Exploring the Emergence of Complexity in Vesicle Traffic Networks through Molecular and Topological Constraints

Abstract

The Endomembrane Trafficking machinery is a defining complex feature of Eukaryotes. This Intracellular Trafficking is regulated by Specificity Modules that are the budding and Fusion Machinery. Along the path of Eukarya evolution, various questions have been raised regarding the emergence of complexity, creation of new organelles, and retargeting of vesicle pathways in eukaryotes. While these complex features have been ascribed to Eukaryotic success in the Phanerozoic era and have been studied with various approaches, this thesis is an attempt at using the simple yet mathematically rich framework of Graph theoretic Boolean Modelling of the vesicle trafficking. Using Boolean modeling of cargo flows we can get to a molecular representation of the network and its specificity modules. The creation of the molecular regulatory landscape of graphs has allowed us to study how topological changes in vesicle pathways are constrained at the molecular level and functionally. We discover how the emergence of molecular properties takes place across various kinds of cells from the underlying constraints of Biophysical properties upon which a Graph is considered a valid cell. We also try resurrecting intermediates in the path of emergence of topological properties starting from the basic biochemical interactions in a genome, and how it implicates the creation of a non-endosymbiotic compartment or pathways to an engulfed compartment through the raw material of existing molecular machinery following specific genetic events.