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 genea	Product or function	Expression ratiosb at:
		5 min	15 min	30 min	60 min
Transport/binding
Cm
pbuG	Hypoxanthine/guanine permease	1.7	3.2	1.0	1.5
pbuX	Xanthine permease	1.4	7.2	1.0	1.2
pyrP	Uracil permease	1.8	7.6	1.9	3.0
yhcA	Similar to multidrug resistance protein	1.1	2.4	1.8	2.1
yxjA	Similar to pyrimidine nucleoside transport	1.1	3.1	1.5	2.1
Em
pbuG	Hypoxanthine/guanine permease	1.1	5.7	1.1	0.1
pbuX	Xanthine permease	1.0	3.4	1.7	0.1
opuAB	Glycine betaine ABC transporter (permease)	1.3	3.7	1.3	0.4
ycgO	Similar to proline permease	0.8	2.4	1.6	0.6
yxjA	Similar to pyrimidine nucleoside transport	1.6	10.0	2.1	2.4
Gm
dppB	Dipeptide ABC transporter (permease)	0.6	0.2	1.2	1.8
malP	Phosphotransferase system maltose-specific enzyme IICB component	0.8	0.5	0.8	1.4
nagP	Phosphotransferase system N-acetylglucosamine-specific enzyme IICB component	0.8	0.4	1.1	1.7
ptsI	Phosphotransferase system enzyme I	1.5	0.6	1.2	1.0
yclN	Similar to ferrichrome ABC transporter (permease)	0.8	0.5	0.6	0.8
Metabolism of carbohydrates
Cm
mleA	Malolactic enzyme	1.3	6.1	28.4	0.5
mtlD	Mannitol-1-phosphate dehydrogenase	0.8	1.3	1.8	2.5
nagB	N-Acetylglucosamine-6-phosphate isomerase	1.0	1.8	4.7	5.3
pckA	Phosphoenolpyruvate carboxykinase	1.0	1.3	1.5	1.3
yvfV	Similar to glycolate oxidase	1.3	3.4	4.7	0.4
Em
citB	Aconitate hydratase (aconitase)	2.7	1.0	1.2	0.4
iolB	Myoinositol catabolism	1.0	0.8	1.1	0.3
iolD	Myoinositol catabolism	1.0	0.9	0.9	0.4
iolE	Myoinositol catabolism	1.1	0.6	1.4	0.3
lacA	β-Galactosidase	1.0	0.9	1.1	0.4
Gm
citB	Aconitate hydratase (aconitase)	1.3	0.6	0.7	1.4
icd	Isocitrate dehydrogenase	1.3	0.5	0.7	1.2
mdh	Malate dehydrogenase	1.5	0.5	0.6	1.2
pckA	Phosphoenolpyruvate carboxykinase	1.5	0.7	0.6	0.9
pfkA	6-Phosphofructokinase	1.9	0.4	0.7	2.9
Protein synthesis
Cm
infC	Initiation factor IF-3	1.2	1.9	2.1	1.5
rplA	Ribosomal protein L1 (BL1)	1.3	3.3	1.7	1.6
rplK	Ribosomal protein L11 (BL11)	1.6	3.4	1.5	2.1
rplT	Ribosomal protein L20	1.1	3.4	1.6	1.9
rplU	Ribosomal protein L21 (BL20)	1.5	2.0	1.3	1.5
Em
rplC	Ribosomal protein L3 (BL3)	1.4	3.1	1.6	0.3
rplU	Ribosomal protein L21 (BL20)	1.3	4.3	1.7	0.5
rpsD	Ribosomal protein S4 (BS4)	1.3	5.9	1.2	0.5
rpsF	Ribosomal protein S6 (BS9)	1.9	9.4	3.5	2.9
rpsL	Ribosomal protein S12 (BS12)	1.5	2.8	1.3	0.2
Gm
rplB	Ribosomal protein L2 (BL2)	1.7	0.6	1.5	0.7
rplJ	Ribosomal protein L10 (BL5)	2.2	0.5	2.4	0.4
rplQ	Ribosomal protein L17 (BL15)	1.3	0.4	1.5	0.6
rplR	Ribosomal protein L18	1.8	0.5	1.6	0.7
rpsK	Ribosomal protein S11 (BS11)	1.7	0.4	1.6	0.7
Metabolism of amino acids
Cm
glnA	Required for transduction of the nitrogen regulation signal to GlnR and TnrA	0.9	0.9	0.7	0.4
glyA	Glycine requirement; indirect activation of KinB	0.9	1.0	0.6	0.5
goxB	Oxidation of sarcosine (N-methylglycine), N-ethylglycine, and glycine; lower activities on d-alanine, d-valine, and d-proline	1.1	0.9	0.7	0.2
pepT	Putative; Zn2+-dependent metalloenzyme; N-terminal region stabilizes Zn2+-binding	0.9	0.4	0.6	0.4
rocA	Sigma-L-dependent; positively regulated by RocR and AhrC (ARG recognition site located immediately upstream of the transcriptional start point)	1.0	1.7	2.7	0.6
Em
glyA	Serine hydroxymethyltransferase	1.1	1.0	1.4	0.4
hisD	Histidinol dehydrogenase	1.0	1.4	1.6	0.5
rocA	Pyrroline-5 carboxylate dehydrogenase	1.5	0.9	1.1	0.2
rocD	Ornithine aminotransferase	1.0	1.2	1.3	0.3
rocG	Glutamate dehydrogenase	0.9	1.0	1.4	0.3
Purine and pyrimidine     biosynthesis
Cm
purD	Phosphoribosylglycinamide synthetase	1.1	2.2	1.7	1.4
pyrB	Aspartate carbamoyltransferase	1.1	1.8	1.2	1.1
pyrF	Orotidine 5′-phosphate decarboxylase	1.0	1.8	1.3	1.8
pyrG	CTP synthetase	1.8	7.6	1.9	3.0
pyrP	Uracil permease	0.8	1.7	0.9	0.8
Em
purC	Phosphoribosylaminoimidazole succinocarboxamide synthetase	0.9	1.2	1.2	0.5
purE	Phosphoribosylaminoimidazole carboxylase I	1.0	2.1	1.2	0.3
purN	Phosphoribosylglycinamide formyltransferase	1.2	1.6	1.8	0.3
pyrAB	Carbamoyl-phosphate synthetase (catalytic subunit)	1.1	1.8	1.7	0.5
pyrD	Dihydroorotate dehydrogenase (catalytic subunit)	1.0	1.6	1.4	0.3
Heat shock proteins
Cm
clpQ	Two-component ATP-dependent protease (N-terminal serine protease)	0.8	0.9	0.6	1.0
clpX	ATP-dependent Clp protease ATP-binding subunit (class III heat shock protein)	1.2	0.6	0.6	0.8
dnaK	Class I heat shock protein (molecular chaperone)	1.2	0.7	1.0	0.7
groES	Class I heat shock protein (chaperonin)	1.1	0.2	0.3	0.3
nadE	NH3-dependent NAD+ synthetase; strongly induced in response to heat, ethanol, and salt stress or after starvation for glucose	1.0	1.0	0.7	0.7
Gm
clpP	ATP-dependent Clp protease proteolytic subunit (class III heat shock protein)
0.1× MIC		1.4	0.6	0.7	2.1
0.25× MIC		1.3	0.8	1.1	3.7
0.4× MIC		1.4	1.4	1.2	4.5
clpX	ATP-dependent Clp protease ATP-binding subunit (class III heat shock protein)	1.4	0.6	0.9	1.5
ykrL	Similar to heat shock protein	0.8	1.3	1.1	1.5

^aCm, chloramphenicol; Em, erythromycin; Gm, gentamicin. Concentrations of 0.4×, 0.5×, and 0.4× MIC, respectively, were used unless indicated otherwise.

^bValues 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.