: -CH2O - anadph + bproduct + catp + dnadh + eco2 2O + 2NADPH + CO 2 2O ATP + CO 2

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Juniper Oliver
5 years ago
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1 Supplementary Notes In the calculations below metabolism is assumed to be respiro-fermentative in nature, which is generally the case under high glycolytic flux and is the best case scenario for pathways requiring ATP. Elemental balances for oxygen and hydrogen have not been considered, as they are embedded in the redox balance. In case of redox deficient pathways, reducing equivalents are assumed to be generated via oxidation of substrate completely to CO via the pentose phosphate pathway leading to NADPH per glucose molecule oxidized. To account for extra ATP/CTP requirement it is assumed that each glucose molecule leads to formation of 9.85 ATP molecules 5 via respiration. The substrate requirement for energy is taken into account while calculating pathway yields for energy deficient pathways. The constraint that net ATP, NADH and NADPH accumulation is zero for the system gives us a set of 3 equations for determining the individual rates of the reactions below (i.e., v, v and v 3 ), which can then be solved to finally obtain redox-constrained pathway yields. It needs to be noted that thermodynamic constraints may place the maximum yield limits even lower than that calculated by pure energy balance in this paper. Y P calculation: : -CHO - anadph + bproduct + catp + dnadh + eco () : -CH O + NADPH + CO () 3 : -CH O + 4.8ATP + CO (3) Here equation () represents the stoichiometric pathway balance for product formation. The coefficients a, b, c, d, e would be product and pathway specific. The coefficients a, c and d signify NADPH requirement, ATP production and NADH production per C-mol of substrate (glucose) respectively. Equation () accounts for substrate consumption for supply of NADPH. Equation (3) is included in calculations only when the coefficient c in equation is negative i.e. ATP is required for product synthesis. Pathway yield can be expressed as: v = Y = Y P Y.. v+ v + v3 + a / ( c /4.8) if c<0 else c=0 (4) Where Y is product yield based on equation () alone. It can be seen that for a = 0 and c 0, Y P =Y. Y P,G calculation: 4 : -CHO - ATP - NADH + CH8 3O (Glycerol) (5) 3 3 Equation 5 is for glycerol production for purpose of co-factor regeneration. As previously, equation (3) is included in calculations only when (d-c) is positive. v = Y = Y v v v v a d c d P,G Y / + (( )/4.8) + if (d-c)>0 else (d-c)=0 3 (6) Nature Biotechnology: doi:0.038/nbt.055

2 Expressions for P,G are same as obtained for Y P,G, with only difference being in values of a and d adjusted to reflect co-factor imbalance. P,G,X calculation: α x ε : -CH O - ATP + CH O N (Biomass) + NADH + CO ( + ε) ( + ε) ( + ε) ( + ε) (7) Equation (7) represents biomass formation due to ATP production. Here α represents mol ATP required per mol C fixed as biomass, ε represents fraction of carbon lost to CO in process of biomass formation and x is calculated from redox balance of the equation as: 4 (+ ε ) κ 4 (+ ε) = κ + x x = (8) Where, κ is the degree of reduction of biomass. Values of α =.4 mol ATP/mol C in biomass; ε = 0.; and κ =4. were assumed in current model 8. Since biomass formation has been attributed to excess ATP production equation (3) will not be included in Y P,G,X CI calculation. v ( α + x) Y = Y. = Y. v + v + v + v ( + a / )( α + x ) + c (3 x+ + ε ) + d (3 α ( + ε )) P,G,X CI 4 5 (9) One needs to be careful that none of the reaction rates above i.e. v,v,v 3,v 4,v 5 are allowed to be negative while deriving the yields. In case any of the rates are negative the corresponding reaction should be left out of calculations. A quick way to check if v 5 is applicable is to check if (c-d) is positive, because only then there will be excess ATP available for biomass formation. Pathway efficiency (η i ) is defined as the ratio of yield (Y i ) to maximum yield Y E. Stoichiometric coefficients assumed and the yields calculated are summarized in supplementary tables S, S, S3, S4 and S5. Thought the black-box stoichiometric calculations presented here are crude approximations of the actual metabolism of a cell, nonetheless they provide a good starting tool for discriminating pathways before venturing into actual pathway construction without resorting to large scale metabolic networks. Same calculations can also be used as a tool to check the consistency of experimental data after incorporating reactions accounting for all the major products. Nature Biotechnology: doi:0.038/nbt.055

3 pglucose+ qnadph rproduct+ sco + tatp+ unadh (0) Table S: Stoichiometric Coefficients as per equation (0) accounting for co-factor imbalance Name (pathway) Formula Glucose C 6 H O 6 NADPH Product CO ATP NADH Ethanol C H 6 O 0 0 butanol (Clostridial) C 4 H 0 O 0 0 Isobutanol (via valine) C 4 H 0 O -methylbutanol(via isoleucine) C 5 H O methylbutanol(via leucine) C 5 H O Isopentenol(Mevalonate) C 5 H 0 O Isopentenol(MEP-DOXP) C 5 H 0 O -3 0 Fatty Alcohol C 6 H 34 O Succinate C 4 H 6 O Lysine C 6 H 4 O N Citrate C 6 H 8 O Glutamate C 5 H 0 O 4 N Hydroxybutyric acid C 4 H 8 O Nature Biotechnology: doi:0.038/nbt.055

4 Table S: Stoichiometric coefficients normalized per glucose carbon atom accounting for co-factor imbalance based on equation () Name (pathway) a b c d e Ethanol butanol (Clostridial) Isobutanol (via valine) methylbutanol(via isoleucine) methylbutanol(via leucine) Isopentenol(Mevalonate) Isopentenol(MEP-DOXP) Fatty Alcohol Succinate Lysine Citrate Glutamate Hydroxybutyric acid Nature Biotechnology: doi:0.038/nbt.055

5 Table S3: Stoichiometric coefficients normalized per glucose carbon atom without cofactor imbalance based on equation () Name (pathway) a b c d e Ethanol butanol (Clostridial) Isobutanol (via valine) methylbutanol(via isoleucine) methylbutanol(via leucine) Isopentenol(Mevalonate) Isopentenol(MEP-DOXP) Fatty Alcohol Succinate Lysine Citrate Glutamate Hydroxybutyric acid Nature Biotechnology: doi:0.038/nbt.055

6 Table S4: Pathway Yields under different scenarios for various biochemicals in mol/mol of glucose P,G,X Name (pathway) Formula Y E Y P Y P,G P,G Ethanol C H 6 O butanol (Clostridial) C 4 H 0 O Isobutanol (via valine) C 4 H 0 O methylbutanol(via isoleucine) C 5 H O methylbutanol(via leucine) C 5 H O Isopentenol(Mevalonate) C 5 H 0 O Isopentenol(MEP-DOXP) C 5 H 0 O Fatty Alcohol C 6 H 34 O Succinate C 4 H 6 O Lysine C 6 H 4 O N Citrate C 6 H 8 O Glutamate C 5 H 0 O 4 N Hydroxybutyric acid C 4 H 8 O Nature Biotechnology: doi:0.038/nbt.055

7 Table S5: Pathway Yields under different scenarios for various biochemicals in g/g of glucose P,G,X Name (pathway) Formula Y E Y P Y P,G P,G Ethanol C H 6 O butanol (Clostridial) C 4 H 0 O Isobutanol (via valine) C 4 H 0 O methylbutanol(via isoleucine) C 5 H O methylbutanol(via leucine) C 5 H O Isopentenol(Mevalonate) C 5 H 0 O Isopentenol(MEP-DOXP) C 5 H 0 O Fatty Alcohol C 6 H 34 O Succinate C 4 H 6 O Lysine C 6 H 4 O N Citrate C 6 H 8 O Glutamate C 5 H 0 O 4 N Hydroxybutyric acid C 4 H 8 O Nature Biotechnology: doi:0.038/nbt.055

E.coli Core Model: Metabolic Core

1 E.coli Core Model: Metabolic Core 2 LEARNING OBJECTIVES Each student should be able to: Describe the glycolysis pathway in the core model. Describe the TCA cycle in the core model. Explain gluconeogenesis.