Mitochondria, popularly known as powerhouse of the cell, contain specialised mitoribosomes that synthesise essential membrane proteins. These essential proteins are required to form enzyme complexes, which carry out the process of oxidative phosphorylation (OXPHOS). OXPHOS is carried out by five enzyme complexes (Complex I-V), out of which complex I, III and IV pump protons during electron transfer from NADH to O₂ and complex V uses the generated proton gradient to synthesise ATP. Cryo-EM, as a revolutionary technique in structural biology made it possible to determine the structures of mitoribosome assembly intermediates and respiratory chain supercomplexes. These structures have allowed us to investigate the mitoribosome biogenesis pathway in human and yeast and to gain deeper insights into the architecture of supercomplexes. In the first area of research, using cryo-EM we were for the first time able to capture mitoribosomes in different late stages of assembly and to determine their high-resolution structures with novel factors bound. Investigation of this process was previously unreachable due to lack of techniques to trap these mitoribosome complexes in different states of assembly. The structures of these assembly intermediates establish the role of assembly factors such as MALSU1, LOR8F8, mt-ACP, MTG1 and mitoribosomal proteins (MRPs) in mitoribosome biogenesis and to ensure proper maturation of each subunit, reflecting their role in regulating translation. Furthermore, genetic deletion studies of MTG1 and uL16m in yeast show the importance of transiently acting factors and MRPs in the mitoribosome assembly process and their effects on translation. The assembly pathway of mitoribosomes is critical for protein synthesis since defects in the translation process causes inherited human pathologies. Therefore, elucidation of mitoribosomal biogenesis pathways may also contribute to the development of potential new therapeutic opportunities. In the second research area, structures of the respiratory chain supercomplex from yeast were determined. These are the first near-atomic resolution structures that show organization of complex III and complex IV into two distinct classes that form higher order assemblies (III₂IV₁and III₂IV₂). Moreover, the architecture of the supercomplex structures differs from the previously determined respirasomes (I₁III₂IV₁) structures in mammals. We obtained a near-atomic resolution structure of the yeast complex IV, revealed core protein-protein and protein-lipid interactions that hold the supercomplex together. Moreover we found novel subunits required for supercomplex formation in S. cerevisiae. The last part of my study focuses on cryo-EM sample method development where we could successfully demonstrate the usefulness of a simple pressure-assisted sample preparation method for microcrystals, proteins and mitochondria. Our findings show great resolution improvements of selected area electron diffraction patterns of microcrystals, a significant reduction in needed sample concentration for single particle studies and an enrichment of gold nano-particles for tomographic studies.

Mitochondria are eukaryotic organelles with a multitude of functions including biosynthesis of molecules and cellular regulation. Most prominently though is their role in energy conversion which culminates with the production of ATP, the universal molecular unit of currency. This is done through several metabolic pathways, including the pyruvate dehydrogenase bridging reaction, the citric acid cycle and the oxidative phosphorylation. In the latter pathway, electrons are transferred from electron carriers formed in the previous pathways and shuttled trough a chain of protein complexes (complex I – complex IV) via the mobile electron carriers coenzyme Q and cytochrome c. Collectively this is known as the respiratory chain. This process harnesses energy from the transferred electrons to translocate protons across the mitochondrial inner membrane, forming an electrochemical gradient that the ATP synthase uses to generate ATP. In this thesis we study parts of these metabolic pathways both structurally and functionally, using a combination of cryo-EM, biochemistry and cell biology. In the first project we used cryo-EM to solve the structure of the pyruvate dehydrogenase complex of E. coli, gaining new insight into how the flexible lipoyl-domain interacts with the active site of the core of the complex. We could determine that this interaction is mediated through electrostatic interaction formed between an acidic patch of amino acids of the lipoyl-domain and positively charged amino acids on the core. In the second project we again employed cryo-EM, this time to solve the structure of the yeast respiratory supercomplex, and for the first time we could obtain a near-atomic resolution structure of how complex III and complex IV in yeast interact with each other to form respiratory supercomplexes. Two forms of these higher order assemblies exist in the respiratory chain of yeast (CIII₂/CIV and CIII₂/CIV₂), which assembles very differently compared to the mammalian CI/CIII₂/CIV respirasome. The main interaction point of the yeast supercomplexes occurs between the subunits Cor1 and Cox5a. Through selective point mutations, we were able to disrupt this interaction and effectively hinder supercomplex formation in yeast. Using biochemistry and cell biology on such disrupted cells, we could determine that supercomplexes form to facilitate better diffusion of cytochrome c between the individual complexes of the supercomplex. In the third project we look at how manganese toxicity impacts the respiratory chain in yeast on a molecular level. By combining proteomics, biochemistry and metal analyses, we found that manganese overload causes mismetalation of Coq7, an essential subunit of the coenzyme Q synthesis pathway, which causes a loss of the electron carrier between complex II and complex III. This loss of coenzyme Q could be restored when cells were augmented with Coq7 overexpression, which restored functional respiration and prevented age-related cell death.