Table 3.
Comparison of gene expression of selected N metabolism genes during N starvation and during N-replete growth on different N sources
| MED4 | MIT9313 | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Function | Gene | N stress | K-means cluster | Urea | Cyanate | N stress | K-means cluster | Urea | Nitrite |
| Regulation | |||||||||
| N regulator | ntcA | 21.86** (6 h) | 2 | NS | NS | 11.71** (12 h) | 1 | NS | 2.69** |
| C–N balance | glnB | 7.26** (6 h) | 2 | NS | NS | NS | 4 | −3.07** | −2.62** |
| glnB cluster | PMM1462 | 48.84** (6 h) | 1 | NS | NS | − | − | − | − |
| PMT1480 | − | − | − | − | NS | 4 | −2.32** | −2.31** | |
| PMT1479 | − | − | − | − | −46.21** (48 h) | 7 | −2.07* | −3.32** | |
| Sigma factors | PMM1289 | 2.85** (6 h) | 5 | NS | NS | − | − | − | − |
| PMM1697 | 2.84** (12 h) | 5 | NS | NS | − | − | − | − | |
| PMM1629 | −6.73** (24 h) | 7 | NS | NS | − | − | − | − | |
| PMT0346 | − | − | − | − | 4.20** (24 h) | 2 | NS | NS | |
| PMT2246 | − | − | − | − | 3.01** (24 h) | 2 | NS | NS | |
| Transport | |||||||||
| Ammonium | amt1 | 2.12** (6 h) | 5 | NS | NS | 4.89** (12 h) | 2 | NS | NS |
| Urea | urtA | 41.36** (6 h) | 1 | NS | 1.86* | 16.56** (12 h) | 1 | 9.19** | 4.59** |
| Cyanate | cynA | 52.71** (6 h) | 1 | NS | 2.25* | − | − | − | − |
| NO2 | PMT2240 | − | − | − | − | 19.43** (12 h) | 1 | 63.56** | 27.47** |
| NO2 transport partner | PMT2241 | − | − | − | − | 9.58** (12 h) | 2 | 16.80** | 9.25** |
| Bicarbonate | sbtA | −2.51** (12 h) | 6 | NS | NS | −2.79** (48 h) | 5 | NS | NS |
| Nitrogen metabolism | |||||||||
| NO2 reduction | nirA | − | − | − | − | 31.56** (24 h) | 1 | 13.55** | 12.30** |
| Urease | ureA | 3.74** (6 h) | 4 | NS | NS | 2.08** (6 h) | 3 | NS | NS |
| Glutamine syn. | glnA | 33.36** (6 h) | 1 | NS | 2.62** | 4.08** (12 h) | 2 | NS | NS |
| GOGAT | glsF | 2.36* (12 h) | 4 | NS | NS | −3.29** (48 h) | 5 | NS | NS |
| Carbon metabolism | |||||||||
| G-6-P dehydrogenase | zwf | 4.76** (6 h) | 4 | NS | NS | 2.23* (24 h) | 3 | NS | NS |
| Transaldolase | tal | 3.25** (6 h) | 4 | NS | NS | 2.69** (24 h) | 3 | NS | NS |
| 2-Oxoglutarate syn. | icd | 2.46** (6 h) | 5 | NS | NS | −3.03** (48 h) | 4 | NS | NS |
| Anonitate hydratase | acnB | 2.84** (12 h) | 4 | NS | NS | −1.94* (48 h) | 4 | NS | NS |
| Rubisco | rbcL | −19.83** (12 h) | 9 | NS | −2.26** | −2.91** (48 h) | 4 | 2.48* | −2.27* |
| Rubisco | rbcS | −20.82** (12 h) | 9 | NS | −1.92** | −3.10** (48 h) | 4 | 4.23** | NS |
| Carboxysome | csoS1 | −10.56** (48 h) | 8 | NS | −2.17** | NS | None | NS | NS |
| Carboxysome | csoS2 | −5.02** (12 h) | 7 | NS | NS | 2.82** (6 h) | 4 | 4.37** | NS |
| Glycogen syn. | glgA | −2.53** (12 h) | 6 | NS | NS | NS | None | NS | NS |
All expression changes are relative to N-replete growth on NH4. N stress columns show maximum fold change over the time course and the associated time point. Two asterisks (**) denote q<0.01, single asterisk (*) shows 0.01<q<0.05, ‘NS' signifies no significant differential expression (q>0.05) and ‘−' means the gene is not present in that strain.