Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism

Abstract

Genome-scale metabolic models are built using information from an organism's annotated genome and, correspondingly, information on reactions catalyzed by the set of metabolic enzymes encoded by the genome. These models have been successfully applied to guide metabolic engineering to increase production of metabolites of industrial interest. Congruity between simulated and experimental metabolic behavior is influenced by the accuracy of the representation of the metabolic network in the model. In the interest of applying the consensus model of Saccharomyces cerevisiae metabolism for increased productivity of triglycerides, we manually evaluated the representation of fatty acid, glycerophospholipid, and glycerolipid metabolism in the consensus model (Yeast v6.0). These areas of metabolism were chosen due to their tightly interconnected nature to triglyceride synthesis. Manual curation was facilitated by custom MATLAB functions that return information contained in the model for reactions associated with genes and metabolites within the stated areas of metabolism. Through manual curation, we have identified inconsistencies between information contained in the model and literature knowledge. These inconsistencies include incorrect gene-reaction associations, improper definition of substrates/products in reactions, inappropriate assignments of reaction directionality, nonfunctional β-oxidation pathways, and missing reactions relevant to the synthesis and degradation of triglycerides. Suggestions to amend these inconsistencies in the Yeast v6.0 model can be implemented through a MATLAB script provided in theSupplementary Materials, Supplementary Data S1(Supplementary Data are available online at www.liebertpub.com/ind).

Fig. 1.

Curation of cytoplasmic and mitochondrial fatty acid synthesis (FAS) in the Yeast v6.0 model. (a) Reactions in the Yeast v6.0 model relevant to cytoplasmic and mitochondrial FAS. Dashed arrows indicate the net outcome of two reactions (ie, transport and hydrolysis). Mitochondrial FAS reactions leading to production of myristoleate, palmitoleate, and linoleic acid are blocked reactions, as indicated by X's in the figure. (b) Proposed representation of cytoplasmic and mitochondrial FAS. For the sake of space, the repeated reaction sequence of CEM1, OAR1, HTD2, and ETR1 for butanoyl-ACP (C4:0) to octanoyl-ACP is omitted, as indicated by the dashed arrow. The reactions for mitochondrial FAS are blocked reactions, as indicated by X's.

Fig. 2.

Curation of fatty acid elongation in the Yeast v6.0 model. (a) Reactions in the Yeast v6.0 model relevant to fatty acid elongation. As indicated by X's, all of the reactions associated with PHS1 or IFA38 are blocked, as are two of the three reactions associated with ELO1. (b) Proposed representation of fatty acid elongation. For the sake of space, the repeated reaction sequence of (ELO1, FEN1, or SUR4), IFA38, PHS1, and TSC13 for myristoyl-CoA (C14:0) to hexacosanoyl-CoA (C26:0) is omitted, as indicated by the dashed arrow. For this omission, the embedded intermediates of palmitoyl-CoA (C16:0) and stearoyl-CoA (C18:0) are assumed to be also derived from activation of fatty acid originating from the extracellular compartment or from cytoplasmic fatty acid synthesis.

Fig. 3.

Curation of β-oxidation in the Yeast v6.0 model. (a) Reactions in the Yeast v6.0 model relevant to β-oxidation of saturated and unsaturated fatty acids. All of the reactions shown are blocked, as indicated by X's. For the sake of space, the repeated reaction sequence of POX1, FOX2, and POT1 for stearoyl-CoA (C18:0) to octanoyl-CoA (C8:0) is omitted, as indicated by the dashed arrow. (b) Proposed representation of β-oxidation of saturated and unsaturated fatty acids. The metabolites relevant to β-oxidation of oleoyl-CoA are shown in parentheses and are written below the metabolites relevant to β-oxidation of palmitoleoyl-CoA. For the sake of space, dashed arrows are used to condense the combined action of the enzymes of classical β-oxidation (ie, Pox1p, Fox2p, and Pot1p) into a singular illustrated reaction.

Fig. 4.

Curation of glycerolipid metabolism in the Yeast v6.0 model. (a) Reactions in the Yeast v6.0 model relevant to glycerolipid metabolism. Blocked reactions are indicated by X's. (b) Proposed representation of glycerolipid metabolism. The proposed modification expands each of the classes shown in this figure into its constituent species (not shown). For instance, the term phosphatidate in the figure refers to a collection of individual species [eg, phosphatidate (1–16:0, 2–16:1), phosphatidate (1–16:1, 2–16:1), etc].