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

TABLE 3.

Genes differentially expressed in a biofilm versus exponential growth phase

N315 ORFa Common namea Producta,b ERc
Cell envelope and cellular processes
    N315-SA1960 mtlF PTS system, mannitol-specific IIBC component 5.46
    N315-SA1882 kdpD Sensor protein KdpD 5.13
    N315-SA2311 Similar to NAD(P)H-flavin oxidoreductase 2.71
    N315-SA1156 ABC transporter (ATP-binding protein) homolog 2.68
    N315-SA0724 Similar to cell division inhibitor 0.496
    N315-SA2253 opp-1C Oligopeptide transporter putative membrane permease domain 0.490
    N315-SA0567 Similar to iron(III) ABC transporter permease protein 0.474
    N315-SA2216 Similar to ABC transporter, ATP-binding protein 0.471
    N315-SA0980 Similar to ferrichrome ABC transporter 0.471
    N315-SA0981 Similar to ferrichrome ABC transporter 0.468
    N315-SA0592 tagA Teichoic acid biosynthesis protein 0.462
    N315-SA1935 hmrA Similar to amidase 0.442
    N315-SA1169 γ-Aminobutyrate permease 0.425
    N315-SA0243 tagB Similar to teichoic acid biosynthesis protein B 0.423
    N315-SA0110 sirB Lipoprotein 0.399
    N315-SA2100 Similar to autolysin E 0.394
    N315-SA1458 lytH N-Acetylmuramoyl-l-alanine amidase 0.393
    N315-SA0109 sirC Lipoprotein 0.378
    N315-SA0106 lctP l-Lactate permease homolog 0.376
    N315-SA0682 Similar to ditripeptide ABC transporter 0.370
    N315-SA2053 Glucose uptake protein homolog 0.331
    N315-SA0479 nupC Pyrimidine nucleoside transport protein 0.315
    N315-SA0111 sirA Lipoprotein 0.312
    N315-SA2339 Similar to antibiotic transport-associated protein 0.291
    N315-SA0566 Similar to iron-binding protein 0.287
    N315-SA2233 Similar to integral membrane efflux protein 0.281
    N315-SA0325 glpT Glycerol-3-phosphate transporter 0.281
    N315-SA2112 Similar to sodium-dependent transporter 0.278
    N315-SA1025 mraY Phospho-N-muramic acid-pentapeptide translocase 0.265
    N315-SA0600 Similar to pyrimidine nucleoside transporter 0.255
    N315-SA1978 Similar to ferrichrome ABC transporter (permease) 0.203
    N315-SA0010 azlC Similar to amino acid permease 0.161
    N315-SA2300 Similar to glucarate transporter 0.141
    N315-SA0691 sstD Lipoprotein, similar to ferrichrome ABC transporter 0.126
    N315-SA0374 pbuX Xanthine permease 0.089
    N315-SA0579 Similar to Na+/H+ antiporter 0.080
    N315-SA0411 ndhF NADH dehydrogenase subunit 5 0.065
    N315-SA2302 stpC Similar to ABC transporter 0.046
    N315-SA2303 smpC Similar to membrane-spanning protein 0.041
Information pathways
    N315-SA1883 kdpE KDP operon transcriptional regulatory protein 5.42
    N315-SA2429 ArgR Similar to arginine repressor 3.92
    N315-SA2296 Similar to transcriptional regulator, MerR family 3.72
    N315-SA2418 Similar to two-component response regulator 2.13
    N315-SA0460 pth Peptidyl-tRNA hydrolase 0.490
    N315-SA0652 Similar to transcription regulation protein 0.452
    N315-SA1853 Similar to DNA mismatch repair protein MutS 0.445
    N315-SA1287 asnS Asparaginyl-tRNA synthetase 0.441
    N315-SA0348 Similar to transcription terminator 0.440
    N315-SA2358 Similar to transcriptional regulator (TetR/AcrR family) 0.382
    N315-SA1697 Similar to protein-tyrosine phosphatase 0.364
    N315-SA1120 Similar to transcription regulator GntR family 0.354
    N315-SA0298 pfoR Similar to regulatory protein PfoR 0.333
    N315-SA1550 tyrS Tyrosyl-tRNA synthetase 0.325
    N315-SA2482 pcp Pyrrolidone-carboxylate peptidase 0.297
    N315-SA1583 rot Repressor of toxins (Rot) 0.295
    N315-SA0653 fruR Similar to transcription repressor of fructose operon 0.229
    N315-SA0904 Probable ATL autolysin transcription regulator 0.191
    N315-SA1725 sspB Staphopain, cysteine proteinase 0.074
Intermediary metabolism
    N315-SA0328 Similar to NADH-dependent FMN reductase 7.25
    N315-SA0122 butA Acetoin (diacetyl)reductase 5.04
    N315-SA2297 Similar to GTP-pyrophosphokinase 3.25
    N315-SA1142 glpD Aerobic glycerol-3-phosphate dehydrogenase 2.97
    N315-SA0016 purA Adenylosuccinate synthase 2.37
    N315-SA2397 Similar to pyridoxal-phosphate-dependent aminotransferase 2.04
    N315-SA2001 Similar to oxidoreductase, aldo/keto reductase family 2.01
    N315-SA1201 trpD Anthranilate phosphoribosyltransferase 0.495
    N315-SA1685 mutY Similar to A/G-specific adenine glycosylase 0.481
    N315-SA2111 Similar to phosphoglycolate phosphatase 0.475
    N315-SA1052 gmk Guanylate kinase homolog 0.462
    N315-SA2279 Similar to phosphomannomutase 0.458
    N315-SA0902 HisC homolog 0.448
    N315-SA0177 argJ Arginine biosynthesis bifunctional protein homolog 0.436
    N315-SA1310 ansA Probable l-asparaginase, gene-ansA 0.429
    N315-SA1309 cmk Cytidylate kinase 0.427
    N315-SA1749 Similar to aspartate transaminase protein 0.423
    N315-SA2140 Similar to esterase 0.412
    N315-SA0507 Similar to N-acyl-l-amino acid amidohydrolase 0.407
    N315-SA0568 Similar to l-2-haloalkanoic acid dehalogenase 0.374
    N315-SA2213 bioB Biotin synthase 0.373
    N315-SA0514 Similar to deoxypurine kinase 0.356
    N315-SA1121 Similar to processing proteinase homolog 0.340
    N315-SA1203 trpF Phosphoriborylanthranilate isomerase 0.323
    N315-SA2342 thgA Similar to O-acetyltransferase 0.280
    N315-SA0511 Similar to UDP-glucose 4-epimerase-related protein 0.256
    N315-SA1202 trpC Indole-3-glycerol phosphate synthase 0.246
    N315-SA2395 ldh l-Lactate dehydrogenase 0.213
    N315-SA0180 bmQ Similar to branched-chain amino acid transport system carrier protein 0.192
    N315-SA1200 trpG Anthranilate synthase component II 0.120
    N315-SA1199 trpE Similar to anthranilate synthase component I 0.101
    N315-SA0373 xprT Xanthine phosphoribosyltransferase 0.077
Other functions
    N315-SA0899 sspC Cysteine protease 7.24
    N315-SA0900 sspB Cysteine protease precursor 7.03
    N315-SA0150 cap5G Capsular polysaccharide synthesis enzyme 4.80
    N315-SA2006 Similar to MHC class II analog 4.69
    N315-SA0149 cap5F Capsular polysaccharide synthesis enzyme 4.58
    N315-SA0148 cap5E Capsular polysaccharide synthesis enzyme 4.05
    N315-SA0146 cap5C Capsular polysaccharide synthesis enzyme 3.31
    N315-SA0147 cap5D Capsular polysaccharide synthesis enzyme 3.30
    N315-SA0145 cap5B Capsular polysaccharide synthesis enzyme Cap5B 2.43
    N315-SA0144 cap5A Capsular polysaccharide synthesis enzyme 2.34
    N315-SA0841 Similar to cell surface protein Map-w 2.22
    N315-SA1709 Similar to ferritin 2.18
    N315-SA0754 Similar to lactococcal prophage ps3 protein 05 0.498
    N315-SA1835 int Similar to integrase (pathogenicity island SaPln1), gene = int 0.431
    N315-SA1559 Similar to smooth muscle caldesmon 0.426
    N315-SA0797 nifU-3 Similar to nitrogen fixation protein NifU 0.407
    N315-SA0780 Similar to hemolysin 0.331
    N315-SA0746 nuc Staphylococcal nuclease 0.170
    N315-SA1766 HP (bacteriophage φN315) 0.069
    N315-SA1775 Similar to scaffolding protein (bacteriophage φN315) 0.048
    N315-SA1765 HP (bacteriophage φN315) 0.042
    N315-SA1777 HP (bacteriophage φN315) 0.038
    N315-SA1771 HP (bacteriophage φN315) 0.036
    N315-SA1762 HP (bacteriophage φN315) 0.036
Similar to unknown proteins
    N315-SA0326 CHP (lactoylglutathione lyase and related lyases) 7.94
    N315-SA0327 CHP (flavin-dependent oxidoreductases) 7.50
    N315-SA2479 CHP 5.04
    N315-SA0007 Predicted sugar kinase 4.57
    N315-SA0380 CHP (pathogenicity island SaPln2) 3.07
    N315-SA0381 CHP (pathogenicity island SaPln2) 2.80
    N315-SA1235 CHP 2.04
    N315-SA1890 CHP 2.03
    N315-SA0230 CHP 2.02
    N315-SA0941 CHP 0.497
    N315-SA0467 CHP (predicted ATPase of the PP-loop superfamily) 0.489
    N315-SA1838 CHP (predicted metal-dependent membrane protease) 0.481
    N315-SA2487 rarD Similar to RarD protein 0.462
    N315-SA1696 CHP 0.453
    N315-SA1448 CHP (TPR repeat-containing proteins) 0.452
    N315-SA0329 CHP 0.445
    N315-SA2328 CHP (putative effector of murein hydrolase, LrgB) 0.434
    N315-SA0979 CHP 0.433
    N315-SA1928 HP 0.421
    N315-SA1601 crcB CHP (integral membrane protein) 0.404
    N315-SA2377 CHP 0.398
    N315-SAS081 CHP (ATPase involved in DNA repair) 0.391
    N315-SA0334 CHP (Sec-independent protein secretion pathway) 0.378
    N315-SA2305 CHP 0.372
    N315-SA0840 CHP (phospholipid-binding protein) 0.370
    N315-SA1903 CHP 0.366
    N315-SA0543 CHP (uncharacterized BCR) 0.353
    N315-SA0413 CHP 0.332
    N315-SA0341 Similar to low-temperature requirement A protein 0.329
    N315-SA0345 CHP (methionine synthase I) 0.324
    N315-SA0257 CHP (SAM-dependent methyltransferases) 0.323
    N315-SA2096 CHP 0.320
    N315-SA0773 CHP (predicted membrane protein) 0.312
    N315-SA2212 Similar to 8-amino-7-oxononanoate synthase 0.303
    N315-SA1252 CHP (histone acetyltransferase) 0.298
    N315-SA2452 CHP (domain typically associated with flavoprotein oxygenases) 0.282
    N315-SA0870 CHP (predicted permease) 0.267
    N315-SA0335 CHP (Sec-independent protein secretion pathway) 0.265
    N315-SA0556 CHP 0.203
    N315-SA0753 CHP (lysine efflux permease) 0.179
    N315-SA2219 CHP (uncharacterized membrane protein) 0.133
    N315-SA0739 CHP 0.129
    N315-SAS001 CHP 0.128
    N315-SA0412 CHP 0.078
No similarity
    N315-SAS016 HP 12.74
    N315-SA0883 HP 5.97
    N315-SA1233 HP 2.25
    N315-SA0414 HP 0.496
    N315-SA2126 HP 0.495
    N315-tRNA12 tRNA-Pro 0.491
    N315-SA1943 HP 0.491
    N315-SA1215 HP 0.486
    N315-tRNA11 tRNA-Arg 0.479
    N315-SA0613 HP 0.470
    N315-SA2485 HP 0.457
    N315-SA0088 HP 0.443
    N315-tRNA57 tRNA-Lys 0.416
    N315-tRNA47 tRNA-Leu 0.409
    N315-SA1607 HP 0.402
    N315-SA0955 HP 0.372
    N315-tRNA07 tRNA-Thr 0.355
    N315-SA0105 HP 0.344
    N315-SA2118 HP 0.335
    N315-SA0336 HP 0.326
    N315-SA0363 HP 0.321
    N315-SA2055 HP 0.321
    N315-SA2224 HP 0.309
    N315-SA2249 HP 0.259
    N315-SA0749 HP 0.233
    N315-tRNA06 tRNA-Val 0.219
    N315-SA0748 HP 0.214
    N315-SA0889 HP 0.179
    N315-SA2488 HP 0.157
    N315-SA1778 HP (bacteriophage φN315) 0.089
    N315-SA1768 HP (bacteriophage φN315) 0.050
    N315-SA1770 HP (bacteriophage φN315) 0.050
    N315-SA1774 HP (bacteriophage φN315) 0.046
    N315-SA1776 HP (bacteriophage φN315) 0.044
    N315-SAS060 HP (bacteriophage φN315) 0.041
    N315-SA1769 HP (bacteriophage φN315) 0.040
    N315-SA1773 HP (bacteriophage φN315) 0.032
    N315-SA1772 HP (bacteriophage φN315) 0.031
    N315-SA1767 HP (bacteriophage φN315) 0.027
No N315 ORF
set5 100% protein ID Set5, exotoxin 5, and HsdM-like protein gene 40.43
sspA 99.4% protein ID S. aureus glutamic acid-specific protease 7.19
cap8H 100% protein ID to capsular polysaccharide synthase enzyme Cap8H 5.11
cap8J 100% protein ID to capsular polysaccharide synthesis enzyme Cap8J 4.52
58.1% protein ID malofactic enzyme, Oenococcus oeni bacteria 3.05
68.1% protein ID SA0329 CHP 2.39
92.8% protein ID MW1748 HP 2.25
84.4% protein ID MW0360 HP 2.16
96.7% protein ID to MW2134 HP 0.500
95.6% protein ID SA2230 0.473
58.4% protein ID BH3950 transposase (10), Bacillus halodurans 0.467
49.1% protein ID MW2618 0.463
COL-SA1788 HP 0.434
87.6% protein ID MW0584 0.423
COL-SA2299 HP 0.421
Similar to splE 62.6% protein ID serine protease SplE 0.420
97.7% protein ID to SA1559 0.419
26.9% protein ID MW2498 0.418
COL-SA0866 HP 0.411
Serine protease 55.4% protein ID serine protease SplB 0.409
96% protein ID MW2325 0.387
95.5% protein ID MW0355 HP 0.371
22.2% protein ID SA0283 HP 0.345
89.4% protein ID SA0553 CHP 0.338
78.2% protein ID MW1720 HP 0.315
COL-SA1556 HP 0.311
99.4% protein ID to MW0053 CHP 0.308
45.9% protein ID BH3950 transposase (10), Bacillus halodurans 0.290
97.7% protein ID MW0355 HP 0.289
splB 97.7% protein ID to serine protease SplB 0.280
79.2% protein ID MW1043 HP 0.270
COL-SA2728 HP 0.237
99.5% id to SAV1992 HP 0.209
37.3% protein ID MW1769 HP 0.202
COL-SA1140 sai-1 29-kDa cell surface protein 0.164
85.2% protein ID MW1042 HP 0.141
99.5% protein ID MWP018 0.138
99.8% protein ID MWP016 S. aureus plasmid pMW2 0.096
93.4% protein ID SAV1953 φPVL ORF 20 and 21 homolog 0.079
Mu50-SAV1953 φPVL ORF 20 and 21 homolog 0.071
100% protein ID to MWP017 HP 0.070
100% protein ID MW1894 HP 0.060
78% protein ID MW1892 HP 0.055
83.2% protein ID SA1763 HP 0.032
100% protein ID SAP019 HP, S. aureus N315 plasmid N315B 0.031
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.