[NiFe] Group 1h-hydrogenase
This entry was last updated at: Feb. 9, 2018, 3:51 a.m.
Properties
| Group | [NiFe] Group 1: Respiratory H2-uptake [NiFe] hydrogenases |
| Subgroup | [NiFe] Group 1h: Actinobacteria-type |
| Function | Hydrogenotrophic respiration using O2 as terminal electron acceptor. Enzyme scavenges electrons from atmospheric H2 to fuel respiratory chain during carbon-starvation. Route of electron transfer unresolved. |
| Activity | H2-uptake (unidirectional, high-affinity) |
| Oxygen tolerance | O2-tolerant or O2-insensitive |
| Localisation | Membrane-associated? |
Distribution
| Ecosystem distribution | Upland soils, plant tissues, possibly surface waters |
| Taxonomic distribution | Widespread among obligately aerobic soil bacteria, especially Actinobacteria, Acidobacteria, and Chloroflexi |
Genetic Organisation
e.g. Mycobacterium smegmatis (WP_003893634.1):
Architecture
| Structures |
|
| Subunits | 3? |
| Subunit description | HyhL (hydrogenase large subunit) HyhS (hydrogenase small subunit) HyhE (putative iron-sulfur protein and proposed physiological electron acceptor) |
| Catalytic site | [NiFe]-centre |
| FeS clusters | Proximal: 3Cys1Asp[4Fe4S] Medial: 4Cys[4Fe4S] Distal: 3Cys1His[4Fe4S] |
Important Notes
The Robiginitalea biformata and Sulfolobus islandicus enzymes are relatively distantly related to the main group. No studies have yet tested whether these enzymes have a H2-scavenging role like other Group 1h [NiFe]-hydrogenases. They may instead represent founding members of a functionally-distinct lineage.
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_048100378.1 | Acidianus copahuensis | [NiFe] Group 1h | Crenarchaeota | Sulfolobales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_021597135.1 | Actinomadura madurae | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_026402909.1 | Actinomadura rifamycini | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_018330638.1 | Actinomycetospora chiangmaiensis | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_020516695.1 | Actinoplanes globisporus | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_026468830.1 | Amycolatopsis balhimycina | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007034607.1 | Amycolatopsis decaplanina | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_013225646.1 | Amycolatopsis mediterranei | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_027944444.1 | Amycolatopsis taiwanensis | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_004559486.1 | Amycolatopsis vancoresmycina | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_013806771.1 | Amycolicicoccus subflavus | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003801347.1 | Arthrobacter globiformis | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_014376814.1 | Blastococcus saxobsidens | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_012934014.1 | Conexibacter woesei | [NiFe] Group 1h | Actinobacteria | Solirubrobacterales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_011603554.1 | Frankia alni | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_018502886.1 | Frankia sp. BCU110501 | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007516725.1 | Frankia sp. CN3 | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_020460087.1 | Frankia sp. EAN1pec | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_006543203.1 | Frankia sp. EUN1f | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_013423858.1 | Frankia sp. EuI1c | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_009739394.1 | Frankia sp. QA3 | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_006334825.1 | Gordonia rhizosphera | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_014267363.1 | Granulicella mallensis | [NiFe] Group 1h | Acidobacteria | Acidobacteriales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007904650.1 | Ktedonobacter racemifer | [NiFe] Group 1h | Chloroflexi | Ktedonobacteriales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_009061231.1 | Methylacidiphilum fumariolicum | [NiFe] Group 1h | Verrucomicrobia | Methylacidiphiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_016920676.1 | Methylocystis parvus | [NiFe] Group 1h | Alphaproteobacteria | Rhizobiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_029651411.1 | Methylocystis sp. SB2 | [NiFe] Group 1h | Alphaproteobacteria | Rhizobiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_014892893.1 | Methylocystis sp. SC2 | [NiFe] Group 1h | Alphaproteobacteria | Rhizobiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003612931.1 | Methylosinus trichosporium | [NiFe] Group 1h | Alphaproteobacteria | Rhizobiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_011724971.1 | Mycobacterium avium | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_014815377.1 | Mycobacterium chubuense | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007775170.1 | Mycobacterium colombiense | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_014942609.1 | Mycobacterium indicus | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_023372393.1 | Mycobacterium kansasii | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_015355236.1 | Mycobacterium liflandii | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_020728307.1 | Mycobacterium marinum | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007171456.1 | Mycobacterium parascrofulaceum | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_005141693.1 | Mycobacterium rhodesiae | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003894103.1 | Mycobacterium smegmatis | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003926809.1 | Mycobacterium thermoresistibile | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_006242884.1 | Mycobacterium tusciae | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003933589.1 | Mycobacterium vaccae | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_003922139.1 | Mycobacterium xenopi | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_020823195.1 | Mycobacterium yongonense | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_008474746.1 | Nitrolancea hollandica | [NiFe] Group 1h | Chloroflexi | Sphaerobacterales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_025349261.1 | Nocardia nova | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_017611790.1 | Nocardiopsis salina | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_020540932.1 | Nonomuraea coxensis | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_007412921.1 | Pedosphaera parvula | [NiFe] Group 1h | Verrucomicrobia | Verrucomicrobiales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
| WP_028930304.1 | Pseudonocardia asaccharolytica | [NiFe] Group 1h | Actinobacteria | Actinomycetales | Aerobic Uptake | Tolerant | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | [FeS] protein |
Literature
Genetics:
- Berney, M., Greening, C., Hards, K., Collins, D., and Cook, G.M. (2014) Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis. Environ. Microbiol. 16: 318-330.
- Constant, P., Chowdhury, S.P., Hesse, L., and Conrad, R. (2011) Co-localization of atmospheric H2 oxidation activity and high affinity H2-oxidizing bacteria in non-axenic soil and sterile soil amended with Streptomyces sp. PCB7. Soil Biol. Biochem. 43: 1888-1893.
- Constant, P., Chowdhury, S.P., Hesse, L., Pratscher, J., and Conrad, R. (2011) Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H2-oxidizing bacteria. Appl. Environ. Microbiol. 77: 6027-6035.
- 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.
- Khdhiri, M., Hesse, L., Popa, M.E., Quiza, L., Lalonde, I., Meredith, L.K., Röckmann, T., and Constant, P. (2015) Soil carbon content and relative abundance of high affinity H2-oxidizing bacteria predict atmospheric H2 soil uptake activity better than soil microbial community composition. Soil Biol. Biochem. 85: 1-9.
Physiology:
- Berney, M., Greening, C., Conrad, R., Jacobs, W.R., and Cook, G.M. (2014) An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia. Proc. Natl. Acad. Sci. U. S. A. 111: 11479-11484.
- Constant, P., Chowdhury, S.P., Pratscher, J., and Conrad, R. (2010) Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ. Microbiol. 12: 821-829.
- Constant, P., Poissant, L., and Villemur, R. (2008) Isolation of Streptomyces sp. PCB7, the first microorganism demonstrating high-affinity uptake of tropospheric H2. ISME J. 2: 1066-1076.
- Kanno, M., Constant, P., Tamaki, H., and Kamagata, Y. (2016) Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. Environ. Microbiol. 18: 2495-2506.
- Greening, C., Berney, M., Hards, K., Cook, G.M., and Conrad, R. (2014) A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. Proc. Natl. Acad. Sci. U. S. A. 111: 4257-61.
- Greening, C., Carere, C.R., Rushton-Green, R., Harold, L.K., Hards, K., Taylor, M.C., Morales, S.E., Stott, M.B., and Cook, G.M. (2015) Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging. Proc. Natl. Acad. Sci. 112: 10497-10502.
- Greening, C., Constant, P., Hards, K., Morales, S.E., Oakeshott, J.G., Russell, R.J., Berney, M., Conrad, R., and Cook, G.M. (2015) Atmospheric hydrogen scavenging: from enzymes to ecosystems. Appl. Environ. Microbiol. 81: 1190-1199.
- Greening, C., Villas-Bôas, S.G., Robson, J.R., Berney, M., and Cook, G.M. (2014) The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2. PLoS One 9: e103034.
- Ji, M., Greening, C., Vanwonterghem, I., Carere, C.R., Bay, S.K., Steen, J.A., Montgomery, K., Lines, T., Beardall, J., van Dorst, J., and Snape, I. (2017) Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature 552: 400-403
- Liot, Q. and Constant, P. (2015) Breathing air to save energy - new insights into the ecophysiological role of high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis. Microbiologyopen 5: 47-59
- Meredith, L.K., Rao, D., Bosak, T., Klepac-Ceraj, V., Tada, K.R., Hansel, C.M., et al. (2014) Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria. Environ. Microbiol. Rep. 6: 226-238.
- Mohammadi, S., Pol, A., van Alen, T.A., Jetten, M.S., and den Camp, H.J.O. (2017) Methylacidiphilum fumariolicum SolV, a thermoacidophilic ‘Knallgas’ methanotroph with both an oxygen-sensitive and-insensitive hydrogenase. ISME J. 11: 945-958.
Biochemistry:
- Schäfer, C., Bommer, M., Hennig, S.E., Jeoung, J.-H., Dobbek, H., and Lenz, O. (2016) Structure of an actinobacterial-type [NiFe]-hydrogenase reveals insight into O2-tolerant H2 oxidation. Structure 24: 285-292
- Schäfer, C., Friedrich, B., and Lenz, O. (2013) Novel, oxygen-insensitive group 5 [NiFe]-hydrogenase in Ralstonia eutropha. Appl. Environ. Microbiol. 79: 5137-5145.