TABLE 2.

Transcriptional response of S. aureus 8325 to 0.8 μg/ml ciprofloxacin

ORF and functional categoryGeneAnnotationFold change
30 min120 min
General metabolism
    Down-regulated ORFs
        SACOL2094atpCATP synthase F1, epsilon subunit1.3−1.6
        SACOL2095atpDATP synthase F1, beta subunit1.1−1.4
        SACOL2096atpGATP synthase F1, gamma subunit1.3−1.9
        SACOL2097atpAATP synthase F1, alpha subunit1.1−1.6
        SACOL2098atpHATP synthase F1, delta subunit1.1−2.0
        SACOL2099atpFATP synthase F0, B subunit1.2−1.6
        SACOL2100atpEATP synthase F0, C subunit1.2−1.9
        SACOL2101atpBATP synthase F0, A subunit1.4−1.6
        SACOL0494nuoFNADH dehydrogenase subunit L1.1−2.2
        SACOL0975Coenzyme A disulfide reductase−1.2−2.5
        SACOL2392narINitrate reductase gamma chain−2.8−5.7
        SACOL2393narJSimilar to nitrate reductase delta chain−2.6−9.7
        SACOL2394narHNitrate reductase beta chain−2.1−7.7
        SACOL2395narGRespiratory nitrate reductase, alpha subunit1.0−4.9
    Up-regulated ORFs
        SA1245sucA2-Oxoglutarate dehydrogenase, E1 component1.72.5
        SACOL1158sdhCSuccinate dehydrogenase cytochrome b5582.02.1
        SACOL1159sdhASuccinate dehydrogenase1.82.1
        SACOL1160sdhB1.62.5
        SACOL1262sucCSuccinyl-CoA synthetase beta subunit2.11.7
        SACOL1263sucDSuccinyl-CoA synthetase alpha subunit1.83.0
        SACOL1385acnAAconitate hydratase1.82.7
        SACOL1448sucBDihydrolipoamide acetyltransferase1.63.3
        SACOL1449sucA1.62.5
        SACOL1741icdIsocitrate dehydrogenase1.32.1
        SACOL1908fumC1.72.1
        SACOL2424bioW6-Carboxyhexanoate-CoA ligase8.47.8
        SACOL2426bioBBiotin synthase8.86.9
        SACOL2427bioAAdenosylmethionine-8-amino-7-oxononanoate aminotransferase7.810.2
        SACOL2428bioDDethiobiotin synthase8.57.4
DNA metabolism
    Down-regulated ORFs
        SACOL1267topATopoisomerase I−1.6−2.3
        SACOL1269xerCXerC site-specific recombinase−1.7−2.0
        SACOL1315hexA−1.1−1.9
        SACOL1316hexB1.1−1.7
        SACOL1523recQ2−1.1−1.5
        SACOL1540xerDa−2.1
        SACOL1564recN1.1−2.1
        SACOL1619dnaGPrimase−1.3−1.5
        SACOL1696ruvB−1.1−1.5
        SACOL18671.0−4.1
    ORFs with no change
        SACOL1931recXRecX regulatory protein−1.2−1.4
        SACOL0751Putative photolyase1.1−1.1
    Up-regulated ORFs
        SACOL0001dnaAChromosomal replication initiation protein−1.12.7
        SACOL0002dnaNDNA polymerase III subunit beta−1.02.6
        SACOL0004recFRecombination protein RecF1.22.8
        SACOL0005gyrBDNA gyrase subunit B1.22.9
        SACOL0006gyrADNA gyrase subunit A−1.02.4
        SACOL0823uvrBExinuclease ABC subunit B2.82.5
        SACOL0824uvrAExinuclease ABC subunit A2.72.9
        SACOL1304recARecombinase A4.94.7
        SACOL1374lexALexA repressor4.13.8
        SACOL1381sbcDSbcD nuclease4.23.4
        SACOL1400UmuC family polymerase7.910.7
        SACOL1955dinBDNA polymerase IV−1.12.2
        SACOL2089Similar to single-stranded DNA binding protein1.62.5
Nucleotide metabolism
    Down-regulated ORFs
        SACOL0018purAAdenylosuccinate synthase−3.8−3.8
        SACOL0458xptXanthine phosphoribosyltransferase1.0−5.3
        SACOL0460guaBInositol-monophosphate dehydrogenase1.1−2.1
        SACOL0554hptHypoxanthine-guanine phosphoribosyltransferase homolog−1.4−2.9
        SACOL1073purEPutative phosphoribosylaminoimidazole carboxylase−7.1−8.7
        SACOL1074purKPhosphoribosylaminoimidazole carboxylase carbon dioxide fixation chain PurK homolog−6.8−12.7
        SACOL1075purCPhosphoribosylaminoimidazole-succinocarboxamide synthase−6.4−11.5
        SACOL1076purSHypothetical protein−6.4−11.0
        SACOL1077purQPhosphoribosylformylglycinamidine synthase I−5.2−11.4
        SACOL1078purLPhosphoribosylformylglycinamidine synthetase−4.4−7.1
        SACOL1079purFPhosphoribosylpyrophosphate amidotransferase−3.3−7.3
        SACOL1080purMPhosphoribosylaminoimidazole synthetase−1.9−5.5
        SACOL1081purNPhosphoribosylglycinamide formyltransferase−1.1−7.2
        SACOL1082purHBifunctional purine biosynthesis protein1.2−3.8
        SACOL1083purDPhosphoribosylamine-glycine ligase PurD1.2−3.1
        SACOL1210pyrRPyrimidine regulatory protein PyrR−5.8−4.3
        SACOL1212pyrBAspartate carbamoyltransferase catalytic subunit−9.3−3.8
        SACOL1214carACarbamoyl-phosphate synthase small subunit−9.6−2.4
        SACOL1215carBCarbamoyl-phosphate synthase large subunit−5.31.1
        SACOL1216pyrFOrotidine-5-phosphate decarboxylase−3.51.3
        SACOL1371guaCGMP oxidoreductase−2.5−4.1
        SACOL1969purBAdenylosuccinate lyase−1.6−2.0
        SACOL2130deoD2Purine nucleoside phosphorylase−1.4−2.6
        SACOL2606pyrDDihydroorotate dehydrogenase−1.7−3.0
        SACOL2635nrdDAnaerobic ribonucleoside triphosphate reductase−1.2−2.0
    Up-regulated ORFs
        SACOL0790.1Putative ribonucleoside reductase 21.53.1
        SACOL0791nrdI1.83.4
        SACOL0792Ribonucleotide reductase alpha subunit2.02.7
        SACOL0793nrdFRibonucleotide reductase beta subunit1.52.3
Lipid biosynthesis
    Down-regulated ORFs
        SACOL0987fabH3-Oxoacyl-(acyl carrier protein) synthase−1.3−4.3
        SACOL0988fabF3-Oxoacyl synthase−1.2−3.3
        SACOL1243plsXFatty acid/phospholipid synthesis protein−1.1−3.8
        SACOL1244fabDMalonyl CoA-acyl carrier protein transacylase−1.1−3.7
        SACOL1245fabG13-oxoacyl-(acyl carrier protein) reductase−1.1−2.3
        SACOL1571accCAcetyl-CoA carboxylase−1.1−2.1
        SACOL1572accBAcetyl-CoA carboxylase biotin carboxyl carrier subunit−1.3−2.3
        SACOL2079cls-2Hypothetical protein−1.4−2.2
Toxin production/resistance and pathogenesis
    Down-regulated ORFs
        SACOL1173hlYAlpha-hemolysin precursor1.4−4.9
        SACOL1812rotRepressor of toxins Rot−1.8−4.1
        SACOL0766saeRResponse regulator1.4−3.4
        SACOL2287sarRStaphylococcal accessory regulator A homolog−1.3−3.1
        SACOL0765saeSHistidine protein kinasea−3.0
        SACOL1060ATL autolysin transcription regulator−1.6−2.4
        SACOL2023agrBAccessory gene regulator protein B−1.6−2.3
        SACOL0672sarAStaphylococcal accessory regulator A−2.1−1.5
        SACOL0754norAQuinolone resistance protein−1.3−2.0
        SACOL0472Exotoxin, putative−3.21.1
        MW0387set21Exotoxin 2; genomic island Nu Sa Alpha2−2.31.1
        MW0385set19Exotoxin 2; genomic island Nu Sa Alpha2−3.31.2
        SACOL0470Exotoxin, putative−2.61.2
    Up-regulated ORFs
        SACOL0096sarSStaphylococcal accessory regulator A homolog−1.32.6
        SACOL1184Exfoliative toxin A3.0a
Phage related
    Up-regulated ORFs
        SAV0910Tail fiber−1.216.2
        SACOL0336Phi PVL ORF 39-like proteina15.4
        SACOL0335Hypothetical protein3.214.4
        MW1926Phi PVL ORF 39-like protein2.914.1
        SAV1991Hypothetical protein2.913.4
        MW1912Phi PVL ORF 61-like protein2.112.6
        SACOL0349Conserved hypothetical protein5.311.9
        MW1896Hypothetical proteina11.8
        SAV1996Phi PVL ORF 32-like protein3.111.6
        MW1932Antirepressor3.411.5
        SAV0911Phi ETA ORF 63-like protein−1.211.2
        SAV0886Large terminase2.511.1
        SACOL0357dut2.510.4
        SACOL0358Hypothetical protein2.710.4
        SACOL0348Conserved hypothetical protein3.510.0
        MW1899Conserved hypothetical proteina10.0
  • a —, microarray signal was below the detection limit.