TABLE 5.

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

Protein encoded by geneCellular role(s)ORFLog2 ratio at:
t0t15t30t60t90
Ornithine carbamoyltransferase (argF-1)aAmino acid biosynthesisEF010500−1.37−2.81−2.19
Cysteine synthase B, putativeAmino acid biosynthesisEF02890000−0.75
Cystathionine beta-lyase (metC)Amino acid biosynthesisEF02900.71000−1.05
Arginine repressor (argR)Amino acid biosynthesisEF0676000−0.940
Aspartate aminotransferase, putativeAmino acid biosynthesisEF0891−1.00−1.08−0.96−0.74−1.03
Phosphomevalonate kinaseBiosynthesis of cofactors/prosthetic groups/carriersEF0902−0.75−0.73000
Thiamin biosynthesis ApbE, putativeBiosynthesis of cofactors/prosthetic groups/carriersEF122500−0.9200
NH3-dependent NAD+ synthetase (nadE)Biosynthesis of cofactors/prosthetic groups/carriersEF26250000−0.88
Phosphomethylpyrimidine kinase (thiD)Biosynthesis of cofactors/prosthetic groups/carriersEF27750−0.83−0.9500
Thiamine-phosphate pyrophosphorylase (thiE)Biosynthesis of cofactors/prosthetic groups/carriersEF27760−0.75−0.7600
Hydroxyethylthiazole kinase, putativeBiosynthesis of cofactors/prosthetic groups/carriersEF27770−0.63−0.7200
Adhesion lipoproteinCell envelopeEF005500−0.8400
Glycosyl hydrolase, family 20Cell envelopeEF0114000−0.870
Surface exclusion protein, putativeCell envelopeEF0146−0.84−0.85−0.7200
Chitinase, family 2Cell envelopeEF0361000−0.86−0.86
Chitin binding protein, putativeCell envelopeEF0362000−1.09−0.96
LemA proteinCell envelopeEF046800−1.1100
Penicillin-binding protein, putativeCell envelopeEF07460−0.73−1.390−0.87
Gram-positive anchor protein, putativeCell envelopeEF0775−0.95−1.10−0.81−0.67−0.91
Membrane protein, putativeCell envelopeEF102700−0.6000
Pheromone cAM373 precursor lipoproteinCell envelopeEF13400−0.79000
CoccolysinCell envelopeEF1818000−0.850
Endocarditis specific antigenCell envelopeEF20760−0.76−0.77−1.12−1.51
DltD proteinCell envelopeEF274600−0.6500
d-Alanyl carrier protein (dltC)Cell envelopeEF2747−0.86−0.79−1.2200
Basic membrane protein DtlBCell envelopeEF274800−0.6500
d-Alanine-activating enzyme, putativeCell envelopeEF274900−0.7400
Sortase family proteinCell envelopeEF305600−0.77−1.56−1.32
Rod shape-determining protein MreDCell envelopeEF3061000−0.93−1.28
Rod shape-determining protein MreCCell envelopeEF3062000−1.01−1.21
Pheromone cAD1 precursor lipoproteinCell envelopeEF32560−0.68−0.7300
Gls24 proteinCellular processesEF00790−1.04−0.97−1.16−1.39
Gls24 proteinCellular processesEF00800−0.98−1.20−1.28−1.87
Regulatory protein, putative (pfoR)Cellular processesEF009700−0.7800
Superoxide dismutase, Mn (sodA)Cellular processesEF04630−0.65000
Low-temperature requirement C protein, putativeCellular processesEF06390000.96−1.21
Polysaccharide lyase, family 8Cellular processesEF08180−0.70−0.890−1.24
Universal stress protein familyCellular processesEF10580−1.20−1.28−1.44−2.27
Streptomycin 3-adenylyltransferase, putativeCellular processesEF1076−0.71−0.97−0.64−0.88−0.77
Autoinducer-2 production protein LuxSCellular processesEF11820−0.68−0.660−0.99
Cold shock protein CspCCellular processesEF19910−0.98000
Negative regulator of genetic competence MecA, putativeCellular processesEF26770000−0.66
Alkyl hydroperoxide reductase, C subunit (ahpC)Cellular processesEF27390−0.70−0.68−0.68−0.68
Dps family proteinCellular processesEF323300−0.7000
Nucleotidyltransferase family proteinCentral intermediary metabolismEF01370−0.69−0.870−0.77
Hydrolase, alpha/beta hydrolase fold familyCentral intermediary metabolismEF102800−0.7000
6-Aminohexanoate-cyclic-dimer hydrolase, putativeCentral intermediary metabolismEF1033000−0.950
Microcompartment proteinCentral intermediary metabolismEF1623−0.66−0.76000
Chromosomal replication initiator protein DnaADNA metabolismEF000100000.65
Thermonuclease precursor (nuc-1)DNA metabolismEF05110000−0.70
Exonuclease RexBDNA metabolismEF11120−0.67−0.6400
MutT/nudix family proteinDNA metabolismEF11410−0.58−0.5900
l-Serine dehydratase, iron-sulfur-dependent, beta subunit (sdhB-1)Energy metabolismEF009800−1.0800
l-Serine dehydratase, iron-sulfur-dependent, alphasubunit (sdhA-1)Energy metabolismEF009900−0.6700
Arginine deiminase (arcA)Energy metabolismEF01040−0.65−1.73−3.16−2.55
Carbamate kinase (arcC-1)Energy metabolismEF010600−0.92−1.99−1.26
Phosphoglycerate mutase 1 (gpm)Energy metabolismEF019500−0.620−0.65
Aldehyde dehydrogenaseEnergy metabolismEF0253−0.74−0.82−0.90−0.72−0.91
l-Lactate dehydrogenase (ldh-2)Energy metabolismEF0641000−0.78−0.75
Phosphoglucomutase/phosphomannomutase family proteinEnergy metabolismEF0677000−1.160
Aldehyde-alcohol dehydrogenase (adhE)Energy metabolismEF090000−0.7700
Methylglyoxal synthase (mgsA)Energy metabolismEF0939−0.88−1.10−0.96−0.85−0.96
Beta-phosphoglucomutase (pgmB)Energy metabolismEF0956000−0.901.27
Glycosyl hydrolase, family 65Energy metabolismEF0957000−1.121.36
Glycosyl hydrolase, family 1Energy metabolismEF1020000−1.930
Aldose 1-epimerase (galM)Energy metabolismEF1068−0.84−1.07−0.720−0.75
Iron-sulfur cluster binding proteinEnergy metabolismEF110900−0.7800
NADH peroxidase (npr)Energy metabolismEF121100−0.590−0.73
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
Glyceraldehyde 3-phosphate dehydrogenase (gap-1)Energy metabolismEF15260000−0.98
Pyruvate formate-lyase activating enzyme (pflA)Energy metabolismEF1612000−0.730
Formate acetyltransferase (pflB)Energy metabolismEF1613000−0.860
Alcohol dehydrogenase, zinc containingEnergy metabolismEF182600−0.84−0.70−1.01
Mannose-6-phosphate isomerase, class I (manA)Energy metabolismEF2589000−0.690
Glycerate kinase, putativeEnergy metabolismEF2646000−1.650.70
Endo-beta-N-acetylglucosaminidaseEnergy metabolismEF2863000−1.390
Ribokinase (rbsK)Energy metabolismEF2961000−1.32−1.16
Glycosyl hydrolase, family 65Energy metabolismEF3157000−1.340
Lipase/acylhydrolaseFatty acid and phospholipid metabolismEF01690000−1.00
IS1216, transposaseOther categoriesEF051400−0.63−0.81−0.81
Transposase, putativeOther categoriesEF09130−0.69000
Aminopeptidase C (pepC)Protein fateEF03020000−0.82
Rotamase family proteinProtein fateEF06850−0.60−0.75−0.80−1.01
Preprotein translocase, YajC subunit, putativeProtein fateEF08970000−0.83
Signal peptidase IProtein fateEF11110−0.66000
Serine proteinase, V8 familyProtein fateEF1817000−0.860
Serine protease DO (htrA)Protein fateEF3027000−0.670
Peptidase, M20/M25/M40 familyProtein fateEF317800−0.62−0.80−1.32
Cysteinyl-tRNA synthetase (cysS)Protein synthesisEF004500−0.5900
RNA methyltransferase, TrmH familyProtein synthesisEF00470−0.60−0.6100
Tyrosyl-tRNA synthetase (tryS-1)Protein synthesisEF0633000−0.67−1.61
Glutamyl-tRNA (Gln) amidotransferase, C subunit (gatC)Protein synthesisEF07240−0.65−0.6800
Ribosomal protein L25 (rplY)Protein synthesisEF0820000.68−1.01−2.07
Alanyl-tRNA synthetase (alaS)Protein synthesisEF13790000−0.69
Ribosomal subunit interface protein (yfiA)Protein synthesisEF17640−0.78000
Aspartyl-tRNA synthetase (aspS)Protein synthesisEF19700000−0.77
Tryptophanyl-tRNA synthetaseProtein synthesisEF222800−0.6200
Ribosomal protein L33 (rpmG-3)Protein synthesisEF28560−0.98000
Threonyl-tRNA synthetase (thrS)Protein synthesisEF28580−0.72−0.64−0.90−1.20
Valyl-tRNA synthetase (valS)Protein synthesisEF2931000−0.670
Seryl-tRNA synthetase (serS-2)Protein synthesisEF3292000−0.67−0.83
Ribosomal protein L34 (rpmH)Protein synthesisEF33330−0.61000
Adenylosuccinate synthetase (purA)Purine/pyrimidine/nucleoside/nucleotideEF00140−0.73−0.730−0.70
Phosphopentomutase (deoB)Purine/pyrimidine/nucleoside/nucleotideEF018500−0.6900
Ribonucleoside-diphosphate reductase 2, beta subunit (nrdF)Purine/pyrimidine/nucleoside/nucleotideEF0470000−0.800
Ribonucleoside-diphosphate reductase 2, alpha subunit (nrdE)Purine/pyrimidine/nucleoside/nucleotideEF0471000−0.69−0.79
Ribonucleoside-diphosphate reductase 2, NrdH-redoxin (nrdH)Purine/pyrimidine/nucleoside/nucleotideEF04730−0.590−0.80−0.83
Aspartate carbamoyltransferase (pyrB)Purine/pyrimidine/nucleoside/nucleotideEF17190−0.63000
Pyrimidine operon regulatory protein PyrR (pyrR)Purine/pyrimidine/nucleoside/nucleotideEF17210−0.82000
Inosine-uridine-preferring nucleoside hydrolasePurine/pyrimidine/nucleoside/nucleotideEF1921000−0.920
Anaerobic ribonucleoside-triphosphate reductase (hrdD)Purine/pyrimidine/nucleoside/nucleotideEF2754000−0.96−0.83
Anaerobic ribonucleoside-triphosphate reductase activating protein (nrdG)Purine/pyrimidine/nucleoside/nucleotideEF2755000−0.96−1.14
Transcriptional regulator, Cro/CI familyRegulatory functionsEF01290−0.69−0.7300
Transcriptional regulator, Cro/CI familyRegulatory functionsEF08690−0.64000
Transcriptional regulator, DeoR familyRegulatory functionsEF1124−0.79−0.84−0.680−0.71
Transcriptional regulator, LysR familyRegulatory functionsEF130300−0.8700
Transcriptional regulator, Cro/CI familyRegulatory functionsEF2142−0.670−0.6700
Transcriptional regulator, Cro/CI familyRegulatory functionsEF23380−0.79−0.600−0.88
Transcriptional regulator, Cro/CI familyRegulatory functionsEF25440−0.75000
Transcriptional regulatorRegulatory functionsEF27030−0.65−0.8400
Transcriptional regulator, AraC familyRegulatory functionsEF2711000−1.000
Transcriptional antiterminator, bglG familyRegulatory functionsEF2966000−1.08−1.28
DNA-binding response regulatorRegulatory functionsEF32890000−0.84
PTS system, mannose-specific IIAB componentSignal transductionEF0020000−0.880
PTS system, mannose-specific IIC componentSignal transductionEF0021000−1.221.04
PTS system, mannose-specific IID componentSignal transductionEF0022000−1.341.04
PTS system, mannitol-specific IIBC componentSignal transductionEF04110000−0.73
PTS system, IID componentSignal transductionEF0553000−0.730
PTS system, IIABC componentSignal transductionEF0958000−1.270
PTS system, IIB componentSignal transductionEF1012000−2.910
PTS system, IIB componentSignal transductionEF1017000−2.750
PTS system, IIA componentSignal transductionEF1018000−2.680
PTS system, IIC componentSignal transductionEF1019000−3.280
Response regulatorSignal transductionEF13360−0.79−0.6000
Response regulatorSignal transductionEF1633−0.80−1.06−0.92−0.80−0.86
PTS system, IIA componentSignal transductionEF180100−0.6900
PTS system, IIBC componentSignal transductionEF2213000−1.830
PTS system, IID componentSignal transductionEF302900−0.6600
Sensor histidine kinaseSignal transductionEF32900000−0.97
RNA polymerase sigma-54 factor (rpoN)TranscriptionEF07820−0.76−0.6400
RNA polymerase sigma-70 factor, ECF subfamilyTranscriptionEF318000−1.1200
ABC transporter, ATP-binding proteinTransport and binding proteinEF005600−0.7500
ABC transporter, permease proteinTransport and binding proteinEF01790−0.59000
Amino acid ABC transporter, amino acid-binding/ permease proteinTransport and binding proteinEF024700−0.6800
Na+/H+ antiporter (nhaC-1)Transport and binding proteinEF0402000−1.10−0.98
Cation ABC transporter, permease proteinTransport and binding proteinEF057600−0.6200
ABC transporter, ATP-binding proteinTransport and binding proteinEF0793−0.85−0.92−0.860−0.75
Amino acid ABC transporter, ATP-binding proteinTransport and binding proteinEF08920−0.61000
Peptide ABC transporter, peptide-binding proteinTransport and binding proteinEF0907000−0.67−1.39
ABC transporter, ATP-binding/TOBE domain proteinTransport and binding proteinEF0938000−1.390
Mn2+/Fe2+ transporter, NRAMP familyTransport and binding proteinEF10570−1.13−1.12−1.23−1.78
ABC transporter, ATP-binding/permease proteinTransport and binding proteinEF1100−0.76−0.86−0.7000
Phosphotransferase enzyme II, B component SgaB (sgaB)Transport and binding proteinEF1128−0.86−0.74000
ABC transporter, permease proteinTransport and binding proteinEF12540000−0.88
Cation-transporting ATPase, E1-E2 familyTransport and binding proteinEF12680−0.64−0.7200
Magnesium-translocating P-type ATPaseTransport and binding proteinEF1304−0.84−1.01−1.3100
ABC transporter, ATP-binding proteinTransport and binding proteinEF13310−0.79−0.6900
Sugar ABC transporter, permease proteinTransport and binding proteinEF134400.620−0.931.25
Sugar ABC transporter, sugar-binding proteinTransport and binding proteinEF1345000−1.390
Magnesium-translocating P-type ATPaseTransport and binding proteinEF135200−0.6200
V-type ATPase, subunit FTransport and binding proteinEF149200−0.8600
ABC transporter, ATP-binding proteinTransport and binding proteinEF1673−0.650−0.8200
Uracil permeaseTransport and binding proteinEF17200−0.60000
Phosphate ABC transporter, phosphate-binding proteinTransport and binding proteinEF175900−0.6100
ABC transporter, permease protein, putativeTransport and binding proteinEF204900−1.1800
ABC transporter, ATP-binding proteinTransport and binding proteinEF205000−1.1600
ABC transporter, ATP-binding proteinTransport and binding proteinEF2074000−0.70−0.76
ABC transporter, permease proteinTransport and binding proteinEF2081000−0.680
ABC transporter, ATP-binding proteinTransport and binding proteinEF239400−0.6100
Permease, GntP familyTransport and binding proteinEF2647000−2.311.32
ABC transporter, ATP-binding proteinTransport and binding proteinEF276900−0.6000.72
Ribose uptake protein, putativeTransport and binding proteinEF2959000−1.19−0.77
Ribose transporter protein RbsDTransport and binding proteinEF296000−0.70−1.48−1.30
Peptide ABC transporter, peptide-binding proteinTransport and binding proteinEF3106000−1.88−1.13
Peptide ABC transporter, permease proteinTransport and binding proteinEF3107000−1.75−0.82
Peptide ABC transporter, permease proteinTransport and binding proteinEF3108000−2.19−0.87
Peptide ABC transporter, ATP-binding proteinTransport and binding proteinEF3109000−1.330
Peptide ABC transporter, ATP-binding proteinTransport and binding proteinEF3110000−1.65−0.86
Cytosine permease, putativeTransport and binding proteinEF3277−0.80−0.74000
AMP-binding family proteinUnknown functionEF045200−0.6100
OsmC/Ohr family proteinUnknown functionEF045300.95−1.05−1.16−1.67
Acetyltransferase, GNAT familyUnknown functionEF0678000−1.320
Oxidoreductase, aldo/keto reductase 2 familyUnknown functionEF0877000−0.670
Pentapeptide repeat family proteinUnknown functionEF0905−0.81−1.04−0.920−0.75
N-acyl-d-amino-acid deacylase family proteinUnknown functionEF1062−0.92−1.02000
Acetyltransferase, GNAT familyUnknown functionEF1075−0.87−0.97−0.790−0.78
Acetyltransferase, GNAT familyUnknown functionEF1077−0.64−0.92−0.6400
YkgG family proteinUnknown functionEF1110−0.67−0.71000
Oxidoreductase, aldo/keto reductase familyUnknown functionEF11380000−0.77
HesA/MoeB/ThiF family proteinUnknown functionEF13290−0.58−0.6400
CelC-related proteinUnknown functionEF2440000−1.310
PDZ domain proteinUnknown functionEF24500000−0.68
HD domain proteinUnknown functionEF24700000−0.80
Aldehyde oxldoreductase, putativeUnknown functionEF257000−0.8000
Hydrolase, haloacid dehalogenase-like familyUnknown functionEF26810−0.86000
Oxidoreductase, Gfo/Idh/MocA familyUnknown functionEF27340000−0.76
Thioredoxin reductase/glutathione-related proteinUnknown functionEF273800−0.6200
DNA-binding protein, putativeUnknown functionEF293300−0.6900
Glyoxalase family proteinUnknown functionEF3092000−0.710
Hydrolase, haloacid dehalogenase-like familyUnknown functionEF3158000−1.16−0.72
Cell-envelope-associated acid phosphataseUnknown functionEF324500−0.7800
Gp35Viral functionsEF21430−0.59−0.5900
  • a Gene names in parentheses.