Systems biology of mitochondrial dysfunction

The human body consumes vast amounts of metabolites that are transformed into one another, modified to useful building blocks and broken down to harvest their energy. Mitochondria are at the core of this metabolic turnover and oxidative phosphorylation provides most cellular ATP in almost all human tissues. Despite the variability of metabolite and oxygen supply, mitochondria can readily adapt to their cellular niche. This requires a general flexibility in the expression patterns of the roughly 1,150 mitochondrial proteins, and fine tuning of protein actions. Failure to meet the cellular metabolic demand causes a wide range of tissue specific symptoms in human.

This thesis explores the use of high­throughput omics techniques in understanding enzy­ matic remodeling during mitochondrial disease. In the first part, I introduce the reader to the concepts of systems biology, and broadly discuss current methods and tools with a focus on mitochondria. Then, I describe the fine­tuning of mitochondrial function by post­translational modifications, in particular protein methylation and phosphorylation, and how this links to the large metabolic network of the one­carbon cycle. I conclude with primers on mitochondria in development and mitochondrial RNA metabolism. After that, I will present four publications in light of the discussed concepts and methods:

In study I, we find that the highly abundant metabolite S­adenosylmethionine is indis­ pensable for mitochondrial function. Its cytoplasmic production controls mitochondrial func­ tion by regulating iron­sulfur clusters biosynthesis and stability of the electron transport chain complex I, which has implications during ageing and cancer development. We apply a novel labeling method and mass spectrometry­based proteomics to identify 205 high­confidence methylation sites on mitochondrial proteins in fruit flies, and validate several by targeted pro­ teomics in mouse and human. In study II, we describe SILAF, a novel and highly efficient method to label amino acids in the fruit fly proteome. We exploit SILAF to characterize the mitochondrial phosphoproteome in a fly model of mitochondrial disease, and we pinpoint two regulatory phosphorylation sites. In study III, we investigate the role of the scaffold protein SQSTM1/p62 in neuronal de­ velopment. We find that the protein is required for differentiation of patient­derived neuronal epithelial stem cells, caused by an impaired switch from glycolytic to oxidative metabolism. In study IV, we use various fruit fly models to examine the interactions of proteins in mi­ tochondrial RNA metabolism. Using transcriptomics, we identify leakage of double­stranded RNA into the cytosol when mitochondrial RNA degradation is impaired and we suggest that this contributes to increased susceptibility to infection upon mitochondrial dysfunction.

Our studies take a novel view on mitochondrial dysfunction, and our post­translational modification screens give insight into a novel layer of complexity in the cell. The studies expose the opportunities and challenges of data­driven life science and can serve as a primer towards a digital representation of mitochondrial disease.

List of scientific papers

I. Schober FA*, Moore D*, Atanassov I, Moedas MF, Clemente P, Végvári Á, El­Fissi N, Filograna R, Bucher A­L, Hinze Y, The M, Hedman E, Chernogubova E, Begzati A, Wibom R, Jain M, Nilsson R, Käll L, Wedell A, Freyer C†, & Wredenberg A† (2021). The One­Carbon Pool Controls Mitochondrial Energy Metabolism via Complex I and Iron­Sulfur Clusters. Science Advances. 7:eabf0717. *These authors contributed equally. †Corresponding authors.
https://doi.org/10.1126/sciadv.abf0717

II. Schober FA*, Atanassov I*,†, Moore D, Calvo-Garrido J, Moedas MF, Wedell A, Freyer C†, & Wredenberg A† (2021). Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits. Molecular and Cellular Proteomics. 20:100065. *These authors contributed equally. †Corresponding authors.
https://doi.org/10.1016/j.mcpro.2021.100065

III. Calvo-Garrido J*, Maffezzini C*, Schober FA, Clemente P, Uhlin E, Kele M, Stran­neheim H, Lesko N, Bruhn H, Svenningsson P, Falk A, Wedell A, Freyer C†, & Wre­denberg A† (2019). SQSTM1/p62­Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation. Stem Cell Reports. 12(4):696–711. *These authors contributed equally. †Corresponding authors.
https://doi.org/10.1016/j.stemcr.2019.01.023

IV. Pajak A*, Laine I*, ClementeP,El-­Fissi N, Schober FA, Maffezzini C, Calvo-Garrido J, Wibom R, Filograna R, Dhir A, Wedell A, Freyer C†, & Wredenberg A† (2019). Defects of mitochondrial RNA turnover lead to the accumulation of double­stranded RNA in vivo. PLOS Genetics. 15(7): e1008240. *These authors contributed equally. †Corresponding authors.
https://doi.org/10.1371/journal.pgen.1008240