Supporting Information
In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories
Meiyappan Lakshmanan, Kai Yu, Lokanand Koduru, Dong-Yup Lee
Table S1. List of free exchange fluxes in E. coli iJR904 model during simulations
Table S2. List of free exchange fluxes in B. subtilis iYO844 model during simulations
Table S3. List of free exchange fluxes in S. cerevisiae iMM904 model during simulations
Table S4. List of free exchange fluxes in P. pastoris iPP618 model during simulations
Table S5. Top 4 CMA identified CSE targets and the % increase of NADP(H) flux sum and growth in the mutant strains with respect to the wild-type
Table S6. Effect of different carbon substrates on NADPH flux-sum and its dependent product synthesis under aerobic and anaerobic conditions
Table S7. The % increase of NADP(H) flux sum and product synthesis in the GAPD cofactor engineered mutant strains with respect to the wild-type
Table S1. List of free exchange fluxes in E. coli iJR904 model during simulations
S. No. / Reactions / Reaction name1 / EX_fe2(e) / Fe2+ exchange
2 / EX_h2o(e) / H2O exchange
3 / EX_h(e) / H+ exchange
4 / EX_k(e) / K+ exchange
5 / EX_na1(e) / Sodium exchange
6 / EX_nh4(e) / Ammonia exchange
7 / EX_pi(e) / Phosphate exchange
8 / EX_so4(e) / Sulfate exchange
Table S2. List of free exchange fluxes in B. subtilis iYO844 model during simulations
S. No. / Reactions / Reaction name1 / EX_ca2(e) / Calcium exchange
2 / EX_fe3(e) / Fe3 exchange
3 / EX_h2o(e) / H2O exchange
4 / EX_h(e) / H exchange
5 / EX_k(e) / K exchange
6 / EX_mg2(e) / Mg exchange
7 / EX_na1(e) / Sodium exchange
8 / EX_nh4(e) / Ammonium exchange
9 / EX_pi(e) / Phosphate exchange
10 / EX_so4(e) / Sulfate exchange
Table S3. List of free exchange fluxes in S. cerevisiae iMM904 model during simulations
S. No. / Reactions / Reaction name1 / EX_fe2(e) / Fe2 exchange
2 / EX_h2o(e) / H2O exchange
3 / EX_h(e) / H exchange
4 / EX_k(e) / K exchange
5 / EX_na1(e) / Sodium exchange
6 / EX_nh4(e) / Ammonia exchange
7 / EX_pi(e) / Phosphate exchange
8 / EX_so4(e) / Sulfate exchange
Table S4. List of free exchange fluxes in P. pastoris iPP618 model during simulations
S. No. / Reactions / Reaction name1 / EX_fe2(e) / Fe2 exchange
2 / EX_h(e) / H exchange
3 / EX_h2o(e) / H2O exchange
4 / EX_na1(e) / Sodium exchange
5 / EX_nh4(e) / Ammonia exchange
6 / EX_pi(e) / Phosphate exchange
7 / EX_so4(e) / Sulfate exchange
Table S5. Top 4 CMA identified CSE targets and the % increase of NADP(H) flux sum and growth in the mutant strains with respect to the wild-type
Organism / Substrate / Aerobic / AnaerobicCSE Target / (% increase) / CSE Target / (% increase)
NADPH basal flux-sum / Growth rate / NADPH basal flux-sum / Growth rate
E. coli / Glucose / GAPD / 41.20 / 5.73 / GAPD / 263.80 / 9.58
PDH / 5.51 / 5.51 / PDH / 8.19 / 6.97
THRD / 1.74 / 0 / MTHFR2 / 0.97 / -0.11
PGCD / 1.15 / 1.15 / MDH / 0.40 / 0.40
Glycerol / GAPD / 172.26 / 0 / GAPD / 96.84 / 0
PGCD / 54.84 / 0 / GLYCD / 6.82 / 0
GLYCD / 51.87 / 0 / MDH / 0.85 / 0
MDH / 51.72 / 0 / PGCD / 0.64 / 0
Xylose / GAPD / 47.57 / 6.17 / GAPD / 309.02 / 9.58
PDH / 7.44 / 6.16 / PDH / 8.19 / 6.97
MTHFD / 1.18 / -0.56 / MTHFR / 0.97 / -0.11
PGCD / 1.15 / 1.15 / MDH / 0.40 / 0.40
B. subtilis / Glucose / GAPD / 384.45 / 2.94 / NA / NA / NA
PDH / 249.57 / 2.94 / NA / NA / NA
LLEUD / 81.94 / -3.03 / NA / NA / NA
G3PD / 7.87 / -0.29 / NA / NA / NA
Glycerol / PDH / 573.09 / 0 / NA / NA / NA
PGCD / 504.53 / 0 / NA / NA / NA
MDH / 74.12 / 0 / NA / NA / NA
HISTD / 73.30 / 0 / NA / NA / NA
Xylose / GAPD / 405.98 / 2.94 / NA / NA / NA
PDH / 262.36 / 2.94 / NA / NA / NA
LLEUD / 81.94 / -3.03 / NA / NA / NA
G3PD / 7.87 / -0.29 / NA / NA / NA
S. cerevisiae / Glucose / GAPD / 356.69 / 0.22 / ADHE / 557.250 / 8.11
MDH / 266.65 / 0.22 / GAPD / 329.280 / 8.11
HSD / 5.79 / -0.18 / PDHm / 164.135 / -0.44
MDHm / 5.64 / 0.22 / GLUS / 159.585 / 0
Glycerol / GAPD / 132.90 / 0 / NA / NA / NA
MDH / 42.06 / 0 / NA / NA / NA
PDHm / 30.13 / 0 / NA / NA / NA
G5SD / 29.07 / 0 / NA / NA / NA
Xylose / GAPD / 6.31 / 9.04 / GAPD / 16.650 / 16.660
XYLTD / 2.25 / 8.83 / - / - / -
HSD / 1.47 / -0.18 / - / - / -
MDHm / 0.11 / 0.43 / - / - / -
P. pastoris / Glucose / GAPD / 71.03 / 5.11 / GAPD / 598.50 / 7.90
MDH / 11.16 / 5.11 / ADHE / 568.57 / 7.90
ADHE / 8.37 / 5.12 / HSD / 4.73 / -0.45
HSD / 4.90 / -0.30 / MDH / 4.66 / 4.66
Glycerol / GAPD / 69.74 / 0 / GAPD / 1180.15 / 0
PGCD / 3.15 / 0 / PGCD / 561.73 / 0
MDH / 1.13 / 0 / MTHFD / 559.35 / 0
MTHFD / 1.13 / 0 / FDH / 559.35 / 0
Xylose / NA / NA / NA / NA / NA / NA
NA / NA / NA / NA / NA / NA
NA / NA / NA / NA / NA / NA
NA / NA / NA / NA / NA / NA
Table S6. Effect of different carbon substrates on NADPH flux-sum and its dependent product synthesis under aerobic and anaerobic conditions
Organism / Substrate / Shikimate / LycopeneAerobic / Anaerobic / Aerobic / Anaerobic
Product flux (mmol gDCW-1 hr-1) / NADPH flux-sum (mmol gDCW-1 hr-1) / Product flux (mmol gDCW-1 hr-1) / NADPH flux-sum (mmol gDCW-1 hr-1) / Product flux (mmol gDCW-1 hr-1) / NADPH flux-sum (mmol gDCW-1 hr-1) / Product flux (mmol gDCW-1 hr-1) / NADPH flux-sum (mmol gDCW-1 hr-1)
E. coli / Glucose / 12.22 / 14.5 / 8.1726 / 9.075 / 2.9478 / 25.86 / 1.7928 / 15.24
Glycerol / 13.56 / 28.51 / 4.948 / 25.72 / 3.464 / 30.04 / 1.5788 / 33.14
Xylose / 12.233 / 14.41 / 7.4126 / 8.2159 / 2.9133 / 25.49 / 1.5978 / 13.58
S. cerevisiae / Glucose / 12.58 / 13.31 / 7.738 / 7.836 / 2.633 / 31.83 / 0.78 / 11.968
Glycerol / 13.8 / 14.96 / NA / NA / 2.5195 / 38.41 / NA / NA
Xylose / 12.067 / 32.075 / 3.5826 / 23.722 / 2.3766 / 48.75 / 0.3813 / 24.64
P. pastoris / Glucose / 12.26 / 12.75 / 7.5 / 7.939 / 2.584 / 33.67 / 1.111 / 13.77
Glycerol / 13.35 / 33.64 / 4.09 / 13.35 / 2.903 / 43.5 / 0.7894 / 21
Xylose / NA / NA / NA / NA / NA / NA / NA / NA
B. subtilis / Glucose / 12.55 / 13.44 / NA / NA / 2.846 / 23.45 / NA / NA
Glycerol / 13.88 / 33.43 / NA / NA / 3.3569 / 38.86 / NA / NA
Xylose / 12.59 / 13.221 / NA / NA / 2.8256 / 23.23 / NA / NA
Table S7. The % increase of NADP(H) flux sum and product synthesis in the GAPD cofactor engineered mutant strains with respect to the wild-type
Organism / Substrate / Shikimate / LycopeneAerobic / Anaerobic / Aerobic / Anaerobic
Product flux (% increase) / NADPH flux-sum (% increase) / Product flux (% increase) / NADPH flux-sum (% increase) / Product flux (% increase) / NADPH flux-sum (% increase) / Product flux (% increase) / NADPH flux-sum (% increase)
E. coli / Glucose / 1.11 / 30.55 / 10.89 / 132.51 / 1.30 / 11.10 / 21.04 / 61.22
Glycerol / 0 / 51.25 / 0 / 20.06 / 0 / 0 / 0 / 1.18
Xylose / 0.83 / 35.67 / 12.88 / 170.15 / 1.26 / 13.57 / 25.01 / 87.63
S. cerevisiae / Glucose / 1.43 / 19.08 / 25.87 / 157.15 / 6.15 / 15.46 / 74.95 / 168.47
Glycerol / 0 / 217.45 / NA / NA / 10.54 / 87.22 / NA / NA
Xylose / 3.42 / 3.38 / 138.37 / 20.90 / 14.15 / 10.17 / 193.63 / 51.42
P. pastoris / Glucose / 1.63 / 32.78 / 21 / 164.34 / 5.21 / 0.86 / 43.29 / 140.23
Glycerol / 0 / 53.12 / 0 / 107.79 / 3.86 / 62.51 / 0 / 216.67
Xylose / NA / NA / NA / NA / NA / NA / NA / NA
B. subtilis / Glucose / 0.96 / 39.58 / NA / NA / 1.12 / 30.96 / NA / NA
Glycerol / 0 / 55.31 / NA / NA / 0 / -29.41 / NA / NA
Xylose / 0.79 / 42.42 / NA / NA / 1.08 / 33.88 / NA / NA