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Deciphering and reversing the consequences of mitochondrial DNA damage

Periodic Reporting for period 4 - RevMito (Deciphering and reversing the consequences of mitochondrial DNA damage)

Reporting period: 2018-12-01 to 2020-03-31

More than one in 5000 people may be afflicted by mitochondrial diseases that lead to a variety of debilitating symptoms. Mutations causing mitochondrial disorders are localized to both the mitochondrial and the nuclear genomes, and with the application of next generation sequencing-based approaches, additional genes continue to be linked to mitochondrial dysfunction. While some mutations can more generally affect energy production by, for example, diminishing the synthesis of mitochondria-encoded protein products or hampering mitochondrial DNA replication, other mutations block specific mitochondrial complexes and activities. Beyond heritable mitochondrial disorders, mitochondrial dysfunction can be caused by antiviral drugs and by drugs targeting tumors. There are few to no treatment options for most mitochondrial diseases. Consequently, increased effort toward discovery and rational formulation of new treatments for mitochondria-associated illness is clearly warranted.

The overall objective of this project is to understand the cellular outcomes of mitochondrial disease. Toward this goal, we use mammalian cells and also budding yeast, a model system that has been historically invaluable in understanding mitochondrial assembly and dysfunction. Our specific focus is the relationship between mitochondrial dysfunction and intracellular signaling, protein transit to mitochondria, and proteostasis. Furthermore, we take unbiased approaches that are designed to reveal new and unexpected genes that control the response to mitochondrial dysfunction.

During the course of this grant action, we were indeed able to better understand the links between sugar sensation, protein import to mitochondria, and the outcome of mitochondrial dysfunction. Moreover, we were able to identify an additional protein, a lysine methyltransferase, which seems to impinge upon the outcome of mitochondrial dysfunction. We helped to illuminate how mitochondrial contact sites promote the intracellular distribution of mitochondrial metabolites. Finally, we developed novel approaches toward prediction of which mtDNA variants are likely to cause disease, and our studies of mitochondrial evolution are likely to provide further insight into key aspects of mitochondrial disease.
Several important advances have been made within the context of this grant. We have successfully investigated the link between glucose sensation in yeast and the outcome of mtDNA deletion. In this course of this work, we have generated an expanded view of the genes and pathways activated or inactivated by removal of the mitochondrial genome. Furthermore, we have developed a novel approach to studying protein insertion at the surface of organelles, and we have applied this workflow to the study of a conserved protein involved in yeast mitochondrial division. We performed pioneering studies demonstrating that hydrophobic stretches obtained from prokaryotic proteins can insert at the mitochondrial outer membrane. We have proposed a new hypothesis related to mitochondrial evolution, and we continue to make headway in our search for new nuclear genes controlling the outcome of mitochondrial dysfunction. Most recently, we developed new methodologies, dependent upon machine learning and novel metrics of conservation, that allow prediction of whether human mitochondrial DNA variants are likely to be deleterious. This work is currently under commercialization.

Certainly, the work funded by the ERC has been impactful, resulting in nine peer-reviewed publications, one pre-print submitted for peer-review, one book chapter accepted for publication, and several other manuscripts nearing completion and submission. This work has also been disseminated in the context of over 30 conferences and seminars. Active work continues on the important topics considered with the support of this EU funding.
Beyond the cessation of this project, we expect further advances beyond the state-of-the-art. We have identified candidate genes and pathways that are likely to be relevant for controlling the outcome of mitochondrial dysfunction. Moreover, we can use the tools developed within this project to continue our investigation of protein targeting to mitochondria, and we can extend our studies of protein trafficking to other organelles, such as the peroxisome, another key metabolic organelle. Our novel phylogenetic methods will continue to allow highly accurate predictions of variant pathogenicity, and our work has additional importance in the field of molecular ecology, as exemplified by our recently accepted paper focused upon the hummingbird mitochondrial genome.
Transcriptomic changes upon modulation of nutrient sensing in cells lacking mitochondrial DNA
Machine learning prediction of protein-coding variants in mtDNA
Substitution mutant analysis of the Fis1 tail anchor