Table 2. Differentially expressed genes that are proposed to contribute to putrescine homeostasis.
A positive number means more transcripts in the ΔspeB (lower putrescine) strain.
| Gene (function) | log2FC | FDR |
|---|---|---|
| Polyamine synthesis | ||
| speA (putrescine) | 0.99 | 0.003 |
| speC (putrescine) | 1.43 | 3E-4 |
| speD (spermidine) | –0.83 | 0.01 |
| speF (putrescine) | 1.05 | 0.007 |
| rpmH (inhibitor of SpeA and SpeC) | –2.77 | 2E-4 |
| rpsT (inhibitor of SpeA and SpeC) | –1.92 | 8E-4 |
| Polyamine transport | ||
| potABCD* (spermidine) | –2.17 | 3E-4 |
| potE (putrescine) | 2.07 | 2E-4 |
| potFGHI* (putrescine) | 1.41 | 4E-4 |
| plaP (putrescine) | 1.11 | 0.005 |
| sapBCDF* (putrescine export) | –1.18 | 8E-4 |
| Arginine synthesis | ||
| argA_2 (synthesis) | 1.77 | 0.001 |
| argB (synthesis) | 1.87 | 0.002 |
| argC (synthesis) | 2.86 | 0.005 |
| argD (synthesis) | 1.41 | 0.001 |
| argF (synthesis) | 1.63 | 0.01 |
| argG (synthesis) | 2.32 | 0.002 |
| argH (synthesis) | 0.97 | 0.001 |
| argI (synthesis) | 1.95 | 0.018 |
| argR (repressor of arginine regulon) | –1.35 | 4E-4 |
| Glutamate generation | ||
| glsA (glutamine degradation) | 2.16 | 5E-4 |
| glnG (regulation of ammonia assimilation) | –1.59 | 0.022 |
| TCA cycle/electron transport | ||
| acnA (TCA cycle) | –1.04 | 8E-4 |
| acnB (TCA cycle) | –1.96 | 2E-4 |
| fumA (TCA cycle) | –1.50 | 6E-4 |
| fumB (TCA cycle) | –1.49 | 0.003 |
| gltA (TCA cycle) | –1.64 | 2E-4 |
| icdA (TCA cycle) | –1.32 | 0.002 |
| sdhCDAB-sucABCD* (TCA cycle) | –3.88 | 5E-5 |
| nuo operon* (electron transport) | –0.82 | 0.004 |
| menFDHBCE* (electron transport) | –0.8 | 0.005 |
| ubiEJB* (electron transport) | –0.93 | 0.004 |
| cyoABCD* (electron transport) | –1.41 | 9E-4 |
| hemCD* (heme) | –2.05 | 2E-4 |
| Iron transport | ||
| exbBD* (transport of all iron chelates) | –2.33 | 4E-5 |
| tonB (transport of all iron chelates) | –1.9 | 4E-5 |
| entCEBA* (enterochelin iron) | –5.2 | 7E-6 |
| fecABCDE * (ferric citrate) | –4.4 | 3E-5 |
| fecIR (regulators, ferric citrate) | –4.4 | 6E-6 |
| feoABC* (ferrous iron) | –3.4 | 7E-4 |
| fur (regulator, iron assimilation) | –0.40 | 0.11 |
| Magnesium and phosphate transport | ||
| mgtA (magnesium) | 5.90 | 5E-6 |
| phoQ (regulator, magnesium) | 0.79 | 0.009 |
| pstSCAB* (phosphate) | 3.61 | 0.01 |
| phoBR* (regulator, phosphate assimilation) | 2.80 | 0.02 |
*
Values for transcripts of the first gene of the operon are given. Results for other genes of the operon are in Supplementary file 2.