Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BiolD, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.

The mitochondrial oxidative phosphorylation system comprises complexes assembled from subunits derived from mitochondrial and nuclear gene expression. Both genetic systems are coordinated by feedback loops, which control the synthesis of specific mitochondrial encoded subunits. Here, we studied how this occurs in the case of cytochrome b, a key subunit of mitochondrial complex III. Our data suggest the presence of a molecular rheostat consisting of two translational activators, Cbp3-Cbp6 and Cbs1, which operates at the mitoribosomal tunnel exit to connect translational output with assembly efficiency. When Cbp3-Cbp6 is engaged in assembly of cytochrome b, Cbs1 binds to the tunnel exit to sequester the cytochrome b-encoding mRNA, repressing its translation. After mediating complex III assembly, binding of Cbp3-Cbp6 to the tunnel exit replaces Cbs1 and the bound mRNA to permit cytochrome b synthesis. Collectively, the data indicate the molecular wiring of a feedback loop to regulate synthesis of a mitochondrial encoded protein.

Mitochondria possess their own genome, remnant of the ancestral eubacterial endosymbiont DNA. This mitochondrial genome encodes mostly few key subunits of the respiratory chain. In order to synthesize these few proteins, mitochondria contain a complete gene expression machinery. Crucially, during the evolution, this apparatus dramatically diverged from its bacterial original counterpart, acquiring unique organellar characteristics. Hence, the mechanisms underlying organization and regulation of mitochondrial gene expression are still enigmatic.

In this thesis, I used the model organism Saccharomyces cerevisiae to reveal few aspects of mitochondrial gene expression. Surprisingly, I report that translation initiation strongly diverged from the bacterial one. In fact, the mitochondrial counterpart of the bacterial translation initiation factor 3 is dispensable in yeast. Furthermore, the research made in this work contributed to establish the proximity labelling technique BioID for yeast mitochondrial proteins. This method permitted to analyse extensively the mitochondrial gene expression milieu, creating a comprehensive proximity-based network of factors involved in biogenesis of mitochondrial synthesized proteins. This protein network revealed a unique organization of factors involved in mitochondrial gene expression, meticulously tailored for the synthesis of few organellar proteins. Crucially, we could identify a clear spatial distribution of factors according to their biological function. Moreover, the thesis describes how the polypeptide tunnel exit hosts proteins involved in multiple functions. First, the results show how factors involved in early maturation of Cox1, the core subunit of complex IV of the respiratory chain, reside at the polypeptide tunnel exit. Second, we demonstrate that the synthesis of cytochrome b, subunit of complex III, is also activated at the polypeptide tunnel exit. In fact, proteins taking part in the regulation of mitochondrial gene expression called translational activators interact with this area in an alternate fashion. When synthesis of cytochrome b is repressed, its coding mRNA COB is sequestered at the polypeptide tunnel exit via the binding to Cbs1, a translational activator. The signal that triggers translation initiation is given by Cbp3-Cbp6, a complex that participates in cytochrome b assembly. When a previously synthesized cytochrome b is correctly assembled into complex III, Cbp3-Cbp6 interacts with the polypeptide tunnel exit, forcing the relocation of Cbs1, and making COB mRNA available for a new round of translation. This mechanism represents a unique form of tuning between mitochondrial and nuclear gene expression systems, essential for the correct assembly of complexes made up by proteins of dual origin.

In summary, the work presented in this thesis reveals novel features of the organization and regulation of the mitochondrial gene expression, highlighting many distinctive organellar features. The concepts and techniques presented here will be a starting point to elucidate many unknown aspects of mitochondrial protein synthesis.

Despite recent achievements implicating caspase-2 in tumor suppression, the enzyme stands out from the apoptotic caspase family as a factor whose function requires further clarification. To specify enzyme characteristics through the definition of interacting proteins in apoptotic or non-apoptotic settings, a yeast 2-hybrid (Y2H) screen was performed using the full-length protein as bait. The current report describes the analysis of a captured prey and putative novel caspase-2 interacting factor, the regulatory factor X-associated ankyrin-containing protein (RFXANK), previously associated with CIITA, the transactivator regulating cell-type specificity and inducibility of MHC class II gene expression. The interaction between caspase-2 and RFXANK was verified by co-immunoprecipitations using both exogenous and endogenous proteins, where the latter approach suggested that binding of the components occurs in the cytoplasm. Cellular co-localization was confirmed by transfection of fluorescently conjugated proteins. Enhanced caspase-2 processing in RFXANK-overexpressing HEK293T cells treated with chemotherapeutic agents further supported Y2H data. Yet, no distinct differences with respect to MHC class II expression were observed in plasma membranes of antigen-presenting cells derived from wild type and caspase-2(-/-) mice. In contrast, increased levels of the total MHC class II protein was evident in protein lysates from caspase-2 RNAi-silenced leukemia cell lines and B-cells isolated from gene-targeted mice. Together, these data identify a novel caspase-2-interacting factor, RFXANK, and indicate a potential non-apoptotic role for the enzyme in the control of MHC class II gene regulation.

The oxidative phosphorylation system contains four respiratory chain complexes that connect the transport of electrons to oxygen with the establishment of an electrochemical gradient over the inner membrane for ATP synthesis. Due to the dual genetic source of the respiratory chain subunits, its assembly requires a tight coordination between nuclear and mitochondrial gene expression machineries. In addition, dedicated assembly factors support the step-by-step addition of catalytic and accessory subunits as well as the acquisition of redox cofactors. Studies in yeast have revealed the basic principles underlying the assembly pathways. In this review, we summarize work on the biogenesis of the bc(1) complex or complex III, a central component of the mitochondrial energy conversion system.

The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system's components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.