TABLE 3.
Genes upregulated in the d-serine-treated sample at 30 mina
| Function | Gene name | Product | Fold change at 30 min (P value) |
|---|---|---|---|
| Carbon metabolism and energy generation | aceE | Pyruvate dehydrogenase | 4.2 (P < 0.001) |
| aceF | Pyruvate dehydrogenase | 3.4 (P < 0.001) | |
| dsdX | d-Serine transporter | 15 (P < 0.0005) | |
| dsdA | d-Serine deaminase | 15 (P < 0.0005) | |
| ndh | NADH dehydrogenase II | 3.9 (P < 0.005) | |
| mqo (yojH) | Malate quinone oxidoreductase | 3.8 (P < 0.05) | |
| ackA | Acetate kinase | 3.9 (P < 0.005) | |
| pta | Phosphotransacetylase | 2.3 (P < 0.05) | |
| garL | Glucarate, galactarate, glycerate metabolism | 3.6 (P < 0.001) | |
| garR | Glucarate, galactarate, glycerate metabolism | 2.7 (P < 0.001 | |
| yfiD | Pyruvate formate lyase accessory protein | 3 (P < 0.005) | |
| Methionine synthesis | metE | Tetrahydropteroyltriglutamate methyltransferase | 2.8 (P < 0.001) |
| metB | Cystathionine gamma-synthase | 3.6 (P < 0.001) | |
| metL | Aspartokinase II and homoserine dehydrogenase II | 2.1 (P < 0.001) | |
| metF | 5,10-Methylenetetrahydrofolate reductase | 3.4 (P < 0.001) | |
| sbp | Periplasmic sulfate-binding protein | 3.0 (P < 0.001) | |
| Unknown | c3104 | Adjacent to yfiD | 2.5 (P < 0.05) |
| c0143 | Intergenic to aceE and aceF | 3.6 (P < 0.005) | |
| c4752 | Adjacent to metE | 3.2 (P < 0.001) |
a
Fold changes of an ORF between strains were calculated as the following ratio: average d-serine-treated signal intensity/average water-treated CFT073 signal intensity. Only ORFs that had at least twofold changes, a P value of less than or equal to 0.05, and were called present on at least two biological replicate microarrays were considered significant.