UniKin1 A Universal, Non Species Specific Whole Cell Kinetic Model.

Citation: Murthy, MV, Balan, D, Kamarudin, NJ, Wang, VCC, Tan, XT, Ramesh, A, Chew, SSM, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. UniKin1: A Universal, Non-Species-Specific Whole Cell Kinetic Model. Acta Scientific Microbiology 3(10): 04-08.

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Mathematical models of metabolism can be a useful tool for metabolic engineering. Genome-scale models (GSMs) and kinetic models (KMs) are the two main types of models. GSMs provide steady-state fluxes while KMs provide time-course profile of metabolites, which has more advantage in identifying metabolic bottlenecks. However, KMs require greater degree of accuracy for parameters than GSMs resulting in fewer large-scale KMs than GSMs. Recently, large-scale KMs have been developed but are not based on standard enzymatic rate equations resulting in difficulty in interpreting results in terms of enzyme kinetics. Here, we construct a universal, non-species-specific KM of core metabolism, based on Michaelis-Menten Equation, from glucose to the 20 amino acids and 5 nucleotides based on reactions listed in Kyoto Encyclopaedia of Genes and Genomes (KEGG). Non-species specificity is achieved by using the same Michaelis-Menten constant (Km), turnover number (Vmax), and concentration for each metabolite and enzyme for each equation. This forms a base model for developing species-specific whole cell KMs. The resulting model consists of 566 reactions, 306 metabolites, and 310 enzymes, involving in 1284 metabolite productions, and 1249 metabolite usages. Sensitivity analysis shows that 85% of the metabolite concentration changes with the change of one enzyme kinetic parameter. This forms a base model for developing species-specific whole cell KMs.