TABLE 5.

Genes differentially expressed in a biofilm versus exponential and stationary phase

N315 ORFaCommon nameaProducta,bER vs EPcER vs SPc
Cell envelope and cellular processes
    N315-SA2426 arcD Arginine/ornithine antiporter59.915.49
    N315-SA1881 kdpA Probable potassium-transporting ATPase A chain51.5811.30
    N315-SA1880 kdpB Probable potassium-transporting ATPase B chain30.999.53
    N315-SA1042 pyrP Uracil permease25.547.97
    N315-SA1879 kdpC Probable potassium-transporting ATPase C chain20.828.40
    N315-SA0417Similar to sodium-dependent transporter7.3316.49
    N315-SA2081Similar to urea transporter6.494.65
    N315-SA1688Similar to teichoic acid translocation ATP-binding protein TagH0.470.42
    N315-SA0233PTS enzyme, maltose and glucose specific, factor II homolog0.440.15
    N315-SA0848 oppF Oligopeptide transport system ATP-binding protein homolog0.420.16
    N315-SA0847 oppD Oligopeptide transport system ATP-binding protein homolog0.390.15
    N315-SA0845 oppB Oligopeptide transport system permease protein0.380.16
    N315-SA2242CHP (predicted permease)0.370.35
    N315-SA0846 oppC Similar to oligopeptide transport system permease protein0.370.17
    N315-SA0758Similar to thioredoxin0.280.34
    N315-SA2261Similar to efflux pump0.250.45
    N315-SA2132Similar to ABC transporter (ATP-binding protein)0.240.34
    N315-SA0217Similar to periplasmic iron-binding protein BitC0.230.24
    N315-SA1699Similar to transporter0.200.34
    N315-SA1987 opuD Glycine betaine transporter OpuD homolog0.110.21
Information pathways
    N315-SA2424 acrR Similar to transcription regulator Crp/Fnr family protein48.169.87
    N315-SA1041 pyrR Pyrimidine operon repressor chain A16.056.82
    N315-SA2320Similar to regulatory protein PfoR9.874.66
    N315-SA2502 rnpA RNase P protein component3.825.26
    N315-SA2134Similar to DNA 3-methyladenine glycosidase0.480.40
    N315-SA0815Peptidyl-prolyl cis-trans isomerase homolog0.440.49
    N315-SA2278Similar to mutator protein MutT0.410.41
    N315-SA1626 hsdM Type I restriction enzyme homolog (SaPln3)0.410.48
    N315-SA0097Similar to transcription regulator AraC/XylS family0.400.49
    N315-SA2144Similar to transcriptional regulator (TetR/AcrR family)0.390.37
    N315-SA0189 hsdR Probable type I restriction enzyme restriction chain0.300.36
    N315-SA1806Probable ATP-dependent helicase (bacteriophage φN315)0.290.25
Intermediary metabolism
    N315-SA2427 arcB Ornithine transcarbamoylase124.225.83
    N315-SA2428 arcA Arginine deiminase114.595.45
    N315-SA2425 arcC Carbamate kinase37.875.76
    N315-SA1044 pyrC Dihydroorotase17.846.11
    N315-SA1045 carA Carbamoyl-phosphate synthase small chain13.136.03
    N315-SA1047 pyrF Orotidine-5-phosphate decarboxylase10.654.93
    N315-SA1046 carB Carbamoyl-phosphate synthase large chain10.504.97
    N315-SA2082 ureA Urease gamma subunit9.683.12
    N315-SA2083 ureAB Urease beta subunit9.292.97
    N315-SA1048 pyrE Orotate phosphoribosyltransferase8.944.87
    N315-SA2319 sdhB Similar to beta-subunit of l-serine dehydratase8.904.84
    N315-SA2084 ureC Urease alpha subunit8.403.50
    N315-SA2086 ureF Urease accessory protein8.343.33
    N315-SA2088 ureD Urease accessory protein7.723.67
    N315-SA2085 ureE Urease accessory protein7.262.82
    N315-SA2087 ureG Urease accessory protein6.783.16
    N315-SA2318 sdhA Similar to l-serine dehydratase6.494.24
    N315-SA1043 pyrB Aspartate transcarbamoylase chain A4.696.34
    N315-SA2007Similar to α-acetolactate decarboxylase4.403.09
    N315-SA0821 argH Argininosuccinate lyase3.9314.65
    N315-SA0822 argG Argininosuccinate synthase3.5213.48
    N315-SA2008 budB α-Acetolactate synthase3.292.53
    N315-SA1155 cls Cardiolipin synthetase homolog2.732.28
    N315-SA1160 nuc Thermonuclease2.302.47
    N315-SA2258Similar to diaminopimelate epimerase2.032.60
    N315-SA1940 deoD Purine nucleoside phosphorylase0.460.49
    N315-SA1615 menE O-Succinylbenzoic acid-CoA ligase0.440.21
    N315-SA0925 purH Bifunctional purine biosynthesis protein0.430.04
    N315-SA0241Similar to 4-diphosphocytidyl-2C-methyl-d-erythritol synthase0.420.46
    N315-SA0963 pyc Pyruvate carboxylase0.410.26
    N315-SA0011Similar to homoserine-o-acetyltransferase0.390.44
    N315-SA0534 atoB Acetyl-CoA c-acetyltransferase0.380.43
    N315-SA0920 purQ Phosphoribosylformylglycinamidine synthase I0.370.02
    N315-SA0923 purM Phosphoribosylformylglycinamidine cyclo-ligase0.340.03
    N315-SA0924 purN Phosphoribosylglycinamide formyltransferase0.340.03
    N315-SA0242Similar to xylitol dehydrogenase0.340.44
    N315-SA0921 purL Phosphoribosylformylglycinamidine synthetase0.330.03
    N315-SA0922 purF Phosphoribosylpyrophosphate amidotransferase0.330.03
    N315-SA0344 metE 5-Methyltetrahydropteroyltriglutamate-homocysteine0.280.43
Methyltransferase
    N315-SA0022Similar to 5′-nucleotidase0.260.29
    N315-SA1814Similar to succinyl-diaminopimelate desuccinylase0.230.20
    N315-SA0266CHP (ABC-type multidrug transport system, ATPase component)0.150.23
Other functions
    N315-SA2353 ssaA Similar to secretory antigen precursor3.645.70
    N315-SA0270 ssaA Similar to secretory antigen precursor0.420.39
    N315-SA1629 splC Serine protease0.390.49
    N315-SA0107 spa Immunoglobulin G-binding protein A precursor0.010.04
Similar to unknown proteins
    N315-SA0023CHP0.500.35
    N315-SA0814 kapB CHP0.480.44
    N315-SA1692CHP (putative intracellular protease/amidase)0.460.37
    N315-SA0518CHP (predicted flavoprotein)0.460.43
    N315-SA1612CHP (NTP pyrophosphohydrolases)0.340.17
    N315-SA1133CHP0.320.44
    N315-SA2371CHP0.300.26
    N315-SA0559CHP (histone acetyltransferase HPA2 and related acetyltransferases)0.290.36
    N315-SA0872CHP (enterochelin esterase and related enzymes)0.290.44
    N315-SA2131CHP (ABC-type Na+ efflux pump, permease component)0.270.38
    N315-SA1733CHP0.260.29
    N315-SA2322CHP (permeases of the drug/metabolite transporter superfamily)0.220.45
    N315-SA0269HP0.130.10
    N315-SA0359CHP (uncharacterized membrane protein)0.130.37
No similarity
    N315-SA1049HP7.424.41
    N315-SA0575HP2.142.10
    N315-SA1152HP0.460.46
    N315-SA0752HP0.410.49
    N315-SAS025HP0.390.47
    N315-SA2372HP0.380.28
    N315-SA0364HP0.360.41
    N315-SA1332HP0.340.26
    N315-SA1015HP0.340.23
    N315-SA2373HP0.320.20
    N315-SA0740HP0.290.24
    N315-SA0268HP0.170.17
    N315-SA0267HP0.170.19
    N315-SA1726HP0.080.17
    No N315 ORF
    COL-SA2069HP42.8613.21
87.1% protein ID to Ssp extracellular ECM and plasma-binding protein33.06135.82
No hit in GenPept16.4228.08
mapN 99.7% protein ID to MapN protein14.7635.81
86.9% protein ID to SA1813 (possibly hemolysin)6.8012.73
46.1% protein ID to lin0925 putative membrane protein, Listeria innocua5.7323.61
50.7% protein ID to lin0924, Listeria innocua5.5214.61
63.2% protein ID to MW07684.582.71
    COL-SA1559HP3.682.70
91% protein ID to SA0093 HP0.370.28
41.4% protein ID to HsdS probable restriction modification system0.360.35
45.5% protein ID to SA24900.330.46
    COL-SA1043Glycosyl transferase, group 10.330.15
100% ID to SA18140.310.25
97.9% protein ID to structure of cassette chromosome (SCC)-like element, stra0.300.21
61.3% protein ID to SA0553 CHP0.280.50
    COL-SA0653CHP0.230.46
24.1% protein ID to BdrC3, Borrelia hermsii0.230.34
26.5% protein ID to RSc1168 CHP, Ralstonia solanacearum0.220.43
29.4% protein ID to PF1843 chromosome segregation protein Smc, Pyrococcus furiosus0.220.26
    COL-SA0654CHP0.210.48
50% protein ID to NMB0372 HP, Neisseria meningitidis0.190.48
82.5% protein ID to SA02760.170.26
32.9% protein ID to ParA, B. subtilis0.140.30
    COL-SA0095 spa Immunoglobulin G-binding protein A precursor0.020.08
  • a Based on the published sequence of S. aureus strain N315. For genes not present in N315, the gene name and description given are from the S. aureus strain COL genome, available from The Institute for Genomic Research website (www.tigr.org or by the putative function.

  • b Abbreviations: PTS, phosphotransferase; CHP, conserved hypothetical protein; CoA, coenzyme A; NTP, nucleoside triphosphate; HP, hypothetical protein; ID, identity; ECM, extracellular matrix.

  • c Normalized values based on the expression ratio (ER), which is defined as the expression level in biofilms/expression level in exponential-phase (EP) or stationary-phase (SP) cells.