Unraveling novel roles in the mitochondrial DNA interactome

Sharma, Nupur (2025): Unraveling novel roles in the mitochondrial DNA interactome: functional insights into the Pyruvate Dehydrogenase Complex and Yme2. Dissertation, LMU München: Fakultät für Biologie

Abstract

Mitochondria are dynamic organelles crucial for eukaryotic life, renowned for their role in energy generation via oxidative phosphorylation. At the heart of their functionality, lies the mitochondrial DNA (mtDNA), which encodes key components of the electron transport chain, while the rest are encoded by the nuclear genome, reflecting their dual genetic origin. The mtDNA is organized into a large nucleoprotein complex known as the mitochondrial nucleoid, that is, in turn, a part of a larger, highly-ordered expressosome-like assembly called the MIOREX complex. The MIOREX complex houses the nucleoid, along with a variety of factors involved in mitochondrial gene expression, genome organization, protein biogenesis and the mitoribosome. Although recent efforts have significantly elucidated the components and mechanisms of MIOREX complexes, the complete MIOREX interactome remains elusive, with many of its protein partners and associated molecular mechanisms yet to be identified. This study attempts to characterize two such candidates, which have been previously identified to be present in the mtDNA interactome, and aims at studying their interaction with the mitochondrial genome. The first candidate is the pyruvate dehydrogenase complex (PDHc), that is well-known for its conserved role in glucose metabolism. The findings in this research reveal an additional role for the PDHc in promoting mitochondrial health, by contributing to mtDNA maintenance and associating with the gene expression machinery, which is independent of the traditional metabolic function of the PDHc, and involves interactions with mitochondrial RNA. Moreover, the precise molecular interactions of this complex have been elucidated through biochemical analyses, providing valuable insights into its identity as a bifunctional enzyme. The second candidate, Yme2, an inner mitochondrial membrane protein, has been previously implicated in mitochondrial protein biogenesis, albeit its mechanism of action remains unclear. Through a combination of bioinformatics and mutagenesis approaches, this research identifies that Yme2 contains an RNA recognition motif (RRM) as well as a AAA+ domain. Moreover, the results demonstrate that YME2 engages in genetic interactions with MDM38, MBA1, and OXA1, as well as biochemical interactions with mitochondrial nucleoid-associated proteins, thereby linking Yme2 to the mitochondrial protein biogenesis machinery. Collectively, by examining the interaction dynamics of PDHc and conducting mutational characterization of Yme2, I aim to contribute new perspectives to the field of the mtDNA interactome, thereby advancing research in this domain.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Mitochondria, pyruvate dehydrogenase complex, yme2, mitochondrial DNA, mtDNA
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 15. Mai 2025
• 1. Bericht­erstatter:in: Osman, Christof