A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.

Ulrike Münzner, Edda Klipp, Marcus Krantz

Nature communications 2019 Mar 21

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Understanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with coverage and precision of formulation. Genome-scale models revolutionised the metabolic field and made the first whole-cell model possible. However, the lack of genome-scale models of signalling networks blocks the development of eukaryotic whole-cell models. Here, we present a comprehensive mechanistic model of the molecular network that controls the cell division cycle in Saccharomyces cerevisiae. We use rxncon, the reaction-contingency language, to neutralise the scalability issues preventing formulation, visualisation and simulation of signalling networks at the genome-scale. We use parameter-free modelling to validate the network and to predict genotype-to-phenotype relationships down to residue resolution. This mechanistic genome-scale model offers a new perspective on eukaryotic cell cycle control, and opens up for similar models-and eventually whole-cell models-of human cells.

Citation

Ulrike Münzner, Edda Klipp, Marcus Krantz. A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. Nature communications. 2019 Mar 21;10(1):1308