Evolution of Ras-like GTPase signaling pathways

Abstract

Signalling pathways are networks of interacting proteins that measure and integrate internal and external stimuli and regulate critical cellular processes accordingly. In these pathways intricate feedback loops are often observed and as a result signalling pathways are very complex. Pathways did not appear in its entirety in a single moment in evolution but became increasingly more complex by subsequent addition and removal of components and interactions. By studying the evolution of the individual components of the pathway and their interactions we are able to derive the evolution of the pathway. In this thesis we describe bioinformatic and phylogenetic approaches to study the evolution of interaction networks and the complex Ras signalling pathways. Ras signalling pathways are very complex and are often implicated in cancer as they regulate critical cellular processes such as cell devision, cell differentation and cell death. Understanding the evolution of interaction networks is a crucial for the elucidation of pathway evolution by comparative genomics. We find that the majority of protein-protein interactions in human are not shared with yeast (68%) due to the absence of one or both interactors in yeast. Of the remaining conserved protein pairs that are conserved in yeast about 90% also interact. Therefore we conclude that the evolutionary dynamics of protein complexes are not the result of network rewiring, but due to genomic acquisition or loss of genes coding for subunits. We subsequently studied the evolution of the central components of the Ras-like signalling pathways. The RasGEF, RapGAP and RasGAP protein families are the major regulators of Ras-like GTPases and we find that their evolution is highly intertwined with the Ras-like GTPases themselves. The RasGEFs and GAPs are ancient and originate from before the last common ancestor of eukaryotes. We find evidence that Ras signallingg in animals and fungi differentiated by differential sampling of ancestral RasGEFs and GAPs. The evolution of the RasGEFs and GAPs allow us to reconstruct the evolution of the Ras-like GTPases to before the last common ancestor of eukaryotes. Also we show that specific subtypes of Ras-like GTPases are regulated differently (positively or negatively) based on the expansion of regulatory gene families. We reconstructed the evolution of the TOR signallingg pathway that contains the Rheb GTPase, and show that many components are ancient and highly conserved. New components have been added in animal evolution to allow for new signalling inputs, such as insulin signalling. Duplicationss of AGC kinases early in eukaryotic evolution have greatly increased the complexity of the TOR pathway. Our results demonstrate how a vital signalling pathway can be both highly conserved and flexible in eukaryotes. The results in this thesis not only provides new insights into how the pathway came to be, but also provides a framework onto which experimental data between model organisms can be compared and assessed