Characterization and evolution of mito-nuclear interactions

Since the emergence of the first eukaryotic cell, two genomes have coexisted and coevolved within the same cellular environment, resulting in a complex network of interactions. The aim of my thesis is to investigate these interactions and their biological implications. RNA-RNA interactions play a key role in cellular homeostasis regulation. The Small Mitochondrial Highly Transcribed RNAs (smithRNAs), transcribed from the mitochondrial genome, target nuclear transcripts. However, their regulatory mechanisms are not fully understood. I focused on identifying proteins involved in the maturation and regulation of smithRNAs. To this end, I analyzed RNA immunoprecipitation (RIP) from various organisms and performed co-immunoprecipitation experiments between the identified smithRNAs in R. philippinarum and protein lysates. In the second part of my project, I examined protein-protein interactions between mitochondrial and nuclear OXPHOS subunits. Twelve subunits are encoded by the mitochondrial genome, while approximately 70 are encoded by the nuclear genome. I studied two mito-nuclear discordances in deep lineages, where mitochondrial markers support one phylogenetic hypothesis, but phylogenomic analyses reject it. I analyzed the phylogenetic signal of nuclear OXPHOS genes. In both Bivalvia and Squamata, the close interaction between OXPHOS subunits caused nuclear OXPHOS genes to support the biased mitochondrial topology. The tight interactions between the nuclear and mitochondrial genomes impact many biological processes. By co-opting nuclear proteins, the mitochondrial genome has evolved an internal RNAi pathway, possibly linked to sex determination in R. philippinarum. In snakes, adaptive selection on OXPHOS genes is likely linked to their extreme radiation. Over the course of my three-year project, I explored these interactions, highlighting their importance in key evolutionary processes.