[NiFe] Group 1d-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:26 a.m.

Properties

Group	[NiFe] Group 1: Respiratory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 1d: Oxygen-tolerant
Function	Hydrogenotrophic respiration using O₂ or fumarate as terminal electron acceptors. Enzyme transfers H₂-liberated electrons through cyt b and quinone to terminal reductase.
Activity	H₂-uptake (unidirectional)
Oxygen tolerance	O₂-tolerant
Localisation	Membrane-bound

Distribution

Ecosystem distribution	Diverse soil, aquatic, and host-associated environments
Taxonomic distribution	Widespread among obligately aerobic and facultatively anaerobic bacteria

Genetic Organisation

e.g. Escherichia coli (WP_021522685.1):

Architecture

Structures	3AYX (Hydrogenovibrio marinus, 1.2 Å resolution, active) 3AYZ (Hydrogenovibrio marinus, 1.3 Å resolution, oxidized) 3AYY (Hydrogenovibrio marinus, 1.3 Å resolution, superoxidized) 3RGW (Ralstonia eutropha, 1.5 Å resolution, active) 4IUD (Ralstonia eutropha, 1.5 Å resolution, reduced) 4IUB (Ralstonia eutropha, 1.6 Å resolution, oxidised) 4IUC (Ralstonia eutropha, 1.5 Å resolution, superoxidised) 5ADU (Escherichia coli, 1.1 Å resolution, oxidised) 3UQY (Escherichia coli, 1.5 Å resolution, active) 3USE (Escherichia coli, 1.7 Å resolution, oxidised) 5A4M (Escherichia coli, 1.7 Å resolution, oxidised) 3USC (Escherichia coli, 2.0 Å resolution, superoxidised) 4GD3 (Escherichia coli, 3.3 Å resolution, with cyt b) 4C3O (Salmonella enterica, 3.2 Å resolution, oxidised)
Subunits	3
Subunit description	HyaB (hydrogenase large subunit) HyaA (hydrogenase small subunit) HyaC (cytochrome b subunit)
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 6Cys[4Fe3S] Medial: 3Cys[3Fe4S] Distal: 3Cys1His[4Fe4S]

Sequences in this class

NCBI Accession	Organism	Hydrogenase Class	Phylum	Order	Activity (Predicted)	Oxygen Tolerance (Predicted)	Subunits (Predicted)	Metal Centres (Predicted)	Accessory Subunits (Predicted)
WP_006366944.1	Chlorobium ferrooxidans	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012465814.1	Chlorobium limicola	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_011744848.1	Chlorobium phaeobacteroides	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012501193.1	Chloroherpeton thalassium	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_011358178.1	Pelodictyon luteolum	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012508571.1	Pelodictyon phaeoclathratiforme	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012505437.1	Prosthecochloris aestuarii	[NiFe] Group 1d	Chlorobi	Chlorobiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_009378513.1	Bilophila sp. 4_1_30	[NiFe] Group 1d	Deltaproteobacteria	Desulfovibrionales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_005026843.1	Bilophila wadsworthia	[NiFe] Group 1d	Deltaproteobacteria	Desulfovibrionales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_011526524.1	Lawsonia intracellularis	[NiFe] Group 1d	Deltaproteobacteria	Desulfovibrionales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_027414715.1	Aneurinibacillus terranovensis	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_003397243.1	Anoxybacillus flavithermus	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_019416530.1	Anoxybacillus kamchatkensis	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_009361199.1	Anoxybacillus sp. DT3-1	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_021094790.1	Anoxybacillus sp. SK3-4	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_003330153.1	Bacillus azotoformans	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_019241710.1	Bacillus massilioanorexius	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_020062534.1	Bacillus sp. 123MFChir2	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_015594636.1	Bacillus sp. 1NLA3E	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_013400922.1	Geobacillus sp. Y4.1MC1	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_013876989.1	Geobacillus thermoglucosidasius	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_028552966.1	Paenibacillus sp. UNC451MF	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_023510524.1	Sporolactobacillus laevolacticus	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_010631937.1	Sporolactobacillus vineae	[NiFe] Group 1d	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_025206080.1	Dehalobacter restrictus	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_019226053.1	Dehalobacter sp. E1	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_026156348.1	Dehalobacter sp. FTH1	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_014794600.1	Desulfitobacterium dehalogenans	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_015261076.1	Desulfitobacterium dichloroeliminans	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_005811167.1	Desulfitobacterium hafniense	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_019850866.1	Desulfitobacterium sp. PCE1	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_014826810.1	Desulfosporosinus acidiphilus	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_014904046.1	Desulfosporosinus meridiei	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_014186363.1	Desulfosporosinus orientis	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_009623566.1	Desulfosporosinus sp. OT	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012281726.1	Heliobacterium modesticaldum	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_012282567.1	Heliobacterium modesticaldum	[NiFe] Group 1d	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_004573252.1	Acetonema longum	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_027937761.1	Anaeroarcus burkinensis	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_018702099.1	Anaeromusa acidaminophila	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_006305436.1	Centipeda periodontii	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_015597373.1	Hyphomicrobium denitrificans	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_027889016.1	Megamonas hypermegale	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_005840788.1	Mitsuokella multacida	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_007954318.1	Pelosinus fermentans	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_026762838.1	Selenomonas artemidis	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_019542170.1	Selenomonas bovis	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_006690835.1	Selenomonas flueggei	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_006692428.1	Selenomonas infelix	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b
WP_006696448.1	Selenomonas noxia	[NiFe] Group 1d	Firmicutes	Selenomonadales	Aerobic Uptake	Tolerant	3	[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] cluster	Cytochrome b

Literature

Genetics:

Bernhard, M., Schwartz, E., Rietdorf, J., and Friedrich, B. (1996) The Alcaligenes eutrophus membrane-bound hydrogenase gene locus encodes functions involved in maturation and electron transport coupling. J. Bacteriol. 178: 4522-4529.
Brewin, N.J., DeJong, T.M., Phillips, D.A., and Johnston, A.W.B. (1980) Co-transfer of determinants for hydrogenase activity and nfodulation ability in Rhizobium leguminosarum. Nature 288: 77-79.
Brito, B., Martínez, M., Fernández, D., Rey, L., Cabrera, E., Palacios, J.M., Imperial, J. and Ruiz-Argüeso, T. (1997) Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein NifA. Proc. Acad. Natl. Sci. USA 84: 6019-6024.
Colbeau, A., Kóvacs, K.L., Chabert, J., and Vignais, P.M., 1994. Cloning and sequences of the structural (hupSLC) and accessory (hupDHI) genes for hydrogenase biosynthesis in Thiocapsa roseopersicina. Gene 140: 25-31.
Csaki, R., Hanczar, T., Bodrossy, L., Murrell, J.C., and Kovács, K.L. (2001) Molecular characterization of structural genes coding for a membrane bound hydrogenase in Methylococcus capsulatus (Bath). FEMS Microbiol. Lett. 205: 203-207.
Elsen, S., Dischert, W., Colbeau, A., and Bauer, C.E. (2000) Expression of uptake hydrogenase and molybdenum nitrogenase in Rhodobacter capsulatus is coregulated by the RegB-RegA two-component regulatory system. J. Bacteriol. 182: 2831-2837.
Ford, C.M., Garg, N., Garg, R.P., Tibelius, K.H., Yates, M.G., Arp, D.J., and Seefeldt, L.C. (1990) The identification, characterization, sequencing and mutagenesis of the genes (hupSL) encoding the small and large subunits of the H₂-uptake hydrogenase of Azotobacter chroococcum. Mol. Microbiol. 4: 999-1008.
Friedrich, B., Hogrefe, C., and Schlegel, H.G. (1981) Naturally occurring genetic transfer of hydrogen-oxidizing ability between strains of Alcaligenes eutrophus. J. Bacteriol. 147: 198-205.
Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., and Morales, S.E. (2016) Genomic and metagenomic surveys of hydrogenase distribution indicate H₂ is a widely utilised energy source for microbial growth and survival. ISME J. 10: 761-777.
Gutierrez, D., Hernando, Y., Palacios, J.M., Imperial, J., and Ruiz-Argüeso, T. (1997) FnrN controls symbiotic nitrogen fixation and hydrogenase activities in Rhizobium leguminosarum biovar viciae UPM791. J. Bacteriol. 179: 5264-5270.
Jamieson, D.J., Sawers, R.G., Rugman, P.A., Boxer, D.H. and Higgins, C.F. (1986) Effects of anaerobic regulatory mutations and catabolite repression on regulation of hydrogen metabolism and hydrogenase isoenzyme composition in Salmonella typhimurium. J. Bacteriol. 168: 405-411.
Leclerc, M., Colbeau, A., Cauvin, B., and Vignais, P.M. (1988) Cloning and sequencing of the genes encoding the large and the small subunits of the H₂ uptake hydrogenase (hup) of Rhodobacter capsulatus. Mol. Gen. Genet. 214: 97-107.
King, P.W. and Przybyla, A.E. (1999) Response of hya expression to external pH in Escherichia coli. J. Bacteriol. 181: 5250-5256.
Lim, S.T. (1978) Determination of hydrogenase in free-living cultures of Rhizobium japonicum and energy efficiency of soybean nodules. Plant Physiol. 62: 609-611.
Maier, R.J., Campbell, N.E., Hanus, F.J., Simpson, F.B., Russell, S.A., and Evans, H.J. (1978) Expression of hydrogenase activity in free-living Rhizobium japonicum. Proc. Acad. Natl. Sci. USA 75: 3258-3262.
Menon, N.K., Robbins, J., Wendt, J.C., Shanmugam, K.T., and Przybyla, A.E. (1991) Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1. J. Bacteriol. 173: 4851-4861.
Menon, N.K., Robbins, J., Peck, H.D., Chatelus, C.Y., Choi, E.S., and Przybyla, A.E. (1990) Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames. J. Bacteriol. 172: 1969-1977.
Nelson, L.M. and Salminen, S.O. (1982) Uptake hydrogenase activity and ATP formation in Rhizobium leguminosarum bacteroids. J. Bacteriol. 151: 989-995.
Palacios, J.M., Murillo, J., Leyva, A., Ditta, G. and Ruiz-Argüeso, T. (1990) Differential expression of hydrogen uptake (hup) genes in vegetative and symbiotic cells of Rhizobium leguminosarum. Mol. Gen. Genet. 221: 363-370.
Pandelia, M.E., Lubitz, W., and Nitschke, W. (2012) Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O₂-tolerance? BBA Bioenergetics 1817: 1565-1575.
Sayavedra-Soto, L.A., Powell, G.K., Evans, H.J., and Morris, R.O. (1988) Nucleotide sequence of the genetic loci encoding subunits of Bradyrhizobium japonicum uptake hydrogenase. Proc. Natl. Acad. Sci. USA 85: 8395-8399.
Schwartz, E., Henne, A., Cramm, R., Eitinger, T., Friedrich, B., and Gottschalk, G. (2003) Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H₂-based lithoautotrophy and anaerobiosis. J. Mol. Biol. 332: 369-383.
Ueda, Y., Yamamoto, M., Urasaki, T., Arai, H., Ishii, M., and Igarashi, Y. (2007) Sequencing and reverse transcription-polymerase chain reaction (RT-PCR) analysis of four hydrogenase gene clusters from an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6. J. Biosci. Bioeng. 104: 470-475.
Uffen, R.L., Colbeau, A., Richaud, P., and Vignais, P.M. (1990) Cloning and sequencing the genes encoding uptake-hydrogenase subunits of Rhodocyclus gelatinosus. Mol. Gen. Genet. 221: 49-58.

Physiology:

Aguilar, O.M., Yates, M.G., and Postgate, J.R. (1985) The beneficial effect of hydrogenase in Azotobacter chroococcum under nitrogen-fixing, carbon-limiting conditions in continuous and batch cultures. Microbiol. 131: 3141-3145.
Albrecht, S.L., Maier, R.J., Hanus, F.J., Russell, S.A., Emerich, D.W., and Evans, H.J. (1979) Hydrogenase in Rhizobium japonicum increases nitrogen fixation by nodulated soybeans. Science 203: 1255-1257.
Ballantine, S.P. and Boxer, D.H. (1985) Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12. J. Bacteriol. 163: 454-459.
Bowman, L., Balbach, J., Walton, J., Sargent, F., and Parkin, A. (2016) Biosynthesis of Salmonella enterica [NiFe]-hydrogenase-5: probing the roles of system-specific accessory proteins. J. Biol. Inorg. Chem. 21: 865-873.
Brøndsted, L. and Atlung, T. (1994) Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli. J. Bacteriol. 176: 5423-5428.
Brugna-Guiral, M, Tron, P, Nitschke, W., Stetter, K.-O., Burlat, B., Guigliarelli, B, Bruschi, M., and Giudici-Orticoni, M.T. (2003) [NiFe] hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics. Extremophiles 7: 147-157.
Carere, C.R., Hards, K., Houghton, K.M., Power, J.F., McDonald, B., Collet, C., Gapes, D.J., Sparling, R., Boyd, E.S., Cook, G.M., Greening, C., and Stott, M.B. (2017) Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. ISME J. 11: 2599-2610.
Colbeau, A., Kelley, B.C., and Vignais, P.M. (1980) Hydrogenase activity in Rhodopseudomonas capsulata: relationship with nitrogenase activity. J. Bacteriol. 144: 141-148.
Colbeau, A. and Vignais, P.M. (1983) The membrane-bound hydrogenase of Rhodopseudomonas capsulata is inducible and contains nickel. BBA Prot. Struct. Mol. Enzymol. 748: 128-138.
De Bont, J.A.M. (1976) Hydrogenase activity in nitrogen-fixing methane-oxidizing bacteria. Antonie van Leeuwenhoek 42: 255-259.
Friedrich, C.G., Friedrich, B. and Bowien, B. (1981) Formation of enzymes of autotrophic metabolism during heterotrophic growth of Alcaligenes eutrophus. Microbiol. 122: 69-78.
Guiral, M., Tron, P., Aubert, C., Gloter, A., Iobbi-Nivol, C., and Giudici-Orticoni, M.T. (2005) A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J. Biol. Chem. 280: 42004-42015.
Guiral, M., Tron, P., Belle, V., Aubert, C., Léger, C., Guigliarelli, B., Giudici-Orticoni, M.T. (2006) Hyperthermostable and oxygen resistant hydrogenases from a hyperthermophilic bacterium Aquifex aeolicus: physicochemical properties. Int. J. Hydrogen Energy 31: 1424-1431.
Hanczár, T., Csáki, R., Bodrossy, L., Murrell, C.J., and Kovács, K.L. (2002) Detection and localization of two hydrogenases in Methylococcus capsulatus (Bath) and their potential role in methane metabolism. Arch. Microbiol. 177: 167-172.
Hanus, F.J., Maier, R.J., and Evans, H.J. (1979) Autotrophic growth of H₂-uptake-positive strains of Rhizobium japonicum in an atmosphere supplied with hydrogen gas. Proc. Acad. Natl. Sci. USA 76: 1788-1792.
Hedrich, S. and Johnson, D.B. (2013) Aerobic and anaerobic oxidation of hydrogen by acidophilic bacteria. FEMS Microbiol. Lett. 349: 40-45.
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Shah, N.N., Hanna, M.L., Jackson, K.J., and Taylor, R.T. (1995) Batch cultivation of Methylosinus trichosporium OB3B: IV. Production of hydrogen-driven soluble or particulate methane monooxygenase activity. Biotechnol. Bioengineer. 45: 229-238.
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Zbell, A.L. and Maier, R.J. (2009) Role of the Hya hydrogenase in recycling of anaerobically produced H₂ in Salmonella enterica serovar Typhimurium. Appl. Environ. Microbiol. 75: 1456-1459.

Biochemistry:

Adams, M.W. and Hall, D.O. (1979) Purification of the membrane-bound hydrogenase of Escherichia coli. Biochem. J. 183: 11-22.
Adams, M.W.W. and Hall, D.O. (1977) Isolation of the membrane-bound hydrogenase from Rhodospirillum rubrum. Biochem. Biophys. Res. Commun. 77: 730-737.
Adams, M.W. and Hall, D.O. (1979) Properties of the solubilized membrane-bound hydrogenase from the photosynthetic bacterium Rhodospirillum rubrum. Arch. Biochem. Biophys. 195: 288-299.
Adamson, H., Robinson, M., Wright, J.J., Flanagan, L.A., Walton, J., Elton, D., Gavaghan, D.J., Bond, A.M., Roessler, M.M., and Parkin, A. (2017) Retuning the catalytic bias and overpotential of a [NiFe]-hydrogenase via a single amino acid exchange at the electron entry/exit site. J. Am. Chem. Soc. 139: 10677-10686.
Arp, D.J., McCollum, L.C., and Seefeldt, L.C. (1985) Molecular and immunological comparison of membrane-bound, H₂-oxidizing hydrogenases of Bradyrhizobium japonicum, Alcaligenes eutrophus, Alcaligenes latus, and Azotobacter vinelandii. J. Bacteriol. 163: 15-20.
Bernhard, M., Benelli, B., Hochkoeppler, A., Zannoni, D., and Friedrich, B. (1997) Functional and structural role of the cytochrome b subunit of the membrane-bound hydrogenase complex of Alcaligenes eutrophus H16. Eur. J. Biochem. 248: 179-186.
Bowman, L., Flanagan, L., Fyfe, P.K., Parkin, A., Hunter, W.N., and Sargent, F. (2014) How the structure of the large subunit controls function in an oxygen-tolerant [NiFe]-hydrogenase. Biochem. J. 458: 449-458.
Bürstel, I., Siebert, E., Frielingsdorf, S., Zebger, I., Friedrich, B., and Lenz, O. (2016) CO synthesized from the central one-carbon pool as source for the iron carbonyl in O₂-tolerant [NiFe]-hydrogenase. Proc. Natl. Acad. Sci. USA 113: 14722-14726.
Brooke, E.J., Evans, R.M., Islam, S.T., Roberts, G.M., Wehlin, S.A., Carr, S.B., Phillips, S.E., and Armstrong, F.A. (2016) Importance of the active site “canopy” residues in an O₂-tolerant [NiFe]-hydrogenase. Biochem. 56: 132-142.
Colbeau, A., Chabert, J. and Vignais, P.M. (1983) Purification, molecular properties and localization in the membrane of the hydrogenase of Rhodopseudomonas capsulata. BBA Prot. Struct. Mol. Enzymol. 748: 116-127.
Cracknell, J.A., Wait, A.F., Lenz, O., Friedrich, B., and Armstrong, F.A. (2009) A kinetic and thermodynamic understanding of O2 tolerance in [NiFe]-hydrogenases. Proc. Natl. Acad. Sci. USA 106: 20681-20686.
Eguchi, S., Yoon, K.S. and Ogo, S. (2012) O₂-stable membrane-bound [NiFe] hydrogenase from a newly isolated Citrobacter sp. S-77. J. Biosci. Bioengin. 114: 479-484.
Evans, R.M., Parkin, A., Roessler, M.M., Murphy, B.J., Adamson, H., Lukey, M.J., Sargent, F., Volbeda, A., Fontecilla-Camps, J.C., and Armstrong, F.A. (2013) Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen-the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases. J. Am. Chem. Soc. 135: 2694-2707.
Flanagan, L.A., Wright, J.J., Roessler, M.M., Moir, J.W., and Parkin, A. (2016) Re-engineering a NiFe hydrogenase to increase the H₂ production bias while maintaining native levels of O₂ tolerance. Chem. Commun. 52: 9133-9136.
Frielingsdorf, S. et al. (2014). Reversible [4Fe-3S] cluster morphing in an O₂-tolerant [NiFe] hydrogenase. Nature Chem. Biol. 10: 378-385.
Frielingsdorf, S., Schubert, T., Pohlmann, A., Lenz, O., and Friedrich, B. (2011) A trimeric supercomplex of the oxygen-tolerant membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha H16. Biochem. 50: 10836-10843.
Fritsch, J., Lenz, O., and Friedrich, B. (2013) Structure, function and biosynthesis of O₂-tolerant hydrogenases. Nature Rev. Microbiol. 11: 106-114.
Fritsch, J., Scheerer, P., Frielingsdorf, S., Kroschinsky, S., Friedrich, B., Lenz, O., and Spahn, C.M. (2011) The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre. Nature 479: 249-252.
Fritsch, J., Lenz, O., and Friedrich, B. (2011) The maturation factors HoxR and HoxT contribute to oxygen tolerance of membrane-bound [NiFe] hydrogenase in Ralstonia eutropha H16. J. Bacteriol. 193: 2487-2497.
Goldet, G., Wait, A.F., Cracknell, J.A., Vincent, K.A., Ludwig, M., Lenz, O., Friedrich, B., and Armstrong, F.A. (2008) Hydrogen production under aerobic conditions by membrane-bound hydrogenases from Ralstonia species. J. Am. Chem. Soc. 130: 11106-11113.
Goris, T., Wait, A.F., Saggu, M., Fritsch, J., Heidary, N., Stein, M., Zebger, I., Lendzian, F., Armstrong, F.A., Friedrich, B., and Lenz, O. (2011) A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase. Nature Chem. Biol. 7: 310-318.
Guiral, M., Tron, P., Belle, V., Aubert, C., Léger, C., Guigliarelli, B., and Giudici-Orticoni, M.T. (2006) Hyperthermostable and oxygen resistant hydrogenases from a hyperthermophilic bacterium Aquifex aeolicus: physicochemical properties. Int. J. Hydrogen Energy 31: 1424-1431.
Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., and Scheerer, P. (2016) Krypton derivatization of an O₂-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic tunnel network for gas transport. Angewandte Chemie 55: 5586-5590.
Knüttel, K. Schneider, K., Schlegel, H.G., and Müller, A. (1989) The membrane-bound hydrogenase from Paracoccus denitrificans. Eur. J. Biochem. 179: 101-108.
Ludwig, M., Cracknell, J.A., Vincent, K.A., Armstrong, F.A., and Lenz, O. (2009) Oxygen-tolerant H₂ oxidation by membrane-bound [NiFe] hydrogenases of Ralstonia species coping with low level H₂ in air. J. Biol. Chem. 284: 465-477.
Lukey, M.J., Parkin, A., Roessler, M.M., Murphy, B.J., Harmer, J., Palmer, T., Sargent, F., and Armstrong, F.A. (2010). How Escherichia coli is equipped to oxidize hydrogen under different redox conditions. J. Biol. Chem. 285: 3928-3938.
Lukey, M.J., Roessler, M.M., Parkin, A., Evans, R.M., Davies, R.A., Lenz, O., Friedrich, B., Sargent, F., and Armstrong, F.A. (2011) Oxygen-tolerant [NiFe]-hydrogenases: the individual and collective importance of supernumerary cysteines at the proximal Fe-S cluster. J. Am. Chem. Soc. 133: 16881-16892.
Madigan, M.T. and Gest, H. (1979) Growth of the photosynthetic bacterium Rhodopseudomonas capsulata chemoautotrophically in darkness with H₂ as the energy source. J. Bacteriol. 137: 524-530.
Murphy, B.J., Sargent, F., and Armstrong, F.A. (2014) Transforming an oxygen-tolerant [NiFe] uptake hydrogenase into a proficient, reversible hydrogen producer. Energy Environ. Sci. 7: 1426-1433.
Pandelia, M.E., Fourmond, V., Tron-Infossi, P., Lojou, E., Bertrand, P., Léger, C., Giudici-Orticoni, M.T., and Lubitz, W. (2010) Membrane-bound hydrogenase I from the hyperthermophilic bacterium Aquifex aeolicus: enzyme activation, redox intermediates and oxygen tolerance. J. Am. Chem. Soc. 132: 6991-7004.
Parkin, A., Bowman, L., Roessler, M.M., Davies, R.A., Palmer, T., Armstrong, F.A., and Sargent, F. (2012) How Salmonella oxidises H₂ under aerobic conditions. FEBS Lett. 586: 536-544.
Radu, V., Frielingsdorf, S., Evans, S.D., Lenz, O., and Jeuken, L.J. (2014) Enhanced oxygen-tolerance of the full heterotrimeric membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. J. Am. Chem. Soc. 136: 8512-8515.
Schink, B. and Schlegel, H.G. (1979) The membrane-bound hydrogenase of Alcaligenes eutrophus. I. Solubilization, purification, and biochemical properties. BBA Enzymol. 567: 315-324.
Seefeldt, L.C. and Arp, D.J. (1986) Purification to homogeneity of Azotobacter vinelandii hydrogenase: a nickel and iron containing αβ dimer. Biochimie 68: 25-34.
Sezer, M., Frielingsdorf, S., Millo, D., Heidary, N., Utesch, T., Mroginski, M.A., Friedrich, B., Hildebrandt, P., Zebger, I., and Weidinger, I.M. (2011) Role of the HoxZ subunit in the electron transfer pathway of the membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha immobilized on electrodes. J. Phys. Chem. B 115: 10368-10374.
Shomura, Y., Yoon, K.S., Nishihara, H., and Higuchi, Y. (2011) Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase. Nature 479: 253-256.
So, K., Hamamoto, R., Takeuchi, R., Kitazumi, Y., Shirai, O., Endo, R., Nishihara, H., Higuchi, Y., and Kano, K., 2016. Bioelectrochemical analysis of thermodynamics of the catalytic cycle and kinetics of the oxidative inactivation of oxygen-tolerant [NiFe]-hydrogenase. J. Electroanalytical Chem. 766: 152-161.
Vincent, K.A., Cracknell, J.A., Lenz, O., Zebger, I., Friedrich, B., and Armstrong, F.A. (2005) Electrocatalytic hydrogen oxidation by an enzyme at high carbon monoxide or oxygen levels. Proc. Acad. Natl. Sci. USA 102: 16951-16954.
Vincent, K.A., Parkin, A., Lenz, O., Albracht, S.P., Fontecilla-Camps, J.C., Cammack, R., Friedrich, B., and Armstrong, F.A. (2005) Electrochemical definitions of O₂ sensitivity and oxidative inactivation in hydrogenases. J. Am. Chem. Soc. 127: 18179-18189.
Volbeda, A., Amara, P., Darnault, C., Mouesca, J.M., Parkin, A., Roessler, M.M., Armstrong, F.A., and Fontecilla-Camps, J.C. (2012) X-ray crystallographic and computational studies of the O₂-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Proc. Natl. Acad. Sci. USA 109: 5305-5310.
Volbeda, A., Darnault, C., Parkin, A., Sargent, F., Armstrong, F.A., and Fontecilla-Camps, J.C. (2013) Crystal structure of the O₂-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b. Structure 21: 184-190.
Wulff, P., Day, C.C., Sargent, F., and Armstrong, F.A. (2014) How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases. Proc. Natl. Acad. Sci. USA 111: 6606-6611.
Wulff, P., Thomas, C., Sargent, F., and Armstrong, F.A. (2016) How the oxygen tolerance of a [NiFe]-hydrogenase depends on quaternary structure. J. Biol. Inorg. Chem. 21: 121-134.
Yoon, K.S., Fukuda, K., Fujisawa, K., and Nishihara, H. (2011) Purification and characterization of a highly thermostable, oxygen-resistant, respiratory [NiFe]-hydrogenase from a marine, aerobic hydrogen-oxidizing bacterium Hydrogenovibrio marinus. Int. J. Hydrogen Energy 36: 7081-7088.

Chemistry:

Fritsch, J. et al. (2011) [NiFe] and [FeS] cofactors in the membrane-bound hydrogenase of Ralstonia eutropha investigated by X-ray absorption spectroscopy: insights into O₂-tolerant H₂ cleavage. Biochem. 50: 5858-5869.
Pandelia, M.E., Bykov, D., Izsak, R., Infossi, P., Giudici-Orticoni, M.T., Bill, E., Neese, F., and Lubitz, W. (2013) Electronic structure of the unique [4Fe-3S] cluster in O₂-tolerant hydrogenases characterized by ⁵⁷Fe Mössbauer and EPR spectroscopy. Proc. Natl. Acad. Sci. USA 110: 483-488.
Pandelia, M.E., Infossi, P., Giudici-Orticoni, M.T., and Lubitz, W. (2010) The oxygen-tolerant hydrogenase I from Aquifex aeolicus weakly interacts with carbon monoxide: an electrochemical and time-resolved FTIR study. Biochem. 49: 8873-8881.
Pandelia, M.E., Infossi, P., Stein, M., Giudici-Orticoni, M.T., and Lubitz, W. (2012) Spectroscopic characterization of the key catalytic intermediate Ni-C in the O₂-tolerant [NiFe] hydrogenase I from Aquifex aeolicus: evidence of a weakly bound hydride. Chem. Commun. 48: 823-825.
Radu, V., Frielingsdorf, S., Lenz, O., and Jeuken, L.J. (2016) Reactivation from the Ni-B state in [NiFe] hydrogenase of Ralstonia eutropha is controlled by reduction of the superoxidised proximal cluster. Chem. Commun. 52: 2632-2635.
Roessler, M.M., Evans, R.M., Davies, R.A., Harmer, J., and Armstrong, F.A. (2012) EPR spectroscopic studies of the Fe-S clusters in the O₂-tolerant [NiFe]-hydrogenase Hyd-1 from Escherichia coli and characterization of the unique [4Fe-3S] cluster by HYSCORE. J. Am. Chem. Soc. 134: 15581-15594.
Saggu, M., Teutloff, C., Ludwig, M., Brecht, M., Pandelia, M.E., Lenz, O., Friedrich, B., Lubitz, W., Hildebrandt, P., Lendzian, F., and Bittl, R. (2010) Comparison of the membrane-bound [NiFe] hydrogenases from R. eutropha H16 and D. vulgaris Miyazaki F in the oxidized ready state by pulsed EPR. Phys. Chem. Chem. Phys. 12: 2139-2148.
Saggu, M., Zebger, I., Ludwig, M., Lenz, O., Friedrich, B., Hildebrandt, P., and Lendzian, F. (2009) Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16. J. Biol. Chem. 284: 16264-16276.
Siebert, E. et al. (2015) Resonance Raman spectroscopic analysis of the [NiFe] active site and the proximal [4Fe-3S] cluster of an O₂-tolerant membrane-bound hydrogenase in the crystalline state. J. Phys. Chem. 119: 13785-13796.
Wisitruangsakul, N., Lenz, O., Ludwig, M., Friedrich, B., Lendzian, F., Hildebrandt, P., and Zebger, I. (2009) Monitoring catalysis of the membrane-bound hydrogenase from Ralstonia eutropha H16 by surface-enhanced IR absorption spectroscopy. Angewandte Chemie 48: 611-613.