Systems biology of protein synthesis and secretion in yeast

Abstract: Protein synthesis and secretion is a vital process to maintain cell function. As it demands numerous building blocks, cofactors and chaperones generated from metabolism and translation, the process is intertwined with metabolic and regulatory networks. To obtain an overall understanding of the protein synthesis and secretory system, multi-omics data are coupled with mathematical modeling to systematically quantify cellular resource reallocation in response to recombinant protein production and/or nutrient starvation. In this thesis, we mainly use two recombinant proteins, α-amylase and insulin precursor, as model proteins to study the protein synthesis and secretion process in a model organism Saccharomyces cerevisiae. We find that the central metabolism is reprogrammed at a large scale to relieve the oxidative stress caused by recombinant protein production, and the activation of Gcn2p-mediated signaling pathway plays a crucial role in reshaping metabolism. As protein folding is often considered the flux controlling step in protein synthesis and secretion, we further identify two routes of the protein folding pathway to improve protein production, namely through improved folding capacity and increased folding precision, respectively. Additionally, protein translation is the initial step of protein synthesis. We find that cells maintain large and unequally distributed reserves in translational capacity by stepwise reducing nitrogen availability. Moreover, we also construct a proteome-constrained genome-scale protein secretory model for S. cerevisiae (pcSecYeast) to perform secretory simulations and provide genomic targets for cell engineering. Our findings elucidate the global responses to various perturbations on protein synthesis and secretion and provide valuable novel insights that can be leveraged for improving recombinant protein production.