Table 1.
NtrC/Nac-activated operons
| b no. | Coding strand | Name | Description | Control* | References
for control
|
|
|---|---|---|---|---|---|---|
| Nitrogen | Other | |||||
| b0336-7 | + | codBA | Cytosine transport, deaminase | Nac | (2) | (19)† |
| b0450-1 | + | glnK-amtB | N-regulation and NH3transport | NtrC | (13) | |
| b0652-5 | − | gltIJKL | Glutamate transport | NtrC?‡ | (11) | (20) |
| b0809-11 | − | glnHPQ | Glutamine transport | NtrC | (21, 22) | (21–23) |
| b0854-7 | + | potFGHI | Putrescine transport | NtrC | (24) | |
| b0929 | − | ompF | Outer membrane protein F | Nac?§ | (25)† | |
| b1006-12 | − | ycdGHIJKLM | Hypothetical proteins | NtrC | ¶ | |
| b1217-8 | + | chaBC | Cation transport regulator | NtrC?‡ | ||
| b1243-7 | + | oppABCDF | Oligopeptide transport | Nac?§ | (20, 26–29)† | |
| b1440-4 | + | ydcSTUV | Putrescine/spermidine transport (30) | Nac | (23) | |
| b1483-8 | − | ddpXABCDE | d-ala-d-ala dipeptide transport and dipeptidase | NtrC | ¶ | (10, 31) |
| b1744-8 | − | astCADBE | Arginine catabolism | NtrC | (32–34) | (32) |
| b1783-4 | + | yeaGH | Hypothetical proteins | NtrC? | ¶ | † |
| b1932 | + | yedL | Hypothetical protein | Nac | ||
| b1987 | − | cbl | Regulator for sulfur metabolism | NtrC‖ | (35) | |
| b1988 | − | nac | N-regulation | NtrC‖ | (2, 36) | |
| b2306-9 | − | hisJQMP | Histidine transport | NtrC** | (37–39) | (38, 39)† |
| b2310 | − | argT | Basic amino acid transport | NtrC | (37–39) | (38, 39)† |
| b2393 | + | nupC | Nucleoside transport | Nac | (40) | |
| b2661-4 | + | gabDTPC | γ-aminobutyric acid transport and catabolism | Nac | (41–43) | (23, 42, 43) |
| b3073 | + | ygjG | Probable ornithine aminotransferase | NtrC | † | |
| b3268-71 | + | yhdWXYZ | Polar amino acid transport (30) | NtrC | ||
| b3540-4 | − | dppABCDF | Dipeptide transport | Nac?§ | (20, 29, 44)† | |
| b3868-70 | − | glnALG | NH3 assimilation and N-regulation | NtrC | (45–47) | (47)† |
| b4207-8 | + | fklB-cycA | Peptidyl-prolyl isomerase; d-ala,d-ser,gly transport | Nac | ||
| Total: 25 operons; 75 genes | ||||||
Derived from Table 3. To avoid making the summary list artificially long, six operons (11 genes) in this table were excluded because it was difficult to assign their control and little is known about them. These are b1034-35, b1296, b1384 (feaR), b2875-76, b2882-85, and b3512. See Xi et al. (48) for recent information on b2875-76 and b2882-85. In addition, annotations (6) for the following operons have been changed: gltIJKL, oppABCDF, yeaGH, hisJQMP, gabDTPC, yhdWXYZ, and fklB-cycA.
Assessed as described in Materials and Methods.
RNA levels in an ntrC strain were ≥2-fold different for cells grown on glutamine versus ammonia (experiment i).
Some data from the second set of PCR products of poor quality; hard to assess NtrC versus Nac control.
At least one gene in these operons also appears to be NtrC-controlled, which is unlikely biologically; Nac control is in accord with known forms of control for these operons (see references), which involve sigma factors other than σ54.
The nac promoter is NtrC-activated (2). The cbl gene is probably expressed from the nac promoter under nitrogen-limiting conditions.
The NtrC-controlled promoter may be upstream of argT (38).