TABLE 3.

Transcriptional profiles of RpoBA621E mutation-related strains

ORF IDGeneProductsRatio of signal intensitya
N315ΔIP-rpoB621E/N315ΔIP10*3d1-SA182614A-rpoB621E/10*3d1-SA182614A-rpoB621A10*3d1/ N315ΔIP
Purine metabolism
    SA0016purAAdenylosuccinate synthase0.360.640.76
    SA0373xprTXanthine phosphoribosyltransferase0.640.400.12
    SA0374pbuXXanthine permease0.550.420.10
    SA0375guaBInositol-monophosphate dehydrogenase0.900.500.18
    SA0376guaAGMP synthase (glutamine hydrolyzing)0.880.650.23
    SA0468Hypoxanthine-guanine phosphoribosyltransferase homologue1.511.181.53
    SA0916Similar to phosphoribosylaminoimidazole carboxylase PurE0.840.800.72
    SA0917purKPhosphoribosylaminoimidazole carboxylase carbon dioxide-fixation chain PurK homolog0.930.540.43
    SA0918purCPhosphoribosylaminoimidazolesuccinocarboxamide synthetase homolog1.000.570.43
    SA0919Conserved hypothetical protein0.960.690.45
    SA0920purQPhosphoribosylformylglycinamidine synthase I PurQ1.100.520.32
    SA0922purFPhosphoribosylpyrophosphate amidotransferase PurF0.810.520.26
    SA0923purMPhosphoribosylformylglycinamidine cyclo-ligase PurM0.770.540.29
    SA0924purNPhosphoribosylglycinamide formyltransferase0.790.560.30
    SA0925purHBifunctional purine biosynthesis protein PurH0.750.590.33
    SA0926purDPhosphoribosylamine-glycine ligase PurD0.610.550.36
    SA1052gmkGuanylate kinase homolog0.810.910.81
    SA1172Similar to GMP reductase0.340.370.57
    SA1173Conserved hypothetical protein0.280.330.58
    SA1461aptAdenine phosphoribosyl transferase0.941.301.41
Pyrimidine metabolism
    SA0440tmkThymidylate kinase homolog0.640.600.74
    SA0719trxBThioredoxine reductase0.450.460.68
    SA1041pyrRPyrimidine operon repressor chain A0.170.350.82
    SA1042pyrPUracil permease0.140.210.41
    SA1043pyrBAspartate transcarbamoylase chain A0.130.220.41
    SA1044pyrCDihydroorotase0.150.250.39
    SA1045pyrAACarbamoyl-phosphate synthase small chain0.180.280.40
    SA1046pyrABCarbamoyl-phosphate synthase large chain0.180.320.38
    SA1047pyrFOrotidine-5-phosphate decarboxylase0.220.400.40
    SA1048pyrEOrotate phosphoribosyltransferase0.200.430.41
    SA1049Hypothetical protein0.220.420.47
    SA1439udkUridine kinase0.680.741.32
    SA2375Similar to dihydroorotate dehydrogenase0.620.750.56
Arginine metabolism and urea cycle
    SA0175Conserved hypothetical protein0.340.420.24
    SA0176Similar to N-acetylglutamate 5-phosphotransferase0.630.760.64
    SA0177argJArginine biosynthesis bifunctional protein homolog0.610.760.64
    SA0178argCN-acetylglutamate gamma-semialdehyde dehydrogenase0.590.730.65
    SA0179Ornithine aminotransferase0.640.800.82
    SA0821argHArgininosuccinate lyase0.440.540.27
    SA0822argGArgininosuccinate synthase0.480.590.29
    SA2082ureAUrease gamma subunit0.370.260.28
    SA2083ureBUrease beta subunit0.230.190.24
    SA2084ureCUrease alpha subunit0.300.210.24
    SA2085ureEUrease accessory protein UreE0.260.190.24
    SA2086ureFUrease accessory protein UreF0.300.270.29
    SA2087ureGUrease accessory protein UreG0.440.330.32
    SA2088ureDUrease accessory protein UreD0.390.300.32
    SA2428arcAArginine deiminase2.822.751.45
    SA2429Similar to arginine repressor3.626.202.27
Galactose metabolism
    SA0123Similar to UDP-glucose 4-epimerase (gale-1)0.340.450.41
    SA0236Similar to PTS fructose-specific enzyme IIBC component0.680.830.82
    SA0237Similar to PTS, galactitol-specific IIB component0.650.710.93
    SA0238gatCProbable PTS galactitol-specific enzyme IIC component0.640.811.28
    SA1521pfk6-Phosphofructokinase0.770.600.53
    SA1991lacG6-Phospho-beta-galactosidase0.330.731.75
    SA1992lacEPTS system, lactose-specific IIBC component0.350.631.40
    SA1993lacFPTS system, lactose-specific IIA component0.320.621.38
    SA1994lacDTagatose 1,6-diphosphate aldolase0.390.591.25
    SA1995lacCTagatose-6-phosphate kinase0.380.561.22
    SA1996lacBGalactose-6-phosphate isomerase LacB subunit0.420.531.17
    SA1997lacAGalactose-6-phosphate isomerase LacA subunit0.420.541.10
    SA2288gtaBUTP-glucose-1-phosphate uridyltransferase0.630.690.53
Nitrogen metabolism
    SA0008hutHHistidine ammonia-lyase1.271.501.25
    SA0171fdhNAD-dependent formate dehydrogenase0.810.781.18
    SA0774ABC transporter ATP-binding protein homolog2.852.953.28
    SA0775FeS assembly protein SufD2.843.053.71
    SA0776Aminotransferase NifS homolog2.763.123.41
    SA0777Similar to nitrogen fixation protein NifU2.583.153.44
    SA0778sufBFeS assembly protein SufB2.272.913.23
    SA0779Hypothetical protein1.912.112.30
    SA0819gudBNAD-specific glutamate dehydrogenase1.782.141.75
    SA1241Similar to nitric-oxide reductase2.371.422.29
    SA1310ansAProbable l-asparaginase1.311.361.18
dlt operon
    SA0792Hypothetical protein1.562.120.98
    SA0793dltAd-alanine-d-alanyl carrier protein ligase1.612.270.88
    SA0794dltBDltB membrane protein1.602.540.81
    SA0795dltCd-alanyl carrier protein1.552.600.83
    SA0796dltDPoly(glycerophosphate chain) d-alanine transfer protein1.442.520.84
sigB operon
    SA1869sigBSigma factor B2.962.051.19
    SA1870rsbWAnti-sigmaB factor3.151.901.14
    SA1871rsbVAnti-sigmaB factor antagonist2.641.741.22
    SA1872rsbUSigmaB regulation protein RsbU2.081.621.22
Riboflavin (vitamin B2) metabolism
    SA1586ribH6,7-Dimethyl-8-ribityllumazine synthase1.751.882.03
    SA1588ribBRiboflavin synthase alpha chain1.921.942.20
    SA1589ribDRiboflavin-specific deaminase2.032.042.08
    SA1587ribARiboflavin biosynthesis protein2.181.992.16
Phylloquinone (vitamin K1) and menaquinone (vitamin K2) metabolism
    SA0898menBNaphthoate synthase1.081.301.33
    SA1303gerCBMenaquinone biosynthesis methyltransferase1.141.001.16
    SA0895Similar to menaquinone-specific isochorismate synthase1.791.442.66
    SA1616Hypothetical protein1.852.122.37
    SA0897Similar to prolyl aminopeptidase (EC 3.4.11.5)1.911.741.91
    SA0896menDMenaquinone biosynthesis protein1.931.652.33
    SA1615menEO-succinylbenzoic acid-coenzyme A (CoA) ligase2.121.762.18
    SA1614menCO-succinylbenzoic acid (OSB) synthetase2.141.651.78
Citrate cycle (TCA cycle)
    SA0944phdBPyruvate dehydrogenase E1 component beta subunit1.250.970.90
    SA0945pdhCDihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E21.281.020.97
    SA0946pdhDDihydrolipoamide dehydrogenase component of pyruvate dehydrogenase E30.901.041.11
    SA0994sdhCSuccinate dehydrogenase cytochrome b-5581.721.131.50
    SA0995sdhASuccinate dehydrogenase flavoprotein subunit1.651.311.50
    SA0996sdhBSuccinate dehydrogenase iron-sulfur protein subunit1.051.581.88
    SA1088sucCSuccinyl-CoA synthetase (beta subunit)1.461.541.59
    SA1089sucDsuccinyl-CoA synthetase (alpha subunit)1.111.521.62
    SA1131Similar to 2-oxoacid ferredoxin oxidoreductase, alpha subunit1.491.251.77
    SA1132Similar to 2-oxoacid ferredoxin oxidoreductase, beta subunit1.391.371.74
    SA1184citBAconitate hydratase1.071.111.59
    SA1244odhBDihydrolipoamide succinyltransferase1.661.741.44
    SA1245odhA2-Oxoglutarate dehydrogenase E11.361.451.24
    SA1349Dihydrolipoamide dehydrogenase1.540.931.16
    SA1517citCIsocitrate dehyrogenase1.171.272.02
    SA1518citZCitrate synthase II1.031.182.11
    SA1609pckAPhosphoenolpyruvate carboxykinase (ATP)1.270.821.10
Cell envelope and cellular processes
    SA0111sirALipoprotein2.322.190.65
    SA0126Similar to capsular polysaccharide synthesis protein 14H0.300.440.44
    SA0127Similar to capsular polysaccharide synthesis protein 14H0.360.480.43
    SA0265lytMPeptidoglycan hydrolase2.152.061.72
    SA0295Similar to outer membrane protein precursor3.293.731.03
    SA0423sle1Hypothetical protein, similar to autolysin (N-acetylmuramoyl-l-alanine amidase)2.762.752.89
    SA0457gcaDUDP-N-acetylglucosamine pyrophosphorylase2.001.591.25
    SA0523Similar to poly(glycerol-phosphate) alpha-glucosyltransferase (teichoic acid biosynthesis)3.254.101.72
    SA0620stcASecretory antigen SsaA homolog1.813.163.05
    SA0905atlAutolysin (N-acetylmuramyl-l-alanine amidase and endo-β-N-acetylglucosaminidase)3.281.891.88
    SA1023ftsLCell division protein0.490.450.70
    SA1026murDUDP-N-acetylmuramoylalanine-d-glutamate ligase2.161.371.29
    SA1027div1bCell division protein, FtsQ homolog2.281.321.19
    SA1212opp-2DOligopeptide transport ATPase1.902.312.01
    SA1267ebhASimilar to streptococcal adhesin Emb0.300.120.64
    SA1898Similar to SceD precursor (lytic transglycosylase)2.352.244.50
    SA2097ssaA homologSimilar to secretory antigen precursor SsaA8.168.046.00
    SA2356isaAImmunodominant antigen A0.380.601.22
    SA2442Preprotein translocase secA homolog2.571.881.23
    SA2446Similar to preprotein translocase secY2.012.082.10
    SA2455Capsular polysaccharide biosynthesis, capC0.370.410.44
    SA2456Capsular polysaccharide biosynthesis, capB0.380.380.40
    SA2457Capsular polysaccharide biosynthesis, capA0.400.360.41
Other functions
    SA0128sodMSuperoxide dismutase1.512.042.12
    SA0222coaStaphylocoagulase precursor0.460.640.14
    SA0309gehGlycerol ester hydrolase; lipase2.292.030.83
    SA0519sdrCSer-Asp rich fibrinogen-binding3.353.041.15
    SA0520sdrDSer-Asp rich fibrinogen-binding6.259.580.58
    SA0521sdrEpfam04650, YSIRK-type signal peptide3.213.300.52
    SA0641mgrATranscriptional regulator, MarR family1.814.001.74
    SA0723clpPATP-dependent Clp protease proteolytic subunit homolog0.460.711.00
    SA0743graBSimilar to staphylocoagulase precursor0.230.220.31
    SA0746Staphylococcal nuclease2.354.540.74
    SA1145Hfq, an abundant, ubiquitous RNA-binding protein0.300.410.70
    SA1396bexGTP-binding protein Era homolog2.021.391.48
    SA1452csbDSigmaB-controlled gene product3.041.821.60
    SA1549Similar to serine proteinase Do, heat shock protein HtrA0.480.650.56
    SA1559Similar to smooth muscle caldesmon2.791.440.93
    SA1577sasCHypothetical protein, similar to FmtB protein0.410.380.83
    SA1617Similar to latent nuclear antigen4.693.161.90
    SA1709Similar to ferritin1.532.242.84
    SA1941dpsGeneral stress protein 20U1.763.994.28
    SA1964fmtBFmtB protein0.300.250.47
    SA1984asp23Alkaline shock protein 23, ASP233.262.001.25
    SA2284Similar to accumulation-associated protein0.050.450.02
    SA2285Similar to accumulation-associated protein AAP0.050.500.02
    SA2286sarTHelix-turn-helix multiple antibiotic resistance protein0.451.030.36
    SA2287sarUHelix-turn-helix multiple antibiotic resistance protein0.070.920.08
    SA2290fnbBFibronectin-binding protein homolog5.692.931.67
    SA2423clfBClumping factor B4.073.791.08
    SA2430aurZinc metalloproteinase aureolysin6.027.321.90
    SA2431isaBImmunodominant antigen B2.284.161.07
  • a Signal intensity ratios of strains with RpoB621E versus those with RpoB621A.