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) |