Table 1.
Confirmed-lethal single-gene deletion strains from Patrick et al. (Patrick et al., 2007) with the corresponding multicopy suppressors (MS) and representative subsets of predicted compensating reactions. Biomass growth rate in the disrupted network computed using FBA is presented as a percentage of the wild type strain growth rate.
| Deletion | Deficient Reactions | MS | MS Biomass | Compensating Reactions |
|---|---|---|---|---|
| ΔilvA (4.3.1.19) | L-threonine → 2-oxobutanoate + NH4+ | tdcB (4.3.1.17, 4.3.1.19) | 100.00% | L-threonine → 2-oxobutanoate + NH4+ |
| 100.47% | L-allo-threonine → 2-oxobutanoate + NH4+ | |||
| ΔilvE (2.6.1.42) | (S)-3-methyl-2-oxopentanoate + L-glutamate → 2-oxoglutarate + L-isoleucine 3-methyl-2-oxobutanoate + L-glutamate → 2-oxoglutarate + L-valine |
avtA (2.6.1.66) | 100.00% | (S)-3-methyl-2-oxopentanoate + L-alanine → L-isoleucine + pyruvate |
| 100.79% | 3 3-methyl-2-oxobutanoate + 2 L-alanine → 2 L-isoleucine + 3 pyruvate | |||
| ΔglnA (6.3.1.2) | ATP + L-glutamate + NH4+ → ADP + L-glutamine + H+ + PO43- | asnB (6.3.5.4) | 100.94% | AMP + L-asparagine + L-glutamate + P2O74- → L-aspartate + ATP + L-glutamine + H2O |
| 101.26% | L-glutamate + NH4+ → L-glutamine + H2O | |||
| 99.38% | AMP + L-asparagine + D-glucose 1-phosphate + L-glutamate → ADP-glucose + L-aspartate + L-glutamine + H2O | |||
| (and others) | ||||
| ΔilvD (4.2.1.9) | (R)-2,3-dihydroxy-3-methylbutanoate → 3-methyl-2-oxobutanoate + H2O (R)-2,3-dihydroxy-3-methylpentanoate → (S)-3-methyl-2-oxopentanoate + H2O |
avtA (2.6.1.66) | 100.23% | 2 Pyruvate + 3 L-valine → 2 (S)-3-methyl-2-oxopentanoate + 3 L-alanine 2 4-methyl-2-oxopentanoate + 3 L-alanine → 2 pyruvate + 3 L-valine |
| 100.23% | 3 3-methyl-2-oxobutanoate + 2 L-alanine → 2 L-isoleucine + 3 pyruvate 2 L-leucine + 3 Pyruvate → 3 3-methyl-2-oxobutanoate + 2 L-alanine |
|||
| (other combinations may be possible) | ||||
| ΔhisH (4.3.2.10, 3.5.1.2) | L-glutamine + phosphoribulosylformimino-AICAR-phosphate → AICAR + erythro-imidazole-glycerol-phosphate + L-glutamate + H+ | hisF (4.3.2.10) | 100.02% | L-glutamine + phosphoribulosylformimino-AICAR-phosphate → AICAR + erythro-imidazole-glycerol-phosphate + L-glutamate |
| 100.02% | L-glutamine + phosphoribosylformiminoaicar-phosphate → AICAR + erythro-imidazole-glycerol-phosphate + L-glutamate | |||
| 100.05% | L-glutamine + 2 phosphoribulosylformimino-AICAR-phosphate → (S)-2-hydroxyglutarate + 2 AICAR + 2 erythro-imidazole-glycerol-phosphate | |||
| (and others) | ||||
| ΔpabA (2.6.1.85) | chorismate + L-glutamine → 4-amino-4-deoxychorismate + L-glutamate | pabB (2.6.1.85) | 100.00% | chorismate + L-glutamine → 4-amino-4-deoxychorismate + L-glutamate |
| 100.00% | 2 chorismate + L-glutamine → 2 4-amino-4-deoxychorismate + (S)-2-hydroxyglutarate | |||
| 100.00% | chorismate + L-glutamine → 4-amino-4-deoxychorismate + O-acetyl-L-serine | |||
| 100.00% | L-asparagine + chorismate → 4-amino-4-deoxychorismate + L-aspartate | |||
| 100.00% | L-glutamine + isochorismate → 4-amino-4-deoxychorismate + L-glutamate | |||
| 100.00% | L-glutamine + prephenate → 4-amino-4-deoxychorismate + L-glutamate | |||