Table 3. Summary of the qRT-PCR results.
Experimental conditions and the target mRNA are indicated along with the number of 5′-GCU sites in the target mRNA. The fold changes indicate the changes in enrichment (not necessarily changes in transcription) after differential mRNA decay by RNase MqsR and were calculated as described earlier (Pfaffl, 2001) relative to the house-keeping gene (rrsG), which was used to normalize the data. Values less than one are indicated as negative fold changes (i.e., mRNA levels were reduced relative to other mRNA). The specificity of the qRT-PCR products was verified by a melting curve analysis.
| Conditions | Target mRNA | Fold change | 5′-GCU site |
|---|---|---|---|
| BW25113/pBS(Kan)-mqsR vs. BW25113/pBS(Kan) | ghoT | 40 ± 1 | 0 |
| ghoS | 8 ± 1 | 3 | |
| 1 mM IPTG for 60 min | ompA | −4.5 ± 1 | 27 |
| ompT | 3 ± 2 | 14 | |
| ompF | −2 ± 1 | 20 | |
| kilR | 10.8 ± 0.4 | 0 | |
| ralR | 12 ± 1 | 0 | |
| yciG | 11 ± 1 | 0 | |
|
| |||
| BW25113 wild-type | mqsR | 18 ± 2 | 1 |
| ghoT | 40 ± 1 | 0 | |
| 2 μg/mL nalidixic acid for 90 min vs. no nalidixic acid | ompA | 1 ± 1 | 27 |
|
| |||
| BW25113 wild-type | mqsR | 20 ± 2 | 1 |
| ghoT | 48 ± 2 | 0 | |
| 10 μg/mL azlocillin for 90 min vs. no azlocillin | ompA | −1 ± 1 | 27 |
|
| |||
| BW25113 wild-type | mqsR | 4.6 ± 0.6 | 1 |
| 20 mM H2O2 for 5 min vs. no H2O2 | ghoT | 6 ± 2 | 0 |