TABLE 1.

Expression ratios of genes involved in transport/binding, metabolism of carbohydrates, protein synthesis, metabolism of amino acids, purine/pyrimidine synthesis, and heat shock proteins in response to the highest tested concentrations of chloramphenicol, erythromycin, or gentamicin

Function, antibiotic, and geneaProduct or functionExpression ratiosb at:
5 min15 min30 min60 min
Transport/binding
    Cm
        pbuGHypoxanthine/guanine permease1.73.21.01.5
        pbuXXanthine permease1.47.21.01.2
        pyrPUracil permease1.87.61.93.0
        yhcASimilar to multidrug resistance protein1.12.41.82.1
        yxjASimilar to pyrimidine nucleoside transport1.13.11.52.1
    Em
        pbuGHypoxanthine/guanine permease1.15.71.10.1
        pbuXXanthine permease1.03.41.70.1
        opuABGlycine betaine ABC transporter (permease)1.33.71.30.4
        ycgOSimilar to proline permease0.82.41.60.6
        yxjASimilar to pyrimidine nucleoside transport1.610.02.12.4
    Gm
        dppBDipeptide ABC transporter (permease)0.60.21.21.8
        malPPhosphotransferase system maltose-specific enzyme IICB component0.80.50.81.4
        nagPPhosphotransferase system N-acetylglucosamine-specific enzyme IICB component0.80.41.11.7
        ptsIPhosphotransferase system enzyme I1.50.61.21.0
        yclNSimilar to ferrichrome ABC transporter (permease)0.80.50.60.8
Metabolism of carbohydrates
    Cm
        mleAMalolactic enzyme1.36.128.40.5
        mtlDMannitol-1-phosphate dehydrogenase0.81.31.82.5
        nagBN-Acetylglucosamine-6-phosphate isomerase1.01.84.75.3
        pckAPhosphoenolpyruvate carboxykinase1.01.31.51.3
        yvfVSimilar to glycolate oxidase1.33.44.70.4
    Em
        citBAconitate hydratase (aconitase)2.71.01.20.4
        iolBMyoinositol catabolism1.00.81.10.3
        iolDMyoinositol catabolism1.00.90.90.4
        iolEMyoinositol catabolism1.10.61.40.3
        lacAβ-Galactosidase1.00.91.10.4
    Gm
        citBAconitate hydratase (aconitase)1.30.60.71.4
        icdIsocitrate dehydrogenase1.30.50.71.2
        mdhMalate dehydrogenase1.50.50.61.2
        pckAPhosphoenolpyruvate carboxykinase1.50.70.60.9
        pfkA6-Phosphofructokinase1.90.40.72.9
Protein synthesis
    Cm
        infCInitiation factor IF-31.21.92.11.5
        rplARibosomal protein L1 (BL1)1.33.31.71.6
        rplKRibosomal protein L11 (BL11)1.63.41.52.1
        rplTRibosomal protein L201.13.41.61.9
        rplURibosomal protein L21 (BL20)1.52.01.31.5
    Em
        rplCRibosomal protein L3 (BL3)1.43.11.60.3
        rplURibosomal protein L21 (BL20)1.34.31.70.5
        rpsDRibosomal protein S4 (BS4)1.35.91.20.5
        rpsFRibosomal protein S6 (BS9)1.99.43.52.9
        rpsLRibosomal protein S12 (BS12)1.52.81.30.2
    Gm
        rplBRibosomal protein L2 (BL2)1.70.61.50.7
        rplJRibosomal protein L10 (BL5)2.20.52.40.4
        rplQRibosomal protein L17 (BL15)1.30.41.50.6
        rplRRibosomal protein L181.80.51.60.7
        rpsKRibosomal protein S11 (BS11)1.70.41.60.7
Metabolism of amino acids
    Cm
        glnARequired for transduction of the nitrogen regulation signal to GlnR and TnrA0.90.90.70.4
        glyAGlycine requirement; indirect activation of KinB0.91.00.60.5
        goxBOxidation of sarcosine (N-methylglycine), N-ethylglycine, and glycine; lower activities on d-alanine, d-valine, and d-proline1.10.90.70.2
        pepTPutative; Zn2+-dependent metalloenzyme; N-terminal region stabilizes Zn2+-binding0.90.40.60.4
        rocASigma-L-dependent; positively regulated by RocR and AhrC (ARG recognition site located immediately upstream of the transcriptional start point)1.01.72.70.6
    Em
        glyASerine hydroxymethyltransferase1.11.01.40.4
        hisDHistidinol dehydrogenase1.01.41.60.5
        rocAPyrroline-5 carboxylate dehydrogenase1.50.91.10.2
        rocDOrnithine aminotransferase1.01.21.30.3
        rocGGlutamate dehydrogenase0.91.01.40.3
Purine and pyrimidine     biosynthesis
    Cm
        purDPhosphoribosylglycinamide synthetase1.12.21.71.4
        pyrBAspartate carbamoyltransferase1.11.81.21.1
        pyrFOrotidine 5′-phosphate decarboxylase1.01.81.31.8
        pyrGCTP synthetase1.87.61.93.0
        pyrPUracil permease0.81.70.90.8
    Em
        purCPhosphoribosylaminoimidazole succinocarboxamide synthetase0.91.21.20.5
        purEPhosphoribosylaminoimidazole carboxylase I1.02.11.20.3
        purNPhosphoribosylglycinamide formyltransferase1.21.61.80.3
        pyrABCarbamoyl-phosphate synthetase (catalytic subunit)1.11.81.70.5
        pyrDDihydroorotate dehydrogenase (catalytic subunit)1.01.61.40.3
Heat shock proteins
    Cm
        clpQTwo-component ATP-dependent protease (N-terminal serine protease)0.80.90.61.0
        clpXATP-dependent Clp protease ATP-binding subunit (class III heat shock protein)1.20.60.60.8
        dnaKClass I heat shock protein (molecular chaperone)1.20.71.00.7
        groESClass I heat shock protein (chaperonin)1.10.20.30.3
        nadENH3-dependent NAD+ synthetase; strongly induced in response to heat, ethanol, and salt stress or after starvation for glucose1.01.00.70.7
    Gm
        clpPATP-dependent Clp protease proteolytic subunit (class III heat shock protein)
            0.1× MIC1.40.60.72.1
            0.25× MIC1.30.81.13.7
            0.4× MIC1.41.41.24.5
        clpXATP-dependent Clp protease ATP-binding subunit (class III heat shock protein)1.40.60.91.5
        ykrLSimilar to heat shock protein0.81.31.11.5
  • a Cm, chloramphenicol; Em, erythromycin; Gm, gentamicin. Concentrations of 0.4×, 0.5×, and 0.4× MIC, respectively, were used unless indicated otherwise.

  • b Values shown are the relative transcript levels of treated samples over untreated samples, with values more than one indicating induction and values less than one indicating repression in the antibiotic-treated samples. Bold numbers represent the average expression ratios from two experiments 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.