TABLE 1.
T. maritima ORFs differentially regulated in biofilma
| Gene description | Source of gene description (reference) | Gene ID | Fold change | −Log10P value |
|---|---|---|---|---|
| Upregulated in biofilmb | ||||
| Aspartate dehydrogenase | (124) | TM1643 | 27.9 | 16.3 |
| ThiH protein, putative | 28% identity, 347 aa with E. coli ThiH (53, 104) conserved CX3CX2C [4Fe-4S] cluster binding motif | TM1267 | 8.9 | 15.4 |
| Nicotinate-nucleotide pyrophosphorylase (NadC) | Crystallized (GI:34811257; 1O4U_A, 1O4U_B) | TM1645 | 8.1 | 9.1 |
| Hypothetical protein | (65) | TM1266 | 7.2 | 10.0 |
| Quinolinate synthetase A (NadA) | 54% identity, 298 aa with P. abyssi (PAB2345) and P. horikoshii (PH0013), 3 conserved cysteines | TM1644 | 7.1 | 11.9 |
| Cellobiose phosphorylase | (79) | TM1848 | 6.9 | 12.9 |
| Cation-transporting ATPase, P-type | COG2217, 30% identity, 724 aa with E. coli ZntA (93) | TM0317 | 6.6 | 14.1 |
| SufD homolog, similar to ABC permease components | COG0719 | TM1370 | 6.3 | 12.0 |
| SufB homolog, similar to ABC ATP-binding components | (80) | TM1369 | 6.3 | 15.0 |
| Iron(II) transport protein B (FeoB) | 33% identity, 718 aa with E. coli FeoB (43, 60) | TM0051 | 5.4 | 12.4 |
| l-Lactate dehydrogenase | (72) | TM1867 | 5.1 | 11.0 |
| Ubiquinone/menaquinone methyltransferase | COG0500, SAM-dependent methyltransferases, 53% identity, 452 aa with PF0738 | TM0318 | 5.0 | 11.4 |
| Biotin synthetase, putative (BioB homolog) | 22% identity, 281 aa with E. coli BioB (108) conserved CX3CX2C motif, CX2C motif | TM1269 | 5.0 | 8.6 |
| IscS/SufS homolog, cysteine desulfurase | (59) | TM1371 | 4.8 | 13.9 |
| Sms/RadA homolog, DNA recombination/repair protein | 39% identity, 452 aa with E. coli Sms/RadA (6), conserved CX2CX10CX2C motif is a zinc finger in E. coli Sms/RadA | TM0199 | 4.6 | 12.4 |
| FTR1, predicted high-affinity Fe2+/Pb2+ permease | 25% identity 228 aa with S. cerevisiae Ftr1p; two conserved REXXE iron-binding motifs (95) | TM0417 | 4.4 | 8.5 |
| Esterase, putative | (65) | TM0053 | 4.1 | 8.8 |
| Iron(II) transport protein A (FeoA) | 42% identity 57 aa with E. coli FeoA (43) | TM0050 | 4.0 | 12.2 |
| Cysteine synthase (CysK) | Crystal structure (GI:34810052, IO58A-IO8D) | TM0665 | 3.9 | 12.0 |
| Serine acetyltransferase (CysE) | 43% identity, 195 aa with S. xylosus CysE (26) | TM0666 | 3.9 | 9.3 |
| FpaA family protein, contains flavodoxin domain and β-metallo-lactamase domain | COG0426, 28% identity, 366 aa with D. gigas ROO (27) | TM0755 | 3.8 | 8.5 |
| Hypothetical protein | (65), 32% identity, 78 aa with TTE1569 | TM1268 | 3.7 | 6.6 |
| Uncharacterized homolog of γ-carboxymuconolactone decarboxylase | COG0599 | TM0316 | 3.6 | 9.1 |
| NADH oxidase | 46% identity, 440 aa with T. neapolitana NADH: polysulfide oxidoreductase | TM0395 | 3.5 | 9.0 |
| Ubiquinone/menaquinone biosynthesis methyltransferase, putative (UbiE homolog) | COG2226 | TM0753 | 3.3 | 10.1 |
| HycB domain containing protein, related to hydrogenase components | COG1142, 2 CX2CX2CX3C motifs, 1 CX2CX7CX2C motif, 1 CX2CX4CX3C motif | TM0396 | 3.2 | 10.8 |
| Heavy metal binding protein | (65) | TM0320 | 3.2 | 9.2 |
| Uncharacterized conserved protein | COG3862, CX2CX3C motif | TM1434 | 3.2 | 8.5 |
| Predicted zinc-dependent protease | COG2738 | TM1511 | 3.1 | 11.0 |
| NAD+-dependent α-glucuronidase | (99) | TM0752 | 3.1 | 7.9 |
| Protein containing Bcp domain and nitroreductase domain | COG1225 (Bcp domain), COG0778 (nitroreductase domain) | TM0386 | 3.0 | 3.1 |
| Hypothetical protein | (65) | TM0338 | 3.0 | 7.9 |
| Hypothetical protein | (65) | TM0052 | 3.0 | 10.1 |
| Predicted GTPase | COG1160 | TM0445 | 2.9 | 10.8 |
| β-d-Galactosidase | 40% identity, 670 aa with B. stearothermophilus β-galactosidase (36) | TM0310 | 2.9 | 9.5 |
| IscU/SufA homolog, iron-sulfur cluster assembly scaffold | 3 conserved cysteines bind a [2Fe-2S] cluster (8, 58) | TM1372 | 2.9 | 5.9 |
| Uncharacterized conserved protein | COG0011, pfam01910, localized with TauABC (4 species) | TM0486 | 2.9 | 9.4 |
| ABC transporter, permease protein, TauC family | COG0600 | TM0485 | 2.9 | 11.1 |
| ATP-dependent Clp protease, ATPase subunit, ClpA homolog | COG0542 | TM0198 | 2.8 | 9.2 |
| Glutamate synthase domain 3 (GltB) | COG0070 | TM0394 | 2.8 | 6.5 |
| Possible endonuclease or sugar phosphate isomerase | COG1082, pfam01261 | TM0422 | 2.8 | 6.3 |
| Hypothetical protein | (65) | TM0054 | 2.8 | 10.2 |
| Predicted membrane protein | COG3462 | TM0315 | 2.8 | 12.2 |
| Uncharacterized conserved protein | COG0718 | TM0687 | 2.8 | 7.9 |
| Cystathionine γ-synthase/β-lyase | COG0626 | TM1270 | 2.7 | 9.3 |
| Predicted transcriptional regulator, ACR/TetR related | pfam00440 | TM0823 | 2.7 | 9.2 |
| Sugar ABC transporter, permease protein, UpgA family | COG1175 | TM0419 | 2.7 | 11.0 |
| Sugar ABC transporter, periplasmic sugar-binding protein, MalE-related | COG2182 | TM0418 | 2.7 | 6.9 |
| ABC transporter, ATP-binding subunit, TauA family | COG0715 | TM0484 | 2.6 | 5.9 |
| Hypothetical protein | (65) | TM0714 | 2.6 | 9.2 |
| Thioredoxin peroxidase | COG1225, 59% identity, 157 aa with T. acidophilum (Tal1368M) | TM0780 | 2.6 | 12.8 |
| Hypothetical protein | (65) | TM0319 | 2.6 | 6.6 |
| Predicted HHH nucleic acid binding protein | COG1623, pfam02457 | TM0200 | 2.6 | 5.7 |
| Glycerol uptake facilitator protein | COG0580 | TM1429 | 2.5 | 7.6 |
| FixX homolog, putative ferredoxin | COG2440, CX3CX4CX3CC motif, CX2CX2CX3C motif | TM1533 | 2.5 | 5.3 |
| FixC homolog | 42% identity, 438 aa with A. caulinodans FixC (4) | TM1532 | 2.5 | 7.9 |
| PotD, spermidine/putrescine ABC transporter, PBP | 39% identity, 320 aa with E. coli potD (45) | TM1375 | 2.5 | 2.6 |
| Transcriptional regulator, biotin repressor family | Crystallized (GI:22218828, 1J5YA) | TM1602 | 2.4 | 9.7 |
| Predicted CAAX amino-terminal protease | pfam0257 | TM1529 | 2.4 | 10.0 |
| RAD55-related, RecA superfamily ATPase | COG0467, 78% identity, 235 aa with PH0824, PAB2180, PH1931 | TM0370 | 2.4 | 7.4 |
| Pyridine nucleotide-disulfide oxidoreductase, putative | pfam00070 | TM0754 | 2.4 | 5.9 |
| Oxidoreductase, aldo/keto reductase family | COG0467 | TM1743 | 2.4 | 7.2 |
| NADH:polysulfide oxidoreductase | 86% identity, 440 aa with T. neapolitana (GI:21702687) | TM0379 | 2.3 | 8.5 |
| Hypothetical protein | (65) | TM0002 | 2.3 | 9.4 |
| Heat shock operon repressor HrcA | (65, 78) | TM0851 | 2.3 | 7.3 |
| Conserved hypothetical protein, GGDEF domain | COG2199, pfam00990 | TM1588 | 2.3 | 7.5 |
| Glutamate synthase domain 2, GltB | COG0069, pfam01645, CX2CX2C motif | TM0397 | 2.3 | 7.9 |
| UDP-sugar disphosphatase precursor | 38% identity, 504 aa with E. coli UshA (11) | TM1878 | 2.3 | 7.9 |
| Putative endonuclease | COG1833, pfam01986 | TM0664 | 2.3 | 10.5 |
| Uncharacterized conserved protein | COG4198, pfam06245 | TM1510 | 2.3 | 6.1 |
| Membrane bound protein LytR, putative transcriptional regulator | COG1316, pfam03816 | TM1866 | 2.3 | 9.8 |
| FixA homolog, electron transfer flavoprotein | 45% identity, 241 aa with A. caulinodans FixA (4) | TM1530 | 2.3 | 1.9 |
| Sugar ABC transporter, ATP-binding protein, MalK homolog | COG3839 | TM0421 | 2.3 | 11.3 |
| Heat shock protein, class I | (62) | TM0374 | 2.3 | 8.5 |
| Conserved hypothetical protein | (65) | TM0387 | 2.3 | 7.8 |
| Predicted coenzyme A-binding protein | COG1832 | TM1435 | 2.2 | 7.3 |
| Conserved hypothetical protein | pfam03706 | TM1390 | 2.2 | 10.2 |
| Hypothetical protein | (65) | TM1534 | 2.2 | 12.3 |
| Frameshift | (65) | TM0621 | 2.2 | 5.2 |
| Glutamate synthase domain 1, GltB | COG0067 | TM0398 | 2.2 | 5.2 |
| Putative sensor histidine kinase | (65) | TM0187 | 2.2 | 5.3 |
| Conserved hypothetical protein | pfam01139 | TM1357 | 2.1 | 8.8 |
| ABC transporter, ATP-binding subunit, SalX domain | COG1136 | TM0352 | 2.1 | 9.2 |
| Endoglucanase (extracellular) | (15, 57) | TM1525 | 2.1 | 8.6 |
| Iron(III) ABC transporter, ATP-binding protein, putative | COG1120, 50% identity, 242 aa with P. furiosis (PF0909) | TM0191 | 2.1 | 7.3 |
| Putative transcriptional regulator | COG1318, 58% identity, 150 aa with P. horikoshii (PH0283) | TM0369 | 2.1 | 8.0 |
| Iron-sulfur cluster-binding protein, putative | COG2768, 2 CX2CX2CX3C motifs (65) | TM0034 | 2.1 | 6.0 |
| Heat shock serine protease, periplasmic | (46, 47) | TM0571 | 2.1 | 9.3 |
| Hypothetical protein | (65) | TM0003 | 2.0 | 8.7 |
| Permease, putative | COG0477, 36% identity, 409 aa with B. subtilis YceI (50) | TM1603 | 2.0 | 7.7 |
| Octaprenyl pyrophosphate synthase | (32, 51) | TM1535 | 2.0 | 7.6 |
| Membrane protein, putative | COG3374 | TM1536 | 2.0 | 8.5 |
| ABC transporter, ATP-binding protein, TauB family | COG1116 | TM0483 | 2.0 | 10.2 |
| RNA polymerase σA factor | (13, 65) | TM1451 | 2.0 | 10.9 |
| Putative Holliday junction resolvase | COG0816 | TM1545 | 2.0 | 10.9 |
| ABC transporter, permease subunit, SalY family | COG0577 | TM0351 | 2.0 | 8.9 |
| Down-regulated in biofilmc | ||||
| K+ channel, beta subunit | COG0667, pfam00248 | TM0313 | −2.0 | 9.3 |
| Cyclomaltodextrinase | (54) | TM1835 | −2.0 | 9.6 |
| Putative regulator, XRE family HTH | COG1917, pfam1381 | TM0656 | −2.0 | 6.7 |
| Hypothetical protein | (65) | TM0794 | −2.1 | 6.9 |
| Predicted dehydrogenase | COG0673, 67% identity, 325 aa with P. furiosus (PF0554) | TM0312 | −2.1 | 5.6 |
| (3R)-Hydroxymyristoyl-(acyl carrier protein) dehydratase | COG0764 (65) | TM0801 | −2.1 | 10.1 |
| Uncharacterized conserved protein | COG3906 | TM0606 | −2.1 | 8.5 |
| Bacteriocin | 33% identity, 251 aa to B. linens linocin M18 (109) | TM0785 | −2.2 | 11.4 |
| Maltose ABC transporter, permease protein | (118) | TM1836 | −2.2 | 2.0 |
| Predicted glycosyltransferase | COG0438, pfam00534 | TM0392 | −2.2 | 7.3 |
| Hypothetical protein | (65) | TM1241 | −2.4 | 7.4 |
| Uncharacterized conserved protein | COG3471 | TM0786 | −2.4 | 6.0 |
| Ribosomal protein L7/L12 | (65) | TM0457 | −2.5 | 9.3 |
| Ribosomal protein L10 | (65) | TM0456 | −2.6 | 9.0 |
| Cold shock protein | (76, 120) | TM1874 | −2.8 | 9.6 |
| Rubredoxin | 68% identity, 51 aa with P. furiosis rubredoxin PF1282 (9, 21), 2 conserved CXXC motifs | TM0659 | −3.1 | 9.9 |
| Superoxide reductase (neelaredoxin) | 57% identity, 128 aa with P. furiosis SOR (PF1281) (38, 125) | TM0658 | −3.5 | 11.4 |
| Rubrerythrin | 58% identity, I65 aa with A. fulgidus rubrerythrin (AF1640) (115) | TM0657 | −3.7 | 7.8 |
| NADPH-dependent alkyl hydroperoxide reductase | 69% identity, 214 aa with P. horikoshii (PH1217) (44) | TM0807 | −6.0 | 9.4 |
| Protein distantly related to bacterial ferritins | COG2406, 82% identity, 183 aa with M. acetivorans strain CZA (MA2882) | TM0560 | −11.6 | 14.5 |
a
Locus description based on conserved domain searches (CDD, NCBI) and similarity to characterized proteins. Species used: Archaeoglobus fulgidus, Azorhizobium caulinodans, Brevibacterium linens, Bacillus stearothermophilus, Bacillus subtilis, Desulfovibrio gigas, Escherichia coli K-12, Methanosarcina acetivorans strain C2A, Pyrococcus furiosus, Pyrococcus horikoshii, Pyrococcus abyssi, Thermoplasma acidophilum, Thermotoga neapolitana, Saccharomyces cerevisiae, and Staphylococcus xylosus. Bcp, bacterioferritin comigratory protein.
b
Genes up-regulated 2.0-fold or greater in biofilm. Significance based on Bonferroni-corrected significance criterion with −log10 P value of >4.6.
c
Genes down-regulated 2.0-fold or greater in biofilm. Significance based on Bonferroni-corrected significance criterion with −log10 P value of >4.6.