TABLE 4.

Log2 ratios of genes whose transcription increased at one or more of the five time points (altogether 90 min) at which the effect of erythromycin treatment was studied, sorted by functional category (cellular role)

Protein encoded by geneCellular role(s)ORFLog2 ratio at:
t0t15t30t60t90
Cystathionine beta-lyase (metC)aAmino acid biosynthesisEF02900.71000−1.05
Prephenate dehydrogenaseAmino acid biosynthesisEF15650.710000
Cobyric acid synthase, putativeBiosynthesis of cofactors/prosthetic groups/carriersEF258600.870.8600
Alanine racemase (alr)Cell envelopeEF0849000.780.871.11
Membrane protein, putativeCell envelopeEF086000000.77
Glycosyl transferase, group 2 family proteinCell envelopeEF088700.6100.980
Extracellular protein, putativeCell envelopeEF094400.72000
UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (murG)Cell envelopeEF099400.64000
Membrane protein, putativeCell envelopeEF13840000.790.81
Bacterial sugar transferaseCell envelopeEF217700.750.7100
Glycosyl transferase, group 1 family proteinCell envelopeEF2890000.6000
Glycosyl transferase, group 1 family proteinCell envelopeEF2891000.690.830
Membrane proteinCell envelopeEF31760.740000
Adhesion lipoproteinCell envelope/cellular processesEF32060000.960.70
NAD-dependent epimerase/dehydratase family proteinCell envelope/energy metabolismEF2165000.7400.71
Cell division protein, FtsW/RodA/SpovE familyCellular processesEF13000000.861.23
MsrC protein, putativeCellular processesEF14131.882.963.243.363.44
Beta-lactamase, putativeCellular processesEF1502000.6200
Competence protein (comG3)Cellular processesEF2044000.6500.76
Competence protein (comG2)Cellular processesEF20450000.730.85
Competence protein (comG1)Cellular processesEF2046000.730.900
Chromosome partitioning protein ParBCellular processesEF329800000.69
ATPase, ParA familyCellular processesEF329900000.89
Drug resistance transporter, EmrB/QacA family proteinCellular processes/transport and binding proteinEF0420000.690.980
Multidrug resistance protein, putativeCellular processes/transport and binding proteinEF107800.781.241.180.93
Drug resistance transporter, EmrB/QacA family proteinCellular processes/transport and binding proteinEF1370000.830.970.68
Cell division ABC transporter, permease protein FtsX, putativeCellular processes/transport and binding proteinEF176000.801.130.720.69
Glycerol dehydrogenase, putativeCentral intermediary metabolismEF1358000.6600
Alkaline phosphatase (phoZ)Central intermediary metabolismEF29730.790.850.620.700
Heptaprenyl diphosphate synthase, component II, putativeCentral intermediary metabolismEF32600.830.840.8400
Chromosomal replication initiator protein DnaADNA metabolismEF000100000.65
MutT/nudix family proteinDNA metabolismEF078000.7000.950
DNA repair exonuclease family proteinDNA metabolismEF09720001.010
DNA polymerase III, alpha subunit (dnaE)DNA metabolismEF104400.6500.710
Endonuclease III (nth)DNA metabolismEF1155000.6600
ATP-dependent DNA helicase RecQDNA metabolismEF154500.760.881.001.08
MutT/nudix family proteinDNA metabolismEF158700000.78
Site-specific recombinase, phage integrase familyDNA metabolismEF16480000.730.81
Endonuclease IV (nfo)DNA metabolismEF173600.610.750.670
Site-specific recombinase, phage integrase familyDNA metabolismEF20430000.660
Toprim domain proteinDNA metabolismEF23050000.760.76
A/G-specific adenine glycosylase (mutY)DNA metabolismEF270400.650.6800
Regulatory protein RecX, putativeDNA metabolismEF270500.6500.940
ExonucleaseDNA metabolismEF27360.9100.9700
ATP-dependent DNA helicase RecGDNA metabolismEF311300.6000.740.69
Beta-phosphoglucomutase (pgmB)Energy metabolismEF0956000−0.901.27
Glycosyl hydrolase, family 65Energy metabolismEF0957000−1.121.36
Galactose-1-phosphate uridylyltransferase (galT)Energy metabolismEF1071000.6000
Glycosyl hydrolase, family 13Energy metabolismEF1347000−0.990.80
Glucan 1,6-alpha-glucosidase, putativeEnergy metabolismEF1348000−1.010.77
Glycosyl hydrolase, family 13Energy metabolismEF1349000−0.990.93
Glycosyl hydrolase, family 4Energy metabolismEF141100000.87
Ferredoxin (fer)Energy metabolismEF1543000.600.790
Glycosyl hydrolase, family 1Energy metabolismEF160600.690.700.700
Glycerate kinase, putativeEnergy metabolismEF2646000−1.650.70
3-Oxoacyl-(acyl-carrier-protein) synthase II (fabF-1)Fatty acid and phospholipid metabolismEF028300.83000
Holo-(acyl-carrier-protein) synthase (acpS)Fatty acid and phospholipid metabolismEF0848000.690.670.91
Cardiolipin synthetase, putativeFatty acid and phospholipid metabolismEF160800.710.6300
1-Acyl-sn-glycerol-3-phosphate acyltransferase, putativeFatty acid and phospholipid metabolismEF269101.060.650.741.09
Enoyl-(acyl-carrier-protein) reductase II (fabK)Fatty acid and phospholipid metabolismEF288300.670.7200.89
Fatty acid/phospholipid synthesis protein PlsXFatty acid and phospholipid metabolismEF3112000.6400
TraE protein, putativeOther categoriesEF2320000.610.690
ATP-dependent Clp protease, ATP-binding subunit ClpEProtein fateEF0706000.7900
DnaJ proteinProtein fateEF131000000.79
Heat shock protein HslVProtein fateEF16470000.740
Signal recognition particle protein (ffh)Protein fateEF170000.740.800.811.05
Preprotein translocase, SecE subunitProtein fateEF2730000.751.170.71
Signal peptidase IProtein fateEF307300.64000.72
Ribosomal protein L18 (rplR)Protein synthesisEF022300.660.7500
Ribosomal protein S5 (rpsE)Protein synthesisEF022400.580.6400
Ribosomal protein L30 (rpmD)Protein synthesisEF022500.600.6100
Ribosomal protein L15 (rplO)Protein synthesisEF022600.660.9200
Ribosomal protein L27 (rpmA)Protein synthesisEF097000.73000
Ribosomal protein S16 (rpsP)Protein synthesisEF1694000.7300
Ribosome recycling factor (frr)Protein synthesisEF2395000.810.770
Translation elongation factor Ts (tsf)Protein synthesisEF239700.720.8200
Ribosomal-protein-alanine acetyltransferase, putativeProtein synthesisEF247300.6300.750
Ribosomal-protein-alanine acetyltransferase, putativeProtein synthesisEF247400000.66
Tryptophanyl-tRNA synthetase (trpS)Protein synthesisEF267900.861.231.010.82
Ribosomal protein L33 (rpmG-2)Protein synthesisEF2731000.620.991.17
Ribosomal protein S4 (rpsD)Protein synthesisEF30700000.660
Dihydroorotate dehydrogenase (pyrD-1)Purine/pyrimidine/nucleoside/nucleotideEF028500.820.6700
Dihydroorotate dehydrogenase (pyrD-2)Purine/pyrimidine/nucleoside/nucleotideEF171400.71000
Dihydroorotase (pyrC)Purine/pyrimidine/nucleoside/nucleotideEF171800000.66
Phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK-2)Purine/pyrimidine/nucleoside/nucleotideEF236200000.68
Xanthine phosphoribosyltransferase (xpt)Purine/pyrimidine/nucleoside/nucleotideEF2365000.791.040
Uridylate kinase (pyrH)Purine/pyrimidine/nucleoside/nucleotideEF239600.760.6800
Inosine-uridine preferring nucleoside hydrolasePurine/pyrimidine/nucleoside/nucleotideEF2587000.7900.90
2′,3′-Cyclic-nucleotide 2′-phosphodiesterase, putativePurine/pyrimidine/nucleoside/nucleotideEF290200000.80
Transcriptional regulator, DeoR familyRegulatory functionsEF07190001.780
Transcriptional regulator, PemK familyRegulatory functionsEF0850000.670.840.95
DNA-binding response regulatorRegulatory functionsEF1050000.7600
Transcriptional regulator, Cro/CI familyRegulatory functionsEF136900.681.181.401.13
Transcription antiterminator BglG family proteinRegulatory functionsEF151500.690.6200.89
Protease synthase and sporulation negative regulatory protein pai 1Regulatory functionsEF159000.700.650.660.87
Sucrose operon repressor ScrR (scrR-1)Regulatory functionsEF1604000.651.050.75
Transcriptional regulator (codY)Regulatory functionsEF1645000.690.730.78
Transcriptional regulator, TetR familyRegulatory functionsEF20660000.680
Phosphosugar-binding transcriptional regulator, putativeRegulatory functionsEF225900000.70
Transcriptional regulator, Cro/CI familyRegulatory functionsEF265300000.94
Transcriptional regulator, Cro/CI familyRegulatory functionsEF285200000.93
Zinc-binding transcriptional regulator, Cro/CI familyRegulatory functionsEF327200.84000
PTS system component, mannose-specific IIC componentSignal transductionEF0021000−1.221.04
PTS system, mannose-specific IID componentSignal transductionEF0022000−1.341.04
PTS system, fructose-specific family, IIABC componentSignal transductionEF07170000.900
PTS system, IIABC componentSignal transductionEF0958000−1.270
Sensor histidine kinaseSignal transductionEF1051000.6900
Sensor histidine kinaseSignal transductionEF1261000.6500
PTS system, IIABC componentSignal transductionEF151601.131.441.061.06
PTS system, IIC componentSignal transductionEF297800000.66
PTS system, IIB componentSignal transductionEF297900.690.7200.94
ATP-dependent RNA helicase, DEAD/DEAH box familyTranscriptionEF08460000.680
Transcription termination factor RhoTranscriptionEF1170000.6800.84
ATP-dependent helicase, DEAH-box family, putativeTranscriptionEF321400.62000
Iron compound ABC transporter, substrate-binding proteinTransport and binding proteinEF018800000.82
Na+/H+ antiporter (nhaC-2)Transport and binding proteinEF063600.6401.010
Sodium/dicarboxylate symporter family proteinTransport and binding proteinEF074401.441.200.870.71
Amino acid ABC transporter, ATP-binding proteinTransport and binding proteinEF0760000.6300
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF078900.701.081.090
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF0790000.750.960
Potassium uptake proteinTransport and binding proteinEF087200.65000
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF09410000.720
Amino acid permease family proteinTransport and binding proteinEF1103000.840.930.66
ABC transporter, ATP-binding proteinTransport and binding proteinEF12550.940.75000
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF134100.69000
Sugar ABC transporter, permease proteinTransport and binding proteinEF134400.620−0.931.25
Cadmium-translocating P-type ATPaseTransport and binding proteinEF14000.650.710.860.781.09
V-type ATPase, subunit BTransport and binding proteinEF149900000.79
Iron compound ABC transporter, ATP-binding proteinTransport and binding proteinEF1639000.6200.95
Iron compound ABC transporter, permease proteinTransport and binding proteinEF164000.600.740.671.04
ABC transporter, ATP-binding/permease protein, MDR familyTransport and binding proteinEF173201.180.860.781.69
ABC transporter, ATP-binding/permease protein, MDR familyTransport and binding proteinEF173301.130.950.811.54
Amino acid permease family proteinTransport and binding proteinEF2047000.901.210
Transport ATP-binding protein CydD, putativeTransport and binding proteinEF2058000.6800
Transport ATP-binding protein CydC, putativeTransport and binding proteinEF2059000.6100.83
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF22260001.000.70
Xanthine permeaseTransport and binding proteinEF23640.7300.971.070
Amino acid permeaseTransport and binding proteinEF237700.630.740.920
ABC transporter, permease proteinTransport and binding proteinEF2485000.6200
AzlC proteinTransport and binding proteinEF25090000.750
Glycine betaine/l-proline transport ATP binding subunitTransport and binding proteinEF26410001.300
Glycine betaine/l-proline ABC transporter, glycine betaine/l-proline-binding/permease proteinTransport and binding proteinEF2642000.821.750.86
Permease, GntP familyTransport and binding proteinEF2647000−2.311.32
Spermidine/putrescine ABC transporterTransport and binding proteinEF264900001.05
Spermidine/putrescine ABC transporterTransport and binding proteinEF265000000.92
Spermidine/putrescine ABC transporterTransport and binding proteinEF265100000.94
Spermidine/putrescine ABC transporterTransport and binding proteinEF265200000.67
ABC transporter, ATP-binding proteinTransport and binding proteinEF27200.930.691.120.860.80
ABC transporter, ATP-binding proteinTransport and binding proteinEF276900−0.6000.72
Ion transporter, putativeTransport and binding proteinEF285400000.72
Potassium uptake protein TrkATransport and binding proteinEF291000.650.840.861.15
ABC transporter, ATP-binding proteinTransport and binding proteinEF2986000.6200
Cytosine/purines, uracil, thiamine, allantoin permease family proteinTransport and binding proteinEF300000000.82
Formate/nitrite transporter family proteinTransport and binding proteinEF30690.820.8700.730.66
Iron compound ABC transporter, permease proteinTransport and binding proteinEF308500000.69
ABC transporter, permease proteinTransport and binding proteinEF3199000.9801.26
ABC transporter, ATP-binding proteinTransport and binding proteinEF320000.700.8600.94
ABC transporter, permease proteinTransport and binding proteinEF320800.710.9800
Oxidoreductase, DadA familyUnknown functionEF04140000.720
LysM domain proteinUnknown functionEF04430.851.211.301.030
Glyoxalase family proteinUnknown functionEF066600.71000
Methyltransferase, putativeUnknown functionEF06910000.750
Type 2 phosphatidic acid phosphatase family proteinUnknown functionEF07960000.690
DegV family proteinUnknown functionEF119100000.77
Metallo-beta-lactamase YycJUnknown functionEF1197000.900.930.92
GTP-binding proteinUnknown functionEF1527000.770.680.74
GTPase, putativeUnknown functionEF1549000.7100
Acetyltransferase, GNAT familyUnknown functionEF158900001.00
LacX protein, putativeUnknown functionEF164400.640.700.810
Lipase/acylhydrolase, putativeUnknown functionEF1683000.6900.67
GTP-binding proteinUnknown functionEF19160.991.021.391.091.18
GTP-binding protein LepAUnknown functionEF2352000.631.040
Diacylglycerol kinase catalytic domain proteinUnknown functionEF26610000.860.92
Oxidoreductase, pyridine nucleotide-disulfide familyUnknown functionEF289900.750.731.061.02
Glucose-inhibited division protein B (gidB)Unknown functionEF330000000.67
  • a Gene names in parentheses.