130 Chapter 5 ABSTRACT Peroxisomes play a key role in fatty acid metabolism and are crucial for oxidation of very-long-chain fatty acids, branched-chain fatty acids and bileacid intermediates. The importance of peroxisomes is highlighted by the number of diseases caused by disruptions of peroxisomal biogenesis and metabolism. Computational models of metabolism are used to simulate metabolite concentrations and fluxes in response to e.g. pathogenic mutations, gene-expression regulation or nutritional or pharmacological interventions. No computational kinetic model has yet been described for the peroxisomal β-oxidation. Here, we first reviewed the kinetic properties of the enzymes involved in the peroxisomal β-oxidation of straight-chain fatty acids. To acquire a deeper understanding of the pathway, we developed a detailed kinetic computation model. The model is composed of reversible kinetic equations and kinetic parameters, obtained from the literature, that describe the behavior of the enzymes. To obtain a full kinetic dataset, it was necessary to combine data from mouse, rat and human enzymes. The model predicts the concentrations of the different metabolites and the fluxes through the enzymes at steady state. Metabolic control analysis revealed acyl-CoA oxidase 1 (ACOX1) to be the enzyme with the highest flux control coefficient of the pathway (0.58). This partially supports the prevailing hypothesis that ACOX1 is a rate-limiting enzyme of the pathway, although we show that it is not the only one. 3-Ketoacyl-CoA thiolase 1 (ACAA1) was found to be the second enzyme with control in the pathway, with a flux control coefficient of 0.42. The rest of enzymes did not exert any control. Integration of proteomics data from hepatic organoids allowed to build context-specific models. Simulations of these models predicted that amino-acid restriction led to a reduction in the metabolic flux of the pathway, which could be rescued by supplementation of docosahexaenoic acid (DHA). Interestingly, differential regulation was observed between the different intermediate metabolites of the pathway in response to amino-acid restriction and rescue by DHA. This study describes -to the best of our knowledge- the first detailed kinetic model of the peroxisomal β-oxidation of straight-chain fatty acids. It can be a powerful tool to investigate different metabolic diseases in which the enzymes in the pathway are implicated, as well as therapeutic approaches or nutritional interventions.
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