TABLE 3.

Genes differentially expressed in a biofilm versus exponential growth phase

N315 ORFaCommon nameaProducta,bERc
Cell envelope and cellular processes
    N315-SA1960 mtlF PTS system, mannitol-specific IIBC component5.46
    N315-SA1882 kdpD Sensor protein KdpD5.13
    N315-SA2311Similar to NAD(P)H-flavin oxidoreductase2.71
    N315-SA1156ABC transporter (ATP-binding protein) homolog2.68
    N315-SA0724Similar to cell division inhibitor0.496
    N315-SA2253 opp-1C Oligopeptide transporter putative membrane permease domain0.490
    N315-SA0567Similar to iron(III) ABC transporter permease protein0.474
    N315-SA2216Similar to ABC transporter, ATP-binding protein0.471
    N315-SA0980Similar to ferrichrome ABC transporter0.471
    N315-SA0981Similar to ferrichrome ABC transporter0.468
    N315-SA0592 tagA Teichoic acid biosynthesis protein0.462
    N315-SA1935 hmrA Similar to amidase0.442
    N315-SA1169γ-Aminobutyrate permease0.425
    N315-SA0243 tagB Similar to teichoic acid biosynthesis protein B0.423
    N315-SA0110 sirB Lipoprotein0.399
    N315-SA2100Similar to autolysin E0.394
    N315-SA1458 lytH N-Acetylmuramoyl-l-alanine amidase0.393
    N315-SA0109 sirC Lipoprotein0.378
    N315-SA0106 lctP l-Lactate permease homolog0.376
    N315-SA0682Similar to ditripeptide ABC transporter0.370
    N315-SA2053Glucose uptake protein homolog0.331
    N315-SA0479 nupC Pyrimidine nucleoside transport protein0.315
    N315-SA0111 sirA Lipoprotein0.312
    N315-SA2339Similar to antibiotic transport-associated protein0.291
    N315-SA0566Similar to iron-binding protein0.287
    N315-SA2233Similar to integral membrane efflux protein0.281
    N315-SA0325 glpT Glycerol-3-phosphate transporter0.281
    N315-SA2112Similar to sodium-dependent transporter0.278
    N315-SA1025 mraY Phospho-N-muramic acid-pentapeptide translocase0.265
    N315-SA0600Similar to pyrimidine nucleoside transporter0.255
    N315-SA1978Similar to ferrichrome ABC transporter (permease)0.203
    N315-SA0010 azlC Similar to amino acid permease0.161
    N315-SA2300Similar to glucarate transporter0.141
    N315-SA0691 sstD Lipoprotein, similar to ferrichrome ABC transporter0.126
    N315-SA0374 pbuX Xanthine permease0.089
    N315-SA0579Similar to Na+/H+ antiporter0.080
    N315-SA0411 ndhF NADH dehydrogenase subunit 50.065
    N315-SA2302 stpC Similar to ABC transporter0.046
    N315-SA2303 smpC Similar to membrane-spanning protein0.041
Information pathways
    N315-SA1883 kdpE KDP operon transcriptional regulatory protein5.42
    N315-SA2429 ArgR Similar to arginine repressor3.92
    N315-SA2296Similar to transcriptional regulator, MerR family3.72
    N315-SA2418Similar to two-component response regulator2.13
    N315-SA0460 pth Peptidyl-tRNA hydrolase0.490
    N315-SA0652Similar to transcription regulation protein0.452
    N315-SA1853Similar to DNA mismatch repair protein MutS0.445
    N315-SA1287 asnS Asparaginyl-tRNA synthetase0.441
    N315-SA0348Similar to transcription terminator0.440
    N315-SA2358Similar to transcriptional regulator (TetR/AcrR family)0.382
    N315-SA1697Similar to protein-tyrosine phosphatase0.364
    N315-SA1120Similar to transcription regulator GntR family0.354
    N315-SA0298 pfoR Similar to regulatory protein PfoR0.333
    N315-SA1550 tyrS Tyrosyl-tRNA synthetase0.325
    N315-SA2482 pcp Pyrrolidone-carboxylate peptidase0.297
    N315-SA1583 rot Repressor of toxins (Rot)0.295
    N315-SA0653 fruR Similar to transcription repressor of fructose operon0.229
    N315-SA0904Probable ATL autolysin transcription regulator0.191
    N315-SA1725 sspB Staphopain, cysteine proteinase0.074
Intermediary metabolism
    N315-SA0328Similar to NADH-dependent FMN reductase7.25
    N315-SA0122 butA Acetoin (diacetyl)reductase5.04
    N315-SA2297Similar to GTP-pyrophosphokinase3.25
    N315-SA1142 glpD Aerobic glycerol-3-phosphate dehydrogenase2.97
    N315-SA0016 purA Adenylosuccinate synthase2.37
    N315-SA2397Similar to pyridoxal-phosphate-dependent aminotransferase2.04
    N315-SA2001Similar to oxidoreductase, aldo/keto reductase family2.01
    N315-SA1201 trpD Anthranilate phosphoribosyltransferase0.495
    N315-SA1685 mutY Similar to A/G-specific adenine glycosylase0.481
    N315-SA2111Similar to phosphoglycolate phosphatase0.475
    N315-SA1052 gmk Guanylate kinase homolog0.462
    N315-SA2279Similar to phosphomannomutase0.458
    N315-SA0902HisC homolog0.448
    N315-SA0177 argJ Arginine biosynthesis bifunctional protein homolog0.436
    N315-SA1310 ansA Probable l-asparaginase, gene-ansA0.429
    N315-SA1309 cmk Cytidylate kinase0.427
    N315-SA1749Similar to aspartate transaminase protein0.423
    N315-SA2140Similar to esterase0.412
    N315-SA0507Similar to N-acyl-l-amino acid amidohydrolase0.407
    N315-SA0568Similar to l-2-haloalkanoic acid dehalogenase0.374
    N315-SA2213 bioB Biotin synthase0.373
    N315-SA0514Similar to deoxypurine kinase0.356
    N315-SA1121Similar to processing proteinase homolog0.340
    N315-SA1203 trpF Phosphoriborylanthranilate isomerase0.323
    N315-SA2342 thgA Similar to O-acetyltransferase0.280
    N315-SA0511Similar to UDP-glucose 4-epimerase-related protein0.256
    N315-SA1202 trpC Indole-3-glycerol phosphate synthase0.246
    N315-SA2395 ldh l-Lactate dehydrogenase0.213
    N315-SA0180 bmQ Similar to branched-chain amino acid transport system carrier protein0.192
    N315-SA1200 trpG Anthranilate synthase component II0.120
    N315-SA1199 trpE Similar to anthranilate synthase component I0.101
    N315-SA0373 xprT Xanthine phosphoribosyltransferase0.077
Other functions
    N315-SA0899 sspC Cysteine protease7.24
    N315-SA0900 sspB Cysteine protease precursor7.03
    N315-SA0150 cap5G Capsular polysaccharide synthesis enzyme4.80
    N315-SA2006Similar to MHC class II analog4.69
    N315-SA0149 cap5F Capsular polysaccharide synthesis enzyme4.58
    N315-SA0148 cap5E Capsular polysaccharide synthesis enzyme4.05
    N315-SA0146 cap5C Capsular polysaccharide synthesis enzyme3.31
    N315-SA0147 cap5D Capsular polysaccharide synthesis enzyme3.30
    N315-SA0145 cap5B Capsular polysaccharide synthesis enzyme Cap5B2.43
    N315-SA0144 cap5A Capsular polysaccharide synthesis enzyme2.34
    N315-SA0841Similar to cell surface protein Map-w2.22
    N315-SA1709Similar to ferritin2.18
    N315-SA0754Similar to lactococcal prophage ps3 protein 050.498
    N315-SA1835 int Similar to integrase (pathogenicity island SaPln1), gene = int0.431
    N315-SA1559Similar to smooth muscle caldesmon0.426
    N315-SA0797 nifU-3 Similar to nitrogen fixation protein NifU0.407
    N315-SA0780Similar to hemolysin0.331
    N315-SA0746 nuc Staphylococcal nuclease0.170
    N315-SA1766HP (bacteriophage φN315)0.069
    N315-SA1775Similar to scaffolding protein (bacteriophage φN315)0.048
    N315-SA1765HP (bacteriophage φN315)0.042
    N315-SA1777HP (bacteriophage φN315)0.038
    N315-SA1771HP (bacteriophage φN315)0.036
    N315-SA1762HP (bacteriophage φN315)0.036
Similar to unknown proteins
    N315-SA0326CHP (lactoylglutathione lyase and related lyases)7.94
    N315-SA0327CHP (flavin-dependent oxidoreductases)7.50
    N315-SA2479CHP5.04
    N315-SA0007Predicted sugar kinase4.57
    N315-SA0380CHP (pathogenicity island SaPln2)3.07
    N315-SA0381CHP (pathogenicity island SaPln2)2.80
    N315-SA1235CHP2.04
    N315-SA1890CHP2.03
    N315-SA0230CHP2.02
    N315-SA0941CHP0.497
    N315-SA0467CHP (predicted ATPase of the PP-loop superfamily)0.489
    N315-SA1838CHP (predicted metal-dependent membrane protease)0.481
    N315-SA2487 rarD Similar to RarD protein0.462
    N315-SA1696CHP0.453
    N315-SA1448CHP (TPR repeat-containing proteins)0.452
    N315-SA0329CHP0.445
    N315-SA2328CHP (putative effector of murein hydrolase, LrgB)0.434
    N315-SA0979CHP0.433
    N315-SA1928HP0.421
    N315-SA1601 crcB CHP (integral membrane protein)0.404
    N315-SA2377CHP0.398
    N315-SAS081CHP (ATPase involved in DNA repair)0.391
    N315-SA0334CHP (Sec-independent protein secretion pathway)0.378
    N315-SA2305CHP0.372
    N315-SA0840CHP (phospholipid-binding protein)0.370
    N315-SA1903CHP0.366
    N315-SA0543CHP (uncharacterized BCR)0.353
    N315-SA0413CHP0.332
    N315-SA0341Similar to low-temperature requirement A protein0.329
    N315-SA0345CHP (methionine synthase I)0.324
    N315-SA0257CHP (SAM-dependent methyltransferases)0.323
    N315-SA2096CHP0.320
    N315-SA0773CHP (predicted membrane protein)0.312
    N315-SA2212Similar to 8-amino-7-oxononanoate synthase0.303
    N315-SA1252CHP (histone acetyltransferase)0.298
    N315-SA2452CHP (domain typically associated with flavoprotein oxygenases)0.282
    N315-SA0870CHP (predicted permease)0.267
    N315-SA0335CHP (Sec-independent protein secretion pathway)0.265
    N315-SA0556CHP0.203
    N315-SA0753CHP (lysine efflux permease)0.179
    N315-SA2219CHP (uncharacterized membrane protein)0.133
    N315-SA0739CHP0.129
    N315-SAS001CHP0.128
    N315-SA0412CHP0.078
No similarity
    N315-SAS016HP12.74
    N315-SA0883HP5.97
    N315-SA1233HP2.25
    N315-SA0414HP0.496
    N315-SA2126HP0.495
    N315-tRNA12tRNA-Pro0.491
    N315-SA1943HP0.491
    N315-SA1215HP0.486
    N315-tRNA11tRNA-Arg0.479
    N315-SA0613HP0.470
    N315-SA2485HP0.457
    N315-SA0088HP0.443
    N315-tRNA57tRNA-Lys0.416
    N315-tRNA47tRNA-Leu0.409
    N315-SA1607HP0.402
    N315-SA0955HP0.372
    N315-tRNA07tRNA-Thr0.355
    N315-SA0105HP0.344
    N315-SA2118HP0.335
    N315-SA0336HP0.326
    N315-SA0363HP0.321
    N315-SA2055HP0.321
    N315-SA2224HP0.309
    N315-SA2249HP0.259
    N315-SA0749HP0.233
    N315-tRNA06tRNA-Val0.219
    N315-SA0748HP0.214
    N315-SA0889HP0.179
    N315-SA2488HP0.157
    N315-SA1778HP (bacteriophage φN315)0.089
    N315-SA1768HP (bacteriophage φN315)0.050
    N315-SA1770HP (bacteriophage φN315)0.050
    N315-SA1774HP (bacteriophage φN315)0.046
    N315-SA1776HP (bacteriophage φN315)0.044
    N315-SAS060HP (bacteriophage φN315)0.041
    N315-SA1769HP (bacteriophage φN315)0.040
    N315-SA1773HP (bacteriophage φN315)0.032
    N315-SA1772HP (bacteriophage φN315)0.031
    N315-SA1767HP (bacteriophage φN315)0.027
No N315 ORF
set5 100% protein ID Set5, exotoxin 5, and HsdM-like protein gene40.43
sspA 99.4% protein ID S. aureus glutamic acid-specific protease7.19
cap8H 100% protein ID to capsular polysaccharide synthase enzyme Cap8H5.11
cap8J 100% protein ID to capsular polysaccharide synthesis enzyme Cap8J4.52
58.1% protein ID malofactic enzyme, Oenococcus oeni bacteria3.05
68.1% protein ID SA0329 CHP2.39
92.8% protein ID MW1748 HP2.25
84.4% protein ID MW0360 HP2.16
96.7% protein ID to MW2134 HP0.500
95.6% protein ID SA22300.473
58.4% protein ID BH3950 transposase (10), Bacillus halodurans0.467
49.1% protein ID MW26180.463
COL-SA1788HP0.434
87.6% protein ID MW05840.423
COL-SA2299HP0.421
Similar to splE62.6% protein ID serine protease SplE0.420
97.7% protein ID to SA15590.419
26.9% protein ID MW24980.418
COL-SA0866HP0.411
Serine protease55.4% protein ID serine protease SplB0.409
96% protein ID MW23250.387
95.5% protein ID MW0355 HP0.371
22.2% protein ID SA0283 HP0.345
89.4% protein ID SA0553 CHP0.338
78.2% protein ID MW1720 HP0.315
COL-SA1556HP0.311
99.4% protein ID to MW0053 CHP0.308
45.9% protein ID BH3950 transposase (10), Bacillus halodurans0.290
97.7% protein ID MW0355 HP0.289
splB 97.7% protein ID to serine protease SplB0.280
79.2% protein ID MW1043 HP0.270
COL-SA2728HP0.237
99.5% id to SAV1992 HP0.209
37.3% protein ID MW1769 HP0.202
COL-SA1140 sai-1 29-kDa cell surface protein0.164
85.2% protein ID MW1042 HP0.141
99.5% protein ID MWP0180.138
99.8% protein ID MWP016 S. aureus plasmid pMW20.096
93.4% protein ID SAV1953 φPVL ORF 20 and 21 homolog0.079
Mu50-SAV1953φPVL ORF 20 and 21 homolog0.071
100% protein ID to MWP017 HP0.070
100% protein ID MW1894 HP0.060
78% protein ID MW1892 HP0.055
83.2% protein ID SA1763 HP0.032
100% protein ID SAP019 HP, S. aureus N315 plasmid N315B0.031
  • 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 (http://www.tigr.org) or by the putative function.

  • b Abbreviations: PTS, phosphotransferase; HP, hypothetical protein; CHP, conserved hypothetical protein; SAM, S-adenosylmethionine; 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.