Table 2.
The ca. 200 identified genes required for methane formation and energy conservation in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. The number of CDS that remain to be identified are given in parentheses. For functions, see Figure 2. H4MPT, tetrahydromethanopterin; MFR, methanofuran.
| Proteins | Genes in M. marburgensis | Genes in M. thermautotrophicus | |||
|---|---|---|---|---|---|
| (MTBMA_c) | Number of CDS | (MTH) | |||
| H2 activation | |||||
|
| |||||
| MvhADG: F420-non reducing [NiFe]-hydrogenase associated with | 15190–15160 (mvhDGAB) (MvhB is a polyferredoxin) | 4 | 1136–1133 | ||
| HdrABC: heterodisulfide reductase | 17680, 04500, 04490 | 3 | 1381, 1879, 1878 | ||
| FrhABG: F420-reducing [NiFe]-hydrogenase; synthesis regulated by nickel | 16860–16830 (frhADGB) (FrhD is an endopeptidase) | 5 | 1300–1297 | ||
| Hmd: [Fe]-hydrogenase (H2-forming methylene-H4MPT dehydrogenase); synthesis regulated by nickel | 15260 | 1 | 1142 | ||
| EhaA-T: Energy-converting [NiFe]-hydrogenase; membrane-associated; Na+-dependent; mainly anabolic function | 07840–08030 | 20 | 384–404 (EhaP twice) |
||
| EhbA-Q: Energy-converting [NiFe]-hydrogenase; membrane-associated; Na+-dependent; mainly anabolic function | 16230–16390 | 17 | 1251–1235 | ||
| Nickel-responsive transcriptional regulator NikR | 07330, 09830, 11340 | 3 | 603, 739 | ||
|
| |||||
| CO2 reduction to methane | |||||
|
| |||||
| FwdA-DFGH: Tungsten-dependent formyl-MFR dehydrogenase; formed constitutively | 01390–01450 (fwdHFGDACB) | 7 | 1553–1559 | ||
| FwdA/FmdBCE: Molybdenum-dependent formyl-MFR dehydrogenase; formed only in the presence of molybdate, involving DNA-binding protein Tfx | 13050–13070 (fmdECB) | 3 | 917–919 | ||
| 13040 | 1 | 916 | |||
| Ftr: Formylmethanofuran: H4MPT formyltransferase | 16460 | 1 | 403 | ||
| Mch: Methenyl-H4MPT cyclohydrolase | 11690 | 1 | 773 | ||
| Mtd: F420-dependent methylene-H4MPT dehydrogenase; synthesis regulated by nickel | 00500 | 1 | 1464 | ||
| Mer: F420-dependent methylene-H4MPT reductase | 03270 | 1 | 1752 | ||
| MtrA-H: Methyl-H4MPT:coenzyme M methyltransferase; membrane-associated; Na+-dependent | 15400–15470 (mtrHGFABCDE) | 7 | 1156–1163 | ||
| McrABG: Methyl-coenzyme M reductase isoenzyme I; contains 5 posttranslational modifications | 15480–15520 (mcrAGCDB) | 5 | 1164–1168 | ||
| (McrCD of unknown function) | (5) | ||||
| MrtABG: Methyl-coenzyme M reductase isoenzyme II; contains 5 posttranslational modifications | 15120–15150 (mrtAGDB) | 4 | 1129–1132 | ||
| (MrtD of unknown function) | |||||
| AtwA: Mcr/Mrt-activating enzyme A2 | 13970, 06010 | 2 | 151, 454, 1015 | ||
| Putative transcriptional regulator of the mcr operon | 05760 | 1 | 126 | ||
|
| |||||
| Electron transport | |||||
|
| |||||
| 6[4Fe4S] polyferredoxin (EhaP); | See above | See above | |||
| 8[4Fe4S] polyferredoxin (FwdF); | |||||
| 10[4Fe4S] polyferredoxin (EhaQ); | |||||
| 12[4Fe4S] polyferredoxin (MvhB); | |||||
| 14[4Fe4S] polyferredoxin (EhbK) | |||||
| 2[4Fe4S] ferredoxins | 00530, 03900, 07270, 14890 | 4 | 1468, 1819, 278, 1106 | ||
| 6[4Fe4S] polyferredoxin | 08040 | 1 | 405 | ||
| 8[4Fe4S] polyferredoxin | 17360 | 1 | 1345 | ||
|
| |||||
| ADP phosphorylation via the Na+-motive force (generated in the MtrA-H-catalyzed reaction; see above) | |||||
|
| |||||
| AhaA-IK: A1A0 ATP synthase complex; membrane-associated; Na+-dependent? | 13380–13470 (ahaGDBAFCEKIH) | 10 | 952–961 | ||
| NhaA: Sodium ion/proton antiporter; pH regulation | 11540 | 1 | 760 | ||
|
| |||||
| Synthesis of prosthetic groups of methanogenic enzymes | |||||
|
| |||||
| [NiFe] center of the [NiFe]-hydrogenases | 9 | ||||
| CarAB: Carbamoyl-phosphate synthase | 13790–13800 | 996–998 (996+997 = CarB) | |||
| HypA-F: Hydrogenase maturation factors | 11790, 11780, 02320, 14600,06550 or 01080, 16720 | 783, 782, 1649, 1072, 205 or 1525, 1287 | |||
| FrhD and HycI: endopeptidases | See above and 11320 | See above and 737 | |||
| FeGP cofactor of Hmd | 8 | ||||
| HcgA-G: Hmd co-occurring proteins | 15270–15320, 15200 (hcgABCFED,G) | 1143–1148, 1137 | |||
| HmdII and HmdIII | 00970, 08950 | 1512, 504 | |||
| FeS-centers of hydrogenases, Fmd, Fwd, Hdr and ferredoxins | 3 | ||||
| IscS/SufS: Cysteine desulfurase | 17750 | 1389 | |||
| SufB/D and SufC | 15340, 15330 | 1150, 1149 | |||
| ApbC: Putative iron-sulfur cluster transfer protein | Not found | 1176 | |||
| Molybdopterin cofactor of formyl-MFR dehydrogenase | 10 | ||||
| MoaABCE | 01360, 04310, 12050, 05990 | 1550, 1861, 809, 149 | |||
| MoeAB | 13850 or 17560, 01580 | 1003 or 1369, 1571 | |||
| MobAB | 05930 or 09160, 01370 | 143 or 528, 1551 | |||
| B12 cofactor of methyltransferase MtrA-H | 4 | ||||
| HemA: Glutamyl-tRNA reductase | 13940 | 1012 | |||
| HemB: δ-Aminolevulinic acid dehydratase | 11390 | 744 | |||
| HemC: Porphobilinogen deaminase | 12690 | 874 | |||
| HemD: Uroporphyrinogen-III synthase | 06170 | 166 | |||
| CysG1: Uroporphyrin-III C-methyltransferase (precorrin-2 synthesis) | 06180 | 1 | 167 | ||
| CbiX: Sirohydrochlorin cobalt chelatase | 17830 | 14 | 1397 | ||
| CbiL: Precorrin-2 C(20)-methyltransferase | 17380 | 1348 | |||
| CbiH: Precorrin-3B C17 methylase | 17900 | 1403 | |||
| CbiG: Cobalamin biosynthesis protein | 17950 | 1408 | |||
| CbiF: Precorrin-4 methylase | 09820 | 602 | |||
| CbiD: Precorrin-6A synthase | 12040 | 808 | |||
| CbiE: Precorrin-6Y methylase | 00990 | 1514 | |||
| CbiJ: Precorrin-6X reductase | 13840 | 1002 | |||
| CbiT: Cobalt-precorrin-6Y C(15)-methyltransferase | 05960 | 146 | |||
| CbiC: Precorrin-8X methylmutase | 06760 | 227 | |||
| CbiA: Cobyrinic acid a,c-diamide synthase | 00460 | 1460 | |||
| CobS: Cobalamin-5-phosphate synthase | 14960 | 1112 | |||
| CbiB: Cobalamin biosynthesis protein | 17960 | 1409 | |||
| CobN: Cobalamin biosynthesis protein | 06860 or 09040 or 17530 | 237 or 514 or 1363 | |||
| F430 cofactor of methyl-coenzyme reductases Biosynthesis starts from uroporphyrinogen-III, probably 7 reactions are involved | ? | (7) | ? | ||
|
| |||||
| Coenzyme biosynthesis | |||||
|
| |||||
| Coenzyme F420 | 6 | ||||
| CofA: Lactaldehyde dehydrogenase | 13630 | 978 | |||
| CofB: l-Lactate kinase | ? | (1) | ? | ||
| CofC: 2-phospho-l-lactate guanylyltransferase | 09930 | 613 | |||
| CofD: LPPG:FO 2-phospho-l-lactate transferase | 14000 | 1018 | |||
| CofE: F420-0: γ-glutamyl ligase | 14010 | 1019 | |||
| CofGH: FO synthase | 15760,12170 | 1198, 820 | |||
| Methanofuran | 1 | ||||
| MfnA: l-Tyrosine decarboxylase | 15000 | 1116 | |||
| and estimated 7 unknown proteins | ? | (7) | ? | ||
| Methanopterin | 3 | ||||
| MptA: GTP cyclohydrolase | 15740 | 1196 | |||
| MptB: Cyclic phosphodiesterase | 02460 | 1668 | |||
| RFAP: Ribofuranosylaminobenzene 5′-P-synthase | 12280 | 830 | |||
| and estimated 7 unknown proteins | ? | (7) | ? | ||
| Coenzyme M | 5 | ||||
| ComA: Phosphosulfolactate synthase | 02530 | 1674 | |||
| ComB: 2-Phosphosulfolactate phosphatase | 15590 | 1182 | |||
| ComC: Sulfolactate dehydrogenase | 15830 | 1205 | |||
| ComDE: Sulfopyruvate decarboxylase | 15840,15850 | 1206, 1207 | |||
| ComF: Sulfoacetaldehyde dehydrogenase | ? | (1) | ? | ||
| Coenzyme B | 4 | ||||
| LeuA homolog: Isopropylmalate synthase | 00630 or 02150 | 1481 or 1630 | |||
| LeuB homolog: Isopropylmalate dehydrogenase | 17740 or 06370 | 1388 or 184 | |||
| LeuCD homolog: Isopropylmalate isomerase | 02160 or 17720, 12270 or 17730 | 1386 or 1631, 829 or 1387 | |||
| and estimated 2 unknown proteins | ? | (2) | ? | ||
|
| |||||
| Ion transport systems | |||||
|
| |||||
| Ni2+ ABC transporter NikMNOQ (=CbiM1N1O1Q1) | 02830–02860 | 4 | 1704–1707 | ||
| Co2+ ABC transporter CbiM2N2O2Q2 | 05800–05830 | 4 | 130–133 | ||
| Fe2+ ABC transporter FeoAB | 17520, 17510 | 2 | 1362, 1361 | ||
| Zn2+ ABC transporter ZnuABC/ZupT | 09840–09860, 08660 | 4 | 604–606, 473 | ||
| Mg2+ transporter MgtE | 10010 | 1 | 620 | ||
| Ca2+ transporter (ATPase) | 13830 | 1 | 1001 | ||
| K+ transporter TrkAH | 16520, 16510 | 2 | 1265, 1264 | ||
| MoO4 2− ABC transporter ModA1B1C1 | 13080, 13090, 13110 | 3 | 920, 921, 924 | ||
| WO4 2− ABC transporter ModA2B2C2 | 08720–08740 | 3 | 477–479 | ||
| HPO4
2− ABC transport system PstABCS1S2/PhoU1U2 Putative transcriptional regulator of the pst/phu operon |
03020–03070, 03090 03000 |
8 | 1727–1732, 1734 1724 |
||