All Roads Lead to the Non-Coding RNome : Evolution of Multicellularity and Host Response to Bacterial Infection

Abstract: The ability to control gene expression is fundamental for all living organisms. Therefore, a large variety of regulatory mechanisms exist in each cell which are essential for e.g. developmental processes and to quickly adapt to different cellular stresses such as infection. Today we know that much of this regulation depends on non-coding (nc)RNAs. However, the function and evolutionary origin of many ncRNAs remains to be understood.The work presented in this thesis revolves around the evolutionary group of Dictyostelia. These social amoebae grow as single cells but initiate a multicellular development program when food runs low. The evolutionary position of Dictyostelia within Amoebozoa together with their multicellular development make these organisms relevant for investigating the evolution of ncRNAs and their association with multicellularity. Furthermore, the dictyostelid Dictyostelium discoideum is one of few organisms besides plants and animals were miRNAs have been identified. It is also an established model organism, well-adapted for laboratory growth and detailed molecular work.In this thesis, we investigate the biogenesis of miRNAs in D. discoideum and show that the Dicer-like protein DrnB is essential for global miRNA maturation. Next, we study the evolution of another ncRNA, Class I RNAs, and show that these are conserved in all dictyostelids and likely emerged in their last common ancestor. Lastly, we utilize the D. discoideum infection model to study the regulation of messenger RNAs and ncRNAs upon infection by Mycobacterium marinum and Legionella pneumophila to improve our understanding of the complex interactions between host and pathogen. We show that the two bacteria induce distinct mRNA regulation in D. discoideum. In addition, we detected high levels of specific tRNA halves generated in the host in response to M. marinum but not L. pneumophila or bacteria utilized as food. Despite the large evolutionary distances, the regulation of both mRNAs and ncRNAs in D. discoideum was, in many aspects, representative for the regulation in macrophages after infection.In conclusion, by using a seemingly simple group of organisms, social amoebae, this thesis work addresses major questions such as the role of ncRNA in multicellular evolution and the intricate host-pathogen interplay during bacterial infection.