Table 6 Genes encoding putative hydrogenases, sensory
hydrogenases, and NADH:Fd oxidoreductases using ferredoxin, coenzyme F 420 , and NAD(P)H as electron carriers Organism Hydrogenase and NADH:Fd oxidoreductase classification and corresponding genes [NiFe] H2ase [FeFe] H2ase NFO Fd-dependent ech and mbh G4 F420-dependentG3and otherG1 Bifurcating SensoryA NAD(P)H-dependent Fd-dependent rnf-type Standard free energy (ΔG°’)* −3.0 11 +7.5** NA 18.1 18.1 −21.1*** Ca. bescii DSM 6725 Athe_1082-Athe_1087 Athe_1297- Athe_1299 A1 TR(M3) Athe_1292 D M2e TGF-beta assay Ca. saccharolyticus DSM 8903 Csac_1534-Csac_1539 Csac_1862- Csac_1864 A1 TR(M3) Csac_1857 D M2e P. furiosus DSM 3638 PF1423- PF1436 PF0891- PF0894 G3 this website PF1329- PF1332 G3 Th. kodakaraensis KOD1 TK2080- TK2093 TK2069-TK2072 G3 T. neapolitana DSM 4359 CTN_1067- CTN1069 TTH CTN_1071- CTN_1072 CD(M2f) CTN_0485 TTH CTN_0437-CTN_0442 T. petrophila RKU-1 Tpet_1367- Tpet_1369 TTH Tpet_1371- Tpet_1372 CD(M2f) Tpet_0723 TTH Tpet_0675-Tpet_0680 T. maritima MSB8 TM1424- TM1426 TTH TM1420- TM1422 CD(M2f) TM0201 TTH TM0244- TM0249 Cal.subterraneus subsp. tengcongensis MB4 TTE0123- TTE0134 TTE0892- TTE0894 A1 TR(M3)
TTE0887 D M2e TTE0697 CD(M2f) E. harbinense YUAN-3 T Ethha_2614- Ethha_2616 A8 TR(M3) Ethha_0052 CD(M2f) Ethha_2293 A7 D(M3) Ethha_0031 B2 M2a C. cellulolyticum H10 Ccel_1686- Ccel_1691 Ccel_1070-Ccel_1071 G1 Ccel_2303- Ccel_2305 A8 TR(M3) Ccel_2300- Ccel_2301 CD(M2f) Ethha_2695 B3 M3a Ccel_3363- Ccel_3371 Ccel_2232- Ccel_2234 A1 TR(M3) Ccel_2467- Ccel_2468 A1 TR(M3) C. phytofermentans
ISDg Cphy_1730-Cphy_1735 Cphy_0087- Cphy_0089 A8 TR(M3) Cphy_0092- Cphy_0093 CD(M2f) Cphy_2056 A5 M2c Cphy_0211-Cphy_0216 Cphy_3803- Cphy_3805 A1 TR(M3) Cphy_3798 D M2e Cthe_3003-Cthe_3004 Cphy_0090 B1 M3a C. RXDX-101 cell line thermocellum ATCC 27405 Cthe_3013-Cthe_3024 Cthe_0428- Cthe_0430 A8 TR(M3) Cthe_0425- Cthe_0426 CD(M2f) Cthe_2430-Cthe_2435 Cthe_0340- Cthe_0342 A1 TR(M3) Cthe_0335 D M2e C. thermocellum DSM 4150 CtherDRAFT_2162-CtherDRAFT_2173 CtherDRAFT_1101-CtherDRAFT_1103 DNA ligase A8 TR(M3) CtherDRAFT_1098-CtherDRAFT_1099 CD(M2f) YesB CtherDRAFT_0369-CtherDRAFT_0375 CtherDRAFT_2978 A1 TR(M3) Ta. pseudethanolicus 39E Teth39_0221 CD(M2f) Teth39_2119-Teth39_2124 Teth39_1456- Teth39_1458 A1 TR(M3) Teth39_1463 D M2e G. thermoglucosidasius C56-YS93 B. cereus ATCC 14579 AGroup D M2e hydrogenases are poorly characterized and do not contain a PAS/PAC-sensory domain. However, given their proximity to protein kinases and bifurcating hydrogenases, and their phylogenetic proximity to group C D(M2f) sensory hydrogenases (Additional file 3) we have classified them as sensory hydrogenases. BVerified by microarray and proteomic analysis (unpublished).