title: Genome-scale modeling of the protein secretory machinery in yeast.
abstract: The protein secretory machinery in Eukarya is involved in post-translational modification (PTMs) and sorting of the secretory and many transmembrane proteins. While the secretory machinery has been well-studied using classic reductionist approaches, a holistic view of its complex nature is lacking. Here, we present the first genome-scale model for the yeast secretory machinery which captures the knowledge generated through more than 50 years of research. The model is based on the concept of a Protein Specific Information Matrix (PSIM: characterized by seven PTMs features). An algorithm was developed which mimics secretory machinery and assigns each secretory protein to a particular secretory class that determines the set of PTMs and transport steps specific to each protein. Protein abundances were integrated with the model in order to gain system level estimation of the metabolic demands associated with the processing of each specific protein as well as a quantitative estimation of the activity of each component of the secretory machinery.
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Amir
authors.initials: A
authors.lastname: Feizi
authors.forename: Tobias
authors.initials: T
authors.lastname: Österlund
authors.forename: Dina
authors.initials: D
authors.lastname: Petranovic
authors.forename: Sergio
authors.initials: S
authors.lastname: Bordel
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D003198:Computer Simulation; D004734:Energy Metabolism; D063990:Gene Ontology; D016681:Genome, Fungal / Q000235:genetics*; D006801:Humans; D060847:Metabolic Engineering; D008954:Models, Biological; D021381:Protein Transport; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins