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

GeneaProduct or functionAntibioticb (MIC)Relative expression levelsc at:
5 min15 min30 min60 min
Highly expressed genes
    dctPC4-dicarboxylate transport proteinCm (0.25×)0.41.10.72.1
Cm (0.4×)0.41.43.43.5
Em (0.25×)0.70.44.224.7
Em (0.5×)0.80.92.820.4
Gm (0.25×)0.50.21.23.9
Gm (0.4×)0.60.41.14.3
    yheHSimilar to ABC transporter (ATP-binding protein)Cm (0.05×)1.11.73.62.2
Cm (0.25×)1.07.219.417.7
Cm (0.4×)1.14.512.214.4
    yheISimilar to ABC transporter (ATP-binding protein)Cm (0.05×)1.31.53.52.1
Cm (0.25×)1.28.416.721.3
Cm (0.4×)1.17.019.120.7
    yolFUnknownEm (0.1×0.80.21.02.8
Em (0.25×)0.90.31.55.4
Em (0.5×)0.70.61.46.4
    ysbAAntiholin-like membrane proteinCm (0.05×)0.30.62.31.2
Cm (0.25×)0.30.81.13.0
Cm (0.4×)0.71.33.24.0
Em (0.1×)1.10.22.03.1
Em (0.25×)1.20.12.66.6
Em (0.5×)1.30.21.87.8
Gm (0.1×)0.80.21.02.7
Gm (0.25×)0.90.31.16.4
Gm (0.4×)0.90.21.05.0
    ysbBAntiholin-like membrane proteinCm (0.05×)0.30.86.01.1
Cm (0.25×)0.30.81.24.2
Cm (0.4×)0.81.17.28.6
Em (0.1×)1.30.12.13.0
Em (0.25×)1.30.12.98.2
Em (0.5×)1.11.10.31.9
Gm (0.1×)0.80.21.12.4
Gm (0.25×)1.11.01.06.2
Gm (0.4×)0.90.20.84.2
    yxiEInduced by phosphate starvation independently ofGm (0.1×)0.90.60.82.1
sigma-B and PhoPR; similar to unknown proteinsGm (0.25×)0.90.50.84.1
Gm (0.4×)1.20.50.73.9
Transcriptional regulators
    lmrATranscriptional repressor of the lincomycin operonCm (0.05×)1.31.01.21.1
Cm (0.25×)0.81.01.20.9
Cm (0.4×)1.31.11.01.0
Em (0.1×)0.82.10.90.7
Em (0.25×)1.02.61.11.0
Em (0.5×)1.23.41.31.0
Gm (0.1×)0.92.31.00.9
Gm (0.25×)1.32.11.10.8
Gm (0.4×)0.91.91.10.8
    lmrBdDrug export proteinCm (0.05×)0.90.90.81.3
Cm (0.25×)0.80.70.60.9
Cm (0.4×)0.90.60.61.1
Em (0.1×)0.81.70.91.2
Em (0.25×)1.12.61.01.1
Em (0.5×)1.12.11.21.1
Gm (0.1×)0.92.00.90.9
Gm (0.25×)0.81.71.00.9
Gm (0.4×)0.91.31.00.9
    pyrRTranscriptional attenuator and uracilCm (0.05×)0.91.91.61.1
phosphoribosyltransferase activity (minor)Cm (0.25×)1.33.91.71.8
Cm (0.4×)1.45.71.72.3
Em (0.1×)1.24.41.00.7
Em (0.25×)1.34.81.00.4
Em (0.5×)1.33.31.80.4
Gm (0.1×)2.21.70.70.8
Gm (0.25×)1.54.70.91.0
Gm (0.4×)1.51.50.91.1
  • a Representative genes in each category showed consistent and reproducible 1.5 fold regulation in at least one condition of each antibiotic treatment.

  • b Cm, chloramphenicol; Em, erythromycin; Gm, gentamicin.

  • c 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.

  • d The lmrB gene does not encode a transcriptional regulator but is in the same operon with lmrA, a transcriptional regulator.