TABLE 4.

Genes differentially expressed in a biofilm versus stationary growth phase

N315 ORFaCommon nameaProducta,bERc
Cell envelope and cellular processes
    N315-SA0655 fruA Fructose-specific permease14.43
    N315-SA0263Similar to proton antiporter efflux pump9.55
    N315-SA2142 semB Similar to multidrug resistance protein4.96
    N315-SA0293Similar to formate transporter NirC4.64
    N315-SA1140 glpF Glycerol uptake facilitator4.40
    N315-SA2185 narG Respiratory nitrate reductase alpha chain4.08
    N315-SA2183 narJ Similar to nitrate reductase delta chain3.87
    N315-SA2184 narH Nitrate reductase beta chain NarH3.56
    N315-SA2053Glucose uptake protein homolog3.55
    N315-SA0166Similar to nitrate transporter3.39
    N315-SA0167Similar to membrane lipoprotein SrpL3.29
    N315-SA0702 llm Lipophilic protein affecting bacterial lysis rate and methicillin resistance level2.83
    N315-SA2222Similar to bicyclomycin resistance protein TcaB2.75
    N315-SA0411 ndhF NADH dehydrogenase subunit 52.41
    N315-SA2176 narK Nitrite extrusion protein2.16
    N315-SA1960 mtlF PTS system, mannitol-specific IIBC component0.486
    N315-SA1381 pbp3 Penicillin-binding protein 30.482
    N315-SA1219Similar to phosphate ABC transporter0.463
    N315-SA2311Similar to NAD(P)H-flavin oxidoreductase0.460
    N315-SA0367Similar to nitroflavin reductase0.410
    N315-SA1982Similar to transporter0.397
    N315-SA0260Similar to ribose transporter RbsU0.385
    N315-SA2074 modA Probable molybdate-binding protein0.384
    N315-SA1848 amt Probable ammonium transporter0.343
    N315-SA0138Similar to alkylphosphonate ABC transporter0.323
    N315-SA2203EmrB/QacA subfamilySimilar to multidrug resistance protein0.304
    N315-SA0420Similar to ABC transporter ATP-binding protein0.286
    N315-SA0422Similar to lactococcal lipoprotein0.272
    N315-SA0421Similar to ABC transporter permease protein0.256
    N315-SA0589Similar to ABC transporter ATP-binding protein0.163
    N315-SA0849Similar to peptide-binding protein OppA0.148
Information pathways
    N315-SA0653 fruR Similar to transcription repressor of fructose operon14.57
    N315-SA0476Similar to transcription regulator GntR family4.98
    N315-SA1058 def Similar to polypeptide deformylase2.35
    N315-SA0460 pth Peptidyl-tRNA hydrolase2.07
    N315-SA1516 phoP Alkaline phosphatase synthesis transcriptional regulatory protein0.479
    N315-SA0130Similar to trehalose operon transcriptional repressor0.477
    N315-SA1805Repressor homolog (bacteriophage φN315)0.390
    N315-SAS042 rpmG 50S ribosomal protein L330.362
    N315-SA1394 glyS Glycyl-tRNA synthetase0.351
    N315-SA1149 glnR Glutamine synthetase repressor0.319
    N315-SA1360Xaa-Pro dipeptidase0.294
Intermediary metabolism
    N315-SA0654 fruB Fructose-1-phosphate kinase17.08
    N315-SA1959 glmS Glucosamine-fructose-6-phosphate aminotransferase9.27
    N315-SA0143 adhE Alcohol-acetaldehyde dehydrogenase5.79
    N315-SA2186 nasF Uroporphyrin III C-methyl transferase4.56
    N315-SA2187 nasE Assimilatory nitrite reductase4.15
    N315-SA1929 pyrG CTP synthase3.97
    N315-SA2188 nirB Nitrite reductase3.38
    N315-SA0973 kdtB Phosphopantetheine adenyltransferase homolog2.29
    N315-SA0572Similar to esterase or lipase0.493
    N315-SA0528Similar to hexulose-6-phosphate synthase0.484
    N315-SA1231 dal Similar to alanine racemase0.471
    N315-SA2120Similar to amino acid amidohydrolase0.464
    N315-SA0008 hutH Histidine ammonia-lyase0.461
    N315-SA1584Lysophospholipase homolog0.456
    N315-SA1230 hipO Hippurate hydrolase0.435
    N315-SAS044 dmpI 4-Oxalocrotonate tautomerase0.432
    N315-SA1225 lysC Aspartokinase II0.429
    N315-SA1229 dapD Tetrahydrodipicolinate acetyltransferase0.423
    N315-SA0258 rbsK Probable ribokinase0.422
    N315-SA0820 glpQ Glycerophosphoryl diester phosphodiesterase0.419
    N315-SA0181 entB Similar to isochorismatase0.416
    N315-SA0512 ilvE Branched-chain amino acid aminotroansferase homolog0.415
    N315-SA2204 gpm Phosphoglycerate mutase0.408
    N315-SA1227 dapA Dihydrodipicolinate synthase0.406
    N315-SA2155 mqo Similar to malate:quinone oxidoreductase0.404
    N315-SA1724 purB Adenylosuccinate lyase0.394
    N315-SA0304 nanA N-Acetylneuraminate lyase subunit0.384
    N315-SA1150 glnA Glutamine-ammonia ligase0.362
    N315-SA1531 ald Alanine dehydrogenase0.357
    N315-SA1228 dapB Dihydrodipicolinate reductase0.354
    N315-SA2125 hutG Similar to formiminoglutamase0.353
    N315-SA0098Similar to aminoacylase0.346
    N315-SA2127 rpiA Similar to ribose 5-phosphate isomerase0.341
    N315-SA1226 asd Aspartate semialdehyde dehydrogenase0.341
    N315-SA1545 serA d-3-Phosphoglycerate dehydrogenase0.341
    N315-SA0679 hisC Similar to histidinol-phosphate aminotransferase0.337
    N315-SA0658Similar to plant metabolite dehydrogenases0.335
    N315-SA0656 nagA Probable N-acetylglucosamine-6-phosphate deacetylase0.333
    N315-SA1184 citB Aconitate hydratase0.329
    N315-SA0915 folD FolD bifunctional protein0.326
    N315-SA1858 ilvD Dihydroxy-acid dehydratase0.280
    N315-SA0430 gltB Glutamate synthase large subunit0.263
    N315-SA1614 menC o-Succinylbenzoic acid synthetase0.234
    N315-SA0431 gltD NADH-glutamate synthase small subunit0.199
    N315-SA1553 fhs Formyltetrahydrofolate synthetase0.168
    N315-SA0016 purA Adenylosuccinate synthase0.117
    N315-SA0926 purD Phosphoribosylamine-glycine ligase0.049
    N315-SA0917 purK Phosphoribosylaminoimidazole carboxylase carbon dioxide fixation chain0.034
    N315-SA0916 purE Similar to phosphoribosylaminoimidazole carboxylase0.030
    N315-SA0918 purC Phosphoribosylaminoimidazolesuccinocarboxamide synthetase homolog0.023
Other functions
    N315-SA2460 icaD Intercellular adhesion protein D34.06
    N315-SA1898Similar to SceD precursor26.36
    N315-SA2206 sbi IgG-binding protein26.16
    N315-SA1000Similar to fibrinogen-binding protein11.51
    N315-SA2097Similar to SsaASimilar to secretory antigen precursor4.74
    N315-SA2164Similar to phage infection protein precursor2.80
    N315-SA1382 sodA Superoxide dismutase SodA0.497
    N316-SA1606Plant metabolite dehydrogenase homolog0.480
    N315-SA0841Similar to cell surface protein Map-w0.448
    N315-SA1549 htrA Similar to serine proteinase Do, heat shock protein0.434
    N315-SA2406 gbsA Glycine betaine aldehyde dehydrogenase0.399
    N315-SA0659Similar to CsbB stress response protein0.390
    N315-SA1312 ebpS Elastin-binding protein0.363
    N315-SA0755Similar to general stress protein 1700.340
    N315-SA1170 katA Catalase0.309
    N315-SA0091 plc 1-Phosphatidylinositol phosphodiesterase precursor0.300
    N315-SA2405 betA Choline dehydrogenase0.252
Similar to unknown proteins
    N315-SA0213CHP17.26
    N315-SA2256CHP4.76
    N315-SA0341HP similar to low-temperature requirement A protein3.95
    N315-SA1176CHP3.05
    N315-SA0929CHP3.04
    N315-SA1431CHP3.00
    N315-SA1340CHP (lactoylglutathione lyase)2.53
    N315-SAS027CHP2.50
    N315-SA1932Similar to HP T13D8.31 Arabidopsis thaliana 2.35
    N315-SA1464 yajC CHP (preprotein translocase subunit YajC)2.30
    N315-SA1540CHP (GAF domain-containing protein)2.24
    N315-SA0165Similar to α-helical coiled-coil protein SrpF2.16
    N315-SA0114CHP2.10
    N315-SA0529CHP (predicted sugar phosphate isomerase involved in capsule formation, GutQ)0.486
    N315-SA1019CHP0.467
    N315-SA1737CHP (3-carboxymuconate cylase)0.466
    N315-SA0801CHP (IscA)0.463
    N315-SA1543CHP (predicted redox protein, regulator of disulfide bond formation)0.462
    N315-SA1380CHP (5-formyltetrahydrofolate cyclo-ligase)0.454
    N315-SA1129CHP (predicted HD superfamily hydrolase)0.447
    N315-SA0861CHP (hemoglobin-like proteins)0.443
    N315-SA0230CHP0.438
    N315-SA1280CHP0.430
    N315-SA0957CHP0.429
    N315-SA1331CHP (predicted oxidoreductases)0.393
    N315-SA1689CHP0.384
    N315-SA0513CHP (predicted phosphatases, Gph)0.379
    N315-SA2367CHP (predicted hydrolases or acyltransferases)0.356
    N315-SA1167CHP (predicted hydrolases of the HAD superfamily)0.337
    N315-SA1690CHP0.324
    N315-SA0089Similar to DNA helicase0.315
    N315-SA0873CHP0.315
    N315-SA1544Similar to soluble hydrogenase 42-kDa subunit0.314
    N315-SA0741CHP (predicted acetyltransferase)0.310
    N315-SA0362CHP0.310
    N315-SA1281CHP0.310
    N315-SA0649CHP (predicted DNA-binding proteins with PD1-like DNA-binding motif)0.286
    N315-SA0407CHP (chromosome segregation ATPases)0.254
    N315-SA1611CHP (dipeptidyl aminopeptidases/acylaminoacyl-peptidases)0.227
    N315-SA0919CHP (phosphoribosylformylglycinamidine [FGAM] synthase)0.027
No similarity
    N315-SA0663HP7.97
    N315-SA2281HP5.10
    N315-SA0779HP3.44
    N315-SA2376HP3.22
    N315-SA0885HP3.16
    N315-SA1670HP2.80
    N315-SA2126HP2.62
    N315-SA0336HP2.59
    N315-SA0571HP2.37
    N315-SA2058HP2.17
    N315-SA0397 lpl2 HP (pathogenicity island SaPln2)0.488
    N315-SAS031HP0.480
    N315-SA1168HP0.472
    N315-SA0372HP0.468
    N315-SA0404 lpl8 HP (pathogenicity island SaPln2)0.447
    N315-SA1319HP0.421
    N315-SA0090HP0.366
    N315-SA1546HP0.293
    N315-SA0406HP0.258
    N315-SA2497HP0.208
    N315-SA0408HP0.198
    N315-SA2496HP0.188
    No N315 ORF72.4% protein ID to MW104125.20
    COL-SA0674HP6.12
    COL-SA1165HP5.57
98.1% protein ID to MW2274 CHP5.33
98.1% protein ID to NasE assimilatory nitrite reductase4.25
57% protein ID to spyM18_1050 HP, S. pyogenes MGAS82323.55
88.2% protein ID to MW23233.11
100% protein ID to SAP023 S. aureus N315 plasmid pN315B2.32
100% protein ID to MW23960.497
    COL-SA1345HP0.491
100% protein ID to SA1320 HP0.482
100% protein ID to lpl11 HP, S. aureus MW20.465
    COL-SA2676LPXTGLPXTG-motif cell wall anchor domain protein0.456
91.5% protein ID to lpl2 HP, S. aureus N3150.447
    COL-SA0293CHP0.444
39.1% protein ID to lin05-11 Listeria innocua 0.436
26.6% protein ID to LigW 5-carboxyvanillate decarboxylase, Sphingomonas paucimobilis 0.416
92.7% protein ID to Lpl7 HP, S. aureus N3150.405
binL 99.5% protein ID to BinL DNA-invertase, S. aureus plasmid pMW20.394
94.8% protein ID to BinL DNA invertase, S. aureus plasmid pMW20.392
    COL-SA0601HP0.372
89.8% protein ID to Lpl10 HP, S. aureus MW20.364
25.8% protein ID to MA2121 CHP, Methanosarcina acetivorans C2A0.363
88% protein ID to MW1374 CHP0.363
74.8% protein ID to lpl5 HP, S. aureus N3150.331
    COL-SA1343HP0.328
48.6% protein ID to ycnB homolog of multidrug resistance protein B, B. subtilis 0.309
71% protein ID to MW1201 HP0.282
93.5% protein ID to MW0402 HP0.276
84% protein ID to lpl2 HP, S. aureus N3150.261
35.9% protein ID to Cgl0945 putative multicopper oxidases, Corynebacterium glutamicum 0.259
57.8% protein ID to CopB ATPase, Enterococcus hirae 0.214
64.2% protein ID to SA0753 CHP0.191
33.6% protein ID to RtxC, Bradyrhizobium elkanii 0.158
  • 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; IgG, immunoglobulin G; CHP, conserved hypothetical protein; HP, hypothetical protein; HAD, haloacid dehalogenase-family protein; ID, identity.

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