Berzins2022 - Crypthecodinium cohnii: ethanol uptake for production of DHA precursor acetyl-CoA

This model is a supplementary material of publication
“Kinetic and stoichiometric modeling-based analysis of do-cosahexaenoic acid (DHA) production potential by C.cohnii from glycerol, glucose and ethanol”
by Kristaps Berzins, Reinis Muiznieks, Matiss R. Baumanis, Inese Strazdina, Karlis Shvirksts, Santa Prikule, Vytautas Galvanauskas, Daniel Pleissner, Agris Pentjuss, Mara Grube, Uldis Kalnenieks and Egils Stalidzans

This is a kinetic model of Crypthecodinium cohnii central carbon metabolism during fatty acid synthesis. The model is aimed at cytosolic acetyl coenzyme-A production, which is the precursor of fatty acids.

The model contains 35 reactions and 36 species split into three compartments – extracellular, cytosol and mitochondria. It was assumed that dry weight accounts for 33% of wet weight and that 1ml = 1g. The mitochondria volume is 1% of cytosol volume. The model was designed for ethanol as a single substrate. For use of glucose and glycerol as substrates, see MODEL2112280001.

The model is preset for steady state calculation using ethanol.

The model contains 31 global quantities which were used to optimize the model during parameter estimation. These global quantities include amino acid concentrations for each enzyme, the total amino acid concentration used in enzymes, the sum transport reaction variable parameters and the total concentration of species.

All enzymatic reactions contain a parameter k, which can be used for change of enzyme expression levels in case of optimization of product flux or yield. Currently all the parameters k are set for 1, which corresponds to wild-type.

The model was made for steady-state. For ethanol as a substrate a steady-state resolution of 0.1 can be used.