Signaling and Trafficking in Choanoflagellates and Humans: A Study of Conserved Peptide-Binding Domains

Many crucial cellular processes are regulated by signaling and trafficking pathways, which are largely dependent on protein interactions in the cell. These networks are thought to play a crucial role in the evolution of multicellular organisms from their unicellular ancestors. Choanoflagellates are unicellular organisms that can adopt a multicellular state, called a rosette. Though they evolved independently from and prior to the diversification of metazoans, they are the closest extant nonmetazoan ancestor to animals, making them a compelling model for the study of early multicellularity. Here, we look at two structurally conserved peptide-binding domains that both play important roles in cellular signaling and trafficking. PDZ and SH2 domains are peptide-binding domains that have highly conserved structures and are found in humans and choanoflagellates. We analyzed the binding cleft of a non-homologous PDZ domain and compared the binding affinities of that PDZ domain to two human PDZ domains. We also developed a program that looks specifically at the PDZ binding cleft and finds the most similar human PDZ domain to an uncharacterized choanoflagellate PDZ domain, then finds potential endogenous target sequences of the uncharacterized PDZ domain. To assess conservation of PDZ domain structure we solved high-resolution crystal structures of a representative M. brevicollis PDZ domain that is homologous to human Dlg1 PDZ2. We also studied the binding cleft of a conserved SH2 domain from the TEC family of kinases. Overall, we find that interactions between the domain and non-motif residues dramatically influence peptide binding and, using our program, we can begin to predict successful interactions. The evolutionary conservation of PDZ and SH2 domain makes them ideal candidates to study to better understand how the evolution of signaling and trafficking domains and pathways coincided with the emergence of multicellularity.