Table 2.
Glucose perturbation experiments in S. cerevisiae with intracellular metabolome quantification: Stirred tank reactors (STR) operated in chemostat. Shake flasks (SF) in batch conformation. Metabolite pools: glycolysis (GLYCO), tricarboxylic acid cycle (TCA), pentose phosphate pathway (PPP), trehalose cycle (TRE), nucleotides (NUC), Amino acids (AAs). Even though intracellularly localized, variables measured were whole cell, and exceptions are pointed. From the literature pool of articles obtained in the systematic reviewing process, the works displayed measured experimentally intracellular variables such as metabolite concentrations or fluxes. Literature is ordered by glucose input regime.
| Rizzi et al. [25] | Theobald et al. [26] | Vaseghi et al. [21] | Visser et al. [27] | |
|---|---|---|---|---|
| Glucose input regime | Glucose-limited to glucose pulse (0.25 g L−1) | Glucose-limited to glucose pulse (1 g L−1) | Glucose-limited to glucose pulse (1 g L−1) | Glucose-limited to glucose pulse (1 g L−1) |
| Experimental setup | 30 °C, pH5, aerobic, D = 0.1 h−1, STR, direct sampling | 30 °C, pH5, aerobic, D = 0.1 h−1, STR, direct sampling | 30 °C, pH5, aerobic, D = 0.1 h−1, STR, direct sampling | 30 °C, pH5, aerobic, D = 0.05 h−1, STR, BioScope sampling |
| Duration | 500 s | 180 s | 180 s | 80 s |
| Strain | CBS 7336 (ATCC 32167) | CBS 7336 (ATCC 32167) | CBS 7336 (ATCC 32167) | CEN.PK113-7D |
| Measurement technique | Enzymatic assay | Enzymatic assay: metabolites, NAD(H) HPLC: adenine nucleotides | Enzymatic assay: metabolites, NAD(H) | Enzymatic assay: ATP, NADX and G6P MS: glycolytic intermediates |
| Intracellular variables measured | GLYCO: G6P. | GLYCO: G6P, F6P, FBP, GAP, 3PG, PEP, PYR. NUC: NAD(H), AXP (whole cell and cytoplasmic). Pi. | GLYCO: G6P, F6P. PPP: 6PG. NUC: NADP(H). | GLYCO: G6P, F6P, G1P, FBP, 2GP+3PG, PEP, PYR. NUC: ATP, NADX. |
| Glucose input regime | Glucose-limited to glucose pulse (1 g L−1) | Glucose-limited to glucose pulse (1 g L−1) | Glucose-limited to glucose pulse (1 g L−1) | Trehalose-limited to glucose pulse (20 g L−1) |
| Experimental setup | 30 °C, pH5, aerobic, D = 0.05 h−1, STR, BioScope sampling | 30 °C, pH5, aerobic, D = 0.05 h−1, STR, BioScope sampling | 30 °C, pH5, aerobic, D = 0.05 h−1, STR, direct sampling | 30 °C, pH4.8, aerobic, SF, direct sampling. |
| Duration | 180 s | 180 s | 300 s | 30 min |
| Strain | CEN.PK113-7D | CEN.PK113-7D | CEN.PK113-7D | BY4741 |
| Measurement technique | MS | Enzymatic analysis: NAD(H) MS | MS | MS |
| Intracellular variables measured | GLYCO: G6P, F6P, FBP, 2/3PG, PEP, PYR. TCA: ISOCIT, FUM, MAL, AKG, SUC. PPP: 6PG. TRE: G1P, T6P, TRE. NUC: AXP, NADH:NAD ratio. | GLYCO: G6P, F6P, F1,6P2, F2,6P2, 2/3PG, PEP. TCA: ISOCIT, AKG, SUC, FUM, MAL. PPP: 6PG. TRE: G1P, T6P. NUC: AXP, NADH:NAD ratio. | GLYCO: G6P, F6P, F1,6P2, F2,6P2, 2/3PG, PEP. TCA: ISOCIT, AKG, SUC, FUM, MAL. PPP: 6PG. TRE: G1P, T6P. NUC: AXP, NADH:NAD ratio. AAs. | GLYCO: G6P, F6P, FBP, G3P, 2/3PG, PEP. TCA: AKG, MAL. PPP: 6PG, R5P, R1P. TRE: T6P, G1P. NUC: ATP, ADP, AMP, IMP, INO, HYP, GTP, GDP, GMP. |
| Van Heerden et al. [18] | Suarez-Mendez et al. [36], Suarez-Mendez et al. [37] | Canelas et al. [34] | Kumar et al. [35] | |
| Glucose input regime | Glucose-limited to glucose pulse (20 g L−1) | Glucose-limited to feast–famine cycles (0.08 g L−1 max.) | Glucose-limited. Dilution rates from 0.025 to 0.375 h−1 | Glucose-limited. Dilution rates from 0.050 to 0.342 h−1 |
| Experimental setup | 30 °C, pH5, aerobic, D = 0.1 h−1, STR, BioScope sampling | 30 °C, pH5, aerobic, D = 0.1 h−1, STR, direct sampling | 30 °C, pH5, aerobic, STR, direct sampling | 30 °C, pH5, aerobic, STR, direct sampling |
| Duration | 340 s | 400 s | N/A (ss) | N/A (ss) |
| Strain | CEN.PK113-7D | CEN.PK113-7D | CEN.PK113-7D,mtlD1 | CEN.PK113-7D |
| Measurement technique | MS Reaction rates calculated by piecewise affine approximation (13C data) | MS Reaction rates calculated by piecewise affine approximation (13C data) | MS Reaction rates calculated with a stoichiometric model | MS |
| Intracellular variables measured | GLYCO: G6P, F6P, FBP. TRE: G1P, UDPG, T6P, TRE. PPP: 6PG. NUC: AXP, cAMP, UXP, GXP. Fluxes within glycolysis and trehalose cycle. | GLYCO: G6P, F6P, FBP, G3P, GLYC, DHAP, GAP, 2PG, 3PG, PEP, PYR. TCA: CIT, FUM, ISOCIT, MAL, AKG, SUC. PPP: 6PG, E4P, R5P, RBUP5, S7P, X5P. TRE: G1P, UDPG, T6P, TRE. NUC: AXP. Fluxes within glycolysis and trehalose cycle. | GLYCO: G6P, F6P, FBP, F26BP, G3P, DHAP, GAP, 2PG, 3PG, PEP, PYR. TCA: CIT, FUM, ISOCIT, MAL, OAA, SUC. PPP: 6PG, E4P, R5P, RBUP5, S7P, X5P. TRE: G1P, T6P, TRE. NUC: AXP, UXP, cAMP, NAD:NADH ratio. AAs. Fluxes within glycolysis. | GLYCO: G6P, F6P, FBP, G3P, DHAP, 2/3PG, PEP, PYR. TCA: CIT, FUM, OAA, ISOCIT, MAL, AKG, SUC. PPP: 6PG, R5P, RBUP5, S7P. TRE: G1P, UDPG. NUC: AXP, GXP, IXP, TXP, UXP, dAXP, dGXP, dUXP. AAs. |