Exploring Synechocystis' Metabolic Potential in the Optimum

T.R. Maarleveld

GSSMs

The Synechocystis Exploring Synechocystis’ Metabolic model Potential in the Optimum Tip of the Iceberg

TimoTimo Exploring Timo Maarleveld Synechocystis’ optimal solution space Centrum Wiskunde en Informatica, Life Sciences

VU University Amsterdam, IBIVU Systems Bioinformatics

BioSolarCells Cluster Meeting, 18-06-2015 What do we need?

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg 1 genome-scale stoichiometric metabolic model of TimoTimo Synechocystis’ Exploring Synechocystis’ 2 method to explore the metabolic potential in the optimum optimal solution space 2 genome-scale: cover the total metabolic potential that is encoded in the genome of an organism 3 stoichiometric: only relative quantities: A + B → C no kinetics: k1 × A[t] × B[t] dA dB dC assume steady-state: dt = dt = dt = 0 4 predict steady-state flux distributions

Genome-scale stoichiometric models in a nutshell

T.R. Maarleveld

GSSMs The 1 metabolism: the set of life-sustaining chemical Synechocystis model transformations within the cells of living organisms Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space 3 stoichiometric: only relative quantities: A + B → C no kinetics: k1 × A[t] × B[t] dA dB dC assume steady-state: dt = dt = dt = 0 4 predict steady-state flux distributions

Genome-scale stoichiometric models in a nutshell

T.R. Maarleveld

GSSMs The 1 metabolism: the set of life-sustaining chemical Synechocystis model transformations within the cells of living organisms Tip of the Iceberg 2 genome-scale: cover the total metabolic potential that is

TimoTimo encoded in the genome of an organism

Exploring Synechocystis’ optimal solution space 4 predict steady-state flux distributions

Genome-scale stoichiometric models in a nutshell

T.R. Maarleveld

TimoTimo encoded in the genome of an organism Exploring 3 stoichiometric: Synechocystis’ optimal only relative quantities: A + B → C solution space no kinetics: k1 × A[t] × B[t] dA dB dC assume steady-state: dt = dt = dt = 0 Genome-scale stoichiometric models in a nutshell

T.R. Maarleveld

Legend: [e]: Extracellular Visualization of the Metabolic Network of Synechocystis Species PCC 6803 [p]: Periplasm [t]: ylakoid dIDP dITP dAMP Modeling others: Cytoplasm cAMP ATP ADP dADP dATP DNA Sink Reactions Demand Reactions Photosynthesis Pi R1P DNA Ø DNA 5-methylcytosineØ Indole-3-acetamide Indole-3-acetate Imidazole-4-acetaldehyde Imidazole-4-acetate H2O Pi Adenylo Oxidative Phosphorylation ITPIDP FOCYTC6[p] Protein RNA succinate AMP Adenosine Adenine AMP Growing 3-Hydroxy-2 (S)-Methylmalonate PC(r)[p] Ø PHB granule Ø Indole-3-acetaldehyde Periplasm H+[p] PHB granule methylpropanoate semialdehyde 2,5-Diamino-6- Protein ATP ADP (5'-phosphoribosylamino) GTP GMP XMP IMP FAICAR 8-Amino-7-oxo Cyanophycin(n) Ø Cyanophycin(n+2) Ø 2-Phenylacetamide Phenylacetic acid Pimeloyl-CoA 4-pyrimidineone THF nonanoate Phosphatidyl Phosphatidyl Cyt BD PGLipid(16:0) Lipid(18:2[9,12]) PG NDH-1 NDH-2 NDH-1 PQH2[p] Quinol Cyt B6f Cyt C ATPase glycero-P glycero-P 3,4-Dihydroxy 3,4-Dihydroxyphenyl CMP CMP type 4 Oxidase 10-Formyl-THF L-Histidinine α-Ribazole Ø S-Methyl-5-thio-Ru1P Ø L-Lactaldehyde (S)-Propane-1,2-diol Ribo�avin Metabolism GDP Deoxyguanosine SAICAR AICAR mandelaldehyde ethyleneglycol cGMP PPi PPPi 5-Amino-6- 5-Amino-6- sn-Glycerol-3-P sn-Glycerol-3-P (5'-phosphoribitylamino) (5'-phosphoribosylamino) UDP-N-acetylmuramoyl L- UDPMurAc(oyl-L-Ala-D-gamma Pi PPi Inositol 1-phosphate Inositol N4-Acetylamino 4-Acetamido CDP-diacyl CDP-diacyl uracil uracil alanyl-D-glutamyl-L-lysine Glu-L-Lys-D-Ala-D-Ala) butanal butanoate glycerol glycerol H+ P-ribosyl-C- 5-Amino-4-imidazole L-Histidinol L-Histidinol-P H2O SDH dGDP dGTP Aminoimidazole carboxyamide PPi PPi T.R. Maarleveld NADP+ NAD(P)H NAD(P)+ NAD(P)H ADP ATP dTDP-4-oxo-6 dTDP-4-oxo-L-rhamnose dTDP-L-rhamnose D-Tagatose 6-phosphate D-Tagatose 1,6-biphosphate H2O2 Protein Protein deoxy-D-glucose linoleoyl-ACP linoleoyl-ACP 6,7-Dimethyl 5-Amino-6- O2 Hexadecanoyl-ACP Hexadecanoyl-ACPACP ACP CTP (n-C18_2ACP) ACP (n-C18_2ACP) ACP CTP H+ H2 FADH2 FAD 8-(1-D-ribityl) (1-D-ribitylamino) DNA AIR Toxopyrimidine D-erythro-Imidazole 1,2-Diacyl 1,2-Diacyl lumazine uracil Imidazole-acetol-P 3-Octaprenyl-4-hydroxybenzoate 2-Octaprenylphenol sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P O2 H2O glycerol-phosphate NADH NAD+ sn-glycerol-3-P sn-glycerol-3-P Q8H2 L-Tyrosine 2-oxoglutarate L-Phenylalanine Purine Metabolism dTDP-Glc dTDP-Gal NADPH NADP+ UDP-6-sulfo UDP-6-sulfo Cytoplasm Q8H2Q8 Histidine Synthesis UDP UDP FNP-acetamidine UDP-6-sulfoquinovosel quinovosel quinovosel Lipid A FADH2 FAD Ribo�avin 4-Hydroxyphenyl 5-phospho LipidX 1,2-Diacyl 1,2-Diacyl 2-Hydroxy N-Formyl Phosphoribosyl-formimino Phosphoribosyl-formimino Disaccharide Lipid(16:0) SQDG Lipid(18:2[9,12]) SQDG Homogentisate pyruvate L-Glutamate PhPyr GAR ribosylamine sn-glycerol sn-glycerol phenylacetate GAR AICAR-phosphate AICAR-phosphate UDP-Glc UDP-Galα-D-Galactose 1-phosphate Galactose NADP+ NADPH UDP-N-acetylmuramoyl UDP-Gal UDP-Gal NADP+ NAD(P)H NAD(P)+ NAD(P)H Fd(ox) Fd(red) ADP ATP Sucrose-6-P Sucrose L-alanyl-D-glutamate ioredoxin ioredoxin SDH FMN UDP-2,3-bis(3-hydroxy H+ F6P X5P Oxidized Reduced UDP UDP hv hv Prephenate R1P D-Ribose PRPP Phosphoribosyl-ATP Phosphoribosyl-AMP CDP-Glc tetradecanoyl) MGDG Lipid(16:0) MGDG Lipid(18:2[9,12]) glucosamine UDP-Gal UDP-Gal 4-Aminobenzoate Cyanophycin(n+2) Cyanophycin(n+2) ACP UDP-N-acetylmuramoyl Cyt BD FAD UDP UDP 3,4-Dihydroxy-2-butanone 4-P Maltose Glucose GlcGlycP GlcGlyc L-alanine NDH-1 NDH-2 NDH-1 PS II PQH2[t] Quinol Cyt B6f PS I Cyt C ATPase Anthranilate Chorismate ADC Pyruvate HMA DGDG Lipid(16:0) DGDG Lipid(18:1[9,12]) type 3 Oxidase G3P E4P G3P R5P UDP-3-O-(3-hydroxy Fd(red) Fd(ox) N-(5-Phospho-D-ribosyl) Storage Products tetradecanoyl) Chorismate D-glucosamine anthranilate Acetaldehyde N-Acetyl GSSMs D-mannosamine UDP-MurNAc Ru5P 6PGL6PG G6P G1P ADP-Glc Glycogen Branched Glycogen 5-O-(1-Carboxyvinyl) D-Glutamate L-Glutamate FOCYTC6[t] GTP 3-phosphoshikimate ylakoid H2O[t] O2[t] H+[t] H+[t] Pentose Phosphate UDP-3-O-(β- PC(r)[t] 1-(2-Carboxyphenylamino) 2-deoxy F6P S7P X5P N-Acetyl-D- UDP-N-acetyl UDP-N-acetyl-3-(1-carbo hydroxymyristoyl) 1-deoxy-D-ribulose 5-P D-ribose 5-P Pathway Fructose F6P D-Glucosamine 6-P D-Glucosamine 1-P Exchange and Transport Reactions glucosamine-1-P D-glucosamine xyvinyl)-D-glucosamine N-acetylglucosamine 6-Pyruvoyltetra Dihydroneopterin Shikimate-3-P hydropterin Phosphatidyl Phosphatidyl PGLipid(16:1) Lipid(18:3[6,9,12]) PG Ø L-Alanine[e] L-Alanine[p] L-Alanine Sedoheptulose 1,7-PP glycero-P glycero-P Folate Metabolism Deoxyribose GDP-4-dehydro Indoleglycerol-P FBP M6P M1P GDP-Mannose GDP-L-fucose CMP CMP D-rhamnose Shikimate Ø L-Arginine[e] L-Arginine[p] L-Arginine 7,8-Dihydroneopterin Dihydroneopterin-Phosphate Glycolysis Sterol Metabolism sn-Glycerol-3-P sn-Glycerol-3-P L-Serine G3P E4P DHAP CDP-diacyl CDP-diacyl Indole G3P DHAP Zeaxanthin glycerol glycerol Ø Glycine[e] Glycine[p] Glycine Glycolaldehyde Glycolate The G3P L-Serine 3-Dehydroshikimate 3-Dehydroquinate DAHP dTTP DNA Pyruvate G3P PPi PPi cis-hexadec-9-enoyl cis-hexadec-9-enoyl Ø L-Glutamate[e] L-Glutamate[p] L-Glutamate PEP iamine Metabolism ACP (n-C16_1) ACP ACP (n-C16_1) ACP CTP γ-linolenoilACPγACP-linolenoilACP ACP CTP 2-Amino-4-hydroxy 7,8-Dihydropterin L-Tryptophan 13DPG 23DPG β-Cryptoxanthin CO2 Formate Oxalate 4-methyl-5-(2-phos 1,2-Diacyl 1,2-Diacyl 6-hydroxymethyl pyrophosphate Calvin Cycle dTDP dCTP dCDP CDP CMP 1-Deoxy-D-xylulose-5-P iamine-Piamine-PP iamine sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P THF-L-glutamate Folinic acid phoethyl)-thiazole sn-glycerol-3-P sn-glycerol-3-P 7,8-dihydropteridine 5-Methyl-THF Ø L-Glutamine[e] L-Glutamine[p] L-Glutamine 2mahmp PPi Protein β UDP-6-sulfo UDP-6-sulfo Glycine Glyoxylate Glycolate RuBP2PG PG3 3PHP Echinenone -Carotene UDP quinovosel UDP quinovosel Synechocystis Ø L-Histidine[e] L-Histidine[p] L-Histidine Dihydropteroate Dihydrofolate THF 10-Formyl-THF 5,10-Methenyl-THF 5,10-Methylene-THF CTP CYTD 2-C-Methyl-D-erythritol 4-P 1-deoxy-D-xylulose 4-Methyl-5-(2-hydroxyethyl)-thiazole 1,2-Diacyl 1,2-Diacyl ymd dTMP dUTP H2O Lipid(16:1) SQDG Lipid(18:3[6,9,12]) SQDG 2-Hydroxy-3-oxopropanoate sn-glycerol sn-glycerol THF RNA UDP-Gal UDP-Gal S-Lactoyl Methylglyoxal D-Ribose γ-Carotene Ø L-Leucine[e] L-Leucine[p] L-Leucine glutathione Mercaptopyruvate Protein L-Serine Pyruvate Glycerone HPYR Glycerate PG2 UTP CSN 4-(Cytidine 5'-diphospho) UDP UDP L-Cysteine 2-C-methyl-D-erythritol MGDG Lipid(16:1) MGDG Lipid(18:3[6,9,12]) Ø L-Lysine[e] L-Lysine[p] L-Lysine dUMP UDPdUDP UDP-Gal UDP-Gal gamma-Glutamyl S-Lactoyl Lycopene Cys-Gly Glutathione(red) cysteine L-Cysteine Acetyl-serine sn-Glycerol-3-P Glycerol Glyceraldehyde F1P PEP glutathione model UMP Uracil UDP UDP Ø L-Proline[e] L-Proline[p] L-Proline 2-Phospho-4-(cytidine 5'-PP) DGDG Lipid(16:1) DGDG Lipid(18:3[6,9,12]) Glycine Acetate H2S Pyrimidine Metabolism PPi PRPP 2-C-methyl-D-erythritol Neurosporene Glutathione(ox) D-Ala-D-Ala D-Alanine L-Alanine Pyruvate Lactate Ø L-Serine[e] L-Serine[p] L-Serine Orotidine-5-P PPi 5,10-Methylene-THF NADP+ L-Asparagine Protein 2-C-Methyl-D-erythritol 1-Hydroxy-2-methyl ADP 2,4-cyclodiphosphate 2-butenyl 4-PP DAMPP Diplopterol Ø hv[e] hv[p] hv Nicotinamide metabolism Acetyl-P PRPP ζ-Carotene PRPP PPi PPi PRPP Pi DHAP Orotate NADH NADPH ATP Nicotinate Succinate Nicotinamide NMN NAD+ Deamino-NAD+ Quinolinate Iminoaspartate L-Aspartate Geranyl Ø H+[e] H+[p] ribonucleotide Isopentenyl-PP PPiPP Squalene Diploptene NAD+ NADP+ Phyto�uene Phosphatidyl Phosphatidyl AcCoA Acetate Acetaldehyde Ethanol Fumarate PGLipid(18:0) Lipid(18:3[9,12,15]) PG Dihydroorotate NADH NADPH glycero-P glycero-P Ø H2O[e] H2O[p] H2O H2O[t] N-Succinyl-L-2,6 N-Succinyl-L-2- Oxalo CMP CMP ADPribose 1,5-Diaminopentane diaminopimelate amino-6-oxopimelate 4-P-Aspartate β-Alanine acetate Citrate cis-Aconitate L-Aspartate NAD+ NADP+ Tip of the CoA NH4 Cyanate Undecaprenyl-PP PPi Farnesyl-PP Geranylgeranyl-PP Prephytoene-PP Phytoene Protein sn-Glycerol-3-P sn-Glycerol-3-P Ø O2[e] O2[p] O2 O2[t] N-Carbamoyl CDP-diacyl CDP-diacyl Succinyl-CoA Carbamoyl-P AMP meso-Di LL-2,6-Di L-aspartate glycerol glycerol Protein L-Lysine THDP 23DHDP Aspartate-SA β-aminopropion Malate Carotenoid Metabolism UDP-N-acetyl amino aminopimelate iso-Citrate R5P aldehyde CO2 HCO3 PPi PPi Ø CO2[e] CO2[p] CO2 D-glucosamineUDP heptanedioate L-Glutamine 2-oxoglutarate L-Glutamate PyruvateH2O TCA Cycle Isopentenyl-PP all-trans Isopentenyl-PP PPi Phytyl diphosphate α-lineloyl-ACP α-lineloyl-ACP UDP-N-acetylmuramoyl-L-alanyl Decaprenyl-PP Octadecanoyl-ACP Octadecanoyl-ACPACP ACP CTP (n-C18_3ACP) ACP (n-C18_3ACP) ACP CTP UDP-N-acetylmuramoyl Homogentisate Peptidoglycan[p] Peptidoglycan UAAGMDA UAGMDA D-glutamyl-6-carboxy-L-lysyl Heptanedioate Homoserine 1,2-Diacyl 1,2-Diacyl Ø HCO3[e] HCO3[p] HCO3 L-alanyl-D-glutamate Fumarate 2-oxoglutarate sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Iceberg D-alanyl-D-alanine 2,3-Dimethyl PPi sn-glycerol-3-P sn-glycerol-3-P Undecaprenyl-PP Undecaprenyl-P D-Ala-D-Ala 5-phytylquinol 2-Methyl-6-phytylquinol Ø NH4[e] NH4[p] L-Glutamate Glutamyl-5-P Glutamate-5-SA P5C L-Proline Protein UDP-6-sulfo UDP-6-sulfo S-Adenosyl 2-oxoglutarate UDP quinovosel UDP quinovosel P-Homoserine Protein Succinate Succinyl-CoA H2S L-homocysteine 1,2-Diacyl 1,2-Diacyl L-Glutamate Lipid(18:0) SQDG Lipid(18:3[9,12,15]) SQDG Succinate γ-Tocopherol δ-Tocopherol sn-glycerol sn-glycerol Ø NO3[e] NO3[p] NO3 NO2 NH4 AcCoA 1-Pyrroline-3-hydroxy L-Cystathionine S-Adenosylmethionine S-Adenosylmethionine UDP-Gal UDP-Gal Acetate Succinate-SA 4-Aminobutanoate 2-oxoglutarate Hydroxyproline 5-carboxylate Protein L-reonine L-Homocysteine L-Methionine CoA S-Adenosylhomocysteine S-Adenosylhomocysteine Ø Urea[e] Urea[p] Urea L-Glutamate 2-oxoglutarate UDP UDP NADP+ NADPH CO2 CO2 Ornithine α-Tocopherol β-Tocopherol MGDG Lipid(18:0) MGDG Lipid(18:3[9,12,15]) Biotin UDP-Gal UDP-Gal Methionine Acetyl-Glutamate Carbamoyl-P Erythro-4 Ø SO4[e] SO4[p] SO4 2,3-Butanediol R-Acetoin 2-Acetolactate Pyruvate 2-oxobutanoate Hydroxyglutamate Synthesis Acetyl-Glutamate Pi UDP UDP Dethiobiotin 7,8-Diaminononanoate 4-Aminobutanal Urea Cycle DGDG Lipid(18:0) DGDG Lipid(18:3[9,12,15]) Urea TimoTimo Ø Succinate[e] Succinate[p] Succinate (S)-2-Aceto-2- S-Adenosylhomocysteine S-Adenosylmethionine Acetyl-Glutamate-5-P L-Glutamate L-Citrulline CO2 hydroxybutanoate 4-Hydroxy H20 L-Glutamate 2-oxoglutarate Urea 2-oxoglutarate Ø Fumarate[e] Fumarate[p] Fumarate Adenosine-3,5-PP AMP Vitamin B6 Acetyl-Glutamate-5-SA Acetylornithine (R)-2,3-Dihydroxy- FADH2 FAD Ø Ethanol[e] Ethanol[p] Ethanol Sul�te PAPS Pyruvate Glyoxylate Chorismate isovalerate Pyridoxamine Pyridoxamine 5'-P 4-Guanidino 4-Guanidino 4-Guanidino Guanidino Isoleucine L-Arginine Arginino-succinate (R)-2,3-Dihydroxy butanamide butanoate butanal 2-oxopentanoate Phosphatidyl Phosphatidyl Ø Glucose[e] Glucose[p] Glucose Valine 3-methylvalerate PGLipid(18:1) Lipid(18:4[6,9,12,15]) PG ioredoxin ioredoxin Fumarate glycero-P glycero-P Leucine APS Isochorismate CMP CMP Oxidized Reduced Pyridoxal Pyridoxal 5'-P Protein Agmatine Succinate semialdehyde-thiamin diphosphate anion Ø Acetate[e] Acetate[p] Acetate (S)-3-Methyl-2-oxopentanoate sn-Glycerol-3-P sn-Glycerol-3-P CoA 2-Dehydropantoate α-Isopropylmalate 2-Ketovaline iamine-PP L-Glutamate L-Glutamate CDP-diacyl CDP-diacyl Exploring SO4 Urea 2-Succinyl-6-hydroxy glycerol glycerol Ø Citrate[e] Citrate[p] Citrate Pyridoxine Pyridoxine 5'-P NADPH NADP+ Putrescine 2,4-cyclohexadiene PPi PPi 2-oxoglutarate 2-oxoglutarate S-Adenosylmethionine S-Adenosylmethioninamine 1-carboxylate Dephospho-CoA Pantoate 2-Isopropylmaleate L-Valine L-Isoleucine cis-octadec-11-enoyl cis-octadec-11-enoyl Octadecatetra Octadecatetra Ø α-kg[e]α-kg[p] 2-oxoglutarate β-Alanine ACP (n-C18_1) ACP ACP (n-C18_1) ACP CTP enoilACP ACP enoilACP ACP CTP S-Methyl-5-thio-Ru1P S-Methyl-5-thio-R1P 5-Methylthioadenosine 4-(Phosphonooxy) Spermidine 1,2-Diacyl 1,2-Diacyl AMP L-threonine sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Adenine Pi Succinylbenzoate sn-glycerol-3-P sn-glycerol-3-P Ø Malate[e] Malate[p] Malate Pantetheine 4'-P Pantothenate 3-Isopropylmalate Protein Protein Synechocystis’ UDP-6-sulfo UDP-6-sulfo UDP quinovosel UDP quinovosel Ø Sucrose[e] Sucrose[p] Sucrose 4'-Phosphopantothenoyl Succinylbenzoyl-CoA 1,2-Diacyl 1,2-Diacyl 4'-Phosphopantothenate (2S)-2-Isopropyl-3-oxosuccinate 4-Methyl-2-oxopentanoate L-Leucine Lipid(18:1) SQDG Lipid(18:4[6,9,12,15]) SQDG L-cysteine sn-glycerol sn-glycerol UDP-Gal UDP-Gal Ø GlcGlyc[e] GlcGlyc[p] GlcGlyc Uroporphyr Copropor inogen I phyrinogen I AaCoA 3hbCoA PHB granule 1,4-Dihydroxy UDP UDP Porphyrin and chlorophyll 2-naphthoate MGDG Lipid(18:1) MGDG Lipid(18:4[6,9,12,15]) optimal Ø Pyruvate[e] Pyruvate[p] Pyruvate Phytyl diphosphate UDP-Gal UDP-Gal 5-amino Porpho Hydroxy Uroporphyr Coproporphyr Protopor Protopor Proto Biliverdin Bilirubin levulinate bilinogen methylbilane inogen III inogen III inogen IX phyrino IX heme AcCoA malCoA PPi UDP UDP Ø Fructose[e] Fructose[p] Fructose Demethylphylloquinone DGDG Lipid(18:1) DGDG Lipid(18:4[6,9,12,15]) Fatty Acid Biosynthesis S-Adenosylmethionine Ø Cyanate[e] Cyanate[p] Cyanate L-Glutamate Precorrin 2 Mg-protopor Heme O Acetyl-ACP S-Adenosylhomocysteine solution space 1-semialdehyde phyrin IX malACP Vitamin K1 Ø Cobalt[e] Cobalt[p] Cobalt Precorrin 3A Heme A Acetoacetyl 3-oxohexa 3-oxoocta 3-oxodecanoyl 3-oxododeca 3-oxotetra 3-oxohexa 3-oxoocta L-Glutamyl Mg-protopor ACP noyl-ACP noyl-ACP noyl-ACP noyl-ACP decanoyl-ACP decanoyl-ACP decanoylACP Ø Pi[e] Pi[p] Pi tRNA(Glu) phyrin IX Phosphatidyl monomethyl ester Lipid(18:1[9]) PG Precorrin 3B glycero-P Ø K+[e] K+[p] K+ (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy CMP HMA acyl-ACP hexanoyl-ACP octanoyl-ACP decanoyl-ACP dodecanoyl-ACP palmitoylACP octadecanoylACP 13(1)-Hydroxy-Mg sn-Glycerol-3-P Ø Na+[e] Na+[p] Na+ Precorrin 4 protoporphyrin IX CDP-diacyl Soluble Pool 13-monomethyl ester glycerol But-2- trans-Hex trans-oct trans-dec trans-dodec trans-tetradec trans-hexadec trans-octadec γ-linolenoilACP Lipid(18:3[6,9,12]) PPi Ø Fe2+[e] Fe2+[p] Fe2+ enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP Pigment cis-octadec-9-enoyl cis-octadec-9-enoyl Precorrin 5 tRNA-Val ACP (n-C18_1) ACP ACP (n-C18_1) ACP CTP 13(1)-Oxo-Mg Aminoacyl-tRNA biosynthesis Ø Fe3+[e] Fe3+[p] Fe3+ Protein 1,2-Diacyl protoporphyrin IX cis-octadec-9-enoyl linoleoyl-ACP L-Valine L-valyl-tRNA(Val) sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Butyryl-ACP Hexanoyl-ACP Octanoyl-ACP Decanoyl-ACP Dodecanoyl-ACP Tetradecanoyl-ACP Hexadecanoyl-ACP Octadecanoyl-ACP Lipid(18:2[9,12]) sn-glycerol-3-P 13-monomethyl ester ACP (n-C18_1) (n-C18_2ACP) DNA tRNA-Glu Ø Cu2+[e] Cu2+[p] Cu2+ Cu2+[t] Precorrin 6A tRNA-Leu UDP-6-sulfo UDP Biomass speci�c quinovosel RNA L-Glutamate L-Glutamyl-tRNA(Glu) L-leucine L-leucyl-tRNA(Ile) Growth Rate Lipid(16:0) Lipid(18:0) Lipid(18:1[9]) 1,2-Diacyl Divinylproto Protochloro cis-dec-3-enoyl α-lineloyl-ACP Lipid(18:1[9]) SQDG Ø Zn2+[e] Zn2+[p] Zn2+ Lipid(18:3[9,12,15]) sn-glycerol chlorophyllide phyllide ACP (n-C10_1) (n-C18_3ACP) Peptidoglycan Precorrin 6B NADPH tRNA-Ile UDP-Gal malACP L-Glutaminyl-tRNA(Gln) L-Isoleucine L-isoleucyl-tRNA(Ile) Ø Mn2+[e] Mn2+[p] Mn2+ Lipid NADP+ UDP MGDG Lipid(18:1[9]) Chlorophyllide a 3-oxo-cis-dodec 3-oxo-cis-myristol 3-oxo-cis-palm 3-oxo-cis-vacc Octadecatetra UDP-Gal Precorrin 8 Phytyl diphosphate Lipid(18:4[6,9,12,15]) tRNA-Ala tRNA-Lys LPS 5-enoyl-ACP 7-eoyl-ACP 9-eoyl-ACP 11-eoyl-ACP enoilACP Ø Mg2+[e] Mg2+[p] Mg2+ L-Alanine L-alanyl-tRNA(Ala) L-Lysine L-lysyl-tRNA(Lys) UDP Ions PPi Chlorophyll a DGDG Lipid(18:1[9]) Ø Ni2+[e] Ni2+[p] Ni2+ Hydrogenobyrinate tRNA-Asp tRNA-Arg (R)-3-hydroxy-cis (R)-3-hydroxy-cis (R)-3-hydroxy-cis (R)-3-hydroxy-cis dodec-5-enoyl-ACP myristol-7-eoyl-ACP palm-9-eoyl-ACP vacc-11-eoyl-ACP L-Aspartate L-aspartyl-tRNA(Asp) L-Arginine L-arginyl-tRNA(Arg) Ø Ca2+[e] Ca2+[p] Ca2+ Hydrogenobyrinate tRNA-Asn tRNA-Pro a,c diamide trans-3-cis-5 trans-3-cis-7-myris trans-3-cis-9-palm trans-3-cis-11- L-Asparagine L-asparaginyl-tRNA(Asn) L-Proline L-prolyl-tRNA(Pro) Ø CO[e] CO[p] CO dodecenoyl-ACP toleoyl-ACP itoleoyl-ACP vacceoyl-ACP tRNA-Gly tRNA-His Ø H2[e] H2[p] H2 Cob(II)yrinate a,c diamide Glycine glycyl-tRNA(Gly) L-Histidine L-histidyl-tRNA(His) NADH cis-dodec-5-enoyl cis-tetradec-7-enoyl cis-hexadec-9-enoyl cis-octadec-11-enoyl ACP (n-C12_1) ACP (n-C14_1) ACP (n-C16_1) ACP (n-C18_1) Ø Spermidine[e] Spermidine[p] Spermidine tRNA-r tRNA-Phe NAD+ Cob(I)yrinate L-reonine L-threonyl-tRNA(r) L-Phenylalanine L-Phenylalanyl-tRNA(Phe) a,c diamide Ø Putrescine[e] Putrescine[p] Putrescine Lipid(16:1) Lipid(18:1) tRNA-Ser tRNA-Tyr

Ø Molybdate[e] Molybdate[p] Molybdate L-Serine L-seryl-tRNA(Ser) L-Tyrosine L-Tyrosyl-tRNA(Tyr) Adenosyl Adenosyl Adenosyl Adenosyl Adenosine-GDP Vitamin B12 cobyrinate cobyric acid cobinamide cobinamide-P cobinamide coenzyme tRNA-Cys tRNA-Trp a,c diamide Ø 2,3-Butanediol[e] 2,3-Butanediol[p] 2,3-Butanediol[c] L-Cysteine L-cysteinyl-tRNA(Cys) L-Tryptophan L-Tryptophanyl-tRNA(Trp)

2012-2014, Amsterdam, Netherlands tRNA-Met L-reonine Tyrosine (R)-1-Aminopropane L-Methionine L-Methionyl-tRNA(Met) N-Formylmethionyl-tRNA (c) T.R. Maarleveld, [email protected] phosphate 2-yl phosphate

Maarleveld et al, 2014. Plant Physiology A real life example: cyanobacterium Synechocystis

Legend: [e]: Extracellular Visualization of the Metabolic Network of Synechocystis Species PCC 6803 [p]: Periplasm [t]: ylakoid dIDP dITP dAMP Modeling others: Cytoplasm cAMP ATP ADP dADP dATP DNA Sink Reactions Demand Reactions Photosynthesis Pi R1P DNA Ø DNA 5-methylcytosineØ Indole-3-acetamide Indole-3-acetate Imidazole-4-acetaldehyde Imidazole-4-acetate H2O Pi Adenylo Oxidative Phosphorylation ITPIDP FOCYTC6[p] Protein RNA succinate AMP Adenosine Adenine AMP Growing 3-Hydroxy-2 (S)-Methylmalonate PC(r)[p] Ø PHB granule Ø Indole-3-acetaldehyde Periplasm H+[p] PHB granule methylpropanoate semialdehyde 2,5-Diamino-6- Protein ATP ADP (5'-phosphoribosylamino) GTP GMP XMP IMP FAICAR 8-Amino-7-oxo Cyanophycin(n) Ø Cyanophycin(n+2) Ø 2-Phenylacetamide Phenylacetic acid Pimeloyl-CoA 4-pyrimidineone THF nonanoate Phosphatidyl Phosphatidyl Cyt BD PGLipid(16:0) Lipid(18:2[9,12]) PG NDH-1 NDH-2 NDH-1 PQH2[p] Quinol Cyt B6f Cyt C ATPase glycero-P glycero-P 3,4-Dihydroxy 3,4-Dihydroxyphenyl CMP CMP type 4 Oxidase 10-Formyl-THF L-Histidinine α-Ribazole Ø S-Methyl-5-thio-Ru1P Ø L-Lactaldehyde (S)-Propane-1,2-diol Ribo�avin Metabolism GDP Deoxyguanosine SAICAR AICAR mandelaldehyde ethyleneglycol cGMP PPi PPPi 5-Amino-6- 5-Amino-6- sn-Glycerol-3-P sn-Glycerol-3-P (5'-phosphoribitylamino) (5'-phosphoribosylamino) UDP-N-acetylmuramoyl L- UDPMurAc(oyl-L-Ala-D-gamma Pi PPi Inositol 1-phosphate Inositol N4-Acetylamino 4-Acetamido CDP-diacyl CDP-diacyl uracil uracil alanyl-D-glutamyl-L-lysine Glu-L-Lys-D-Ala-D-Ala) butanal butanoate glycerol glycerol H+ P-ribosyl-C- 5-Amino-4-imidazole L-Histidinol L-Histidinol-P H2O SDH dGDP dGTP Aminoimidazole carboxyamide PPi PPi T.R. Maarleveld NADP+ NAD(P)H NAD(P)+ NAD(P)H ADP ATP dTDP-4-oxo-6 dTDP-4-oxo-L-rhamnose dTDP-L-rhamnose D-Tagatose 6-phosphate D-Tagatose 1,6-biphosphate H2O2 Protein Protein deoxy-D-glucose linoleoyl-ACP linoleoyl-ACP 6,7-Dimethyl 5-Amino-6- O2 Hexadecanoyl-ACP Hexadecanoyl-ACPACP ACP CTP (n-C18_2ACP) ACP (n-C18_2ACP) ACP CTP H+ H2 FADH2 FAD 8-(1-D-ribityl) (1-D-ribitylamino) DNA AIR Toxopyrimidine D-erythro-Imidazole 1,2-Diacyl 1,2-Diacyl lumazine uracil Imidazole-acetol-P 3-Octaprenyl-4-hydroxybenzoate 2-Octaprenylphenol sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P O2 H2O glycerol-phosphate NADH NAD+ sn-glycerol-3-P sn-glycerol-3-P Q8H2 L-Tyrosine 2-oxoglutarate L-Phenylalanine Purine Metabolism dTDP-Glc dTDP-Gal NADPH NADP+ UDP-6-sulfo UDP-6-sulfo Cytoplasm Q8H2Q8 Histidine Synthesis UDP UDP FNP-acetamidine UDP-6-sulfoquinovosel quinovosel quinovosel Lipid A FADH2 FAD Ribo�avin 4-Hydroxyphenyl 5-phospho LipidX 1,2-Diacyl 1,2-Diacyl 2-Hydroxy N-Formyl Phosphoribosyl-formimino Phosphoribosyl-formimino Disaccharide Lipid(16:0) SQDG Lipid(18:2[9,12]) SQDG Homogentisate pyruvate L-Glutamate PhPyr GAR ribosylamine sn-glycerol sn-glycerol phenylacetate GAR AICAR-phosphate AICAR-phosphate UDP-Glc UDP-Galα-D-Galactose 1-phosphate Galactose NADP+ NADPH UDP-N-acetylmuramoyl UDP-Gal UDP-Gal NADP+ NAD(P)H NAD(P)+ NAD(P)H Fd(ox) Fd(red) ADP ATP Sucrose-6-P Sucrose L-alanyl-D-glutamate ioredoxin ioredoxin SDH FMN UDP-2,3-bis(3-hydroxy H+ F6P X5P Oxidized Reduced UDP UDP hv hv Prephenate R1P D-Ribose PRPP Phosphoribosyl-ATP Phosphoribosyl-AMP CDP-Glc tetradecanoyl) MGDG Lipid(16:0) MGDG Lipid(18:2[9,12]) glucosamine UDP-Gal UDP-Gal 4-Aminobenzoate Cyanophycin(n+2) Cyanophycin(n+2) ACP UDP-N-acetylmuramoyl Cyt BD FAD UDP UDP 3,4-Dihydroxy-2-butanone 4-P Maltose Glucose GlcGlycP GlcGlyc L-alanine NDH-1 NDH-2 NDH-1 PS II PQH2[t] Quinol Cyt B6f PS I Cyt C ATPase Anthranilate Chorismate ADC Pyruvate HMA DGDG Lipid(16:0) DGDG Lipid(18:1[9,12]) type 3 Oxidase G3P E4P G3P R5P UDP-3-O-(3-hydroxy Fd(red) Fd(ox) N-(5-Phospho-D-ribosyl) Storage Products tetradecanoyl) Chorismate D-glucosamine anthranilate Acetaldehyde N-Acetyl GSSMs D-mannosamine UDP-MurNAc Ru5P 6PGL6PG G6P G1P ADP-Glc Glycogen Branched Glycogen 5-O-(1-Carboxyvinyl) D-Glutamate L-Glutamate FOCYTC6[t] GTP 3-phosphoshikimate ylakoid H2O[t] O2[t] H+[t] H+[t] Pentose Phosphate UDP-3-O-(β- PC(r)[t] 1-(2-Carboxyphenylamino) 2-deoxy F6P S7P X5P N-Acetyl-D- UDP-N-acetyl UDP-N-acetyl-3-(1-carbo hydroxymyristoyl) 1-deoxy-D-ribulose 5-P D-ribose 5-P Pathway Fructose F6P D-Glucosamine 6-P D-Glucosamine 1-P Exchange and Transport Reactions glucosamine-1-P D-glucosamine xyvinyl)-D-glucosamine N-acetylglucosamine 6-Pyruvoyltetra Dihydroneopterin Shikimate-3-P hydropterin Phosphatidyl Phosphatidyl PGLipid(16:1) Lipid(18:3[6,9,12]) PG Ø L-Alanine[e] L-Alanine[p] L-Alanine Sedoheptulose 1,7-PP glycero-P glycero-P Folate Metabolism Deoxyribose GDP-4-dehydro Indoleglycerol-P FBP M6P M1P GDP-Mannose GDP-L-fucose CMP CMP D-rhamnose Shikimate Ø L-Arginine[e] L-Arginine[p] L-Arginine 7,8-Dihydroneopterin Dihydroneopterin-Phosphate Glycolysis Sterol Metabolism sn-Glycerol-3-P sn-Glycerol-3-P L-Serine G3P E4P DHAP CDP-diacyl CDP-diacyl Indole G3P DHAP Zeaxanthin glycerol glycerol Ø Glycine[e] Glycine[p] Glycine Glycolaldehyde Glycolate The G3P L-Serine 3-Dehydroshikimate 3-Dehydroquinate DAHP dTTP DNA Pyruvate G3P PPi PPi cis-hexadec-9-enoyl cis-hexadec-9-enoyl Ø L-Glutamate[e] L-Glutamate[p] L-Glutamate PEP iamine Metabolism ACP (n-C16_1) ACP ACP (n-C16_1) ACP CTP γ-linolenoilACPγACP-linolenoilACP ACP CTP 2-Amino-4-hydroxy 7,8-Dihydropterin L-Tryptophan 13DPG 23DPG β-Cryptoxanthin CO2 Formate Oxalate 4-methyl-5-(2-phos 1,2-Diacyl 1,2-Diacyl 6-hydroxymethyl pyrophosphate Calvin Cycle dTDP dCTP dCDP CDP CMP 1-Deoxy-D-xylulose-5-P iamine-Piamine-PP iamine sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P THF-L-glutamate Folinic acid phoethyl)-thiazole sn-glycerol-3-P sn-glycerol-3-P 7,8-dihydropteridine 5-Methyl-THF Ø L-Glutamine[e] L-Glutamine[p] L-Glutamine 2mahmp PPi Protein β UDP-6-sulfo UDP-6-sulfo Glycine Glyoxylate Glycolate RuBP2PG PG3 3PHP Echinenone -Carotene UDP quinovosel UDP quinovosel Synechocystis Ø L-Histidine[e] L-Histidine[p] L-Histidine Dihydropteroate Dihydrofolate THF 10-Formyl-THF 5,10-Methenyl-THF 5,10-Methylene-THF CTP CYTD 2-C-Methyl-D-erythritol 4-P 1-deoxy-D-xylulose 4-Methyl-5-(2-hydroxyethyl)-thiazole 1,2-Diacyl 1,2-Diacyl ymd dTMP dUTP H2O Lipid(16:1) SQDG Lipid(18:3[6,9,12]) SQDG 2-Hydroxy-3-oxopropanoate sn-glycerol sn-glycerol THF RNA UDP-Gal UDP-Gal S-Lactoyl Methylglyoxal D-Ribose γ-Carotene Ø L-Leucine[e] L-Leucine[p] L-Leucine glutathione Mercaptopyruvate Protein L-Serine Pyruvate Glycerone HPYR Glycerate PG2 UTP CSN 4-(Cytidine 5'-diphospho) UDP UDP L-Cysteine 2-C-methyl-D-erythritol MGDG Lipid(16:1) MGDG Lipid(18:3[6,9,12]) Ø L-Lysine[e] L-Lysine[p] L-Lysine dUMP UDPdUDP UDP-Gal UDP-Gal gamma-Glutamyl S-Lactoyl Lycopene Cys-Gly Glutathione(red) cysteine L-Cysteine Acetyl-serine sn-Glycerol-3-P Glycerol Glyceraldehyde F1P PEP glutathione model UMP Uracil UDP UDP Ø L-Proline[e] L-Proline[p] L-Proline 2-Phospho-4-(cytidine 5'-PP) DGDG Lipid(16:1) DGDG Lipid(18:3[6,9,12]) Glycine Acetate H2S Pyrimidine Metabolism PPi PRPP 2-C-methyl-D-erythritol Neurosporene Glutathione(ox) D-Ala-D-Ala D-Alanine L-Alanine Pyruvate Lactate Ø L-Serine[e] L-Serine[p] L-Serine Orotidine-5-P PPi 5,10-Methylene-THF NADP+ L-Asparagine Protein 2-C-Methyl-D-erythritol 1-Hydroxy-2-methyl ADP 2,4-cyclodiphosphate 2-butenyl 4-PP DAMPP Diplopterol Ø hv[e] hv[p] hv Nicotinamide metabolism Acetyl-P PRPP ζ-Carotene PRPP PPi PPi PRPP Pi DHAP Orotate NADH NADPH ATP Nicotinate Succinate Nicotinamide NMN NAD+ Deamino-NAD+ Quinolinate Iminoaspartate L-Aspartate Geranyl Ø H+[e] H+[p] ribonucleotide Isopentenyl-PP PPiPP Squalene Diploptene NAD+ NADP+ Phyto�uene Phosphatidyl Phosphatidyl AcCoA Acetate Acetaldehyde Ethanol Fumarate PGLipid(18:0) Lipid(18:3[9,12,15]) PG Dihydroorotate NADH NADPH glycero-P glycero-P Ø H2O[e] H2O[p] H2O H2O[t] N-Succinyl-L-2,6 N-Succinyl-L-2- Oxalo CMP CMP ADPribose 1,5-Diaminopentane diaminopimelate amino-6-oxopimelate 4-P-Aspartate β-Alanine acetate Citrate cis-Aconitate L-Aspartate NAD+ NADP+ Tip of the CoA NH4 Cyanate Undecaprenyl-PP PPi Farnesyl-PP Geranylgeranyl-PP Prephytoene-PP Phytoene Protein sn-Glycerol-3-P sn-Glycerol-3-P Ø O2[e] O2[p] O2 O2[t] N-Carbamoyl CDP-diacyl CDP-diacyl Succinyl-CoA Carbamoyl-P AMP meso-Di LL-2,6-Di L-aspartate glycerol glycerol Protein L-Lysine THDP 23DHDP Aspartate-SA β-aminopropion Malate Carotenoid Metabolism UDP-N-acetyl amino aminopimelate iso-Citrate R5P aldehyde CO2 HCO3 PPi PPi Ø CO2[e] CO2[p] CO2 D-glucosamineUDP heptanedioate L-Glutamine 2-oxoglutarate L-Glutamate PyruvateH2O TCA Cycle Isopentenyl-PP all-trans Isopentenyl-PP PPi Phytyl diphosphate α-lineloyl-ACP α-lineloyl-ACP UDP-N-acetylmuramoyl-L-alanyl Decaprenyl-PP Octadecanoyl-ACP Octadecanoyl-ACPACP ACP CTP (n-C18_3ACP) ACP (n-C18_3ACP) ACP CTP UDP-N-acetylmuramoyl Homogentisate Peptidoglycan[p] Peptidoglycan UAAGMDA UAGMDA D-glutamyl-6-carboxy-L-lysyl Heptanedioate Homoserine 1,2-Diacyl 1,2-Diacyl Ø HCO3[e] HCO3[p] HCO3 L-alanyl-D-glutamate Fumarate 2-oxoglutarate sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Iceberg D-alanyl-D-alanine 2,3-Dimethyl PPi sn-glycerol-3-P sn-glycerol-3-P Undecaprenyl-PP Undecaprenyl-P D-Ala-D-Ala 5-phytylquinol 2-Methyl-6-phytylquinol Ø NH4[e] NH4[p] L-Glutamate Glutamyl-5-P Glutamate-5-SA P5C L-Proline Protein UDP-6-sulfo UDP-6-sulfo S-Adenosyl 2-oxoglutarate UDP quinovosel UDP quinovosel P-Homoserine Protein Succinate Succinyl-CoA H2S L-homocysteine 1,2-Diacyl 1,2-Diacyl L-Glutamate Lipid(18:0) SQDG Lipid(18:3[9,12,15]) SQDG Succinate γ-Tocopherol δ-Tocopherol sn-glycerol sn-glycerol Ø NO3[e] NO3[p] NO3 NO2 NH4 AcCoA 1-Pyrroline-3-hydroxy L-Cystathionine S-Adenosylmethionine S-Adenosylmethionine UDP-Gal UDP-Gal Acetate Succinate-SA 4-Aminobutanoate 2-oxoglutarate Hydroxyproline 5-carboxylate Protein L-reonine L-Homocysteine L-Methionine CoA S-Adenosylhomocysteine S-Adenosylhomocysteine Ø Urea[e] Urea[p] Urea L-Glutamate 2-oxoglutarate UDP UDP NADP+ NADPH CO2 CO2 Ornithine α-Tocopherol β-Tocopherol MGDG Lipid(18:0) MGDG Lipid(18:3[9,12,15]) Biotin UDP-Gal UDP-Gal Methionine Acetyl-Glutamate Carbamoyl-P Erythro-4 Ø SO4[e] SO4[p] SO4 2,3-Butanediol R-Acetoin 2-Acetolactate Pyruvate 2-oxobutanoate Hydroxyglutamate Synthesis Acetyl-Glutamate Pi UDP UDP Dethiobiotin 7,8-Diaminononanoate 4-Aminobutanal Urea Cycle DGDG Lipid(18:0) DGDG Lipid(18:3[9,12,15]) Urea TimoTimo Ø Succinate[e] Succinate[p] Succinate (S)-2-Aceto-2- S-Adenosylhomocysteine S-Adenosylmethionine Acetyl-Glutamate-5-P L-Glutamate L-Citrulline CO2 hydroxybutanoate 4-Hydroxy H20 L-Glutamate 2-oxoglutarate Urea 2-oxoglutarate Ø Fumarate[e] Fumarate[p] Fumarate Adenosine-3,5-PP AMP Vitamin B6 Acetyl-Glutamate-5-SA Acetylornithine (R)-2,3-Dihydroxy- � FADH2 FAD Ø Ethanol[e] Ethanol[p] Ethanol Sul te PAPS Pyruvate Glyoxylate Chorismate isovalerate Pyridoxamine Pyridoxamine 5'-P 4-Guanidino 4-Guanidino 4-Guanidino Guanidino Isoleucine L-Arginine Arginino-succinate (R)-2,3-Dihydroxy butanamide butanoate butanal 2-oxopentanoate Phosphatidyl Phosphatidyl Ø Glucose[e] Glucose[p] Glucose Valine 3-methylvalerate PGLipid(18:1) Lipid(18:4[6,9,12,15]) PG ioredoxin ioredoxin Fumarate glycero-P glycero-P Leucine APS Isochorismate CMP CMP Oxidized Reduced Pyridoxal Pyridoxal 5'-P Protein Agmatine Succinate semialdehyde-thiamin diphosphate anion Ø Acetate[e] Acetate[p] Acetate (S)-3-Methyl-2-oxopentanoate sn-Glycerol-3-P sn-Glycerol-3-P CoA 2-Dehydropantoate α-Isopropylmalate 2-Ketovaline iamine-PP L-Glutamate L-Glutamate CDP-diacyl CDP-diacyl Exploring SO4 Urea 2-Succinyl-6-hydroxy glycerol glycerol Ø Citrate[e] Citrate[p] Citrate Pyridoxine Pyridoxine 5'-P NADPH NADP+ Putrescine 2,4-cyclohexadiene PPi PPi 2-oxoglutarate 2-oxoglutarate S-Adenosylmethionine S-Adenosylmethioninamine 1-carboxylate Dephospho-CoA Pantoate 2-Isopropylmaleate L-Valine L-Isoleucine cis-octadec-11-enoyl cis-octadec-11-enoyl Octadecatetra Octadecatetra Ø α-kg[e]α-kg[p] 2-oxoglutarate β-Alanine ACP (n-C18_1) ACP ACP (n-C18_1) ACP CTP enoilACP ACP enoilACP ACP CTP S-Methyl-5-thio-Ru1P S-Methyl-5-thio-R1P 5-Methylthioadenosine 4-(Phosphonooxy) Spermidine 1,2-Diacyl 1,2-Diacyl AMP L-threonine sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Adenine Pi Succinylbenzoate sn-glycerol-3-P sn-glycerol-3-P Ø Malate[e] Malate[p] Malate Pantetheine 4'-P Pantothenate 3-Isopropylmalate Protein Protein Synechocystis’ UDP-6-sulfo UDP-6-sulfo UDP quinovosel UDP quinovosel Ø Sucrose[e] Sucrose[p] Sucrose 4'-Phosphopantothenoyl Succinylbenzoyl-CoA 1,2-Diacyl 1,2-Diacyl 4'-Phosphopantothenate (2S)-2-Isopropyl-3-oxosuccinate 4-Methyl-2-oxopentanoate L-Leucine Lipid(18:1) SQDG Lipid(18:4[6,9,12,15]) SQDG L-cysteine sn-glycerol sn-glycerol UDP-Gal UDP-Gal Ø GlcGlyc[e] GlcGlyc[p] GlcGlyc Uroporphyr Copropor inogen I phyrinogen I AaCoA 3hbCoA PHB granule 1,4-Dihydroxy UDP UDP Porphyrin and chlorophyll 2-naphthoate MGDG Lipid(18:1) MGDG Lipid(18:4[6,9,12,15]) optimal Ø Pyruvate[e] Pyruvate[p] Pyruvate Phytyl diphosphate UDP-Gal UDP-Gal 5-amino Porpho Hydroxy Uroporphyr Coproporphyr Protopor Protopor Proto Biliverdin Bilirubin levulinate bilinogen methylbilane inogen III inogen III inogen IX phyrino IX heme AcCoA malCoA PPi UDP UDP Ø Fructose[e] Fructose[p] Fructose Demethylphylloquinone DGDG Lipid(18:1) DGDG Lipid(18:4[6,9,12,15]) Fatty Acid Biosynthesis S-Adenosylmethionine Ø Cyanate[e] Cyanate[p] Cyanate L-Glutamate Precorrin 2 Mg-protopor Heme O Acetyl-ACP S-Adenosylhomocysteine solution space 1-semialdehyde phyrin IX malACP Vitamin K1 Ø Cobalt[e] Cobalt[p] Cobalt Precorrin 3A Heme A Acetoacetyl 3-oxohexa 3-oxoocta 3-oxodecanoyl 3-oxododeca 3-oxotetra 3-oxohexa 3-oxoocta L-Glutamyl Mg-protopor ACP noyl-ACP noyl-ACP noyl-ACP noyl-ACP decanoyl-ACP decanoyl-ACP decanoylACP Ø Pi[e] Pi[p] Pi tRNA(Glu) phyrin IX Phosphatidyl monomethyl ester Lipid(18:1[9]) PG Precorrin 3B glycero-P Ø K+[e] K+[p] K+ (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy (R)-3-hydroxy CMP HMA acyl-ACP hexanoyl-ACP octanoyl-ACP decanoyl-ACP dodecanoyl-ACP palmitoylACP octadecanoylACP 13(1)-Hydroxy-Mg sn-Glycerol-3-P Ø Na+[e] Na+[p] Na+ Precorrin 4 protoporphyrin IX CDP-diacyl Soluble Pool 13-monomethyl ester glycerol But-2- trans-Hex trans-oct trans-dec trans-dodec trans-tetradec trans-hexadec trans-octadec γ-linolenoilACP Lipid(18:3[6,9,12]) PPi Ø Fe2+[e] Fe2+[p] Fe2+ enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP 2-enoyl-ACP Pigment cis-octadec-9-enoyl cis-octadec-9-enoyl Precorrin 5 tRNA-Val ACP (n-C18_1) ACP ACP (n-C18_1) ACP CTP 13(1)-Oxo-Mg Aminoacyl-tRNA biosynthesis Ø Fe3+[e] Fe3+[p] Fe3+ Protein 1,2-Diacyl protoporphyrin IX cis-octadec-9-enoyl linoleoyl-ACP L-Valine L-valyl-tRNA(Val) sn-Glycerol-3-P 1-Acyl-sn-glycerol-3-P Butyryl-ACP Hexanoyl-ACP Octanoyl-ACP Decanoyl-ACP Dodecanoyl-ACP Tetradecanoyl-ACP Hexadecanoyl-ACP Octadecanoyl-ACP Lipid(18:2[9,12]) sn-glycerol-3-P 13-monomethyl ester ACP (n-C18_1) (n-C18_2ACP) DNA tRNA-Glu Ø Cu2+[e] Cu2+[p] Cu2+ Cu2+[t] Precorrin 6A tRNA-Leu UDP-6-sulfo UDP Biomass speci�c quinovosel RNA L-Glutamate L-Glutamyl-tRNA(Glu) L-leucine L-leucyl-tRNA(Ile) Growth Rate Lipid(16:0) Lipid(18:0) Lipid(18:1[9]) 1,2-Diacyl Divinylproto Protochloro cis-dec-3-enoyl α-lineloyl-ACP Lipid(18:1[9]) SQDG Ø Zn2+[e] Zn2+[p] Zn2+ Lipid(18:3[9,12,15]) sn-glycerol chlorophyllide phyllide ACP (n-C10_1) (n-C18_3ACP) Peptidoglycan Precorrin 6B NADPH tRNA-Ile UDP-Gal malACP L-Glutaminyl-tRNA(Gln) L-Isoleucine L-isoleucyl-tRNA(Ile) Ø Mn2+[e] Mn2+[p] Mn2+ Lipid NADP+ UDP MGDG Lipid(18:1[9]) Chlorophyllide a 3-oxo-cis-dodec 3-oxo-cis-myristol 3-oxo-cis-palm 3-oxo-cis-vacc Octadecatetra UDP-Gal Precorrin 8 Phytyl diphosphate Lipid(18:4[6,9,12,15]) tRNA-Ala tRNA-Lys LPS 5-enoyl-ACP 7-eoyl-ACP 9-eoyl-ACP 11-eoyl-ACP enoilACP Ø Mg2+[e] Mg2+[p] Mg2+ L-Alanine L-alanyl-tRNA(Ala) L-Lysine L-lysyl-tRNA(Lys) UDP Ions PPi Chlorophyll a DGDG Lipid(18:1[9]) Ø Ni2+[e] Ni2+[p] Ni2+ Hydrogenobyrinate tRNA-Asp tRNA-Arg (R)-3-hydroxy-cis (R)-3-hydroxy-cis (R)-3-hydroxy-cis (R)-3-hydroxy-cis dodec-5-enoyl-ACP myristol-7-eoyl-ACP palm-9-eoyl-ACP vacc-11-eoyl-ACP L-Aspartate L-aspartyl-tRNA(Asp) L-Arginine L-arginyl-tRNA(Arg) Ø Ca2+[e] Ca2+[p] Ca2+ Hydrogenobyrinate tRNA-Asn tRNA-Pro a,c diamide trans-3-cis-5 trans-3-cis-7-myris trans-3-cis-9-palm trans-3-cis-11- L-Asparagine L-asparaginyl-tRNA(Asn) L-Proline L-prolyl-tRNA(Pro) Ø CO[e] CO[p] CO dodecenoyl-ACP toleoyl-ACP itoleoyl-ACP vacceoyl-ACP tRNA-Gly tRNA-His Ø H2[e] H2[p] H2 Cob(II)yrinate a,c diamide Glycine glycyl-tRNA(Gly) L-Histidine L-histidyl-tRNA(His) NADH cis-dodec-5-enoyl cis-tetradec-7-enoyl cis-hexadec-9-enoyl cis-octadec-11-enoyl ACP (n-C12_1) ACP (n-C14_1) ACP (n-C16_1) ACP (n-C18_1) Ø Spermidine[e] Spermidine[p] Spermidine tRNA-r tRNA-Phe NAD+ Cob(I)yrinate L-reonine L-threonyl-tRNA(r) L-Phenylalanine L-Phenylalanyl-tRNA(Phe) a,c diamide Ø Putrescine[e] Putrescine[p] Putrescine Lipid(16:1) Lipid(18:1) tRNA-Ser tRNA-Tyr

Maarleveld et al, 2014. Plant Physiology After zooming in

T.R. Maarleveld dTTP DNA Photosynthesis Oxidative Phosphorylation GSSMs FOCYTC6[p] PC(r)[p] dTDP dCTP dCDP CDP CMP Periplasm H+[p] The

Synechocystis NDH-1 NDH-2 NDH-1 PQH2[p] Q Oxi Cyt B6f Cyt C ATPase model type 4 CTP CYTD dTMP dUTP H2O RNA Tip of the SDH H+ NADP+ NADPH NAD(P)+ NAD(P)H ADP ATP D-Ribose Iceberg UTP CSN H+ H2

O2 H2O dUMP UDPdUDP TimoTimo Q8H2Q8 Q8H2 NADPH NADP+ Cytoplasm UMP Uracil Exploring Pyrimidine Metabolism PPi PRPP NADP+ NADPH NAD(P)+ NAD(P)H Fd(red)Fd(ox) ADP ATP Synechocystis’ SDH H+ optimal hv hv Orotidine-5-P PPi solution space NDH-1 NDH-2 NDH-1 PS II PQH2[t] Q Oxi Cyt B6f PS I Cyt C ATPase type 3 PRPP Orotate Succinate Thylakoid H2O[t] O2[t] H+[t] FOCYTC6[t] H+[t] PC(r)[t] Fumarate Dihydroorotate

Maarleveld et al, 2014. Plant Physiology How can we simulate this model?

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space Flux Balance Analysis

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space FBA Flux Balance Analysis

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg

TimoTimo Genome-scale Exploring Synechocystis’ optimal metabolic model solution space

v2 Z FBA Point of optimalv

Solution space defined by Calculate �uxes constraints v that maximize Z 1 Exploring different scenario’s

T.R. Maarleveld Z = max µ GSSMs 0.090 3.5 LLS The Synechocystis 0.075 model 3.0 )

Tip of the − 1 Iceberg 2.5 0.060 TimoTimo 2.0 Exploring 0.045 Synechocystis’ CLLS optimal 1.5 solution space ( mmoluptake gDW h

− 1 0.030 1.0 HCO 3

0.015 0.5 CLS

0.0 0.000 0 10 20 30 40 50 60 Photon flux (mmol gDW h−1 ) Visualization of flux data is now possible with

T.R. Maarleveld

GSSMs

The Synechocystis model 1.0e-9 4.73e-7 0.000224 0.106 50 H+ H2 Tip of the O2 H2O Cytoplasm Q8H2Q8 NADPH NADP+ Iceberg FADFADH2 5.16 4.46e-7 2.31 NADP+ NAD(P)H NAD(P)+ NAD(P)H Fd(red)Fd(ox) ADP ATP SDH 5.3 H+ TimoTimo hv hv

Cyt BD Exploring NDH-1 NDH-2 NDH-1 PS II PQH2[t] Quinol Cyt B6f PS I Cyt C ATPase type 3 Oxidase Synechocystis’ VoNDA 0.0659 5.37 5.37 FOCYTC6[t] optimal Thylakoid H2O[t] O2[t] H+[t] H+[t] PC(r)[t] solution space Visualization of Network DAta Carbon and Light Limiting State

T.R. Maarleveld grey line: flux = 0 1.0e-9 4.75e-7 0.000225 0.107 50.7 GSSMs Photosynthesis The Oxidative Phosphorylation FOCYTC6[p] Synechocystis PC(r)[p] model Periplasm H+[p]

Tip of the NDH-1 NDH-2 NDH-1 PQH2[p] Q Oxi Cyt B6f Cyt C ATPase Iceberg type 4

TimoTimo SDH H+ Exploring NADP+ NADPH NAD(P)+ NAD(P)H ADP ATP 0.0317 Synechocystis’ H+ H2 optimal O2 H2O solution space Q8H2Q8 Cytoplasm Q8H2 NADPH NADP+

4.61 3.15 NADP+ NADPH NAD(P)+ NAD(P)H Fd(red)Fd(ox) ADP ATP SDH H+ hv hv 6.06

NDH-1 NDH-2 NDH-1 PS II PQH2[t] Q Oxi Cyt B6f PS I Cyt C ATPase type 3

6.95 FOCYTC6[t] Thylakoid H2O[t] O2[t] H+[t] 7.02 0.957 H+[t] PC(r)[t] Light limiting state

T.R. Maarleveld grey line: flux = 0 1.0e-9 4.75e-7 0.000225 0.107 50.7 GSSMs Photosynthesis The Oxidative Phosphorylation FOCYTC6[p] Synechocystis PC(r)[p] model Periplasm H+[p]

Tip of the NDH-1 NDH-2 NDH-1 PQH2[p] Q Oxi Cyt B6f Cyt C ATPase Iceberg type 4

TimoTimo SDH H+ Exploring NADP+ NADPH NAD(P)+ NAD(P)H ADP ATP 0.0122 Synechocystis’ H+ H2 optimal O2 H2O solution space Q8H2Q8 Cytoplasm Q8H2 NADPH NADP+

1.77 1.21 NADP+ NADPH NAD(P)+ NAD(P)H Fd(red)Fd(ox) ADP ATP SDH H+ hv hv 2.33

NDH-1 NDH-2 NDH-1 PS II PQH2[t] Q Oxi Cyt B6f PS I Cyt C ATPase type 3

2.67 FOCYTC6[t] Thylakoid H2O[t] O2[t] H+[t] 2.7 0.368 H+[t] PC(r)[t] Carbon Limiting State

T.R. Maarleveld grey line: flux = 0 1.0e-9 4.75e-7 0.000225 0.107 50.7 GSSMs Photosynthesis The Oxidative Phosphorylation FOCYTC6[p] Synechocystis PC(r)[p] model Periplasm H+[p]

Tip of the NDH-1 NDH-2 NDH-1 PQH2[p] Q Oxi Cyt B6f Cyt C ATPase Iceberg type 4

TimoTimo SDH H+ Exploring NADP+ NADPH NAD(P)+ NAD(P)H ADP ATP 0.0441 Synechocystis’ H+ H2 optimal O2 H2O solution space Q8H2Q8 Cytoplasm Q8H2 NADPH NADP+

1.13 3.85 NADP+ NADPH NAD(P)+ NAD(P)H Fd(red)Fd(ox) ADP ATP SDH H+ hv hv 1.58

NDH-1 NDH-2 NDH-1 PS II PQH2[t] Q Oxi Cyt B6f PS I Cyt C ATPase type 3 22.2

23.8 FOCYTC6[t] Thylakoid H2O[t] O2[t] H+[t] 1.58 H+[t] PC(r)[t] Net effect

T.R. Maarleveld

GSSMs

The Synechocystis JPSI/JPSII = 0.058 (LEF gives 1) model JATP/JNADPH = 7.2 (LEF gives 1.28) Tip of the Iceberg PSII: 2 Hc + PQ + H2O + 2 hv → 2 Ht + PQH2 + 0.5 O2 TimoTimo Quinol oxidase: PQH + 0.5 O → H O + PQ Exploring 2 2 2 Synechocystis’ net reaction: 2 H + 2 hv → 2 H optimal c t solution space

net effect: ATP production! Tip of the iceberg

T.R. Maarleveld

GSSMs Genome-scale metabolic reconstruction The

v2 Z Synechocystis FBA Point of model optimal v Solution space Calculate uxes de ned by constraints that maximize Z v Tip of the 1 Iceberg TimoTimo ace Exploring ? Synechocystis’ tion sp optimal solu solution space mal l opti ona ? mensi tidi Mul ? Genome-scale metabolic reconstruction

v2 Z T.R. Maarleveld FBA Point of optimalv

Solution space Calculate �uxes defined by that maximize Z constraints v1 GSSMs

The Rays Synechocystis model

Tip of the Linealities Iceberg Multidimensional optimal solution space Vertices TimoTimo

Exploring Synechocystis’ optimal solution space CoPE FBA

Topological understanding of the metabolic capacity in terms of metabolic flux routes Kelk et al, 2012. Scientific Reports. CoPE-FBA is slow!

T.R. Maarleveld

GSSMs

The Synechocystis Even I'm faster model Tip of the than CoPE-FBA Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space Can we speed-up CoPE-FBA?

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space Our solution: CoPE-FBA 2.0 a.k.a. TimoTimo

T.R. Maarleveld

dTTP DNA GSSMs dTDP dCTP dCDP CDP CMP The Synechocystis CTP CYTD ymd dTMP dUTP model RNA UTP CSN

Tip of the dUMP UDPdUDP Iceberg UMP Uracil PPi PRPP

TimoTimo Orotidine-5-P PPi

PRPP Exploring Orotate Synechocystis’ Succinate Acetaldehyde Ethanol Fum optimal Dihydroorotate solution space TimoTimo How fast is TimoTimo?

T.R. Maarleveld

GSSMs

The Synechocystis model Running time (s) Running time (s) Organism (model) Source CoPE-FBA Kelk et al. 2012 TimoTimo Tip of the S. PC6803 (iTM686) glycogen FAILED 117 Iceberg S. PC6803 (iTM686) light FAILED 26 E. coli (iAF1260,ox) glucose FAILED 36 TimoTimo E. coli (iAF1260,noox) glucose FAILED 27 L. Lactis glucose 432495 16 Exploring S. thermophilus lactose 345362 15 Synechocystis’ M. tuberculosis (iNJ661) glycerol FAILED 41 optimal M. barkeri (iAF692) methanol 265760 12 solution space E. coli (iJR904) malate 324793 10 E. coli (iJR904) fumarate 584690 16 "Faster than lightning", but why?

T.R. Maarleveld GSSMs TimoTimo: The Synechocystis model From days Tip of the Iceberg to minutes TimoTimo

Exploring Synechocystis’ optimal solution space CoPE-FBA approach (in a nutshell)

iAF1260 (glc, aerobic) 5184 CoPE-FBA (weeks) T.R. Maarleveld 2 2 Vertices Subnetworks 3 3 GSSMs 120.932.352 2 6 The 2 Synechocystis 54 model

Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space

Kelk et al, 2012. Scientific Reports TimoTimo uses a divide-and-conquer approach

iAF1260 (glc, aerobic) 5184 CoPE-FBA (weeks) T.R. Maarleveld 2 2 Vertices Subnetworks 3 3 GSSMs 120.932.352 2 6 The 2 Synechocystis 54 model

Tip of the Iceberg Subnetworks TimoTimo

Exploring Synechocystis’ TimoTimo (minutes) optimal 5184 solution space 2 Vertices 2 6+3+5184+3+2+54+2+2 = 5256 3 3 2 6 2 54 Enumerate 0.004% of the vertices to get all

Maarleveld et al, 2015. PLoS Comp. Biol. A real life example: cyanobacterium Synechocystis

T.R. Maarleveld

GSSMs

The Synechocystis model

Tip of the Iceberg

TimoTimo

Exploring Synechocystis’ optimal solution space

Maarleveld et al, 2014. Plant Physiology Why do we have so many ?? We do not have a enough (flux) constraints

Optimal solution space characterization after reversible-reaction splitting

T.R. Maarleveld

GSSMs

The Synechocystis Synechocystis iTM686 model autotrophic (LLS) heterotrophic (glycogen) Tip of the Simulation time (s) 135 228 Iceberg Rays 242 242 TimoTimo Linealities 0 0 Exploring Synechocystis’ Vertices 41.803.776 1.399.652.352 optimal solution space Subnetworks 11 11 We do not have a enough (flux) constraints

Optimal solution space characterization after reversible-reaction splitting

T.R. Maarleveld

GSSMs

Why do we have so many ?? Optimal solution space characterization after reversible-reaction splitting

T.R. Maarleveld

GSSMs

Why do we have so many ?? We do not have a enough (flux) constraints Synechocystis iTM686 growth condition autotrophic (LLS) heterotrophic (glycogen) Vertices 41.803.776 1.399.652.352 min(PL) 184.320 460.800 min(PJ) 24 4

What kind of distributions do you expect?

What’s the effect of secondary objectives?

T.R. Maarleveld

GSSMs PL = |{Ji : Ji 6= 0}| (1) The Synechocystis r model X PJ = |Ji| (2) Tip of the Iceberg i=1 TimoTimo

Exploring Synechocystis’ optimal solution space What kind of distributions do you expect?

What’s the effect of secondary objectives?

T.R. Maarleveld

GSSMs PL = |{Ji : Ji 6= 0}| (1) The Synechocystis r model X PJ = |Ji| (2) Tip of the Iceberg i=1 TimoTimo

Exploring Synechocystis’ optimal Synechocystis iTM686 growth condition solution space autotrophic (LLS) heterotrophic (glycogen) Vertices 41.803.776 1.399.652.352 min(PL) 184.320 460.800 min(PJ) 24 4 What’s the effect of secondary objectives?

T.R. Maarleveld

GSSMs PL = |{Ji : Ji 6= 0}| (1) The Synechocystis r model X PJ = |Ji| (2) Tip of the Iceberg i=1 TimoTimo

What kind of distributions do you expect? Gaussian and bimodal distributions of secondary optimization of vertices

T.R. Maarleveld Õþ GSSMs Õþä autotrophic Õþ¦ The heterotrophic Synechocystis # Vertices Õþó model Õþþ Tip of the Iceberg óþþ TimoTimo

Exploring Synechocystis’ Õ¢þ optimal solution space

Õþþ Vertex Sum of Abs. Fluxes

¢þ

þ ¢ìþ ¢ì¢ ¢¦þ ¢¦¢ Õþþ Õþó Õþ¦ Õþä Õþ Vertex Length # Vertices

; What explains the bimodal distributions? autotrophic growth

T.R. Maarleveld min P max P GSSMs j j 2.72.7 4.24.2 Ø H+[e] H+[p] Ø H+[e] H+[p] The Synechocystis 0.76 0.76 0.76 2.3 2.3 2.3 model Ø H2O[e] H2O[p] H2O Ø H2O[e] H2O[p] H2O

2.2 3.7 Tip of the Na+[p] Na+ Na+[p] Na+ Iceberg H2O 1.5 1.5 H2O TimoTimo Ø CO2[e] CO2[p] CO2 Ø CO2[e] CO2[p] CO2 2.0 3.5 2.2 2.2 2.2 3.7 3.7 Exploring Ø HCO3[e] HCO3[p] HCO3 H+ Ø HCO3[e] HCO3[p] HCO3 H+ Synechocystis’ optimal Na+[p] Na+ Na+Na+[p] solution space − − strategy: minimal HCO3 vs. maximal HCO3 import relative effect: 206 % total effect: 11 % What explains the bimodal distributions? autotrophic growth

T.R. Maarleveld

min Pj max Pj GSSMs 2.72.7 4.24.2 Ø H+[e] H+[p] Ø H+[e] H+[p] The diffusion Synechocystis 0.76 0.76 0.76 2.3 2.3 2.3 Ø H2O[e] H2O[p] H2O Ø H2O[e] H2O[p] H2O model diffusion diffusion 2.2 3.7 Tip of the Na+[p] Na+ Carbonic Na+[p] Na+ Iceberg antiporter anhydrase 1.5 1.5 Ø CO2[e] CO2[p] CO2 H2O Ø CO2[e] CO2[p] CO2 H2O TimoTimo diffusion symporter 2.0 3.5 2.2 2.2 2.2 3.7 3.7 Exploring Ø HCO3[e] HCO3[p] HCO3 H+ Ø HCO3[e] HCO3[p] HCO3 H+ Synechocystis’ Na+[p] Na+ Na+Na+[p] optimal solution space − − strategy: minimal HCO3 vs. maximal HCO3 import some reactions are related to diffusion requires additional expression of transporters and enzymes Summary

T.R. Maarleveld we present GSSMs

The a ready-to-use genome-scale stoichiometric model of the Synechocystis model cyanobacterium Synechocystis with interactive map Tip of the we present a faster and more user-friendly tool to analyze Iceberg

TimoTimo the metabolic potential in the optimum

Exploring Synechocystis’ optimal we can use this to e.g. solution space explore the metabolic potential for producing biofuels obtain a topological understanding of the metabolic capacity investigate flexibility in the optimum Acknowledgments

T.R. Maarleveld

GSSMs

The Synechocystis model Meike Wortel , Brett Olivier, Bas Teusink, Frank Bruggeman (VU) Tip of the Iceberg Arne Reimers (CWI)

TimoTimo

Exploring Maarleveld et al. PLoS Comp. Biol. 2015 - Interplay between Synechocystis’ optimal Constraints, Objectives, and Optimality for Genome-Scale solution space Stoichiometric Models Maarleveld et al. Plant Physiology 2014 - A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

Contact information: t.r.maarleveld[at]cwi.nl Website: memesa-tools.sf.net