Acyl-[acyl-carrier-protein] transporter, mitochondrial
SUBSYSTEM: Thiamine (vitamin B1) metabolism
SUBSYSTEM: Phenylalanine, tyrosine, and tryptophan biosynthesis (aromatic amino acids)
Phospho-2-keto-3-deoxyheptonate aldolase
Methylene-fatty-acyl-phospholipid synthase
SUBSYSTEM: Pyridoxine (vitamin B6) metabolism
SUBSYSTEM: Fructose and mannose metabolism
SUBSYSTEM: Cytosolic fatty acid synthesis
3-oxoacyl-[acyl-carrier-protein] synthase
3-oxoacyl-[acyl-carrier-protein] reductase
Phosphopantothenate-cysteine decarboxylase
SUBSYSTEM: Pantothenate and CoA metabolism
Transport of deoxycytidine, extracellular
Inositol phosphosphingolipids phospholipase C
Probable phosphatidylinositol-4-phosphate 5-kinase MSS4
SUBSYSTEM: Glycine, serine, and threonine metabolism
Transport of deoxyadenosine, extracellular
Glycerophosphoinositol plasma membrane permease
SUBSYSTEM: Starch and sucrose metabolism
Transport of nicotinamide mononucleotide, extracellular
Transport of deoxyuridine, extracellular
Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
Carboxylic acid transporter protein homolog
Inorganic pyrophosphatase, mitochondrial
SUBSYSTEM: Glutamate metabolism (aminosugars metabolism)
SUBSYSTEM: Nicotinic acid synthesis from TRP
Transport of 5,10-methylenetetrahydrofolate, mitochondrial
Model-specific reaction, used to affect NADPH levels by converting NADP+ to NADPH
SUBSYSTEM: Glycerol metabolism (glycerolipid metabolism)
Glycerophosphodiester phosphodiesterase GDE1
6-phosphogluconate dehydrogenase, decarboxylating 2
6-phosphogluconate dehydrogenase, decarboxylating 1
Putative mitochondrial carnitine O-acetyltransferase
SUBSYSTEM: Alanine and aspartate metabolism
SUBSYSTEM: Mitochondrial type II fatty acid synthase
3-oxoacyl-[acyl-carrier-protein] synthase homolog
Transport of tetrahydrofolate, mitochondrial
Phosphatidylserine decarboxylase proenzyme 1, mitochondrial
Phosphatidylserine decarboxylase proenzyme 2
Transport of 2-oxoadipate, mitochondrial
Asparaginyl-tRNA synthetase, cytoplasmic
Dihydroxy-acid dehydratase, mitochondrial
SUBSYSTEM: Branched chain amino acid metabolism (valine, leucine, and isoleucine)
Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
Peroxisomal 2,4-dienoyl-CoA reductase SPS19
Model-specific reaction, used to affect NADH levels by converting NAD+ to NADH
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Transport of dethiobiotin, mitochondrial
Uroporphyrinogen-III C-methyltransferase
Transport of 3-isopropylmalate, mitochondrial
S-(hydroxymethyl)glutathione dehydrogenase
1-phosphatidylinositol-3-phosphate 5-kinase FAB1
Choline/ethanolaminephosphotransferase 1
Enoyl-[acyl-carrier-protein] reductase [NADH]
3-hydroxyacyl-[acyl-carrier-protein] dehydrase
Glycerol-3-phosphate dehydrogenase, mitochondrial
Tryptophanyl-tRNA synthetase, mitochondrial
Transport of deoxyinosine, extracellular
N-terminal acetyltransferase A complex subunit NAT1
SUBSYSTEM: Proteins, peptides and amino acids metabolism
Transport of acetoacetate, mitochondrial
3',5'-cyclic-nucleotide phosphodiesterase 2
Phosphoribosylaminoimidazolecarboxamide formyltransferase
3-methyl-2-oxobutanoate hydroxymethyltransferase
Glutamine-dependent carbamoyl-phosphate synthase
Transport of deoxyguanosine, extracellular
Putative inosine-5'-monophosphate dehydrogenase IMD1
Transport of 2-acetolactate, mitochondrial
Mitochondrial 3-oxoacyl-[acyl-carrier-protein] reductase
Transport of 4-methyl-2-oxopentanoate, mitochondrial
Hypoxanthine-guanine phosphoribosyltransferase
Glycerol-3-phosphate O-acyltransferase 1
Dihydroxyacetone phosphate acyltransferase 1
Dihydrosphingosine 1-phosphate phosphatase
3,4-dihydroxy-2-butanone-4-phosphate synthase
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Acetylornithine aminotransferase, mitochondrial
L-aminoadipate-semialdehyde dehydrogenase
Diacylglycerol pyrophosphate phosphatase 1
Ribonucleoside-diphosphate reductase large chain 1
Ubiquinone biosynthesis monooxygenase COQ6
Uptake of glycerophosphatidyl-D-myo-inositol
Hexaprenyl pyrophosphate synthetase, mitochondrial
Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial
5',5'''-P-1,P-4-tetraphosphate phosphorylase
Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
Excretion of glycerophosphatidyl-D-myo-inositol
Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial
Model-specific reaction, used to affect ATP levels by converting ADT to ATP
Trehalose synthase complex regulatory subunit TPS3
NAD-dependent malic enzyme, mitochondrial
Phosphatidylinositol kinase homolog TOR1
Probable UTP--glucose-1-phosphate uridylyltransferase
Phenylalanyl-tRNA synthetase alpha chain
Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial
Succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial
Model-specific reaction, pools acyl-CoAs
2-octaprenyl-6-methoxyphenol hydroxylase
Pyruvate dehydrogenase E1 component subunit alpha, mitochondrial
Dihydroneopterin triphosphate pyrophosphorylase
UTP--glucose-1-phosphate uridylyltransferase
Excretion of adenosine 3',5'-bisphosphate
Aspartate aminotransferase, mitochondrial
Mannosyl phosphorylinositol ceramide synthase SUR1
Mitochondrial phosphate carrier protein 2
Probable prolyl-tRNA synthetase, mitochondrial
Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial
[Acyl-carrier-protein] acetyltransferase
3-ketodihydrosphingosine reductase TSC10
Model-specific reaction, involved in sphingoglycolipid metabolism
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate
Dolichyl-phosphate-mannose--protein mannosyltransferase 6
Dolichyl-phosphate-mannose--protein mannosyltransferase 5
Dolichyl-phosphate-mannose--protein mannosyltransferase 2
Dolichyl-phosphate-mannose--protein mannosyltransferase 1
Dolichyl-phosphate-mannose--protein mannosyltransferase 4
Dolichyl-phosphate-mannose--protein mannosyltransferase 3
Acetolactate synthase catalytic subunit, mitochondrial
This is a reconstruction of the metabolic network of the yeast Saccharomyces cerevisiae as described in the article: The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S. BMC Syst Biol. 2008 Aug 7;2:71; PMID: 18687109 ,doi: 10.1186/1752-0509-2-71 Abstract: BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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 SBML was downloaded from the BioMet Toolbox page( http://129.16.106.142/models.php?c=S.cerevisiae ) of Jens Nielsen's Lab for Systems Biology at Chalmers University ( http://www.sysbio.se/ ). The parameters LOWER_BOUND and UPPER_BOUND were added as defined in the BioOpt file available from the same page. One error was corrected R_PIxtO (Excretion of phosphate) LOWER_BOUND was changed from 1000 to 0. Parameters FLUX_VALUE were then calculated as defined in "Flux balance analysis: a geometric perspective.", Smallbone K and Simeonidis E, 2009 (J Theor Biol. 2009;258(2):311-5, pmid: 19490860 ). Technical notes: The compartments included here have no volume defined; there are no reliable estimates available for those volumes yet. There are no kinetic functions defined for the reactions because this model only represents the chemical structure of the network (stoichiometry). Reactions for uptake and excretion are defined for some of the metabolites. All uptake reactions are constrained to zero flux and all excretion reactions are unconstrained. All genes are assigned to the cytosol. This has no physiological meaning, but it is necessary for the structure of the model. Biomass equations are available for carbon-limited and nitrogen-limited growth. The nitrogen-limited biomass equation is constrained to zero flux. A few reactions are meant to be used to simulate the effect of for example increased ATP production. They are constrained to zero flux. This SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Glycine dehydrogenase [decarboxylating], mitochondrial
NADPH-dependent 1-acyldihydroxyacetone phosphate reductase
Tryptophanyl-tRNA synthetase, cytoplasmic
S-adenosylmethionine decarboxylase proenzyme
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase
Mitochondrial 2-oxodicarboxylate carrier 1
Mitochondrial 2-oxodicarboxylate carrier 2
Methionyl-tRNA formyltransferase, mitochondrial
Nicotinamide-nucleotide adenylyltransferase 1
Glyceraldehyde-3-phosphate dehydrogenase 3
Glyceraldehyde-3-phosphate dehydrogenase 2
Glyceraldehyde-3-phosphate dehydrogenase 1
5-amino-6-(5-phosphoribosylamino)uracil reductase
Phosphatidylethanolamine N-methyltransferase
Ketol-acid reductoisomerase, mitochondrial
Phosphoadenosine phosphosulfate reductase
Sulfite reductase [NADPH] flavoprotein component
Very long-chain fatty acyl-CoA synthetase
UDP-N-acetylglucosamine pyrophosphorylase
1,3-beta-D-glucan-UDP glucosyltransferase
High-affinity potassium transport protein
External NADH-ubiquinone oxidoreductase 1, mitochondrial
External NADH-ubiquinone oxidoreductase 2, mitochondrial
D-arabinose dehydrogenase [NAD(P)+] heavy chain
Glycylpeptide N-tetradecanoyltransferase
Transport of dihydrofolate, mitochondrial
Peroxisomal acyl-coenzyme A thioester hydrolase 1
Dihydrolipoyl dehydrogenase, mitochondrial
Transport of a-ketoglutarate, extracellular
Transport of a-methylglucoside, extracellular
Model-specific reaction, involved in the elongation of fatty acids
Potassium-activated aldehyde dehydrogenase, mitochondrial
Protein farnesyltransferase subunit beta
Transport of 5-phospho-alpha-D-ribose 1-diphosphate, mitochondrial
NADH-ubiquinone oxidoreductase, mitochondrial
Mitochondrial aspartate-glutamate transporter AGC1
Uncharacterized seryl-tRNA synthetase, cytoplasmic
Valine/tyrosine/tryptophan amino-acid permease
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase 1
Cytochrome b-c1 complex subunit Rieske, mitochondrial
Transport of D-glucosamine 6-phosphate, extracellular
7-keto 8-aminopelargonic acid transporter
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Transport of pantetheine 4'-phosphate, mitochondrial
Transport of nucleosides and deoxynucleoside, extracellular
Methylenetetrahydrofolate dehydrogenase [NAD+]
Homoisocitrate dehydrogenase, mitochondrial
Transport of arabinose (low affinity), extracellular
Transport of 8-amino-7-oxononanoate, extracellular
Asparaginyl-tRNA synthetase, mitochondrial
Isocitrate dehydrogenase [NADP], cytoplasmic
Magnesium-activated aldehyde dehydrogenase, cytosolic
Enoyl-[acyl-carrier protein] reductase [NADPH, B-specific], mitochondrial
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Nicotinate-nucleotide pyrophosphorylase [carboxylating]
N-(5'-phosphoribosyl)anthranilate isomerase
1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
Dihydroxyacetone phosphate acyltransferase 2
Glycerol-3-phosphate O-acyltransferase 2
Inositolphosphorylceramide-B C-26 hydroxylase
3',5'-cyclic-nucleotide phosphodiesterase 1
5-aminolevulinate synthase, mitochondrial
1-phosphofructokinase (fructose 1-phosphate kinase)
Phenylalanyl-tRNA synthetase, mitochondrial
Model-specific reaction, used to group lipid formation for biomass production (nitrogen limited)
Transport of 7,8-diaminononanoate, extracellular
Probable alanine aminotransferase, mitochondrial
Inosine-5'-monophosphate dehydrogenase IMD2
Ethanolamine-phosphate cytidylyltransferase
Transport of oxidized glutathione, extracellular
Asparagine synthetase [glutamine-hydrolyzing] 1
Asparagine synthetase [glutamine-hydrolyzing] 2
Succinate-semialdehyde dehydrogenase [NADP+]
Transport of S-adenosyl-L-methionine, mitochondrial
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
D-lactate dehydrogenase [cytochrome] 1, mitochondrial
Saccharopine dehydrogenase [NAD+, L-lysine-forming]
Inositol-1,4,5-trisphosphate 5-phosphatase 3
Saccharopine dehydrogenase [NADP+, L-glutamate-forming]
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Imidazole glycerol phosphate synthase hisHF
Transport of pimelic acid, extracellular
Transport of pyridine-2,3-dicarboxylate, mitochondrial
Transport of O-acetylcarnitine, mitochondrial
ATP synthase subunit alpha, mitochondrial
Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase
Phospholipid:diacylglycerol acyltransferase
Succinate/fumarate mitochondrial transporter
Carnitine O-acetyltransferase, mitochondrial
Chalmers University of Technology, Gothenburg
Transport of carbon dioxide, extracellular
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Glycerol uptake/efflux facilitator protein
(2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl trihydrogen diphosphate
Malonyl CoA-acyl carrier protein transacylase, mitochondrial
Model-specific reaction, used to group lipid formation for biomass production (carbon limited)
Transport of dicarboxylates, extracellular
Galactose-1-phosphate uridylyltransferase
Uptake of ergosta-5,7,22,24(28)-tetraen-3beta-ol
2-dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
Excretion of ergosta-5,7,22,24(28)-tetraen-3beta-ol
CDP-diacylglycerol--inositol 3-phosphatidyltransferase
Transport of (R)-2-oxoisovalerate, mitochondrial
Carbamoyl-phosphate synthase arginine-specific large chain
Branched-chain-amino-acid aminotransferase, mitochondrial
[Acyl-carrier-protein] malonyltransferase
Transport of glycerone phosphate, mitochondrial
Excretion of nicotinamide mononucleotide
Probable glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial
Mitochondrial thiamine pyrophosphate carrier 1
Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphates
(2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid
Transport of 3-methyl-2-oxobutanoate, mitochondrial
Transport of N-acetylglucosamine, extracellular
CDP-diacylglycerol--serine O-phosphatidyltransferase
Transport of S-adenosyl-L-homocysteine, mitochondrial
1-phosphatidyl-1D-myo-inositol 3-phosphates
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphates
1-phosphatidyl-1D-myo-inositol 4-phosphates
Putative inosine-5'-monophosphate dehydrogenase-like protein
Trehalose synthase complex regulatory subunit TSL1
Inositol-1,4,5-trisphosphate 5-phosphatase
Isocitrate dehydrogenase [NADP], mitochondrial
SUBSYSTEM: Glyoxalate and dicarboxylate metabolism
Hydroxyacylglutathione hydrolase, cytoplasmic isozyme
Glycerol-3-phosphate dehydrogenase [NAD+] 1
Glycerol-3-phosphate dehydrogenase [NAD+] 2, mitochondrial
Phosphatidylglycerol phosphate phosphatase A
Probable inosine-5'-monophosphate dehydrogenase IMD3
Probable inosine-5'-monophosphate dehydrogenase IMD4
Transport of phosphatidate, mitochondrial
Transport of hypoxanthine, extracellular
Deoxyuridine 5'-triphosphate nucleotidohydrolase
N-acetyl-gamma-glutamyl-phosphate reductase
Transport of adenosine 3',5'-bisphosphate, extracellular
Phosphoribosylformylglycinamidine cyclo-ligase
Hydroxyacylglutathione hydrolase, mitochondrial
Mitochondrial oxaloacetate transport protein
Transport of sn-glycerol 3-phosphate, mitochondrial
Glucosamine 6-phosphate N-acetyltransferase
Geranylgeranyl transferase type-2 subunit beta
Transport of (R)-mevalonate, mitochondrial
Indoleamine 2,3-dioxygenase family protein
Ribonucleoside-diphosphate reductase large chain 2
Transport of 2-isopropylmalate, mitochondrial
3-hydroxy-3-methylglutaryl-coenzyme A reductase 2
3-hydroxy-3-methylglutaryl-coenzyme A reductase 1
Phosphoribosylaminoimidazole carboxylase
Phosphoribosylaminoimidazole-succinocarboxamide synthase
Methionyl-tRNA synthetase, mitochondrial
a-ketoglutarate/malate translocator, extracellular
Serine hydroxymethyltransferase, mitochondrial
Phosphoribosylformylglycinamidine synthase
ATP drain flux for constant maintanence requirements
Transport of (S)-3-hydroxy-3-methylglutaryl-CoA, mitochondrial
Phosphoribosylglycinamide formyltransferase
Serine hydroxymethyltransferase, cytosolic
Mannosyl phosphorylinositol ceramide synthase regulatory protein CSG2
Inositol-1,4,5-trisphosphate 5-phosphatase 4
Protoheme IX farnesyltransferase, mitochondrial
Transport of acetaldehyde, extracellular
Phosphatidylinositol 4,5-bisphosphate 5-phosphatase
Transport of 3-methyl-2-oxopentanoate, mitochondrial
3-phosphoshikimate 1-carboxyvinyltransferase
Isoleucyl-tRNA synthetase, mitochondrial
Uptake of 5alpha-ergosta-7,22-dien-3beta-ol
Transport of glyceraldehyde, extracellular
Branched-chain-amino-acid aminotransferase, cytosolic
Excretion of 5alpha-ergosta-7,22-dien-3beta-ol