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Biological Pathways Analysis and Engineering




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                                  ! "#$%&' (  )*                        +      ,    (   +      *     +          E. coli metabolic capabilities                      +      ,    (   +     How can we identify multiple metabolic manipulations for producing a desired product and also computationally evaluate of the consequences of potential network modifications ?  *     +          How can we systematically select the appropriate set of pathways/genes to recombine into existing production systems? Desired Phenotype E. coli metabolic capabilities How can we identify gene knockouts that will force biochemical overproduction by coupling it with cell growth? Desired Phenotype E. coli metabolic capabilities E. coli metabolic capabilities       µ  PEP G6P F16P F6P 13P2DG 3PDGL 2PDGL PEP PYR OA MAL SUCCOA CIT AKG GAP ICIT DHAP GLC PYR D6PGL RL5P X5P S7P E4P F6P GAP R5P D6PGC FUM ACCOA SUCC ACTP AC LAC ETH Escherichia coli Chemical Process Plant + 9:  1  2 "    PEP G6P F16P F6P 13P2DG 3PDGL 2PDGL PEP PYR OA MAL SUCCOA CIT AKG GAP ICIT DHAP GLC PYR D6PGL RL5P X5P S7P E4P F6P GAP R5P D6PGC FUM ACCOA SUCC ACTP AC LAC ETH 0 2 4 6 8 10 12 14 0 0.2 0.4 0.6 0.8 1 1.2 Growth Rate (1/hr) 1,3 PD Production Limits (mmol/hr)Complete E. coli network Basis: 10 mmol/hr glucose, 1 gDW cells Maximum Growth: E. coli (wild type) GL3P Non-E. coli reaction Glycerol GPP1& 2 3-HP dhaB 1,3 PD dhaT Non-E. coli genes/enzymes: GPP1&2: glycerol-3-phosphatase dhaB: glycerol dehydratase dhaT: 1,3 PD oxidoreductase Klebsiella pneumoniae Klebsiella pneumoniae Saccharomyces cerevisiae PEP G6P F16P F6P 13P2DG 3PDGL 2PDGL PEP PYR OA MAL SUCCOA CIT AKG GAP ICIT DHAP GLC PYR D6PGL RL5P X5P S7P E4P F6P GAP R5P D6PGC FUM ACCOA SUCC ACTP AC LAC ETH + 9:  1  2 "      GLAL Basis: 10 mmol/hr glucose, 1 gDW cells Maximum Biomass : 1,3 PD: 1.05 hr-1 0.00 mmol/hr “Wild” type: Maximum Biomass : 1,3 PD: 0.21 hr-1 9.66 mmol/hr Mutant A: Mutant A: (3) Fructose-1,6-bisphosphatase (fbp) or Fructose-1,6-bisphosphate aldolase (fba) (2) Phosphoglycerate kinase (pgk) or Glyceraldehyde-3-phosphate dehydrogenase (gapA, gapC1C2) (1) Aldehyde dehydrogenase (adhC) GL3P Non-E. coli reaction Glycerol 2KD6PG Entner-Doudoroff 3-HP 1,3 PD PEP ...





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