GENE_ASSOCIATION: ( YER081W or YIL074C ) SUBSYSTEM: AMINOACID_SYNTHESIS
(R_phosphoglycerate_dehydrogenase)::3 PhosphoGlycerate + NAD+ => 3 PhosphohydroxyPyruvate + H + NADH --> [AminoAcid1]
GENE_ASSOCIATION: ( YGL062W or YBR218C ) SUBSYSTEM: GLYCOLYSIS
(R_pyruvate_carboxylase)::HCO3- + Pyruvate + ATP => Phosphate + Oxaloacetate + ADP
GENE_ASSOCIATION: YER065C SUBSYSTEM: GLYOXYLATE
(R_Isocitrate_lyase)::IsoCitrate => Glyoxylate + Succinate
GENE_ASSOCIATION: ( YJL052W or YJR009C or YGR192C ) SUBSYSTEM: GLYCOLYSIS
(R_glyceraldehyde_3_phosphate_dehydrogenase)::Glyceraldehyde 3 phosphate + Phosphate + NAD => 1,3 BIP Glycerate + NADH + H+
GENE_ASSOCIATION: ( YFL018C and YIL125W and YDR148C ) SUBSYSTEM: TCA
(R_pyruvate_dehydrogenase__dihydrolipoamide_dehydrogenase_)::Oxoglutarate [m] + Coenzyme A [m] + NAD => SuccinylCoA [m] + CO2 + NADH
GENE_ASSOCIATION: YNL241C SUBSYSTEM: NUCLEOTIDE_SYNTHESIS
(R_glucose_6_phosphate_dehydrogenase)::Glucose 6 phosphate + NADP => D 6 phospho gluconoδlactone + NADPH + H+ --> (Nucleotide1)
GENE_ASSOCIATION: YCR010C SUBSYSTEM: OTHERS
(R_acetate_transporter)::Acetate [e] => Acetate
GENE_ASSOCIATION: YPL134C SUBSYSTEM: GLUTAMATE
(R_2_oxodicarboylate_transporter__mitochondrial)::Oxoglutarate [m] => Oxoglutarate
GENE_ASSOCIATION: ( YOR142W and YGR244C ) SUBSYSTEM: TCA
(R_Succinate__CoA_ligase__ADP_forming_)::Succinyl CoA [m] + GDP + Phosphate => Succinate [m] + Coenzyme A [m] + GTP
GENE_ASSOCIATION: YMR105C SUBSYSTEM: GLYCOLYSIS
(R_phosphoglucomutase)::Glucose 1 phosphate => Glucose 6 phosphate
Ray2013 - S.cerevisiae meiosis-specific metabolic network Meiosis is a strongly concerved cell division program that generates haploid gametes from a diploid parental cell. Successful meiosis is the fundamental basis of sexual reproduction. Multiple lines of evidence suggest a tight link between meiosis and metabolism. Here, yeast meiosis is studied to elucidate the link between reproduction and metabolism. Network flux is obtained using GLPK (GNU Linear Programming Kit) supported by the COBRA Toolbox for Matlab. This model is described in the article: Characterization of the metabolic requirements in yeast meiosis. Ray D, Ye P. PLoS One. 2013 May 8;8(5):e63707. Abstract: The diploid yeast Saccharomyces cerevisiae undergoes mitosis in glucose-rich medium but enters meiosis in acetate sporulation medium. The transition from mitosis to meiosis involves a remarkable adaptation of the metabolic machinery to the changing environment to meet new energy and biosynthesis requirements. Biochemical studies indicate that five metabolic pathways are active at different stages of sporulation: glutamate formation, tricarboxylic acid cycle, glyoxylate cycle, gluconeogenesis, and glycogenolysis. A dynamic synthesis of macromolecules, including nucleotides, amino acids, and lipids, is also observed. However, the metabolic requirements of sporulating cells are poorly understood. In this study, we apply flux balance analyses to uncover optimal principles driving the operation of metabolic networks over the entire period of sporulation. A meiosis-specific metabolic network is constructed, and flux distribution is simulated using ten objective functions combined with time-course expression-based reaction constraints. By systematically evaluating the correlation between computational and experimental fluxes on pathways and macromolecule syntheses, the metabolic requirements of cells are determined: sporulation requires maximization of ATP production and macromolecule syntheses in the early phase followed by maximization of carbohydrate breakdown and minimization of ATP production in the middle and late stages. Our computational models are validated by in silico deletion of enzymes known to be essential for sporulation. Finally, the models are used to predict novel metabolic genes required for sporulation. This study indicates that yeast cells have distinct metabolic requirements at different phases of meiosis, which may reflect regulation that realizes the optimal outcome of sporulation. Our meiosis-specific network models provide a framework for an in-depth understanding of the roles of enzymes and reactions, and may open new avenues for engineering metabolic pathways to improve sporulation efficiency. This model is hosted on BioModels Database and identified by: MODEL1303140001 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.
GENE_ASSOCIATION: YDR050C SUBSYSTEM: GLYCOLYSIS
(R_triose_phosphate_isomerase)::Dihydroxyacetone phosphate => Glyceraldehyde 3 phosphate
GENE_ASSOCIATION: YNR016C SUBSYSTEM: LIPID_SYNTHESIS
(R_acetyl_CoA_carboxylase__reversible_reaction)::BCCP biotin CO2 + AcetylCoA + ATP => MalonylCoA + BCCP biotin + phosphate + ADP --> Lipid1
GENE_ASSOCIATION: YLR348C SUBSYSTEM: OTHERS
(R_succinate_transport__mitochondrial)::Succinate + Phosphate [m] => Succinate [m] + Phosphate
GENE_ASSOCIATION: YIL006W SUBSYSTEM: GLYCOGENOLYSIS
(R_pyruvate_mitochondrial_transport_via_proton_symport)::Pyruvate => Pyruvate [m]
GENE_ASSOCIATION: YKL152C SUBSYSTEM: GLYCOLYSIS
(R_phosphoglycerate_mutase)::3 PhosphoGlycerate --> 2 PhosphoGlycerate
GENE_ASSOCIATION: YJR095W SUBSYSTEM: OTHERS
(R_succinate_fumarate_transport__mitochondrial)::Fumarate [m] + Succinate => Fumarate + Succinate [m]
GENE_ASSOCIATION: ( YNL037C and YOR136W ) SUBSYSTEM: TCA
(R_Isocitrate_dehydrogenase__NAD_)::NAD + IsoCitrate [m] => Oxoglutarate [m] + NADH + CO2
GENE_ASSOCIATION: YLR304C SUBSYSTEM: OTHERS
(R_aconitase)::Citrate + H2O => IsoCitrate
GENE_ASSOCIATION: YAL062W SUBSYSTEM: GLUTAMATE
(R_glutamate_dehydrogenase__NADP_)::Oxoglutarate + NH3 + NADPH + H+ => L Glutamate + H2O + NADP
GENE_ASSOCIATION: YDR127W SUBSYSTEM: AMINOACID_SYNTHESIS
(R_3_phosphoshikimate_1_carboxyvinyltransferase__irreversible)::PhosphoenolPyruvate + Skm5p => 3Psme + phosphate --> [AminoAcid5]
GENE_ASSOCIATION: YKL085W SUBSYSTEM: TCA
(R_malate_dehydrogenase__mitochondrial)::Malate [m] + NAD => Oxaloacetate [m] + NADH + H+
GENE_ASSOCIATION: ( YML042W avg YAR035W avg YER024W ) SUBSYSTEM: OTHERS
(R_carnitine_O_acetyltransferase)::AcetylCoA => AcetylCoA [m]
GENE_ASSOCIATION: ( YMR108W and YCL009C ) SUBSYSTEM: AMINOACID_SYNTHESIS
(R_acetolactate_synthase__mitochondrial)::Pyruvate [m] + NADPH + H+ + Glutamate => CO2 + NADP+ + H2O + Alpha ketoglutarate + valine --> [AminoAcid3]
GENE_ASSOCIATION: YBR291C SUBSYSTEM: OTHERS
(R_citrate_transport__mitochondrial)::IsoCitrate [m] => IsoCitrate
GENE_ASSOCIATION: ( YJL052W or YJR009C or YGR192C ) SUBSYSTEM: GLUCONEOGENESIS
(R_glyceraldehyde_3_phosphate_dehydrogenase)::1,3 Biphospho Glycerate + NADH + H+ => Glyceraldehyde 3 phosphate + phosphate + NAD
GENE_ASSOCIATION: YPL262W SUBSYSTEM: TCA
(R_fumarase__mitochondrial)::Fumarate [m] + H2O => Malate [m]
GENE_ASSOCIATION: YKL120W SUBSYSTEM: OTHERS
(R_oxaloacetate_transport__mitochondrial)::Oxaloacetate => Oxaloacetate [m]
GENE_ASSOCIATION: YLR174W SUBSYSTEM: GLUTAMATE
(R_isocitrate_dehydrogenase__NADP_)::IsoCitrate + NADP => Oxoglutarate + CO2 + NADPH
GENE_ASSOCIATION: YLR377C SUBSYSTEM: GLUCONEOGENESIS
(R_fructose_bisphosphatase)::Fructose 1,6 bisphosphate + H2O => Fructose 6 phosphate + phosphate
GENE_ASSOCIATION: YNR001C SUBSYSTEM: TCA
(R_acetyl_CoA_synthetase)::Oxaloacetate [m] + AcetylCoA [m] + H2O => Citrate [m]+ Coenzyme A [m]
GENE_ASSOCIATION: YDR050C SUBSYSTEM: GLUCONEOGENESIS
(R_triose_phosphate_isomerase)::Glyceraldehyde 3 phosphate => Dihydroxyacetone phosphate
GENE_ASSOCIATION: YKL152C SUBSYSTEM: GLUCONEOGENESIS
(R_phosphoglycerate_mutase)::2 PhosphoGlycerate => 3 PhosphoGlycerate
GENE_ASSOCIATION: ( YKL148C and YLL041C and YKL141W and YDR178W ) SUBSYSTEM: TCA
(R_succinate_dehydrogenase)::Succinate [m] + FAD => Fumarate [m] + FADH2
GENE_ASSOCIATION: YKL106W SUBSYSTEM: AMINOACID_SYNTHESIS
(R_aspartate_transaminase)::Oxaloacetate [m] + L Glutamate => 2 Oxoglutarate + L Aspartate --> [AminoAcid4]
GENE_ASSOCIATION: YLR304C SUBSYSTEM: TCA
(R_Aconitate_hydratase)::Citrate [m] + H2O => IsoCitrate [m]
GENE_ASSOCIATION: YKR097W SUBSYSTEM: GLUCONEOGENESIS
(R_phosphoenolpyruvate_carboxykinase)::Oxaloacetate + GTP => CO2 + PhosphoenolPyruvate + GDP
GENE_ASSOCIATION: YCR012W SUBSYSTEM: GLYCOLYSIS
(R_phosphoglycerate_kinase)::1,3 BIP Glycerate + ADP => 3 PhosphoGlycerate + ATP
GENE_ASSOCIATION: YDL022W SUBSYSTEM: LIPID_SYNTHESIS
(R_glycerol_3_phosphate_dehydrogenase__NAD_)::Dihydroxyacetone phosphate + NADH => Glycerol 3 P + NAD --> Lipid3
GENE_ASSOCIATION: YPL262W SUBSYSTEM: OTHERS
(R_oxaloacetate_transport__mitochondrial)::Oxaloacetate [m] => Oxaloacetate
GENE_ASSOCIATION: YCR012W SUBSYSTEM: GLUCONEOGENESIS
(R_phosphoglycerate_kinase)::3 PhosphoGlycerate + ATP => 1,3 Biphospho Glycerate + ADP
GENE_ASSOCIATION: YOL126C SUBSYSTEM: OTHERS
(R_malate_dehydrogenase)::Malate + NAD => Oxaloacetate + NADH + H+
GENE_ASSOCIATION: YJL153C SUBSYSTEM: LIPID_SYNTHESIS
(R_myo_Inositol_1_phosphate_synthase)::Glucose 6 phosphate => Mi1p-D
GENE_ASSOCIATION: YLR027C SUBSYSTEM: AMINOACID_SYNTHESIS
(R_aspartate_transaminase)::Oxaloacetate + L glutamate => 2,Oxoglutarate + L aspartate --> [AminoAcid2]
GENE_ASSOCIATION: YMR105C SUBSYSTEM: GLUCONEOGENESIS
(R_phosphoglucomutase)::Glucose 6 phosphate => Glucose 1 phosphate
GENE_ASSOCIATION: YOR347C SUBSYSTEM: GLYCOLYSIS
(R_pyruvate_kinase)::PhosphoenolPyruvate + ADP + H+ => Pyruvate + ATP
GENE_ASSOCIATION: YMR207C SUBSYSTEM: LIPID_SYNTHESIS
(R_Acetyl_Coa_carboxylase__mitochondrial)::BCCP biotin CO2 + AcetylCoA [m]+ ATP => MalonylCoA + BCCP biotin + phosphate + ADP --> Lipid2
GENE_ASSOCIATION: YKL035W SUBSYSTEM: GLUCONEOGENESIS
(R_glycogen_synthase__UDPGlc_)::Glucose 1 phosphate => Glycogen
GENE_ASSOCIATION: YNL117W SUBSYSTEM: GLYOXYLATE
(R_malate_synthase)::Glyoxylate + AcetylCoA => Malate
GENE_ASSOCIATION: ( YBR126C and YDR074W and YMR261C and YML100W ) SUBSYSTEM: GLUCONEOGENESIS
(R_alpha_alpha_trehalose_phosphate_synthase__UDP_forming_)::UDP D glucose + Glucose 6 phosphate => UDP + α,α trehalose 6 phosphate
GENE_ASSOCIATION: YGR254W SUBSYSTEM: GLUCONEOGENESIS
(R_enolase)::PhosphoenolPyruvate + H2O => 2 PhosphoGlycerate
GENE_ASSOCIATION: YKL060C SUBSYSTEM: GLYCOLYSIS
(R_fructose_bisphosphate_aldolase)::Fructose 1,6 bisphosphate => Dihydroxyacetone phosphate + Glyceraldehyde 3 phosphate
(R_citrate_transport__mitochondrial)::Citrate => Citrate [m]
GENE_ASSOCIATION: YCR005C SUBSYSTEM: OTHERS
(R_acetyl_CoA_synthetase)::Oxaloacetate + AcetylCoA + H2O => Citrate + Coenzyme A
GENE_ASSOCIATION: ( YER178W and YBR221C ) SUBSYSTEM: GLYCOGENOLYSIS
(R_pyruvate_dehydrogenase)::Coenzyme A [m] + NAD + Pyruvate [m] => AcetylCoA [m] + CO2 + NADH
GENE_ASSOCIATION: YKL060C SUBSYSTEM: GLUCONEOGENESIS
(R_fructose_bisphosphate_aldolase)::Dihydroxyacetone phosphate + Glyceraldehyde 3 phosphate => Fructose 1,6 bisphosphate
GENE_ASSOCIATION: YBR196C SUBSYSTEM: GLUCONEOGENESIS
(R_glucose_6_phosphate_isomerase)::Fructose 6 phosphate => Glucose 6 phosphate
GENE_ASSOCIATION: YPR160W SUBSYSTEM: GLYCOLYSIS
(R_glycogen_phosphorylase)::Glycogen => Glucose 1 Phosphate
GENE_ASSOCIATION: YGR254W SUBSYSTEM: GLYCOLYSIS
(R_enolase)::2 PhosphoGlycerate => PhosphoenolPyruvate + H2O
Ray2013 - S.cerevisiae meiosis-specific metabolic network
GENE_ASSOCIATION: YLR153C SUBSYSTEM: OTHERS
(R_acetyl_CoA_synthetase)::Coenzyme A + Acetate + ATP => AcetylCoA + pyrophosphate + AMP
GENE_ASSOCIATION: ( YGR240C and YMR205C ) SUBSYSTEM: GLYCOLYSIS
(R_phosphofructokinase)::Fructose 6 phosphate + ATP => Fructose 1,6 bisphosphate + ADP + H+
GENE_ASSOCIATION: YBR196C SUBSYSTEM: GLYCOLYSIS
(R_glucose_6_phosphate_isomerase)::Glucose 6 phosphate => Fructose 6 phosphate