The vesicle traffic system, a hallmark of eukaryotic cellular complexity, is central to cellular organization and has driven the diversification of eukaryotes. The evolutionary leap from early prokaryotes to eukaryotes introduced sophisticated organelles and advanced cellular functions; however, the absence of evolutionary intermediates between the two leaves unanswered questions about the origins of these complex cellular features and the evolutionary framework underlying vesicle traffic networks. In this work, we model the vesicle traffic system as a graph-based framework that captures the regulatory landscape defined by molecular rules governing vesicle trafficking to identify biologically relevant graph structure. We further extend this framework to explore an evolutionary landscape, mapping potential trajectories from early to complex proto-eukaryotic trafficking systems. This framework provides insights into the molecular principles and topological constraints that shape vesicle traffic networks and traces the emergence of functional features and the first intracellular compartment in the proto-eukaryotic cell, proposing evolutionary paths that lead to increasing cellular complexity.

Distinct amino acids function as private resources or exchanged public goods

Abstract

Cells experience fluctuations in nutrients due to changing environmental conditions. However, the dynamics and nature of amino acids formation, secretion, and consumption in various phases of growth remains unknown. Using Saccharomyces cerevisiae growing in minimal medium, we studied the quantitative changes of intracellular and extracellular amino acids over time. We find that intracellular as well as extracellular abundance of distinct amino acids vary by several orders of magnitude, and that intracellular and extracellular amino acid pools are distinct in composition as well as quantity. Further, we identify hierarchies of amino acid accumulation and utilization. Only some amino acids are secreted, and the extent of their secretion changes at different growth stages. A subset of amino acids are exclusively intracellular, and function as private goods. These are not secreted into the extracellular environment. Using quantitative uptake and flux measurements, we demonstrate the utilization of select amino acids as either public or private goods in relation to specific metabolic outputs. Further, we find that auxotrophic strains of public good amino acids are effectively able to grow in spent media of wild-type cells. This finding provides clear evidence that public goods are secreted and shared, and can sustain auxotrophic growth. Finally, we established effective synthetic cell communities, by pairing auxotrophs of public good amino acids, that can grow together very effectively through resource exchange.

Collectively, we find that in growing cells, distinct amino acids act as private or public good resources, with these roles being critical for unique metabolic functions. Here, we discovered pools of amino acids function as a public and private goods using S. cerevisiae model system.