Table 2.
Gene expression profile in methane-grown cells of M. trichosporium OB3b.
| Gene ID | Predicted function | Gene | Replicate 1 | Replicate 2 |
|---|---|---|---|---|
| METHANE AND METHANOL OXIDATION | ||||
| METTOv1_1270003 | Particulate methane monooxygenase subunit C | pmoC | 123026 | 127241 |
| METTOv1_1270002 | Particulate methane monooxygenase subunit A | pmoA | 37102 | 31813 |
| METTOv1_1270001 | Particulate methane monooxygenase subunit B | pmoB | 27371 | 22917 |
| METTOv1_310040 | Particulate methane monooxygenase subunit C2 | pmoC2 | 532 | 492 |
| METTOv1_50081 | Soluble methane monooxygenase alpha subunit | mmoX | 9 | 8 |
| METTOv1_50082 | Soluble methane monooxygenase beta subunit | mmoY | 13 | 9 |
| METTOv1_50084 | Soluble methane monooxygenase gamma subunit | mmoZ | 20 | 19 |
| METTOv1_240014 | PQQ-dependent methanol dehydrogenase | mxaF | 15313 | 13760 |
| METTOv1_240011 | PQQ-dependent methanol dehydrogenase | mxaI | 24552 | 28474 |
| METTOv1_240012 | Cytochrome c class I | mxaG | 5712 | 6117 |
| METTOv1_240013 | Extracellular solute-binding protein family 3 | mxaJ | 1942 | 1838 |
| METTOv1_240001 | Putative methanol utilization control sensor protein | mxaY | 36 | 41 |
| METTOv1_240002 | Putative two-component response regulator | mxaB | 303 | 317 |
| METTOv1_240003 | MxaH protein, involved in methanol oxidation | mxaH | 399 | 391 |
| METTOv1_240004 | MxaD protein, involved in methanol oxidation | mxaD | 1137 | 1077 |
| METTOv1_240005 | von Willebrand factor type A, involved in methanol oxidation | mxaL | 191 | 201 |
| METTOv1_240006 | Protein of unknown function, involved in methanol oxidation | mxaK | 124 | 132 |
| METTOv1_240007 | von Willebrand factor type A, involved in methanol oxidation | mxaC | 144 | 141 |
| METTOv1_240008 | MxaA protein, involved in methanol oxidation | mxaA | 137 | 127 |
| METTOv1_240009 | MxaS protein, involved in methanol oxidation | mxaS | 202 | 167 |
| METTOv1_240010 | ATPase, involved in methanol oxidation | mxaR | 563 | 538 |
| METTOv1_110056 | Coenzyme PQQ biosynthesis protein A | pqqA | 11857 | 13927 |
| METTOv1_160001 | Coenzyme PQQ biosynthesis protein E | pqqE | 166 | 161 |
| METTOv1_160002 | Coenzyme PQQ biosynthesis protein PqqC/D | pqqC/D | 372 | 344 |
| METTOv1_160003 | Coenzyme PQQ biosynthesis protein B | pqqB | 306 | 313 |
| METTOv1_20046 | Coenzyme PQQ biosynthesis protein F | pqqF | 183 | 185 |
| METTOv1_20047 | Coenzyme PQQ biosynthesis protein G | pqqG | 157 | 142 |
| METTOv1_610028 | Aldehyde dehydrogenase | aldh | 37 | 37 |
| METTOv1_290006 | Aldehyde oxidase | aor | 45 | 38 |
| METTOv1_100046 | Aldehyde dehydrogenase | aldh-F7 | 7 | 9 |
| FORMALDEHYDE OXIDATION | ||||
| METTOv1_40010 | Methenyltetrahydromethanopterin cyclohydrolase | mch | 393 | 312 |
| METTOv1_40011 | Tetrahydromethanopterin-linked C1 transfer pathway protein. Orf5 | orf5 | 128 | 111 |
| METTOv1_40012 | Tetrahydromethanopterin-linked C1 transfer pathway protein, Orf7 | orf7 | 73 | 72 |
| METTOv1_40013 | Formaldehyde activating enzyme | fae1 | 24353 | 24787 |
| METTOv1_40014 | Formaldehyde activating enzyme | fae1-2 | 4024 | 3676 |
| METTOv1_840013 | Formaldehyde activating enzyme homolog | fae2 | 535 | 581 |
| METTOv1_40015 | Tetrahydromethanopterin-linked C1 transfer pathway protein | orf17 | 38 | 45 |
| METTOv1_110058 | Tetrahydromethanopterin formyltransferase, subunit C | fhcC | 535 | 453 |
| METTOv1_110059 | Tetrahydromethanopterin formyltransferase, subunit D | fhcD | 496 | 470 |
| METTOv1_110060 | Tetrahydromethanopterin formyltransferase, subunit A | fhcA | 591 | 546 |
| METTOv1_110061 | Tetrahydromethanopterin formyltransferase, subunit B | fhcB | 620 | 570 |
| METTOv1_560001 | Tetrahydromethanopterin -linked C1 transfer pathway protein | orf9 | 172 | 167 |
| METTOv1_560002 | Methylenetetrahydrofolate dehydrogenase (NAD) | mtdB | 688 | 607 |
| METTOv1_440045 | Ribofuranosylaminobenzene 5′-phosphate synthase | mptG | 94 | 80 |
| FORMATE OXIDATION | ||||
| METTOv1_630016 | Transcriptional regulator, LysR family | fdsR | 52 | 39 |
| METTOv1_630017 | NAD-linked formate dehydrogenase, subunit G | fdsG | 672 | 608 |
| METTOv1_630018 | NAD-linked formate dehydrogenase, subunit B | fdsB | 585 | 531 |
| METTOv1_630019 | NAD-linked formate dehydrogenase, subunit A | fdsA | 593 | 554 |
| METTOv1_370001 | Formate dehydrogenase family accessory protein | fdsC | 210 | 199 |
| METTOv1_370002 | NAD-linked formate dehydrogenase, subunit D | fdsD | 368 | 312 |
| METTOv1_220028 | NAD-linked formate dehydrogenase, subunit A | fdhA2 | 9 | 7 |
| C1-ASSIMILATION:SERINE CYCLE | ||||
| METTOv1_130002 | Phosphoenolpyruvate carboxylase | ppc2 | 104 | 89 |
| METTOv1_400011 | Glycerate kinase | gckA | 229 | 211 |
| METTOv1_400012 | Conserved protein of unknown function | orf1 | 626 | 708 |
| METTOv1_400013 | Malyl-CoA lyase/beta-methylmalyl-CoA lyase | mclA | 1713 | 1615 |
| METTOv1_400014 | Phosphoenolpyruvate carboxylase | ppc1 | 141 | 139 |
| METTOv1_400015 | Malate thiokinase, small subunit | mtkB | 516 | 485 |
| METTOv1_400016 | Malate thiokinase, large subunit | mtkA | 534 | 455 |
| METTOv1_400017 | Methenyltetrahydrofolate cyclohydrolase | fch | 355 | 281 |
| METTOv1_400018 | NADP-dependent methylenetetrahydrofolate dehydrogenase | mtdA | 281 | 243 |
| METTOv1_400019 | 2-Hydroxyacid dehydrogenase NAD-binding | hprA | 375 | 348 |
| METTOv1_400020 | Serine-glyoxylate transaminase | sga | 1840 | 1969 |
| METTOv1_400021 | Formate-tetrahydrofolate ligase | ftfL | 448 | 412 |
| METTOv1_670019 | Serine hydroxymethyltransferase | glyA | 1342 | 1197 |
| METTOv1_20135 | Enolase | eno | 432 | 408 |
| C1-ASSIMILATION:EMP PATHWAY AND PHB CYCLE | ||||
| METTOv1_100079 | Acetyl-CoA acetyltransferase | phaA | 597 | 561 |
| METTOv1_100080 | Acetoacetyl-CoA reductase | phaB | 1160 | 1060 |
| METTOv1_50006 | Crotonase | croR | 235 | 275 |
| METTOv1_110068 | Crotonyl-CoA reductase | ccr | 577 | 523 |
| METTOv1_60013 | Ethylmalonyl-CoA mutase | ecm | 187 | 162 |
| METTOv1_510010 | Methylsuccinyl-CoA dehydrogenase | ibd | 309 | 295 |
| METTOv1_110043 | Mesaconyl-CoA hydratase | meaC | 341 | 317 |
| METTOv1_30129 | Methylmalonyl-CoA epimerase | epm | 428 | 394 |
| METTOv1_220010 | Malyl-CoA lyase/beta-Methylmalyl-CoA lyase | mclA2 | 137 | 135 |
| METTOv1_200020 | Acetyl/propionyl-CoA carboxylase | ppcA | 353 | 310 |
| METTOv1_220035 | Propionyl-CoA carboxylase | ppcB | 472 | 455 |
| METTOv1_50067 | Methylmalonyl-CoA mutase, large subunit | mcmA | 201 | 188 |
| METTOv1_10062 | Methylmalonyl-CoA mutase small subunit B | mcmB | 144 | 144 |
| METTOv1_270063 | 3-Hydroxybutyrate dehydrogenase | bdhA | 235 | 232 |
| METTOv1_130047 | Poly-beta-hydroxybutyrate polymerase | phaC | 30 | 30 |
| METTOv1_200042 | Acetoacetate decarboxylase | aad | 123 | 114 |
| METTOv1_200022 | Acetoacetyl-coenzyme A synthetase | aas | 116 | 114 |
| METTOv1_630008 | Polyhydroxyalkanoate depolymerase | phaZ | 237 | 263 |
| C1-ASSIMILATION: TCA CYCLE | ||||
| METTOv1_360040 | Malate dehydrogenase | mdh | 539 | 473 |
| METTOv1_360041 | Succinyl-CoA synthetase, beta subunit | sucC | 660 | 631 |
| METTOv1_510003 | Succinyl-CoA synthetase, alpha subunit | sucD | 1198 | 1135 |
| METTOv1_510002 | 2-Oxoglutarate dehydrogenase E1 | sucA | 236 | 237 |
| METTOv1_370050 | 2-Oxoglutarate dehydrogenase E2 | sucB | 191 | 181 |
| METTOv1_80046 | Succinate:ubiquinone oxidoreductase | sdhB | 327 | 348 |
| METTOv1_80046 | Succinate:ubiquinone oxidoreductase | sdhA | 311 | 299 |
| METTOv1_80051 | Succinate:ubiquinone oxidoreductase, cytochrome b556 subunit | sdhC | 318 | 329 |
| METTOv1_40061 | Fumarate hydratase | fum | 196 | 185 |
| METTOv1_1080004 | 2-Oxoacid ferredoxin oxidoreductase | ofr | 79 | 77 |
| INTERMEDIARY METABOLISM AND ANAPLEROTIC CO2-FIXATION | ||||
| METTOv1_70038 | Phosphoenolpyruvate synthase | pps | 28 | 26 |
| METTOv1_120036 | Pyruvate carboxylase | pcx | 145 | 140 |
| METTOv1_830002 | Acetyl-coenzyme A carboxylase subunit beta | accD | 246 | 228 |
| METTOv1_380021 | Acetyl-CoA carboxylase subunit alpha | accA | 211 | 204 |
| METTOv1_130018 | Acetyl-CoA carboxylase, biotin carboxyl carrier protein | accB | 307 | 276 |
| METTOv1_150014 | Pyruvate kinase | pyk1 | 245 | 224 |
| METTOv1_340039 | Pyruvate dehydrogenase (acetyl-transferring) E1 | pdhA | 181 | 175 |
| METTOv1_340041 | Pyruvate dehydrogenase subunit beta | pdhB | 160 | 158 |
| METTOv1_340042 | Pyruvate dehydrogenase | pdhC | 101 | 106 |
| METTOv1_350050 | Pyruvate phosphate dikinase | pdk | 50 | 52 |
| METTOv1_80025 | Malic enzyme | mae | 107 | 106 |
| METTOv1_680013 | Phosphoglycerate mutase | gpmA | 136 | 135 |
| METTOv1_100061 | Phosphoglycerate mutase (modular protein) | pgm | 101 | 99 |
| METTOv1_10180 | Phosphoglycerate mutase (modular protein) | pgm | 72 | 65 |
| METTOv1_280049 | Phosphoglycerate kinase | pgk | 199 | 208 |
| METTOv1_280047 | Glyceraldehyde-3-phosphate dehydrogenase | gpd | 391 | 407 |
| METTOv1_620016 | Ribokinase | rik | 140 | 144 |
| METTOv1_620017 | Phosphoribulokinase | prk | 173 | 164 |
| METTOv1_620018 | Transketolase | tkl | 147 | 123 |
| METTOv1_620019 | Fructose-bisphosphate aldolase, class II | fba | 427 | 461 |
| METTOv1_220030 | 6-Phosphofructokinase | pfk | 243 | 239 |
| METTOv1_200031 | Fructose 1,6-bisphosphatase II | glp | 68 | 56 |
| METTOv1_550029 | Glucose-6-phosphate isomerase | pgi | 88 | 84 |
| METTOv1_620022 | Ribulose-phosphate 3-epimerase | rpe | 51 | 53 |
| NITROGEN, Cu, Fe METABOLISM | ||||
| METTOv1_310019 | Nitrate transporter component | nrtA | 151 | 154 |
| METTOv1_310020 | Nitrite reductase (NAD(P)H), large subunit | nasB | 1762 | 1562 |
| METTOv1_310021 | Nitrite reductase (NAD(P)H), small subunit | nasD | 726 | 610 |
| METTOv1_310022 | Nitrate reductase, large subunit | nasA | 646 | 597 |
| METTOv1_130049 | Ammonium transporter | amtB | 2029 | 1766 |
| METTOv1_300058 | Glutamate synthase large subunit (NADPH/GOGAT) | gltB | 199 | 183 |
| METTOv1_300033 | Glutamate synthase small subunit (NADPH/GOGAT) | gltD | 431 | 401 |
| METTOv1_190023 | Glutamate dehydrogenase | gdh | 2 | 2 |
| METTOv1_200046 | Glutamate-ammonia ligase | glnS | 1413 | 1375 |
| METTOv1_200047 | Nitrogen regulatory protein P-II | glnK | 2400 | 2277 |
| METTOv1_200048 | Glutamine synthetase, type I | glnA | 2452 | 2321 |
| METTOv1_280018 | Alanine dehydrogenase | aldA | 29 | 36 |
| METTOv1_80043 | Phosphoserine aminotransferase | serC | 415 | 364 |
| METTOv1_560023 | Cytochrome c′-alpha | cycA | 336 | 370 |
| METTOv1_230076 | Putative oxygenase | 6 | 8 | |
| METTOv1_230077 | Hydroxylamine reductase | hcp | 21 | 16 |
| METTOv1_230078 | Putative transcriptional regulator | nsrR | 38 | 35 |
| METTOv1_730005 | Putative FecR iron sensor protein | fecR | 48 | 58 |
| METTOv1_730006 | Putative TonB-dependent receptor protein | tonB | 382 | 383 |
| METTOv1_CDS4222756D | Methanobactin precursor | Mb | 1439 | 2177 |
| METTOv1_730007 | Putative lyase | 306 | 384 | |
| METTOv1_730008 | Conserved protein of unknown function | hp | 170 | 175 |
| METTOv1_730009 | Conserved protein of unknown function | hp | 116 | 143 |
| METTOv1_660011 | l-Ornithine 5-monooxygenase | pvdA1 | 1410 | 1450 |
| METTOv1_760004 | Putative hydroxy-l-ornithine formylase | pvdF | 2255 | 2676 |
| METTOv1_760006 | l-Ornithine 5-monooxygenase | pvdA2 | 979 | 1116 |
| METTOv1_760007 | Diaminobutyrate-2-oxoglutarate aminotransferase | pvdH | 720 | 770 |
| METTOv1_760008 | Sigma-24 (FecI-like) | pvdS | 1260 | 1522 |
| METTOv1_760009 | Putative pyoverdine ABC export system, permease | pvdE | 532 | 500 |
| METTOv1_760010 | TonB-dependent siderophore receptor | fpvA | 2197 | 2174 |
| METTOv1_760011 | FecR-like protein | fecR | 330 | 321 |
| METTOv1_760012 | FecI-family sigma factor | fecI | 922 | 951 |
| METTOv1_870003 | Ferribactin synthase | pvdL | 433 | 441 |
| METTOv1_870004 | Pyoverdine biosynthesis regulatory protein-TauD/TfdA family protein | 932 | 1039 | |
| METTOv1_870005 | Pyoverdine synthetase, thioesterase component | pvdG | 1542 | 1473 |
| METTOv1_870006 | Integral components of bacterial non-ribosomal peptide synthetases | MbtH | 4176 | 5481 |
| METTOv1_1220001 | Putative pyoverdine sidechain peptide synthetase IV, d-Asp-l-Ser component | pvdI/J | 480 | 564 |
| METTOv1_1220002 | Putative non-ribosomal peptide synthase | pvdJ/D | 379 | 396 |
Values represent reads per kilobase of coding sequence per million (reads) mapped (RPKM).