Table 8 Comparison of FastKnock, OptKnock and experimental results reported in the literature for succinate production. The iJR904 model (Strain0) is used in the in silico experimentations (M9 cultivation medium)
Knockout | Knockout strategy | Method | Biomass formation rate (h−1) | Succinate production rate (mmol.gDW−1 h−1) | yield | SSP (h−1) × 10 | SoGC (h−1) × 100 | CO2 exchange flux (mmol.gDW−1 h−1) |
|---|---|---|---|---|---|---|---|---|
Triple | ADHEr, LDH_D, PTAr | OptKnock [33], FastKnock | 0.08 | 9.37 | 0.94 | 0.75 | 0.79 | −9.36 (uptake) |
ADHEr, LDH_D, PFL | OptKnock, FastKnock (best production rate) | 0.12 | 12.24 | 1.22 | 1.46E | 1.53 | −5.87 (uptake) | |
PTAr, PYK, GLCpts | OptKnock, FastKnock | 0.09 | 9.32 | 0.93 | 0.83 | 0.87 | 3.24 (production) | |
PFL, LDH_D, GLCpts | Experimental [71] (production is lower than considered threshold) | 0.16 | 0.71 | 0.07 | 0.11 | 0.11 | 16.78 (production) | |
ADHEr, ATPS4r, LDH_D | FastKnock (best SoGC) | 0.16 | 8.90 | 0.89 | 1.42 | 3.01 | −8.76 (uptake) | |
Quadruple | PTAr, PYK, ATPS4r, SUCD1i | OptKnock | 0.16 | 1.18 | 0.11 | 0.18 | 0.01 | 9.03 (production) |
ADHEr, LDH_D, PFL, THD2 | FastKnock (best production rate) | 0.11 | 12.72 | 1.27 | 1.39 | 2.85 | −6.12 (uptake) | |
ADHEr, LDH_D, HEX1, THD2 | FastKnock (best SoGC) | 0.13 | 9.88 | 0.98 | 1.28 | 3.09 | −8.77 (uptake) | |
Quintuple | ADHEr, LDH_D, PTAr, PYK, GLCpts | OptKnock, FastKnock | 0.05 | 9.96 | 0.99 | 0.49 | 1.19 | −9.51 (uptake) |
ADHEr, LDH_D, PFL, ACKr, FORt | Experimental [71], FastKnock | 0.08 | 9.57 | 0.95 | 0.76 | 0.80 | −9.16 (uptake) | |
ADHEr, LDH_D, HEX1, THD2, DRPA | FastKnock (best SoGC) | 0.13 | 9.87 | 0.98 | 1.28 | 3.10 | −8.76 (uptake) | |
ADHEr, LDH_D, GLUDy, PFL, THD2 | FastKnock (best production rate) | 0.10 | 12.77 | 1.27 | 1.27 | 2.61 | −6.17 (uptake) |