Shridhar, S.; Kumari, K.; Thattai, M.

Eukaryotic cells are defined by their endomembranes: compartments such as the endoplasmic reticulum (ER), Golgi and endosomes, exchanging cargo via vesicles. The evolutionary origins of endomembrane compartments remain unclear. Here we construct molecular-evolutionary trajectories for the stepwise addition of compartments after the emergence of the proto-ER in an ancestral eukaryote. We represent compartments and vesicles as nodes and edges of a directed graph. Vesicle budding and fusion regulators such as coats and SNAREs control cargo flows and determine compartment compositions. We computationally sample billions of possible graphs, and enumerate how duplication, deletion and mutation of regulators drive graph transitions. We find that evolutionary trajectories display punctuated shifts in compartment composition and number, interspersed with millions of neutral mutations. The first added compartment inherits functions from the proto-ER or plasma membrane, or gains novel functions. Our results show how, given sufficient time, simple molecular steps can generate complex endomembrane systems.