Formal Representation of the High Osmolarity Glycerol Pathway in Yeast

Clemens Kühn [1](
K. V. S. Prasad [2](
Edda Klipp [1](
Peter Gennemark [3][4](

[1] Humboldt University, DE-10115 Berlin, Germany
[2] Chalmers University of Technology, SE-412 96 G\"{o}teborg, Sweden
[3] University of G\"{o}teborg, SE-412 96 G\"{o}teborg, Sweden
[4] Uppsala University, SE-751 06 Uppsala, Sweden


The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system.
This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system. In the commonly used Systems Biology Markup Language (SBML), such a model would need to explicitly enumerate all state variables. The \emph{Kappa} modelling language which we use supports representation of complexes without such enumeration.
To conclude, we compare \emph{Kappa} with a few other modelling languages and software tools that could also be used to represent and model the HOG system.

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Japanese Society for Bioinformatics