The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
© Nookaew et al; licensee BioMed Central Ltd. 2008
Received: 14 March 2008
Accepted: 07 August 2008
Published: 07 August 2008
Up to now, there have been three published versions of a yeast genome-scale metabolic model: iFF708, iND750 and iLL672. All three models, however, lack a detailed description of lipid metabolism and thus are unable to be used as integrated scaffolds for gaining insights into lipid metabolism from multilevel omic measurement technologies (e.g. genome-wide mRNA levels). To overcome this limitation, we reconstructed a new version of the Saccharomyces cerevisiae genome-scale model, iIN800 that includes a more rigorous and detailed description of lipid metabolism.
The reconstructed metabolic model comprises 1446 reactions and 1013 metabolites. Beyond incorporating new reactions involved in lipid metabolism, we also present new biomass equations that improve the predictive power of flux balance analysis simulations. Predictions of both growth capability and large scale in silico single gene deletions by iIN800 were consistent with experimental data. In addition, 13C-labeling experiments validated the new biomass equations and calculated intracellular fluxes. To demonstrate the applicability of iIN800, we show that the model can be used as a scaffold to reveal the regulatory importance of lipid metabolism precursors and intermediates that would have been missed in previous models from transcriptome datasets.
Performing integrated analyses using iIN800 as a network scaffold is shown to be a valuable tool for elucidating the behavior of complex metabolic networks, particularly for identifying regulatory targets in lipid metabolism that can be used for industrial applications or for understanding lipid disease states.
The yeast Saccharomyces cerevisiae is widely used for production of many different commercial compounds such as food, feed, beverages and pharmaceuticals . It also serves as a model eukaryotic organism and has been the subject of more than 40,000 research publications [2, 3]. After the complete genome sequence for yeast was released in 1996 , about 4,600 ORFs were characterized  and yeast contains many genes with human homologs . This has allowed for comparative functional genomics and comparative systems biology between yeast and human. Yeast, for example, has been used to understand the function of complex metabolic pathways that are related to the development of human diseases [5–7].
Several human diseases (e.g. cancer, atherosclerosis, Alzheimer's disease, and Parkinson's disease) are associated with disorders in lipid metabolism [8–10]. The emergence of lipidomics has allowed analysis of lipid metabolism at the systems level [8, 11]. Lipidomics promises to make a significant impact in our understanding of lipid related disease development . As with other high-throughput techniques, however, we hypothesize that one of the main challenges for utilization of lipidome data will be our ability to develop appropriate frameworks to integrate and map data for studying relations between lipid metabolism and other cellular networks.
Previous work has shown that genome-scale metabolic models provide an excellent scaffold for integrating data into single, coherent models . The calculation of Reporter Metabolites using genome-scale metabolic models is an example of how metabolic models can be used to upgrade the information content of omics data . This approach allows mapping of key metabolites and reactions in large metabolic networks when combined with transcriptome  or metabolome data . However, pathways, reactions, and genes that are not included in the metabolic network cannot be queried. Therefore, the Reporter Metabolite algorithm requires a reliable and global genome scale-model to achieve precise and accurate data interpretation.
So far, three yeast genome-scale metabolic models, iFF708, iND750 and iLL672, have been published. All three models, however, lack a detailed description of the lipid metabolism. The first model, iFF708 , consists of 1175 reactions linked to 708 ORFs. iFF708 shows good predictions of many different cellular functions  and gene essentiality predictions . However, almost all intermediate reactions in lipid metabolism were either lumped or neglected. The second model published was iND750 . iND750 is fully compartmentalized, consisting of 1498 reactions linked to 750 ORFs. The model was validated by a large-scale gene deletion study and metabolic phenotypes  and was expanded to include regulation for predicting gene expression and phenotypes of different transcription factor mutants . iND750 contains more reactions and metabolites in lipid metabolism than iFF708, but still lacks a comprehensive description of lipid metabolism. The third published model is iLL672, which is derived from iFF708 and comprises 1038 reactions. Several dead-end reactions of iFF708 were eliminated leading to an improved accuracy of the single gene deletion prediction . However, only minor improvements were made to reactions involved in lipid metabolism. The model was validated using 13C-labeling experiments to study the robustness of different yeast mutants .
Here our objective was to expand the genome-scale metabolic model of yeast to include a detailed description of lipid metabolism for use as a scaffold to integrate omics data. We used iFF708 as a template for building a model based on recent literature that contains new reactions in lipid metabolism and transport relative to all previous models. The new model named iIN800 includes 92 additional ORFs and provides a more detailed structure of lipid metabolism, tRNA synthesis and transport processes than previous models. The biomass composition, which is very important for flux balance analysis and predicting lethality, was also recalculated and improved. iIN800 was validated with large-scale gene deletion data and growth simulation predictions. Simulated intracellular fluxes were also supported by 13C-labeling flux experimental data. Finally, we show that the transcriptome data of yeast cultivated under various growth conditions can be integrated with iIN800 to identify lipid related Reporter Metabolites. We anticipate that iIN800 will be useful as a scaffold for integrating multilevel omic data and that this new model will have a significant impact in the emerging field of lipidomics.
Results and discussion
Model reconstruction and characteristics of iIN800
Comparison of the number of lipid metabolism reactions among yeast genome-scale metabolic models
Mitochondrial fatty acid synthesis
Cytosolic fatty acid synthesis
Fatty acid elongation
Fatty acid activation and beta-oxidation
Phospholipid and TAG synthesis
To compare metabolic characteristics of the different in silico models, lipid metabolism was classified into unique sub-categories (e.g. mitochondrial fatty acid synthesis, ergosterol biosynthesis) (Table 1). Fatty acid synthesis and elongation accounted for three of these sub-categories. In contrast to previous models, iIN800 incorporates fatty acid biosynthesis in both mitochondria and the cytosol. Fatty acid synthesis, which involves iterative malonyl-CoA condensations that result in a growing chain of fatty acids, is catalyzed by four major enzymes: β-ketoacyl-ACP synthase (a condensing enzyme), β-ketoacyl-ACP reductase, β-dehydroxyacyl-ACP dehydratase and enoyl-ACP reductase. In the cytosol, these enzymes are encoded by the multifunctional FAS1 and FAS2. In the mitochondria, however, fatty acid synthesis is carried out by the products encoded by CEM1, OAR1, HTD2 and ETR1. These ORFs were missing from previous models, which prevented simulation of mitochondrial fatty acid synthesis. Fatty acid elongation, which leads to the production of long-chain fatty acids, was not included in iFF708, but was also updated in iIN800. Including fatty acid elongation resulted in the addition of four major biochemical reaction steps: condensing enzyme, 3-ketoacyl-CoA reductase, enoyl-CoA dehydratase and enoyl-CoA reductase . These reactions are carried out by the enzymes encoded by ELO1, ELO2, ELO3, IFA38 and TSC13. While the gene encoding enoyl-CoA dehydratase has not been identified in S. cerevisiae, the reaction was inferred due to the identification of long chain fatty acids in yeast.
β-oxidation is the process where fatty acids, after becoming activated in the form of acyl-CoAs, are broken down to make acetyl-CoA, and ultimately energy. FAT1, encoding an enzyme for long-chain fatty acid activation was missing in iFF708 and iLL672. The genes SPS19, ECI1 and DCI1 are also now included in iIN800. As a result, iIN800 can simulate the oxidation of unsaturated fatty acids.
Sphingolipid synthesis reactions were added to iIN800 according to a recently reported model , resulting in more sphingolipid reactions than the template iFF708. Sphingolipid synthesis is the only sub-category in iIN800 with a significantly lower reaction tally than iND750. This is because iND750 incorporated both C24:0 and C26:0 as very long-chain fatty acids (the back bone of sphingolipids) to produce ceramides. Because the amount of very long chain fatty acids in S. cerevisiae is so low relative to other fatty acid species (<2% of total fatty acid pool) [24, 26], iIN800 treats very long chain fatty acids as a single metabolite. As a result, fewer reactions are present in sphingolipid synthesis.
Relative to other models, only minor changes in the biosynthesis of phospholipids and triacylglycerides as well as ergosterol were introduced in iIN800. However, esterification of sterols and degradation of lipids, which were not included in all other previous models, are present in iIN800 (Table 1). Finally, 26 ORFs encoding for tRNA synthesis and one related enzyme, lipoamide dehydrogenase as well as 14 ORFs encoding transporters were also included in iIN800. The additionally included ORFs and their related references as well as detailed comparisons of reactions in lipid metabolism of all reported models are given in Additional files 1 and 2, respectively.
Structure comparison of S. cerevisiae genome-scale metabolic models
Network characteristics of the reconstructed metabolic network of S. cerevisiae strain iFF708 and iIN800
Cytosolic exchange fluxes
Mitochondrial exchange fluxes
Reactions with ORF assignments
Biochemical and Physical consideration
Improved biomass equation
The biomass equation is crucial for using genome-scale models to simulate growth using flux balance analysis (FBA). Therefore, an important consideration in the development of iIN800 was to address the concern that the biomass composition of S. cerevisiae changes under different growth conditions. For example, during growth on excess glucose the carbohydrate content increases and during growth on excess ammonium the protein content increases.
Growth simulation capability
In silico genome-scale models are most generally used to predict various phenotypes. These include growth rates and extracellular secretion rates of metabolite products, as well as uptake rates of nutrients. In addition, models can be employed to explore active route(s) in metabolic pathways under certain growth conditions as illustrated for a genome-scale metabolic model of E. coli [30–32] as well as for one of the S. cerevisiae genome-scale metabolic models .
Evaluation of large-scale gene deletion
Summary of large-scale single gene deletion evaluation of S. cerevisiae iIN800.
Minimal media on
Number of deletions
Positive prediction rate
Negative prediction rate
Integration of transcriptome data with genome-scale metabolic models
Top thirty Reporter Metabolites calculated from various perturbations. The Reporter Metabolite algorithm was performed with iIN800 and iFF708.
Reductive building phase1
Reductive charging Phase1
a Long-chain carboxylic acid
* Metabolite is contained in iIN800 only
1 = data from Tu, B. P., A. Kudlicki, et al. (2005)
Carbon- and Nitrogen-limited 2
Aerobic and Anaerobic 2
Temperature(30°C and 15°C) 3
First, transcriptome data from the yeast metabolic cycle  were analyzed. Notably, the reporter algorithm identified unique Reporter Metabolites with iIN800 that would have been missed if iFF708 was used as the scaffold (Table 6). The most dramatic difference was observed for the reductive charging phase of the metabolic cell cycle. While both models revealed the importance of regulation controlling the cellular response at glycogen, trehalose, UDP-glucose, glucose-6-P and glucose nodes, only iIN800 was able to identify key intermediates in β-oxidation. For example, iIN800 identified trans-3-acyl-CoAs, trans-2-acyl-CoAs, 3-keto-acyl-CoAs and some fatty acids as Reporter Metabolites (Table 6). This result demonstrates the advantage of expanding the metabolic model to include a much more detailed description of lipid metabolism. Namely, we can now use the genome-scale metabolic model to identify the regulatory importance of lipid precursors and intermediates at different physiological conditions or at different phases of cellular growth. Searching for highly co-regulated subnetworks that implicate lipid genes is also now possible.
Further demonstrations of the applicability of iIN800 as a scaffold to integrate omic data were performed by analyzing transcriptome data derived from nutrient-limited , oxygen-limited  and temperature stress conditions  Previously, mRNA and protein levels of genes and enzymes in fatty acid catabolism have been shown to be significantly different between carbon-limited and nitrogen limited growth . When comparing these conditions, only iIN800 was able to identify fatty acids as Reporter Metabolites (Table 6). In anaerobic yeast cultivation, oleic acid has to be added to the medium because unsaturated fatty acids synthesis is not possible; therefore, the expression of genes in this pathway is induced by the function of the ORE element . Consistent with this observed cellular response, only iIN800, with identified Reporter Metabolites involved in β-oxidation (Table 6). Similarly, iIN800 was able to highlight the importance of unsaturated fatty acids when comparing high and low temperature cultivations (Table 6), which is known to be important for maintaining proper membrane structure and fluidity .
Genome-scale metabolic models have emerged as a valuable tool in the post-genomic era for illustrating whole-cell functions based on the complete network of biochemical reactions. An iterative reconstruction process is required to achieve a comprehensive S. cerevisiae genome-scale metabolic model. In this work, we focused on improving the formulation of lipid metabolism relative to previously published S. cerevisiae genome-scale metabolic models. Validating the model and new biomass equations, the constraint-based simulation of iIN800 showed accurate predictions of cellular growth and is also consistent with 13C-labeling experiments. Furthermore, in silico gene essentialness predictions were found to be in high agreement with in vivo results. Finally, we show that iIN800, being more complete, is a better network scaffold for integration of multilevel omics data.
In conclusion, by incorporating a more complete description of lipid metabolism, iIN800 is positioned to have a broader impact than previously described yeast models. Its capability of predictions were consistent with a number of experimental data both quantitatively (growth rate) and qualitatively (gene essentialness). Moreover, the new model is positioned to be used for studying the regulation and role of lipid metabolism during different growth conditions. With the high degree of homology in lipid metabolism between yeast and humans and emergence of lipidomics, this is expected to allow for new insights into the connection between lipid metabolism and overall cellular function for industrial and medical applications.
Model reconstruction and visualization
Reconstruction of the S. cerevisiae genome-scale metabolic model was done by expanding iFF708 . The additional ORFs included in the expansion procedure were involved in lipid metabolism, tRNA synthesis and lipoamide dehydrogenase. These ORFs were added based on publications listed in Additional file 1. Online resources related to S. cerevisiae, such as SGD , MIPS  and YPD , were also used to confirm the existence of the ORFs and their function. Pathway and reaction databases including KEGG , ExPASy , and Reactome , were used together with research papers to identify relevant information of the additional reactions and metabolites, e.g. stoichiometry and co-factor usage. The expanded iFF708, called iIN800, was visualized by Adobe Illustrator software (Adobe Systems), and then converted to EPS format (Adobe Systems) format which is downloadable as Additional file 6. In this visualization file, it is possible to overlay information about transcription, fluxes etc. A detailed list of metabolic reactions in iIN800 is provided as Additional file 7.
Metabolic modeling and simulations
The reaction set in iIN800 was used for construction of a stoichiometric matrix S(m × n). In the stoichiometric matrix, m = 1013, which is the number of metabolites, and n = 1446, which is the number of metabolic reactions. With an assumption of steady state for all metabolite pools, a linear equation constraining the fluxes in the metabolic network is obtained [30, 47]:
Here v is a vector that contains all the fluxes in the model. Equation 1) has a large number of degrees of freedom, i.e. it is an underdetermined problem, and linear programming was employed to solve the equation system by maximizing an objective function Z (equal to the growth rate), an approach generally referred to as flux balance analysis (FBA) [30, 47]. The problem formulation is described below.
α≤ v≤ β
where α and β are lower and upper bounds of fluxes respectively, ω is a weight vector indicating an amount of desired metabolites for biomass synthesis. For irreversible fluxes semi-positive infinite boundary was applied as 0≤ v≤ ∞, and fully infinite boundaries was applied as -∞ ≤ v≤ ∞ for reversible fluxes. The problem was solved by using the commercial linear programming software package LINDO (Lindo systems Inc., Chicago, IL, USA). The calculated intracellular fluxes were overlaid on the visualized genome-scale map as described previously by the ReMapper software (The software has been developed for visualization of multilevel omics data onto a metabolic map.).
Calculation of biomass composition and sensitivity analysis
The biomass composition was re-calculated in order to improve the prediction of the model during growth at different nutrition-limitations, i.e. carbon- and nitrogen-limited growth condition. The contents of macro-molecules were extracted from the thesis of Schulze  who measured the biomass composition at a dilution rate of 0.1 h-1. The calculations were performed as described previously . The calculation of protein precursors, i.e. amino acids, and carbohydrate precursors, i.e. trehalose, glycogen, manna and glucan, were adopted from Schulze's work . Deoxyribonucleotide and ribonucleotide compositions were calculated from the study of Vaughan-Martini and co-workers . Lipid compositions were calculated from our own measurements of structural lipidomics, which contains phospholipids, triacylglycerol, sterols, sterol-esters, sphingolipids, free fatty acids and fatty acids composition of all measured lipid classes (unpublished data). The impact of the macromolecular composition on biomass yield was explored in aerobically glucose- and ammonium-limited conditions by fixing the specific growth rate and then minimizing the glucose and ammonium uptake rates at both glucose- and ammonium-limited growth conditions. Four parameters were evaluated, namely the protein, RNA, carbohydrate and lipid content of the biomass.
The metabolic capabilities of iIN800 were evaluated by using FBA and linear programming to simulate the biomass flux representing the in silico growth rate, which were derived by maximizing the biomass production. Data from various carbon-limited and nitrogen-limited chemostat experiments performed at either aerobic or anaerobic growth condition were taken from the literature for comparisons (see references in Additional file 3). These data were used to validate the metabolic capabilities of the model by comparing in silico biomass yields with in vivo biomass yields. The in silico biomass yields were calculated by fixing measurable uptake rates of extracellular metabolites, such as glucose, ammonium and oxygen, as well as secretions rates of acetate, glycerol, ethanol, succinate, pyruvate and carbon dioxide. The biomass equation (or flux), which was the objective function, was changed depending on the growth conditions evaluated according to the data provide in Table 4.
Large-scale gene essentiality simulations
The impact of individual gene deletions on cell growth of iIN800 was evaluated by eliminating the reaction(s) corresponding to each gene in the model from the stoichiometric matrix S and then simulating growth of the mutant by FBA. The in silico gene essentialities were simulated for growth on rich- and minimal-medium. For minimal media, different carbon sources (glucose, galactose, glycerol and ethanol), ammonium, sulphate and phosphate were evaluated. For rich media, the uptake fluxes of amino acids, purines and pyrimidines were added as additional constraints as previously described . The in silico simulations were compared to experimental data available in the MIPS and SGD databases and from competitive growth assays  as well as yeast mutant array experiments . The power of iIN800 to predict gene essentiality was evaluated based on the criteria defined as follows:
Accuracy = (TP + TN)/(TP + TN + FP +FN)
Sensitivity = TP/(TP + FN)
Specificity = TN/(TN + FP)
Positive predictive value = TN/(TP + FP)
Negative predictive value = TN/(TN+FN)
Geometric mean = (Sensitivity·Specificity)1/2
where TP = true positive, TN = true negative, FP = false positive, FN = false negative. Positive and negative values referred to viable and lethal phenotype, respectively.
Reporter Metabolite determination
Published microarray data were retrieved from Gene Expression Omnibus (GEO) . The CEL files were normalized by the dChip software  in order to minimize overall intensity variation among a set of chips. The statistical test of significance was done by ANOVA or student t-test for p-value calculation.
Briefly, we describe the Reporter Metabolite calculations. The genome-scale model was converted to a bipartite undirected graph. In this graph each metabolite node has as neighbors the enzymes catalyzing the formation and consumption of the metabolite. The transcriptome data were mapped on the enzyme nodes using the significant values of gene expression. The normal commutative distribution was used to convert the p-values to a Z-score for further calculations. To identify an importance of metabolites in the metabolic network of the particular experimental conditions, the reporter algorithm was applied as described earlier .
Inferring regulatory modules from Reporter Metabolites
The interactome network was initially constructed with data obtained from YPD , ChIP-chip databases  (protein-DNA interaction) and BioGRID  (protein-protein interaction). The candidate genes of high scoring Reporter Metabolites were retrieved from the bipartite metabolite-gene encoding enzyme interaction graph. They were then used to identify subnetworks from the interactome network . Significantly changing p-values from microarray data were mapped on the subnetwork and then also genes having a p-value < 0.01 directly connected with the Reporter Metabolites. The module was visualized by Cytoscape software .
The authors gratefully thank Mikael Rørdam Andersen and Kiran Raosaheb Patil for providing the ReMapper and the Reporter software, respectively. This work is supported by a grant from the National Center for Genetic Engineering and Biotechnology (BIOTEC) (grant number BT-B-06-NG-B5-4602). Intawat Nookaew gratefully acknowledges financial support by Thai Graduate Student Institute Science and Technology (TGIST). Michael C. Jewett is grateful to the NSF International Research Fellowship Program for supporting his work.
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