Prof. Dr. Aleksandra Trifunovic

Research Area: Mitochondrial Stress Responses in Disease and Ageing

Website: Trifunovic Lab

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 reactive oxygen species 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. 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. 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 diseases1. In a different study, we examined the conservation of mitochondrial unfolded protein response (UPRmt) in mammals, as we reported that the pathway for induction of mtUPR differs between C. elegans and mice2-4. We also look for novel pathways involved in the adaptation of cells and organisms to mitochondrial dysfunction that could lead to prolongation of lifespan5, or discovery of novel homeostatic pathways6. Recently, we reported that mitochondrial stress response is regulated by an intricate interplay between three transcription factors: CHOP, C/EBPβ, and ATF47.

3. Possible projects:

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. Thus, deciphering the molecular mechanisms of mitochondrial biogenesis, especially the coordination of two translation systems that ensure correct OXPHOS assembly upon different stresses, is essential for identifying new potential therapeutic targets for different pathological states.

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, a homolog of mammalian SP1 transcription factor, that in turn promotes mitochondrial gene expression and increases mito-biogenesis. In worms 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. We aim to identify signalling cascade that allows a crosstalk between cytoplasmic and mitochondrial translation in both nematode and mammalian system and identify specific conditions leading to its activation.

4. Applied methods and model organisms:

The group mainly uses in vivo model systems, specifically multiple 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, most recently using the CRISPR/Cas9 techniques. The group relies mainly on various molecular biology techniques to understand the complex signalling 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, many different bioenergetic techniques and approaches are established within the lab, and within Collaborative Research Center - SFB1218, the lab provides this expertise to the Cologne research community. These include, in vivo metabolic phenotyping of transgenic mice using indirect calorimetry and detailed analysis of mitochondrial respiratory function using high-resolution respirometry.

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 ability for problem solving through analytical thinking combined with high enthusiasm for scientific research is expected.

6. References:

  1. Dogan, S. A. et al. Tissue-specific loss of DARS2 activates stress responses independently of respiratory chain deficiency in the heart. Cell Metab19, 458-469, doi:10.1016/j.cmet.2014.02.004 (2014).
  2. Becker, C. et al. CLPP deficiency protects against metabolic syndrome but hinders adaptive thermogenesis. EMBO Rep19, e45126, doi:10.15252/embr.201745126 (2018).
  3. Szczepanowska, K. et al. CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels. EMBO J35, 2566-2583, doi:10.15252/embj.201694253 (2016).
  4. Seiferling, D. et al. Loss of CLPP alleviates mitochondrial cardiomyopathy without affecting the mammalian UPRmt. EMBO Rep17, 953-964, doi:10.15252/embr.201642077 (2016).
  5. Herholz, M. et al. KLF-1 orchestrates a xenobiotic detoxification program essential for longevity of mitochondrial mutants. Nat Commun10, 3323, doi:10.1038/s41467-019-11275-w (2019).
  6. Szczepanowska, K. et al. A salvage pathway maintains highly functional respiratory complex I. Nat Commun11, 1643, doi:10.1038/s41467-020-15467-7 (2020).
  7. Kaspar, S. et al. Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. Sci Adv (2021).