caenorhabditis elegans to tackle specific questions of mitochondrial pathophysiology. Many of the transgenic mice models are developed within the group. The group relies mainly on various molecular biology techniques to understand the complex signaling pathways, many of which are specifically developed to understand the mitochondrial physiology. To tackle complex molecular mechanisms of specific processes in details, we often turn to mammalian cell-based models and different biochemical approaches. As one of the main aims is to understand the consequences of energy depletion in cells and the organism as a whole, the lab has established many different bioenergetic approaches in vitro and in vivo, and this expertise are provided to the Cologne research community.

5. Desirable skills and qualifications:

Applicants should have a strong theoretical and practical background in molecular biology, cell biology, genetics and/or biochemistry. A genuine enthusiasm for scientific research is expected. A high ability for problem solving through analytical thinking is beneficial.

6. References:

  1. S. A. Dogan et al., Tissue-specific loss of DARS2 activates stress responses independently of respiratory chain deficiency in the heart. Cell Metab19, 458-469 (2014).
  2.  M. Aradjanski et al., DARS2 protects against neuroinflammation and apoptotic neuronal loss, but is dispensable for myelin producing cells. Hum Mol Genet26, 4181-4189 (2017).
  3.  C. Becker et al., CLPP deficiency protects against metabolic syndrome but hinders adaptive thermogenesis. EMBO Rep19, e45126 (2018).
  4.  K. Szczepanowska et al., CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels. EMBO J35, 2566-2583 (2016).
  5. D. Seiferling et al., Loss of CLPP alleviates mitochondrial cardiomyopathy without affecting the mammalian UPRmt. EMBO Rep17, 953-964 (2016).
  6. M. Herholz et al., KLF-1 orchestrates a xenobiotic detoxification program essential for longevity of mitochondrial mutants. Nat Commun10, 3323 (2019).
  7.  K. Szczepanowska et al., A salvage pathway maintains highly functional respiratory complex I. Nat Commun11, 1643 (2020).
  8. A. Rumyantseva, M. Popovic, A. Trifunovic, CLPP deficiency ameliorates neurodegeneration caused by impaired mitochondrial protein synthesis. Brain145, 92-104 (2022).
  9. S. Kaspar et al., Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. Sci Adv7,  (2021).
  10. M. Croon et al., FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction. Sci Adv8, eabn7105 (2022).