Genome-Scale Modeling of the Protein Secretory Machinery in Yeast
Journal article, 2013

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.

Author

Amir Feizi

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Tobias Österlund

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Dina Petranovic Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Sergio Velasco

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Jens B Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

PLoS ONE

1932-6203 (ISSN)

Vol. 8 5 e63284

Industrial Systems Biology of Yeast and A. oryzae (INSYSBIO)

European Commission (FP7), 2010-01-01 -- 2014-12-31.

Infrastructure

C3SE (Chalmers Centre for Computational Science and Engineering)

Subject Categories

Microbiology

Areas of Advance

Life Science Engineering (2010-2018)

DOI

10.1371/journal.pone.0063284

More information

Created

10/7/2017