[NiFe] Group 1c-hydrogenase

This entry was last updated at: March 2, 2017, 1:49 a.m.

Properties

Group	[NiFe] Group 1: Respiratory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 1c: Hyb-type
Function	Hydrogenotrophic respiration using fumarate, sulfate, or metals as terminal electron acceptors. Route of electron transfer unresolved. Can also fermentatively evolve H₂ under hypoxia.
Activity	H₂-uptake (unidirectional)
Oxygen tolerance	O₂-sensitive
Localisation	Membrane-bound

Distribution

Ecosystem distribution	Animal gastrointestinal tracts, anoxic soils and sediments
Taxonomic distribution	Widespread in Enterobacteria and various sulfate-reducing bacteria

Genetic Organisation

e.g. Escherichia coli (WP_021568771.1):

Architecture

Structures	None
Subunits	4
Subunit description	HybC (hydrogenase large subunit) HybO (hydrogenase small subunit) HybA (iron-sulfur protein and proposed physiological electron acceptor) HybB (transmembrane protein of unresolved function)
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] 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_000083066.1	Shigella sonnei	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_002443827.1	Shimwellia blattae	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004703021.1	Yersinia aldovae	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005275315.1	Yersinia bercovieri	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_013650389.1	Yersinia enterocolitica	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004711883.1	Yersinia frederiksenii	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005188096.1	Yersinia intermedia	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004389983.1	Yersinia kristensenii	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004877367.1	Yersinia mollaretii	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004716848.1	Yersinia rohdei	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_006819763.1	Yokenella regensburgei	[NiFe] Group 1c	Gammaproteobacteria	Enterobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005605173.1	Actinobacillus pleuropneumoniae	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005576256.1	Aggregatibacter actinomycetemcomitans	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_012771488.1	Aggregatibacter aphrophilus	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_006718275.1	Aggregatibacter segnis	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005638557.1	Haemophilus haemolyticus	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_014064532.1	Haemophilus parainfluenzae	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_007243608.1	Haemophilus pittmaniae	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_005760858.1	Pasteurella bettyae	[NiFe] Group 1c	Gammaproteobacteria	Pasteurellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_028581743.1	Desulfobulbus japonicus	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_028579802.1	Desulfobulbus japonicus	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_028583198.1	Desulfobulbus mediterraneus	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_015725977.1	Desulfobulbus propionicus	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_015403419.1	Desulfocapsa sulfexigens	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_023408348.1	Desulfofustis sp. PB-SRB1	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011187820.1	Desulfotalea psychrophila	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_010941450.1	Geobacter sulfurreducens	[NiFe] Group 1c	Deltaproteobacteria	Desulfobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_027371077.1	Desulfovermiculus halophilus	[NiFe] Group 1c	Deltaproteobacteria	Desulfovibrionales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_012468242.1	Geobacter lovleyi	[NiFe] Group 1c	Deltaproteobacteria	Desulfuromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_015721386.1	Geobacter sp. M18	[NiFe] Group 1c	Deltaproteobacteria	Desulfuromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_012774796.1	Geobacter sp. M21	[NiFe] Group 1c	Deltaproteobacteria	Desulfuromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011938839.1	Geobacter uraniireducens	[NiFe] Group 1c	Deltaproteobacteria	Desulfuromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011419537.1	Anaeromyxobacter dehalogenans	[NiFe] Group 1c	Deltaproteobacteria	Myxococcales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_012098324.1	Anaeromyxobacter sp. Fw109-5	[NiFe] Group 1c	Deltaproteobacteria	Myxococcales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_012524582.1	Anaeromyxobacter sp. K	[NiFe] Group 1c	Deltaproteobacteria	Myxococcales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_013010514.1	Denitrovibrio acetiphilus	[NiFe] Group 1c	Deferribacteres	Deferribacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_013886108.1	Flexistipes sinusarabici	[NiFe] Group 1c	Deferribacteres	Deferribacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_022851983.1	Geovibrio sp. L21-Ace-BES	[NiFe] Group 1c	Deferribacteres	Deferribacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011466351.1	Rhodoferax ferrireducens	[NiFe] Group 1c	Betaproteobacteria	Burkholderiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_009206448.1	Sulfuricella denitrificans	[NiFe] Group 1c	Betaproteobacteria	Hydrogenophilales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_015437386.1	Azoarcus sp. KH32C	[NiFe] Group 1c	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_014238024.1	Azospira oryzae	[NiFe] Group 1c	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_027457220.1	Dechloromonas agitata	[NiFe] Group 1c	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011289692.1	Dechloromonas aromatica	[NiFe] Group 1c	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_004378930.1	Thauera phenylacetica	[NiFe] Group 1c	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_015766767.1	Accumulibacter phosphatis	[NiFe] Group 1c	Betaproteobacteria	Unclassified	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_022846122.1	Desulfurobacterium sp. TC5-1	[NiFe] Group 1c	Aquificae	Desulfurobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_013638066.1	Desulfurobacterium thermolithotrophum	[NiFe] Group 1c	Aquificae	Desulfurobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_013537874.1	Thermovibrio ammonificans	[NiFe] Group 1c	Aquificae	Desulfurobacteriales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit
WP_011714122.1	Magnetococcus marinus	[NiFe] Group 1c	Alphaproteobacteria	Magnetococcales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, TM subunit

Literature

Genetics:

Coppi, M.V. (2005) The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiol. 151: 1239-1254.
Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., 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.
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.
Zbell, A.L., Benoit, S.L., and Maier, R.J. (2007) Differential expression of NiFe uptake-type hydrogenase genes in Salmonella enterica serovar Typhimurium. Microbiol. 153: 3508-3516.
Zbell, A.L., Maier, S.E., and Maier, R.J. (2008) Salmonella enterica serovar Typhimurium NiFe uptake-type hydrogenases are differentially expressed in vivo. Infect. Immun. 76: 4445-4454.
Menon, N.K., Chatelus, C.Y., Dervartanian, M., Wendt, J.C., Shanmugam, K.T., Peck, H.D., and Przybyla, A.E. (1994) Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2. J. Bacteriol. 176: 4416-4423.
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.
Richard, D.J., Sawers, G., Sargent, F., McWalter, L., and Boxer, D.H. (1999) Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli. Microbiol. 145: 2903-2912.
Sargent, F., Ballantine, S.P., Rugman, P.A., Palmer, T. and Boxer, D.H. (1998) Reassignment of the gene encoding the Escherichia coli hydrogenase 2 small subunit. Eur. J. Biochem. 255: 746-754.

Physiology:

Ballantine, S.P. and Boxer, D.H. (1985) Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12. J. Bacteriol. 163: 454-459.
Ban, J., Jiang, W., Li, Y., Zhang, Y., and Li, J. (2010) Functional analysis of hydrogenases and their effects on cell growth and magnetosome synthesis in Magnetospirillum gryphiswaldense. Chinese Sci. Bulletin 55: 1271-1277.
Caccavo, F., Lonergan, D.J., Lovley, D.R., Davis, M., Stolz, J.F., and McInerney, M.J. (1994) Geobacter sulfurreducens sp. nov., a hydrogen-and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl. Environ. Microbiol. 60: 3752-3759.
Coppi, M.V., O'Neil, R.A., and Lovley, D.R. (2004) Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens. J. Bacteriol. 186: 3022-3028.
Lamichhane-Khadka, R., Benoit, S.L., Miller-Parks, E.F., and Maier, R.J., 2015. Host hydrogen rather than that produced by the pathogen is important for Salmonella enterica serovar Typhimurium virulence. Infect. Immun. 83: 311-316.
Lamichhane-Khadka, R., Kwiatkowski, A., and Maier, R.J. (2010) The Hyb hydrogenase permits hydrogen-dependent respiratory growth of Salmonella enterica serovar Typhimurium. mBio 1: e00284-10.
Laurinavichene, T.V. and Tsygankov, A.A. (2001) H₂ consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol. Lett. 202: 121-124.
Laurinavichene, T.V., Zorin, N.A., and Tsygankov, A.A. (2002) Effect of redox potential on activity of hydrogenase 1 and hydrogenase 2 in Escherichia coli. Arch. Microbiol. 178: 437-442.
Maier, L. et al. (2013) Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem. Cell Host Microb. 14: 641-651.
Redwood, M.D., Mikheenko, I.P., Sargent, F. and Macaskie, L.E. (2008) Dissecting the roles of Escherichia coli hydrogenases in biohydrogen production. FEMS Microbiol. Lett. 278: 48-55.
Rodrigue, A., Boxer, D.H., Mandrand-Berthelot, M.A., and Wu, L.F. (1996) Requirement for nickel of the transmembrane translocation of NiFe-hydrogenase 2 in Escherichia coli. FEBS Lett. 392: 81-86.
Sawers, R.G., Jamieson, D.J., Higgins, C.F., and Boxer, D.H. (1986) Characterization and physiological roles of membrane-bound hydrogenase isoenzymes from Salmonella typhimurium. J. Bacteriol. 168: 398-404.
Trchounian, K., Soboh, B., Sawers, R.G., and Trchounian, A. (2013) Contribution of hydrogenase 2 to stationary phase H₂ production by Escherichia coli during fermentation of glycerol. Cell Biochem. Biophys. 66: 103-108.
Trchounian, K. and Trchounian, A. (2009) Hydrogenase 2 is most and hydrogenase 1 is less responsible for H₂ production by Escherichia coli under glycerol fermentation at neutral and slightly alkaline pH. Int. J. Hydrogen Energy 34: 8839-8845.
Trchounian, K. and Trchounian, A. (2013) Escherichia coli hydrogenase 4 (hyf) and hydrogenase 2 (hyb) contribution in H₂ production during mixed carbon (glucose and glycerol) fermentation at pH 7.5 and pH 5.5. Int. J. Hydrogen Energy 38: 3921-3929.

Biochemistry:

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.
Muhd Noor, N.D., Nishikawa, K., Nishihara, H., Yoon, K.S., Ogo, S., and Higuchi, Y. (2016) Improved purification, crystallization and crystallographic study of Hyd-2-type [NiFe]-hydrogenase from Citrobacter sp. S-77. Acta Cryst. F: 72: 53-58.