HydDB: A web tool for hydrogenase classification and analysis

Søndergaard, Dan; Pedersen, Christian N. S.; Greening, Chris

doi:10.1101/061994

Cited by 2 publications

(2 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, while [NiFe]-hydrogenases are encoded in archaeal and bacterial genomes [32], no homologues of HycH are encoded in the operons of archaeal hydrogenases. For example, examination of the hydrogenase database HydDB indicates that there are group 4a Hyd enzymes in the archaea species Fervidicoccus fontis and Thermofilum pendens, but these lack HycH [34]. The same applies for other group 4 hydrogenases like those from Pyrococcus furiosus (group 4d).…”

Section: Discussionmentioning

confidence: 91%

The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex

Lindenstrauß

Skorupa

McDowall

et al. 2017

Biochemical Journal

View full text Add to dashboard Cite

The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membranebound formate hydrogenlyase (FHL) complex is the primary hydrogen-producing enzyme in Escherichia coli and is composed of seven subunits mostly encoded within the hycA-I operon for [NiFe]-hydrogenase-3 (Hyd-3). The HycH protein is predicted to have an accessory function and is not part of the final structural FHL complex. In this work, a mutant strain devoid of HycH was characterised and found to have significantly reduced FHL activity due to the instability of the electron transfer subunits. HycH was shown to interact specifically with the unprocessed species of HycE, the catalytic hydrogenase subunit of the FHL complex, at different stages during the maturation and assembly of the complex. Variants of HycH were generated with the aim of identifying interacting residues and those that influence activity. The R70/71/K72, the Y79, the E81 and the Y128 variant exchanges interrupt the interaction with HycE without influencing the FHL activity. In contrast, FHL activity, but not the interaction with HycE, was negatively influenced by H37 exchanges with polar residues. Finally, a HycH Y30 variant was unstable. Surprisingly, an overlapping function between HycH with its homologous counterpart HyfJ from the operon encoding [NiFe]-hydrogenase-4 (Hyd-4) was identified and this is the first example of sharing maturation machinery components between Hyd-3 and Hyd-4 complexes. The data presented here show that HycH has a novel dual role as an assembly chaperone for a cytoplasmic [NiFe]-hydrogenase.

show abstract

Section: Discussionmentioning

confidence: 91%

The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex

Lindenstrauß

Skorupa

McDowall

et al. 2017

Biochemical Journal

View full text Add to dashboard Cite

show abstract

“…The genes of interest were retrieved from the downloaded metagenomes by BLAST using the hhyL, coxL, and rbcL1E gene sequences identified from the Robinson Ridge metagenome as queries. The identity of the retrieved type I coxL and type IE rbcL large subunit genes was confirmed by constructing phylogenetic trees as described above, whereas genes encoding group 1h [NiFe]-hydrogenase large subunits were identified using HydDB 53 . The relative abundance of the three genes was compared with those in five public forest metagenomes (JGI IDs 66726, 69782, 92543, 94443, 109646).…”

mentioning

confidence: 99%

Atmospheric trace gases support primary production in Antarctic desert surface soil

Greening

Vanwonterghem

et al. 2017

Nature

307

306

View full text Add to dashboard Cite

Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities 1-3 . Given that phototroph abundance varies across these Antarctic soils 2,4 , an enduring question is what supports life in those communities with low photosynthetic capacity 3,5 . Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation 6,7 . Soil microcosms aerobically scavenged atmospheric H 2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO 2 fixation. We propose that atmospheric H 2 , CO 2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources 8,9 . Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.Terrestrial Antarctica is among the most extreme environments on Earth. Its inhabitants experience the cumulative stresses of freezing temperatures, limited carbon, nitrogen and water availability, strong UV radiation, and frequent freeze-thaw cycles 2,10,11 . Although it was once believed that these conditions restrict life, we now know that the continent hosts a surprising diversity of macrofauna and microbiota 1,2,12 . Surveys indicate that the phylum-level composition of microbial communities in Antarctic soils is similar to those of temperate soils 3 , but Antarctic communities are highly specialized at the species level and strongly structured by physicochemical factors 1,3,10 . In many Antarctic soils, microorganisms are thought to live in dormant states 2 , with metabolic energy directed towards cell maintenance rather than growth 13 . However, it is unclear how these communities obtain the energy and carbon needed for maintenance, given that these soils are often low in organic carbon and contain few classical primary producers 2,5 .

show abstract

HydDB: A web tool for hydrogenase classification and analysis

Cited by 2 publications

References 48 publications

The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex

The dual-function chaperone HycH improves assembly of the formate hydrogenlyase complex

Atmospheric trace gases support primary production in Antarctic desert surface soil

Contact Info

Product

Resources

About