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J Biol Chem. 2006 Mar;281(12):8024-33. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. Fong SS, Nanchen A, Palsson BO, et al.



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ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 219 R02736+R01528+R00267+R00214
NADPH production rate Minium 183 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 246 R02736+R01528+R00267+R00214
NADPH production rate Minium 196 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 208 R02736+R01528+R00267+R00214
NADPH production rate Minium 192 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 97 R02736+R01528+R00267+R00214
NADPH production rate Minium 58 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum N/A R02736+R01528+R00267+R00214
NADPH production rate Minium 68 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum N/A R02736+R01528+R00267+R00214
NADPH production rate Minium 70 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum N/A R02736+R01528+R00267+R00214
NADPH production rate Minium 67 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 104 R02736+R01528+R00267+R00214
NADPH production rate Minium 63 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 90 R02736+R01528+R00267+R00214
NADPH production rate Minium 68 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 96 R02736+R01528+R00267+R00214
NADPH production rate Minium 61 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 130 R02736+R01528+R00267+R00214
NADPH production rate Minium 49 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 118 R02736+R01528+R00267+R00214
NADPH production rate Minium 53 R02736+R01528
ATP production rate Maximum N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R00267+2.5*R08549-R00405+1.5*R00402+2.5*R00342
+2.5*R00214
ATP production rate Minium N/A -R01786-R04779+2.5*R01061+R01512+R00200+2.5*R00209
+2.5*R08549-R00405+1.5*R00402+2.5*R00342
NADPH production rate Maximum 121 R02736+R01528+R00267+R00214
NADPH production rate Minium 53 R02736+R01528
Growth Condition
Strains Escherichia coli MG1655
Genotype Wild type
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.63/h
Case-specific description Wild type
Growth Condition
Strains Escherichia coli pgi mutant
Genotype pgi gene knock-out
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.17/h
Case-specific description parent mutant
Growth Condition
Strains Escherichia coli pgiE1 mutant
Genotype pgi gene knock-out with endpoints designated E1
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.34/h
Case-specific description evolved mutant(50 days of evolution)
Growth Condition
Strains Escherichia coli pgiE2 mutant
Genotype pgi gene knock-out with endpoints designated E2
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.53/h
Case-specific description evolved mutant(50 days of evolution)
Growth Condition
Strains Escherichia coli ppc mutant
Genotype ppc gene knock-out
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.22/h
Case-specific description parent mutant
Growth Condition
Strains Escherichia coli ppcE1 mutant
Genotype ppc gene knock-out with endpoints designated E1
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.55/h
Case-specific description evolved mutant(45 days of evolution)
Growth Condition
Strains Escherichia coli ppcE2 mutant
Genotype ppc gene knock-out with endpoints designated E2
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.56/h
Case-specific description evolved mutant(45 days of evolution)
Growth Condition
Strains Escherichia coli pta mutant
Genotype pta gene knock-out
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.58/h
Case-specific description parent mutant
Growth Condition
Strains Escherichia coli ptaE1 mutant
Genotype pta gene knock-out with endpoints designated E1
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.64/h
Case-specific description evolved mutant(30 days of evolution)
Growth Condition
Strains Escherichia coli ptaE2 mutant
Genotype pta gene knock-out with endpoints designated E2
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.66/h
Case-specific description evolved mutant(30 days of evolution)
Growth Condition
Strains Escherichia coli tpi mutant
Genotype tpi gene knock-out
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.18/h
Case-specific description parent mutant
Growth Condition
Strains Escherichia coli tpiE1 mutant
Genotype tpi gene knock-out with endpoints designated E1
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.51/h
Case-specific description evolved mutant(50 days of evolution)
Growth Condition
Strains Escherichia coli tpi mutant
Genotype tpi gene knock-out with endpoints designated E2
Culture medium M9 minimal medium supplemented with 2g/L of glucose in 500 ml Erlenmeyer flasks using magnetic stir bars for aeration at 37 Celsius. M9 medium contained (per liter of deionized water)0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4-2H2O,and 3.0 g KH2PO4. The following components were sterilized separately and then added (per liter final volume of medium): 2 ml of 1 M MgSO4, 1ml of 0.1 M CaCl2, 0.3 ml of 1 mM filter sterilized thiamine HCl, and 10 ml of a trace element solution containing (per liter) 1 g of FeCl3-6H2O,0.18 g ZnSO4-7H2O, 0.12 g CuCl2-2H2O, 0.12 g MnSO4-H2O and 0.18 g CoCl2-6H2O. At the startof evolution, initial pre-cultures of each mutant were grown overnight in Luria-Bertani(LB) medium before being transferred to minimal medium for adaptive evolution.
Carbon source Glucose
Growth rate 0.49/h
Case-specific description evolved mutant(50 days of evolution)
Specific Rate (mmol g-1 h-1)
glucose 8.8
acetate 4.5
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 2.3
acetate 0.1
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 5.8
acetate 2.6
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 5.6
acetate 0
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 3
acetate 1.1
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 8.1
acetate 2.2
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 7.8
acetate 2.2
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 9.1
acetate 0.6
Pyruvate 4.3
Specific Rate (mmol g-1 h-1)
glucose 10.3
acetate 0.7
Pyruvate 4.6
Specific Rate (mmol g-1 h-1)
glucose 8.6
acetate 0.7
Pyruvate 2.8
Specific Rate (mmol g-1 h-1)
glucose 2.7
acetate 0.2
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 7.8
acetate 1
Pyruvate 0
Specific Rate (mmol g-1 h-1)
glucose 7.3
acetate 0.9
Pyruvate 0
Source