Title: Study of metabolic network of Cupriavidus necator DSM 545 growing on glycerol applying elementary flux modes and yield space analysis
Journal: Industrial Microbiology and Biotechnology
Authors: Markan Lopara, Ivna Vrana Špoljarića, Nikolina Cepaneca, Martin Kollerb*, Gerhart Brauneggc, Predrag Horvata
a Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6/IV, HR-10000 Zagreb, Croatia
b Institute of Biotechnology and Biochemical Engineering, Graz University of Technology; Petersgasse 12, A- 8010 Graz, Austria
c ARENA, Arbeitsgemeinschaft für Ressourcenschonende & Nachhaltige Technologien, Graz University of Technology; Inffeldgasse 23, 8010 Graz, Austria
d Institute of Chemistry, University of Graz; Stremargasse 16/IV
*Corresponding author: Martin Koller, E-mail:
Metabolic reactions:
(Ei means enzyme that catalyses i-th reaction of metabolic network presented in Fig.1. Arrows indicate relevant directions of reactions)
E1 : Gext + PEP → G6P + Pyr / MR (1)E2 : G6P + NADP → 6PGnat + NADPH / MR (2)
E3 : 6PGnat → KDPG / MR (3)
E4 : KDPG → G3P + Pyr / MR (4)
E5 : 6PGnat + NADP → Ril5P + NADPH + CO2 / MR (5)
E6 : Ril5P ↔ R5P / MR (6)
E7 : Ril5P ↔ X5P / MR (7)
E8 : R5P + X5P ↔ G3P + S7P / MR (8)
E9 : G3P + S7P ↔ E4P + F6P / MR (9)
E10 : X5P + E4P ↔ F6P + G3P / MR (10)
E11 : G6P ↔ F6P / MR (11)
E12 : F16P → F6P / MR (12)
E13 : F16P ↔ G3P + DHAP / MR (13)
E14 : DHAP ↔ G3P / MR (14)
E15 : G3P + NAD+ ↔ BPG + NADH / MR (15)
E16 : BPG + ADP ↔ 3PG + ATP / MR (16)
E17 : 3PG ↔ 2PG / MR (17)
E18 : 2PG ↔ PEP / MR (18)
E19 : PEP + ADP → PYR + ATP / MR (19)
E20 : PYR + NAD+ → AcCoA + NADH / MR (20)
E21 : AcCoA + OXA → CIT + CoA / MR (21)
E22 : CIT ↔ ISC / MR (22)
E23 : ISC + NADP ↔ αKG + NADPH + CO2 / MR (23)
E24 : αKG + CoA + NAD+ → SucCoA + CO2 + NADH / MR (24)
E25 : SucCoA + ADP ↔ CoA + SUC + ATP / MR (25)
E26 : SUC + FAD ↔ FUM + FADH2 / MR (26)
E27 : FUM ↔ MAL / MR (27)
E28 : MAL + NAD+ ↔ OXA + NADH / MR (28)
E29 : ISC → SUC + GLYOX / MR (29)
E30 : AcCoA + GLYOX → CoA + MAL / MR (30)
E31 : Pyr + ATP + CO2 → OXA + ADP / MR (31)
E32 : OXA + ATP → PEP + ADP + CO2 / MR (32)
E33 : αKG + NADPH + NH3 ↔ GLUT + NADP / MR (33)
E34 : GLUT + NH3 + ATP ↔ GLUM + ADP / MR (34)
E35 : 2 AcCoA ↔ AcAcCoA + CoA / MR (35)
E36 : AcAcCoA + NADPH ↔ 3HBCoA + NADP / MR (36)
E37 : 3HBCoA → PHB + CoA / MR (37)
E38 : PHB + NAD → AAC + NADH / MR (38)
E39 : AAC + SucCoA → AcAcCoA + SUC / MR (39)
E40 : 0.021 G6P + 0.09 R5P + 0.036 E4P + 0.007 F6P + 0.013 G3P + 0.15 3PG + 0.052 PEP + 0.283 PYR + 0.179 OXA + 0.832 GLUT + 0.025 GLUM + 0.374 AcCoA + 4.11 ATP + 0.312 NAD+ + 0.826 NADPH → BIO + 0.751 αKG + 0.374 CoA + 4.11 ADP + 0.312 NADH + 0.826 NADP + 0.261 CO2 / MR (40)
E41 : NH3ext → NH3 / MR (41)
E42 : 2 NADH + O2 + 4 ADP → 2 NAD+ + 4 ATP / MR (42)
E43 : NADPH + NAD+ → NADP + NADH / MR (43)
E44 : 2 FADH2 + O2 + 2 ADP → 2 FAD + 2 ATP / MR (44)
E45 : GLY + ATP → GLY3P + ADP / MR (45)
E46 : GLY3P + NAD+ → DHAP + NADH / MR (46)*
E47 : GLYext → GLY / MR (47)
E48 : ATP → ADP / MR (48)
* In case when the FAD/FADH2 pair is considered to take place in reaction of Glycerol 3-phosphate dehydrogenase (GLY-3-P DH) reaction E46 should be written as follows:
E46 : GLY3P + FAD → DHAP + FADH2