Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

Abstract

The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites. The number of gene functions included in the reconstructed network corresponds to approximately 16% of all characterized ORFs in S. cerevisiae. Using the reconstructed network, the metabolic capabilities of S. cerevisiae were calculated and compared with Escherichia coli. The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions.

Figure 1.

Reconstruction of the metabolic network of S. cerevisiae. Based on the available information from the genome annotation, biochemical pathway databases, biochemistry textbooks, and recent publications, a genome-scale metabolic network of S. cerevisiae was designed. Additional physiological constraints were considered and modeled, such as growth and nongrowth-dependent ATP requirements. Compartmentation was included, and cofactor requirements of all model reactions were inspected carefully, thereby, reactions that created a net transhydrogenic effect were additionally constrained. Regulatory information was not included. The picture of the pathway map was taken from the KEGG database (www.genome.ad.jp).

Figure 2.

Reaction classification by number of participating metabolites.

Figure 3.

Number of reactions and ORFs included in the S. cerevisiae metabolic network arranged by enzyme categories. For comparison, data for an E. coli (Edwards and Palsson 2000) metabolic network is shown. (EC 1) Oxidoreductases; (EC 2) transferases; (EC 3) hydrolases; (EC 4) lyases; (EC 5) isomerases; (EC 6) ligases.

Figure 4.

ORFs sorted into the functional categories of MIPS, metabolism (A) and energy (B). (AA) Amino-Acid Metabolism; (N2/S) nitrogen and sulphur metabolism; (N) nucleotide metabolism; (P) phosphate metabolism; (C) C-compound and carbohydrate metabolism; (L) lipid, fatty-acid and isoprenoid metabolism; (V) metabolism of vitamins, cofactors, and prosthetic groups; (S) secondary metabolism; (EMP) glycolysis and gluconeogenesis; (PPP) pentose-phosphate pathway; (TCA) tricarboxylic-acid pathway; (RES) respiration; (FER) fermentation; (ER) metabolism of energy reserves (glycogen, trehalose); (GLYC) glyoxylate cycle; (OX) oxidation of fatty acids; (O) other energy generation activities.

Figure 5.

Maximum precursor and amino acid production in S. cerevisiae and E. coli including nongrowth-specific ATP maintenance (A,B) (in mole/mole glucose). (3PG) 3-Phospho glycerate; (ACCOA) acetyl-CoA; (AKG) 2-Oxoglutarate; (ALA) alanine; (ARG) arginine; (ASN) asparagine; (ASP) aspartate; (CYS) cysteine; (E4P) eErythrose 4 -phosphate; (F6P) fructose 6-phosphate; (G6P) glucose 6-phosphate; (GLN) glutamine; (GLU) glutamate; (GLY) glycine; (HIS) histidine; (ILE) isoleucine; (LEU) leucine; (LYS) lysine; (MET) methionine; (OA) oxaloacetate; (PEP) phosphoenolpyruvate; (PHE) phenylalanine; (PRO) pProline; (PYR) pyruvate; (R5P) ribose 5-phosphate; (SER) serine; (SUCCOA) succinyl-CoA; (T3P1) glyceraldehyde 3-phosphate; (THR) threonine; (TRP) tryptophane; (TYR) tyrosine; (VAL) valine.