[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 |
|
| 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_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_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_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_028840815.1 | Thermodesulfobacterium hveragerdense | [NiFe] Group 1c | Thermodesulfobacteria | Thermodesulfobacteriales | Anaerobic Uptake | Sensitive | 4 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | [FeS] protein, TM subunit |
| WP_029009764.1 | Azospirillum halopraeferens | [NiFe] Group 1c | Alphaproteobacteria | Rhodospirillales | Anaerobic Uptake | Sensitive | 4 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | [FeS] protein, TM subunit |
| WP_029095540.1 | Budvicia aquatica | [NiFe] Group 1c | Gammaproteobacteria | Enterobacteriales | Anaerobic Uptake | Sensitive | 4 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | [FeS] protein, TM subunit |
| WP_029132834.1 | Sedimenticola selenatireducens | [NiFe] Group 1c | Gammaproteobacteria | Alteromonadales | 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.