TABLE 2.
Differential expression of genes in biofilm-bound cells as related to predicted T. maritima operons
| Putative function | Gene ID | Gene description | Fold change | −Log10P valuec |
|---|---|---|---|---|
| Iron transportb | TM0050 | Iron(II) transport protein A (FeoA) | 4.0 | 12.2 |
| TM0051 | Iron(II) transport protein B (FeoB) | 5.4 | 12.4 | |
| TM0052 | Hypothetical protein | 3.0 | 10.1 | |
| TM0053 | Esterase, putative | 4.1 | 8.8 | |
| TM0054 | Hypothetical protein | 2.8 | 10.2 | |
| DNA processingb | TM0198 | ATP-dependent Clp protease, ATPase subunit, ClpA family | 2.8 | 9.2 |
| TM0199 | Sms/RadA homolog, DNA recombination/repair protein | 4.6 | 12.4 | |
| TM0200 | Predicted HHH nucleic acid binding protein | 2.6 | 5.7 | |
| TM0201 | NADP-reducing hydrogenase, subunit D, putative | 1.5 | 2.7 | |
| TM0202 | TauA homolog | 1.7 | 5.5 | |
| Cation transport systemb | TM0315 | Predicted membrane protein | 2.8 | 12.2 |
| TM0316 | Uncharacterized homolog of γ-carboxymuconolactone decarboxylase subunit | 3.6 | 9.1 | |
| TM0317 | Cation-transporting ATPase, P-type | 6.6 | 14.1 | |
| TM0318 | Ubiquinone/menaquinone methyltransferase | 5.0 | 11.4 | |
| TM0319 | Hypothetical protein | 2.6 | 6.6 | |
| TM0320 | Heavy metal binding protein | 3.2 | 9.2 | |
| ABC transporta | TM0351 | ABC transporter, permease subunit, SalY family | 2.0 | 8.9 |
| TM0352 | ABC transporter, ATP-binding subunit, SalX domain | 2.1 | 9.2 | |
| TM0353 | Predicted membrane fusion protein (COG0845) | 1.4 | 6.4 | |
| DNA repaira | TM0369 | Predicted transcriptional regulator | 2.1 | 8.0 |
| TM0370 | RAD55-related, RecA superfamily ATPase (COG0467) | 2.4 | 7.4 | |
| Thermal stress | TM0373 | DnaK protein (62) | 1.9 | 8.5 |
| TM0374 | Heat shock protein, class I | 2.3 | 8.5 | |
| Glutamate synthesisa | TM0394 | Glutamate synthase domain 3 (GltB) | 2.8 | 6.5 |
| TM0395 | NADH oxidase | 3.5 | 9.0 | |
| TM0396 | HycB domain containing protein, related to hydrogenase components | 3.2 | 10.8 | |
| TM0397 | Glutamate synthase domain 2, GltB | 2.3 | 7.9 | |
| TM0398 | Glutamate synthase domain 1, GltB | 2.2 | 5.2 | |
| Sugar and iron transportb | TM0417 | FTR1, predicted high affinity Fe2+/Pb2+ permease | 4.4 | 8.5 |
| TM0418 | Sugar ABC transporter, periplasmic sugar-binding protein, MalE-related | 2.7 | 6.9 | |
| TM0419 | Sugar ABC transporter, permease protein, UpgA family | 2.7 | 11.0 | |
| TM0420 | Sugar ABC transporter, permease protein | 1.4 | 7.6 | |
| TM0421 | Sugar ABC transporter, ATP-binding protein, MalK homolog | 2.3 | 11.3 | |
| TM0422 | Possible endonuclease or sugar phosphate isomerase | 2.8 | 6.3 | |
| Sulfur compound transport systemsa | TM0483 | ABC transporter, ATP-binding protein, TauB family | 2.0 | 10.2 |
| TM0484 | ABC transporter, ATP-binding subunit, TauA family | 2.6 | 5.9 | |
| TM0485 | ABC transporter, permease protein, TauC family | 2.9 | 11.1 | |
| TM0486 | Uncharacterized conserved protein | 2.9 | 9.4 | |
| Oxygen detoxificationa | TM0657 | Rubrerythrin | −3.7 | 7.8 |
| TM0658 | Superoxide reductase (neelaredoxin) | −3.5 | 11.4 | |
| TM0659 | Rubredoxin | −3.1 | 9.9 | |
| Amino acid metabolismb | TM0664 | Putative endonuclease | 2.3 | 10.5 |
| TM0665 | Cysteine synthase | 3.9 | 12.0 | |
| TM0666 | Serine acetyltransferase (CysE) | 3.9 | 9.3 | |
| Oxygen detoxification/electron transferb | TM0752 | NAD+-dependent α-glucuronidase | 3.1 | 7.9 |
| TM0753 | Ubiquinone/menaquinone biosynthesis methyltransferase, putative (UbiE homolog) | 3.3 | 10.1 | |
| TM0754 | Oxidoreductase | 2.4 | 5.9 | |
| TM0755 | FpaA family protein, contains flavodoxin domain and β-metallolactamase domain (COG0426) | 3.8 | 8.5 | |
| Biotin/thiamine-synthesisb | TM1266 | Hypothetical protein | 7.2 | 10.0 |
| TM1267 | ThiH protein, putative | 8.9 | 15.4 | |
| TM1268 | Hypothetical protein | 3.7 | 6.6 | |
| TM1269 | Biotin synthetase, putative (BioB homolog) | 5.0 | 8.6 | |
| TM1270 | Cystathionine γ-synthase/β-lyase | 2.7 | 9.3 | |
| Iron-sulfur cluster assemblya | TM1368 | SufC homolog, similar to ABC ATP-binding components | 1.1 | 2.0 |
| TM1369 | SufB homolog, similar to ABC permease components | 6.3 | 15.0 | |
| TM1370 | SufD homolog, similar to ABC permease components | 6.3 | 12.0 | |
| TM1371 | SufS/IscS homolog, cysteine desulfurase | 4.8 | 13.9 | |
| TM1372 | SufA/IscU homolog, iron-sulfur cluster assembly scaffold | 2.9 | 5.9 | |
| Sugar/electron transfer cascadeb | TM1524 | Endoglucanase (intracellular) | 1.8 | 7.1 |
| TM1525 | Endoglucanase (extracellular) | 2.1 | 8.6 | |
| TM1526 | Hypothetical protein (COG1633) | 1.7 | 6.3 | |
| TM1527 | IscR homolog, putative | 1.8 | 6.0 | |
| TM1528 | 1,4-Dihydroxy-2-naphthoate octaprenyltransferase, MenA homolog | 1.7 | 6.0 | |
| TM1529 | Predicted CAAX amino terminal protease | 2.4 | 10.0 | |
| TM1530 | FixA homolog, electron transfer flavoprotein | 2.3 | 1.9 | |
| TM1531 | FixB homolog, electron transfer flavoprotein | 2.0 | 4.9 | |
| TM1532 | FixC homolog | 2.5 | 7.9 | |
| TM1533 | FixX homolog | 2.5 | 5.3 | |
| TM1534 | Hypothetical protein | 2.2 | 12.3 | |
| TM1535 | Octaprenyl pyrophosphate synthase (OPP) | 2.0 | 7.6 | |
| TM1536 | Putative membrane protein | 2.0 | 8.5 | |
| Nicotinate synthesisb | TM1643 | Aspartate dehydrogenase | 27.9 | 16.3 |
| TM1644 | Quinolinate synthetase A (NadA) | 7.1 | 11.9 | |
| TM1645 | Nicotinate-nucleotide pyrophosphorylase (NadC) | 8.1 | 9.1 | |
| Maltose utilization and transportb | TM1834 | α-glucosidase | −1.5 | 5.1 |
| TM1835 | Cyclomaltodextrinase | −2.0 | 9.6 | |
| TM1836 | Maltose ABC transporter, permease protein | −2.2 | 2.0 | |
| TM1837 | Maltose transport system permease protein | −1.9 | 8.1 | |
| TM1838 | Hypothetical protein | −1.4 | 5.7 | |
| TM1839 | Maltose ABC transporter, periplasmic maltose-binding protein | 1.0 | 0.4 |
a
Complete operon predicted by www.tigr.org. Partial operon predicted by www.tigr.org. Note that some −log10 P values are below the significance criterion Bonferroni factor of 4.6.