Abstract
In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster ovary cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
Highlights
In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway
This pathway is important in biotechnology and the biopharmaceutical industry, since most therapeutic proteins are produced in mammalian cell lines such as HEK-293, PerC6, NS0, and Chinese hamster ovary (CHO) cells, which are capable of folding and adding the necessary post-translational modifications (PTMs) to the target product[2]
We estimated the energetic cost of synthesizing and/or secreting 5641 and 3538 endogenous proteins in the CHO and human secretome and membrane proteome in terms of total number of ATP equivalent molecules consumed. These protein costs were compared to the cost of five recombinant proteins commonly produced in CHO cells (Fig. 1a)
Summary
In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology To interact with their environment, cells produce numerous signaling proteins, hormones, receptors, and structural proteins. The secretory pathway consists of a complex series of processes that predominantly take place in the endoplasmic reticulum (ER), Golgi apparatus, and the endomembrane system This pathway is important in biotechnology and the biopharmaceutical industry, since most therapeutic proteins are produced in mammalian cell lines such as HEK-293, PerC6, NS0, and Chinese hamster ovary (CHO) cells, which are capable of folding and adding the necessary post-translational modifications (PTMs) to the target product[2]. We present the first genome-scale stoichiometric reconstructions and computational models of mammalian metabolism coupled to protein secretion We constructed these for human, mouse, and CHO cells, called RECON2.2s, iMM1685s, and iCHO2048s, respectively. All models and data used in this study are freely available at https://github.com/LewisLabUCSD/ MammalianSecretoryRecon
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