Table 2.
Identification of 10 additional promoter regions belonging to the TnrA primary regulon
| Gene | Sequence of TnrA box1 | TnrA-binding sites2 | Expression ratio3 |
|---|---|---|---|
| Genes positively regulated by TnrA | |||
| appD | -119 TGTAATAATATACAACT | −95 | 0.13 |
| dtpT | -212 TCTAAAATTTTATTAAA; -175 TGTAAGAAAATCTCACG | −271; −151 | 0.33 |
| pucR | -140 TGTCAGTTTATGTAACA | −224 | 0.1 |
| yfiR | -31 GGTAAGAAAATTGCAGA* | −51 | 0.5 |
| ysnD | -141 TGGAAGATTTTATAACA; -97 TGACAGATCATCTTGCA | −142; −76 | 0.33 |
| yrbD | -96 GGTCATATAATGTGACA | −121 | 0.04 |
| Genes negatively regulated by TnrA | |||
| hom | -203 GAGGAGAAAATCTGACT* | −55; −187 | 8 |
| pycA | -87 TGTTTATCTGTAAAAAA* | −87 | 2 |
| yuiA | -78 TGTCACATGATCTGACT | −77 | 3 |
| yvgT | -39 CGTCAGAAAATTTAACA | +53 | 4 |
1
Positions of TnrA boxes are indicated relative to the translational start site (+1) according to (Yoshida et al. 2003) and the RegTransBase database (Cipriano et al. 2013). Asterisks indicate TnrA boxes predicted in this work from the newly defined TnrA box consensus.
2
Positions of in vivo TnrA-binding sites correspond to the top of each peak detected by ChIP-on-chip and are indicated relative to the translational start site (+1).
3
The ratio of expression for each gene (ΔtnrA mutant/wild-type) was calculated as the average of three independent experiments obtained with the luc transcriptional fusions.