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. 2004 Jul;186(14):4665–4684. doi: 10.1128/JB.186.14.4665-4684.2004

TABLE 5.

Genes differentially expressed in a biofilm versus exponential and stationary phase

N315 ORFa Common namea Producta,b ER vs EPc ER vs SPc
Cell envelope and cellular processes
    N315-SA2426 arcD Arginine/ornithine antiporter 59.91 5.49
    N315-SA1881 kdpA Probable potassium-transporting ATPase A chain 51.58 11.30
    N315-SA1880 kdpB Probable potassium-transporting ATPase B chain 30.99 9.53
    N315-SA1042 pyrP Uracil permease 25.54 7.97
    N315-SA1879 kdpC Probable potassium-transporting ATPase C chain 20.82 8.40
    N315-SA0417 Similar to sodium-dependent transporter 7.33 16.49
    N315-SA2081 Similar to urea transporter 6.49 4.65
    N315-SA1688 Similar to teichoic acid translocation ATP-binding protein TagH 0.47 0.42
    N315-SA0233 PTS enzyme, maltose and glucose specific, factor II homolog 0.44 0.15
    N315-SA0848 oppF Oligopeptide transport system ATP-binding protein homolog 0.42 0.16
    N315-SA0847 oppD Oligopeptide transport system ATP-binding protein homolog 0.39 0.15
    N315-SA0845 oppB Oligopeptide transport system permease protein 0.38 0.16
    N315-SA2242 CHP (predicted permease) 0.37 0.35
    N315-SA0846 oppC Similar to oligopeptide transport system permease protein 0.37 0.17
    N315-SA0758 Similar to thioredoxin 0.28 0.34
    N315-SA2261 Similar to efflux pump 0.25 0.45
    N315-SA2132 Similar to ABC transporter (ATP-binding protein) 0.24 0.34
    N315-SA0217 Similar to periplasmic iron-binding protein BitC 0.23 0.24
    N315-SA1699 Similar to transporter 0.20 0.34
    N315-SA1987 opuD Glycine betaine transporter OpuD homolog 0.11 0.21
Information pathways
    N315-SA2424 acrR Similar to transcription regulator Crp/Fnr family protein 48.16 9.87
    N315-SA1041 pyrR Pyrimidine operon repressor chain A 16.05 6.82
    N315-SA2320 Similar to regulatory protein PfoR 9.87 4.66
    N315-SA2502 rnpA RNase P protein component 3.82 5.26
    N315-SA2134 Similar to DNA 3-methyladenine glycosidase 0.48 0.40
    N315-SA0815 Peptidyl-prolyl cis-trans isomerase homolog 0.44 0.49
    N315-SA2278 Similar to mutator protein MutT 0.41 0.41
    N315-SA1626 hsdM Type I restriction enzyme homolog (SaPln3) 0.41 0.48
    N315-SA0097 Similar to transcription regulator AraC/XylS family 0.40 0.49
    N315-SA2144 Similar to transcriptional regulator (TetR/AcrR family) 0.39 0.37
    N315-SA0189 hsdR Probable type I restriction enzyme restriction chain 0.30 0.36
    N315-SA1806 Probable ATP-dependent helicase (bacteriophage φN315) 0.29 0.25
Intermediary metabolism
    N315-SA2427 arcB Ornithine transcarbamoylase 124.22 5.83
    N315-SA2428 arcA Arginine deiminase 114.59 5.45
    N315-SA2425 arcC Carbamate kinase 37.87 5.76
    N315-SA1044 pyrC Dihydroorotase 17.84 6.11
    N315-SA1045 carA Carbamoyl-phosphate synthase small chain 13.13 6.03
    N315-SA1047 pyrF Orotidine-5-phosphate decarboxylase 10.65 4.93
    N315-SA1046 carB Carbamoyl-phosphate synthase large chain 10.50 4.97
    N315-SA2082 ureA Urease gamma subunit 9.68 3.12
    N315-SA2083 ureAB Urease beta subunit 9.29 2.97
    N315-SA1048 pyrE Orotate phosphoribosyltransferase 8.94 4.87
    N315-SA2319 sdhB Similar to beta-subunit of l-serine dehydratase 8.90 4.84
    N315-SA2084 ureC Urease alpha subunit 8.40 3.50
    N315-SA2086 ureF Urease accessory protein 8.34 3.33
    N315-SA2088 ureD Urease accessory protein 7.72 3.67
    N315-SA2085 ureE Urease accessory protein 7.26 2.82
    N315-SA2087 ureG Urease accessory protein 6.78 3.16
    N315-SA2318 sdhA Similar to l-serine dehydratase 6.49 4.24
    N315-SA1043 pyrB Aspartate transcarbamoylase chain A 4.69 6.34
    N315-SA2007 Similar to α-acetolactate decarboxylase 4.40 3.09
    N315-SA0821 argH Argininosuccinate lyase 3.93 14.65
    N315-SA0822 argG Argininosuccinate synthase 3.52 13.48
    N315-SA2008 budB α-Acetolactate synthase 3.29 2.53
    N315-SA1155 cls Cardiolipin synthetase homolog 2.73 2.28
    N315-SA1160 nuc Thermonuclease 2.30 2.47
    N315-SA2258 Similar to diaminopimelate epimerase 2.03 2.60
    N315-SA1940 deoD Purine nucleoside phosphorylase 0.46 0.49
    N315-SA1615 menE O-Succinylbenzoic acid-CoA ligase 0.44 0.21
    N315-SA0925 purH Bifunctional purine biosynthesis protein 0.43 0.04
    N315-SA0241 Similar to 4-diphosphocytidyl-2C-methyl-d-erythritol synthase 0.42 0.46
    N315-SA0963 pyc Pyruvate carboxylase 0.41 0.26
    N315-SA0011 Similar to homoserine-o-acetyltransferase 0.39 0.44
    N315-SA0534 atoB Acetyl-CoA c-acetyltransferase 0.38 0.43
    N315-SA0920 purQ Phosphoribosylformylglycinamidine synthase I 0.37 0.02
    N315-SA0923 purM Phosphoribosylformylglycinamidine cyclo-ligase 0.34 0.03
    N315-SA0924 purN Phosphoribosylglycinamide formyltransferase 0.34 0.03
    N315-SA0242 Similar to xylitol dehydrogenase 0.34 0.44
    N315-SA0921 purL Phosphoribosylformylglycinamidine synthetase 0.33 0.03
    N315-SA0922 purF Phosphoribosylpyrophosphate amidotransferase 0.33 0.03
    N315-SA0344 metE 5-Methyltetrahydropteroyltriglutamate-homocysteine 0.28 0.43
Methyltransferase
    N315-SA0022 Similar to 5′-nucleotidase 0.26 0.29
    N315-SA1814 Similar to succinyl-diaminopimelate desuccinylase 0.23 0.20
    N315-SA0266 CHP (ABC-type multidrug transport system, ATPase component) 0.15 0.23
Other functions
    N315-SA2353 ssaA Similar to secretory antigen precursor 3.64 5.70
    N315-SA0270 ssaA Similar to secretory antigen precursor 0.42 0.39
    N315-SA1629 splC Serine protease 0.39 0.49
    N315-SA0107 spa Immunoglobulin G-binding protein A precursor 0.01 0.04
Similar to unknown proteins
    N315-SA0023 CHP 0.50 0.35
    N315-SA0814 kapB CHP 0.48 0.44
    N315-SA1692 CHP (putative intracellular protease/amidase) 0.46 0.37
    N315-SA0518 CHP (predicted flavoprotein) 0.46 0.43
    N315-SA1612 CHP (NTP pyrophosphohydrolases) 0.34 0.17
    N315-SA1133 CHP 0.32 0.44
    N315-SA2371 CHP 0.30 0.26
    N315-SA0559 CHP (histone acetyltransferase HPA2 and related acetyltransferases) 0.29 0.36
    N315-SA0872 CHP (enterochelin esterase and related enzymes) 0.29 0.44
    N315-SA2131 CHP (ABC-type Na+ efflux pump, permease component) 0.27 0.38
    N315-SA1733 CHP 0.26 0.29
    N315-SA2322 CHP (permeases of the drug/metabolite transporter superfamily) 0.22 0.45
    N315-SA0269 HP 0.13 0.10
    N315-SA0359 CHP (uncharacterized membrane protein) 0.13 0.37
No similarity
    N315-SA1049 HP 7.42 4.41
    N315-SA0575 HP 2.14 2.10
    N315-SA1152 HP 0.46 0.46
    N315-SA0752 HP 0.41 0.49
    N315-SAS025 HP 0.39 0.47
    N315-SA2372 HP 0.38 0.28
    N315-SA0364 HP 0.36 0.41
    N315-SA1332 HP 0.34 0.26
    N315-SA1015 HP 0.34 0.23
    N315-SA2373 HP 0.32 0.20
    N315-SA0740 HP 0.29 0.24
    N315-SA0268 HP 0.17 0.17
    N315-SA0267 HP 0.17 0.19
    N315-SA1726 HP 0.08 0.17
    No N315 ORF
    COL-SA2069 HP 42.86 13.21
87.1% protein ID to Ssp extracellular ECM and plasma-binding protein 33.06 135.82
No hit in GenPept 16.42 28.08
mapN 99.7% protein ID to MapN protein 14.76 35.81
86.9% protein ID to SA1813 (possibly hemolysin) 6.80 12.73
46.1% protein ID to lin0925 putative membrane protein, Listeria innocua 5.73 23.61
50.7% protein ID to lin0924, Listeria innocua 5.52 14.61
63.2% protein ID to MW0768 4.58 2.71
    COL-SA1559 HP 3.68 2.70
91% protein ID to SA0093 HP 0.37 0.28
41.4% protein ID to HsdS probable restriction modification system 0.36 0.35
45.5% protein ID to SA2490 0.33 0.46
    COL-SA1043 Glycosyl transferase, group 1 0.33 0.15
100% ID to SA1814 0.31 0.25
97.9% protein ID to structure of cassette chromosome (SCC)-like element, stra 0.30 0.21
61.3% protein ID to SA0553 CHP 0.28 0.50
    COL-SA0653 CHP 0.23 0.46
24.1% protein ID to BdrC3, Borrelia hermsii 0.23 0.34
26.5% protein ID to RSc1168 CHP, Ralstonia solanacearum 0.22 0.43
29.4% protein ID to PF1843 chromosome segregation protein Smc, Pyrococcus furiosus 0.22 0.26
    COL-SA0654 CHP 0.21 0.48
50% protein ID to NMB0372 HP, Neisseria meningitidis 0.19 0.48
82.5% protein ID to SA0276 0.17 0.26
32.9% protein ID to ParA, B. subtilis 0.14 0.30
    COL-SA0095 spa Immunoglobulin G-binding protein A precursor 0.02 0.08
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.