Prof. Dr. Aleksandra Trifunovic

Research Area: Mitochondrial Biology & Metabolic Diseases


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. Recently, the group has shown that mitochondrial dysfunction is sensed independently of respiratory chain deficiency, questioning the current view on molecular mechanisms contributing to the development of mitochondrial diseases (Dogan et al 2014 Cell Metabolism). 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 mice (Seiferling et al. 2016, EMBO Rep, Szczepanowska et al. EMBO J 2016, Becker et al EMBO Rep 2018). We also look for novel pathways involved in adaptation of cells and organisms to mitochondrial dysfunction that under certain conditions could lead to prolongation of lifespan (Herholz et al. Nat Commun 2019), or discovery of novel homeostatic pathways (Szczepanowska et al. Nat Commun 2020). We continue working on different aspects of mitochondrial communication with the cell and the rest of the organism under physiological and pathophysiological conditions.

3. Possible projects:

  1. 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 and physical exercise, or in 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 nucleolar stress response (NSR), that stabilizes p53 and ultimately induces apoptosis. 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. 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.
  2. In addition to their conventional role of meeting the cell's  energy  requirements, mitochondria also actively regulate innate immune responses against infectious and sterile insults. In fact, it was suggested that mitochondria might regulate the inflammation process toward immunotolerance or immunogenicity. Components of mitochondria, when released or exposed in response to dysfunction or damage, can be directly recognized by receptors of  the innate immune system and trigger an immune response. Several recent studies suggested that dysfunctional mitochondria might activate innate immunity responses, by releasing either mtDNA or dsRNA. Our preliminary data indicated that mitochondrial dsRNA might be released from cells carrying various mutations in different OXPHOS components, and that this causes activation of interferon beta target genes even in the steady state conditions, independent of the mtDNA release. Now, we will investigate dynamics of dsRNA shuttling between different cell compartments with specific focus on PNPT1 (mitochondrial polyribonucleotide nucleotidyltransferase 1), an enzyme responsible for removal of dsRNA inside mitochondria. We hypothesized that PNPT1 gets inactivated by increased citrate accumulation in dysfunctional mitochondria, enabling release into cytoplasm. Based on the preliminary findings and this hypothesis, we aim to dissect the dsRNA signalling cascade by analysing downstream and upstream factors through genetic screens and functional analysis of candidate proteins.

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:

We are seeking a highly motivated PhD candidate to join our team investigating the role of mitochondrial stress responses in disease and ageing. Applicants should have a solid background in molecular biology, cell biology, genetics and/or biochemistry. A strong ability for problem solving through analytical thinking combined with high enthusiasm for scientific research is expected. Experience in working with mouse or C. elegans models is desirable, but not necessary.

6. References:

  1. Szczepanowska K, Senft K, Heidler J, Herholz M, Kukat A, …Wittig I and Trifunovic A. A salvage pathway maintains functional respiratory complex I. Nat Commun. 2020 Apr 2;11(1): 1643.
  2. Herholz, M., Cepeda, E., Baumann, L., Kukat, A., Hermeling, J., Maciej, S., Szczepanowska, K., Pavlenko, V., Frommolt, P., and Trifunovic, A. (2019). KLF-1 orchestrates a xenobiotic detoxification program essential for longevity of mitochondrial mutants. Nat. Commun. 10, 3323.
  3. Becker C, Kukat A, Szczepanowska K, Hermans S, Senft K, Brandscheid CP, Maiti P, and Trifunovic A.(2018) CLPP deficiency protects against metabolic syndrome but hinders adaptive thermogenesis. EMBO Rep. 2018 Mar 27. pii: e45126. doi: 10.15252/embr.201745126. [Epub ahead of print]. PMID: 29588285
  4. Szczepanowska K, Maiti P, Kukat A, Hofetz E, Nolte H, Senft K, Becker C, Ruzzenente B, Hornig-Do HT, Wibom R, Wiesner RJ, Krüger M, Trifunovic A (2016) CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels. EMBO J 35(23): 2566-83
  5. Seiferling D, Szczepanowska K, Becker C, Senft K, Hermans S, Maiti P, Kukat A, Trifunovic A (2016) Loss of ClpP alleviates mitochondrial cardiomyopathy without affecting the mammalian UPRmt. EMBO Rep 17(7): 953-64
  6. Dogan SA, Pujol C, Maiti P, Kukat A, Wang S, Hermans S, Senft K, Wibom R, Rugarli EI, Trifunovic A(2014) Tissue-specific loss of DARS2 activates stress responses independently of respiratory chain deficiency in the heart. Cell Metab 19: 458-69