TABLE 4.
Genes differentially expressed in a biofilm versus stationary growth phase
| N315 ORFa | Common namea | Producta,b | ERc |
|---|---|---|---|
| Cell envelope and cellular processes | |||
| N315-SA0655 | fruA | Fructose-specific permease | 14.43 |
| N315-SA0263 | Similar to proton antiporter efflux pump | 9.55 | |
| N315-SA2142 | semB | Similar to multidrug resistance protein | 4.96 |
| N315-SA0293 | Similar to formate transporter NirC | 4.64 | |
| N315-SA1140 | glpF | Glycerol uptake facilitator | 4.40 |
| N315-SA2185 | narG | Respiratory nitrate reductase alpha chain | 4.08 |
| N315-SA2183 | narJ | Similar to nitrate reductase delta chain | 3.87 |
| N315-SA2184 | narH | Nitrate reductase beta chain NarH | 3.56 |
| N315-SA2053 | Glucose uptake protein homolog | 3.55 | |
| N315-SA0166 | Similar to nitrate transporter | 3.39 | |
| N315-SA0167 | Similar to membrane lipoprotein SrpL | 3.29 | |
| N315-SA0702 | llm | Lipophilic protein affecting bacterial lysis rate and methicillin resistance level | 2.83 |
| N315-SA2222 | Similar to bicyclomycin resistance protein TcaB | 2.75 | |
| N315-SA0411 | ndhF | NADH dehydrogenase subunit 5 | 2.41 |
| N315-SA2176 | narK | Nitrite extrusion protein | 2.16 |
| N315-SA1960 | mtlF | PTS system, mannitol-specific IIBC component | 0.486 |
| N315-SA1381 | pbp3 | Penicillin-binding protein 3 | 0.482 |
| N315-SA1219 | Similar to phosphate ABC transporter | 0.463 | |
| N315-SA2311 | Similar to NAD(P)H-flavin oxidoreductase | 0.460 | |
| N315-SA0367 | Similar to nitroflavin reductase | 0.410 | |
| N315-SA1982 | Similar to transporter | 0.397 | |
| N315-SA0260 | Similar to ribose transporter RbsU | 0.385 | |
| N315-SA2074 | modA | Probable molybdate-binding protein | 0.384 |
| N315-SA1848 | amt | Probable ammonium transporter | 0.343 |
| N315-SA0138 | Similar to alkylphosphonate ABC transporter | 0.323 | |
| N315-SA2203 | EmrB/QacA subfamily | Similar to multidrug resistance protein | 0.304 |
| N315-SA0420 | Similar to ABC transporter ATP-binding protein | 0.286 | |
| N315-SA0422 | Similar to lactococcal lipoprotein | 0.272 | |
| N315-SA0421 | Similar to ABC transporter permease protein | 0.256 | |
| N315-SA0589 | Similar to ABC transporter ATP-binding protein | 0.163 | |
| N315-SA0849 | Similar to peptide-binding protein OppA | 0.148 | |
| Information pathways | |||
| N315-SA0653 | fruR | Similar to transcription repressor of fructose operon | 14.57 |
| N315-SA0476 | Similar to transcription regulator GntR family | 4.98 | |
| N315-SA1058 | def | Similar to polypeptide deformylase | 2.35 |
| N315-SA0460 | pth | Peptidyl-tRNA hydrolase | 2.07 |
| N315-SA1516 | phoP | Alkaline phosphatase synthesis transcriptional regulatory protein | 0.479 |
| N315-SA0130 | Similar to trehalose operon transcriptional repressor | 0.477 | |
| N315-SA1805 | Repressor homolog (bacteriophage φN315) | 0.390 | |
| N315-SAS042 | rpmG | 50S ribosomal protein L33 | 0.362 |
| N315-SA1394 | glyS | Glycyl-tRNA synthetase | 0.351 |
| N315-SA1149 | glnR | Glutamine synthetase repressor | 0.319 |
| N315-SA1360 | Xaa-Pro dipeptidase | 0.294 | |
| Intermediary metabolism | |||
| N315-SA0654 | fruB | Fructose-1-phosphate kinase | 17.08 |
| N315-SA1959 | glmS | Glucosamine-fructose-6-phosphate aminotransferase | 9.27 |
| N315-SA0143 | adhE | Alcohol-acetaldehyde dehydrogenase | 5.79 |
| N315-SA2186 | nasF | Uroporphyrin III C-methyl transferase | 4.56 |
| N315-SA2187 | nasE | Assimilatory nitrite reductase | 4.15 |
| N315-SA1929 | pyrG | CTP synthase | 3.97 |
| N315-SA2188 | nirB | Nitrite reductase | 3.38 |
| N315-SA0973 | kdtB | Phosphopantetheine adenyltransferase homolog | 2.29 |
| N315-SA0572 | Similar to esterase or lipase | 0.493 | |
| N315-SA0528 | Similar to hexulose-6-phosphate synthase | 0.484 | |
| N315-SA1231 | dal | Similar to alanine racemase | 0.471 |
| N315-SA2120 | Similar to amino acid amidohydrolase | 0.464 | |
| N315-SA0008 | hutH | Histidine ammonia-lyase | 0.461 |
| N315-SA1584 | Lysophospholipase homolog | 0.456 | |
| N315-SA1230 | hipO | Hippurate hydrolase | 0.435 |
| N315-SAS044 | dmpI | 4-Oxalocrotonate tautomerase | 0.432 |
| N315-SA1225 | lysC | Aspartokinase II | 0.429 |
| N315-SA1229 | dapD | Tetrahydrodipicolinate acetyltransferase | 0.423 |
| N315-SA0258 | rbsK | Probable ribokinase | 0.422 |
| N315-SA0820 | glpQ | Glycerophosphoryl diester phosphodiesterase | 0.419 |
| N315-SA0181 | entB | Similar to isochorismatase | 0.416 |
| N315-SA0512 | ilvE | Branched-chain amino acid aminotroansferase homolog | 0.415 |
| N315-SA2204 | gpm | Phosphoglycerate mutase | 0.408 |
| N315-SA1227 | dapA | Dihydrodipicolinate synthase | 0.406 |
| N315-SA2155 | mqo | Similar to malate:quinone oxidoreductase | 0.404 |
| N315-SA1724 | purB | Adenylosuccinate lyase | 0.394 |
| N315-SA0304 | nanA | N-Acetylneuraminate lyase subunit | 0.384 |
| N315-SA1150 | glnA | Glutamine-ammonia ligase | 0.362 |
| N315-SA1531 | ald | Alanine dehydrogenase | 0.357 |
| N315-SA1228 | dapB | Dihydrodipicolinate reductase | 0.354 |
| N315-SA2125 | hutG | Similar to formiminoglutamase | 0.353 |
| N315-SA0098 | Similar to aminoacylase | 0.346 | |
| N315-SA2127 | rpiA | Similar to ribose 5-phosphate isomerase | 0.341 |
| N315-SA1226 | asd | Aspartate semialdehyde dehydrogenase | 0.341 |
| N315-SA1545 | serA | d-3-Phosphoglycerate dehydrogenase | 0.341 |
| N315-SA0679 | hisC | Similar to histidinol-phosphate aminotransferase | 0.337 |
| N315-SA0658 | Similar to plant metabolite dehydrogenases | 0.335 | |
| N315-SA0656 | nagA | Probable N-acetylglucosamine-6-phosphate deacetylase | 0.333 |
| N315-SA1184 | citB | Aconitate hydratase | 0.329 |
| N315-SA0915 | folD | FolD bifunctional protein | 0.326 |
| N315-SA1858 | ilvD | Dihydroxy-acid dehydratase | 0.280 |
| N315-SA0430 | gltB | Glutamate synthase large subunit | 0.263 |
| N315-SA1614 | menC | o-Succinylbenzoic acid synthetase | 0.234 |
| N315-SA0431 | gltD | NADH-glutamate synthase small subunit | 0.199 |
| N315-SA1553 | fhs | Formyltetrahydrofolate synthetase | 0.168 |
| N315-SA0016 | purA | Adenylosuccinate synthase | 0.117 |
| N315-SA0926 | purD | Phosphoribosylamine-glycine ligase | 0.049 |
| N315-SA0917 | purK | Phosphoribosylaminoimidazole carboxylase carbon dioxide fixation chain | 0.034 |
| N315-SA0916 | purE | Similar to phosphoribosylaminoimidazole carboxylase | 0.030 |
| N315-SA0918 | purC | Phosphoribosylaminoimidazolesuccinocarboxamide synthetase homolog | 0.023 |
| Other functions | |||
| N315-SA2460 | icaD | Intercellular adhesion protein D | 34.06 |
| N315-SA1898 | Similar to SceD precursor | 26.36 | |
| N315-SA2206 | sbi | IgG-binding protein | 26.16 |
| N315-SA1000 | Similar to fibrinogen-binding protein | 11.51 | |
| N315-SA2097 | Similar to SsaA | Similar to secretory antigen precursor | 4.74 |
| N315-SA2164 | Similar to phage infection protein precursor | 2.80 | |
| N315-SA1382 | sodA | Superoxide dismutase SodA | 0.497 |
| N316-SA1606 | Plant metabolite dehydrogenase homolog | 0.480 | |
| N315-SA0841 | Similar to cell surface protein Map-w | 0.448 | |
| N315-SA1549 | htrA | Similar to serine proteinase Do, heat shock protein | 0.434 |
| N315-SA2406 | gbsA | Glycine betaine aldehyde dehydrogenase | 0.399 |
| N315-SA0659 | Similar to CsbB stress response protein | 0.390 | |
| N315-SA1312 | ebpS | Elastin-binding protein | 0.363 |
| N315-SA0755 | Similar to general stress protein 170 | 0.340 | |
| N315-SA1170 | katA | Catalase | 0.309 |
| N315-SA0091 | plc | 1-Phosphatidylinositol phosphodiesterase precursor | 0.300 |
| N315-SA2405 | betA | Choline dehydrogenase | 0.252 |
| Similar to unknown proteins | |||
| N315-SA0213 | CHP | 17.26 | |
| N315-SA2256 | CHP | 4.76 | |
| N315-SA0341 | HP similar to low-temperature requirement A protein | 3.95 | |
| N315-SA1176 | CHP | 3.05 | |
| N315-SA0929 | CHP | 3.04 | |
| N315-SA1431 | CHP | 3.00 | |
| N315-SA1340 | CHP (lactoylglutathione lyase) | 2.53 | |
| N315-SAS027 | CHP | 2.50 | |
| N315-SA1932 | Similar to HP T13D8.31 Arabidopsis thaliana | 2.35 | |
| N315-SA1464 | yajC | CHP (preprotein translocase subunit YajC) | 2.30 |
| N315-SA1540 | CHP (GAF domain-containing protein) | 2.24 | |
| N315-SA0165 | Similar to α-helical coiled-coil protein SrpF | 2.16 | |
| N315-SA0114 | CHP | 2.10 | |
| N315-SA0529 | CHP (predicted sugar phosphate isomerase involved in capsule formation, GutQ) | 0.486 | |
| N315-SA1019 | CHP | 0.467 | |
| N315-SA1737 | CHP (3-carboxymuconate cylase) | 0.466 | |
| N315-SA0801 | CHP (IscA) | 0.463 | |
| N315-SA1543 | CHP (predicted redox protein, regulator of disulfide bond formation) | 0.462 | |
| N315-SA1380 | CHP (5-formyltetrahydrofolate cyclo-ligase) | 0.454 | |
| N315-SA1129 | CHP (predicted HD superfamily hydrolase) | 0.447 | |
| N315-SA0861 | CHP (hemoglobin-like proteins) | 0.443 | |
| N315-SA0230 | CHP | 0.438 | |
| N315-SA1280 | CHP | 0.430 | |
| N315-SA0957 | CHP | 0.429 | |
| N315-SA1331 | CHP (predicted oxidoreductases) | 0.393 | |
| N315-SA1689 | CHP | 0.384 | |
| N315-SA0513 | CHP (predicted phosphatases, Gph) | 0.379 | |
| N315-SA2367 | CHP (predicted hydrolases or acyltransferases) | 0.356 | |
| N315-SA1167 | CHP (predicted hydrolases of the HAD superfamily) | 0.337 | |
| N315-SA1690 | CHP | 0.324 | |
| N315-SA0089 | Similar to DNA helicase | 0.315 | |
| N315-SA0873 | CHP | 0.315 | |
| N315-SA1544 | Similar to soluble hydrogenase 42-kDa subunit | 0.314 | |
| N315-SA0741 | CHP (predicted acetyltransferase) | 0.310 | |
| N315-SA0362 | CHP | 0.310 | |
| N315-SA1281 | CHP | 0.310 | |
| N315-SA0649 | CHP (predicted DNA-binding proteins with PD1-like DNA-binding motif) | 0.286 | |
| N315-SA0407 | CHP (chromosome segregation ATPases) | 0.254 | |
| N315-SA1611 | CHP (dipeptidyl aminopeptidases/acylaminoacyl-peptidases) | 0.227 | |
| N315-SA0919 | CHP (phosphoribosylformylglycinamidine [FGAM] synthase) | 0.027 | |
| No similarity | |||
| N315-SA0663 | HP | 7.97 | |
| N315-SA2281 | HP | 5.10 | |
| N315-SA0779 | HP | 3.44 | |
| N315-SA2376 | HP | 3.22 | |
| N315-SA0885 | HP | 3.16 | |
| N315-SA1670 | HP | 2.80 | |
| N315-SA2126 | HP | 2.62 | |
| N315-SA0336 | HP | 2.59 | |
| N315-SA0571 | HP | 2.37 | |
| N315-SA2058 | HP | 2.17 | |
| N315-SA0397 | lpl2 | HP (pathogenicity island SaPln2) | 0.488 |
| N315-SAS031 | HP | 0.480 | |
| N315-SA1168 | HP | 0.472 | |
| N315-SA0372 | HP | 0.468 | |
| N315-SA0404 | lpl8 | HP (pathogenicity island SaPln2) | 0.447 |
| N315-SA1319 | HP | 0.421 | |
| N315-SA0090 | HP | 0.366 | |
| N315-SA1546 | HP | 0.293 | |
| N315-SA0406 | HP | 0.258 | |
| N315-SA2497 | HP | 0.208 | |
| N315-SA0408 | HP | 0.198 | |
| N315-SA2496 | HP | 0.188 | |
| No N315 ORF | 72.4% protein ID to MW1041 | 25.20 | |
| COL-SA0674 | HP | 6.12 | |
| COL-SA1165 | HP | 5.57 | |
| 98.1% protein ID to MW2274 CHP | 5.33 | ||
| 98.1% protein ID to NasE assimilatory nitrite reductase | 4.25 | ||
| 57% protein ID to spyM18_1050 HP, S. pyogenes MGAS8232 | 3.55 | ||
| 88.2% protein ID to MW2323 | 3.11 | ||
| 100% protein ID to SAP023 S. aureus N315 plasmid pN315B | 2.32 | ||
| 100% protein ID to MW2396 | 0.497 | ||
| COL-SA1345 | HP | 0.491 | |
| 100% protein ID to SA1320 HP | 0.482 | ||
| 100% protein ID to lpl11 HP, S. aureus MW2 | 0.465 | ||
| COL-SA2676 | LPXTG | LPXTG-motif cell wall anchor domain protein | 0.456 |
| 91.5% protein ID to lpl2 HP, S. aureus N315 | 0.447 | ||
| COL-SA0293 | CHP | 0.444 | |
| 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 N315 | 0.405 | ||
| binL | 99.5% protein ID to BinL DNA-invertase, S. aureus plasmid pMW2 | 0.394 | |
| 94.8% protein ID to BinL DNA invertase, S. aureus plasmid pMW2 | 0.392 | ||
| COL-SA0601 | HP | 0.372 | |
| 89.8% protein ID to Lpl10 HP, S. aureus MW2 | 0.364 | ||
| 25.8% protein ID to MA2121 CHP, Methanosarcina acetivorans C2A | 0.363 | ||
| 88% protein ID to MW1374 CHP | 0.363 | ||
| 74.8% protein ID to lpl5 HP, S. aureus N315 | 0.331 | ||
| COL-SA1343 | HP | 0.328 | |
| 48.6% protein ID to ycnB homolog of multidrug resistance protein B, B. subtilis | 0.309 | ||
| 71% protein ID to MW1201 HP | 0.282 | ||
| 93.5% protein ID to MW0402 HP | 0.276 | ||
| 84% protein ID to lpl2 HP, S. aureus N315 | 0.261 | ||
| 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 CHP | 0.191 | ||
| 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.