TABLE 3.
Expression ratios of genes that were highly expressed or involved in transcription regulatory functions in response to various concentrations of chloramphenicol, erythromycin, or gentamicin
| Genea | Product or function | Antibioticb (MIC) | Relative expression levelsc at:
|
|||
|---|---|---|---|---|---|---|
| 5 min | 15 min | 30 min | 60 min | |||
| Highly expressed genes | ||||||
| dctP | C4-dicarboxylate transport protein | Cm (0.25×) | 0.4 | 1.1 | 0.7 | 2.1 |
| Cm (0.4×) | 0.4 | 1.4 | 3.4 | 3.5 | ||
| Em (0.25×) | 0.7 | 0.4 | 4.2 | 24.7 | ||
| Em (0.5×) | 0.8 | 0.9 | 2.8 | 20.4 | ||
| Gm (0.25×) | 0.5 | 0.2 | 1.2 | 3.9 | ||
| Gm (0.4×) | 0.6 | 0.4 | 1.1 | 4.3 | ||
| yheH | Similar to ABC transporter (ATP-binding protein) | Cm (0.05×) | 1.1 | 1.7 | 3.6 | 2.2 |
| Cm (0.25×) | 1.0 | 7.2 | 19.4 | 17.7 | ||
| Cm (0.4×) | 1.1 | 4.5 | 12.2 | 14.4 | ||
| yheI | Similar to ABC transporter (ATP-binding protein) | Cm (0.05×) | 1.3 | 1.5 | 3.5 | 2.1 |
| Cm (0.25×) | 1.2 | 8.4 | 16.7 | 21.3 | ||
| Cm (0.4×) | 1.1 | 7.0 | 19.1 | 20.7 | ||
| yolF | Unknown | Em (0.1× | 0.8 | 0.2 | 1.0 | 2.8 |
| Em (0.25×) | 0.9 | 0.3 | 1.5 | 5.4 | ||
| Em (0.5×) | 0.7 | 0.6 | 1.4 | 6.4 | ||
| ysbA | Antiholin-like membrane protein | Cm (0.05×) | 0.3 | 0.6 | 2.3 | 1.2 |
| Cm (0.25×) | 0.3 | 0.8 | 1.1 | 3.0 | ||
| Cm (0.4×) | 0.7 | 1.3 | 3.2 | 4.0 | ||
| Em (0.1×) | 1.1 | 0.2 | 2.0 | 3.1 | ||
| Em (0.25×) | 1.2 | 0.1 | 2.6 | 6.6 | ||
| Em (0.5×) | 1.3 | 0.2 | 1.8 | 7.8 | ||
| Gm (0.1×) | 0.8 | 0.2 | 1.0 | 2.7 | ||
| Gm (0.25×) | 0.9 | 0.3 | 1.1 | 6.4 | ||
| Gm (0.4×) | 0.9 | 0.2 | 1.0 | 5.0 | ||
| ysbB | Antiholin-like membrane protein | Cm (0.05×) | 0.3 | 0.8 | 6.0 | 1.1 |
| Cm (0.25×) | 0.3 | 0.8 | 1.2 | 4.2 | ||
| Cm (0.4×) | 0.8 | 1.1 | 7.2 | 8.6 | ||
| Em (0.1×) | 1.3 | 0.1 | 2.1 | 3.0 | ||
| Em (0.25×) | 1.3 | 0.1 | 2.9 | 8.2 | ||
| Em (0.5×) | 1.1 | 1.1 | 0.3 | 1.9 | ||
| Gm (0.1×) | 0.8 | 0.2 | 1.1 | 2.4 | ||
| Gm (0.25×) | 1.1 | 1.0 | 1.0 | 6.2 | ||
| Gm (0.4×) | 0.9 | 0.2 | 0.8 | 4.2 | ||
| yxiE | Induced by phosphate starvation independently of | Gm (0.1×) | 0.9 | 0.6 | 0.8 | 2.1 |
| sigma-B and PhoPR; similar to unknown proteins | Gm (0.25×) | 0.9 | 0.5 | 0.8 | 4.1 | |
| Gm (0.4×) | 1.2 | 0.5 | 0.7 | 3.9 | ||
| Transcriptional regulators | ||||||
| lmrA | Transcriptional repressor of the lincomycin operon | Cm (0.05×) | 1.3 | 1.0 | 1.2 | 1.1 |
| Cm (0.25×) | 0.8 | 1.0 | 1.2 | 0.9 | ||
| Cm (0.4×) | 1.3 | 1.1 | 1.0 | 1.0 | ||
| Em (0.1×) | 0.8 | 2.1 | 0.9 | 0.7 | ||
| Em (0.25×) | 1.0 | 2.6 | 1.1 | 1.0 | ||
| Em (0.5×) | 1.2 | 3.4 | 1.3 | 1.0 | ||
| Gm (0.1×) | 0.9 | 2.3 | 1.0 | 0.9 | ||
| Gm (0.25×) | 1.3 | 2.1 | 1.1 | 0.8 | ||
| Gm (0.4×) | 0.9 | 1.9 | 1.1 | 0.8 | ||
| lmrBd | Drug export protein | Cm (0.05×) | 0.9 | 0.9 | 0.8 | 1.3 |
| Cm (0.25×) | 0.8 | 0.7 | 0.6 | 0.9 | ||
| Cm (0.4×) | 0.9 | 0.6 | 0.6 | 1.1 | ||
| Em (0.1×) | 0.8 | 1.7 | 0.9 | 1.2 | ||
| Em (0.25×) | 1.1 | 2.6 | 1.0 | 1.1 | ||
| Em (0.5×) | 1.1 | 2.1 | 1.2 | 1.1 | ||
| Gm (0.1×) | 0.9 | 2.0 | 0.9 | 0.9 | ||
| Gm (0.25×) | 0.8 | 1.7 | 1.0 | 0.9 | ||
| Gm (0.4×) | 0.9 | 1.3 | 1.0 | 0.9 | ||
| pyrR | Transcriptional attenuator and uracil | Cm (0.05×) | 0.9 | 1.9 | 1.6 | 1.1 |
| phosphoribosyltransferase activity (minor) | Cm (0.25×) | 1.3 | 3.9 | 1.7 | 1.8 | |
| Cm (0.4×) | 1.4 | 5.7 | 1.7 | 2.3 | ||
| Em (0.1×) | 1.2 | 4.4 | 1.0 | 0.7 | ||
| Em (0.25×) | 1.3 | 4.8 | 1.0 | 0.4 | ||
| Em (0.5×) | 1.3 | 3.3 | 1.8 | 0.4 | ||
| Gm (0.1×) | 2.2 | 1.7 | 0.7 | 0.8 | ||
| Gm (0.25×) | 1.5 | 4.7 | 0.9 | 1.0 | ||
| Gm (0.4×) | 1.5 | 1.5 | 0.9 | 1.1 | ||
Representative genes in each category showed consistent and reproducible 1.5 fold regulation in at least one condition of each antibiotic treatment.
Cm, chloramphenicol; Em, erythromycin; Gm, gentamicin.
Values are relative transcript levels of treated samples over untreated samples, with values more than one indicating induction and values less than one indicating repression. Bold numbers represent the average expression ratios from two experiments that are considered significant by SAM and were consistently up- or downregulated in both experiments. The “q values” range from 0.0003 to 0.01, 0.0002 to 0.0017, and 0.0004 to 0.0025 under the conditions shown for chloramphenicol, erythromycin, and gentamicin, respectively.
The lmrB gene does not encode a transcriptional regulator but is in the same operon with lmrA, a transcriptional regulator.