How Escherichia coli is equipped to oxidize hydrogen under different redox conditions.

Lukey, Michael J.; Parkin, Alison; Roessler, Maxie M.; Murphy, Bonnie J.; Harmer, Jeffrey; Palmer, Tracy; Sargent, Frank; Armstrong, Fräser A.

doi:10.1074/jbc.a109.067751

Cited by 57 publications

(131 citation statements)

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“…The results in the present study support the previously made conclusion (11,43,45,54 (24,43,85 (53) and of the membrane-bound type (MBH) from R. eutropha (25,31). Two CN -and one CO at the active site iron were inferred by FTIR (43).…”

Section: Resultssupporting

confidence: 81%

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

et al. 2011

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Molecular features that allow certain [NiFe] hydrogenases to catalyze the conversion of molecular hydrogen (H2) in the presence of dioxygen (O2) were investigated. Using X-ray absorption spectroscopy (XAS), we compared the [NiFe] active site and FeS clusters in the O2-tolerant membrane-bound hydrogenase (MBH) of Ralstonia eutropha and the O2-sensitive periplasmic hydrogenase (PH) of Desulfovibrio gigas. Fe-XAS indicated an unusual complement of iron–sulfur centers in the MBH, likely based on a specific structure of the FeS cluster proximal to the active site. This cluster is a [4Fe4S] cubane in PH. For MBH, it comprises less than ~2.7 Å Fe–Fe distances and additional longer vectors of ≥3.4 Å, consistent with an Fe trimer with a more isolated Fe ion. Ni-XAS indicated a similar architecture of the [NiFe] site in MBH and PH, featuring Ni coordination by four thiolates of conserved cysteines, i.e., in the fully reduced state (Ni-SR). For oxidized states, short Ni−μO bonds due to Ni–Fe bridging oxygen species were detected in the Ni-B state of the MBH and in the Ni-A state of the PH. Furthermore, a bridging sulfenate (CysSO) is suggested for an inactive state (Niia-S) of the MBH. We propose that the O2 tolerance of the MBH is mainly based on a dedicated electron donation from a modified proximal FeS cluster to the active site, which may favor formation of the rapidly reactivated Ni-B state instead of the slowly reactivated Ni-A state. Thereby, the catalytic activity of the MBH is facilitated in the presence of both H2 and O2.

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Section: Resultssupporting

confidence: 81%

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

et al. 2011

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“…However, based on recent models, it is likely that a large proportion is reoxidised through the respiratory Rnf complex, which generates sodium/protonmotive force by coupling Fd red oxidation to NAD C reduction. 26,36 The only quantitatively abundant [NiFe] uptake hydrogenases detected were the oxygen-tolerant respiratory uptake hydrogenases (Group 1d [NiFe]-hydrogenases); 37 such enzymes have been linked to reoxidation of fermentatively-produced H 2 and might also contribute the metabolic flexibility needed for facultative anaerobes such as E. coli to transition between host-associated and free-living states. 38 Between them, such processes would enable the majority of H 2 produced in the human colon to be reoxidised without formation of detectable endproducts.…”

Section: Discussionmentioning

confidence: 99%

H₂metabolism is widespread and diverse among human colonic microbes

et al. 2016

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Microbial molecular hydrogen (H 2 ) cycling is central to metabolic homeostasis and microbial composition in the human gastrointestinal tract. Molecular H 2 is produced as an endproduct of carbohydrate fermentation and is reoxidised primarily by sulfate-reduction, acetogenesis, and methanogenesis. However, the enzymatic basis for these processes is incompletely understood and the hydrogenases responsible have not been investigated. In this work, we surveyed the genomic and metagenomic distribution of hydrogenase-encoding genes in the human colon to infer dominant mechanisms of H 2 cycling. The data demonstrate that 70% of gastrointestinal microbial species listed in the Human Microbiome Project encode the genetic capacity to metabolise H 2 . A wide variety of anaerobicallyadapted hydrogenases were present, with [FeFe]-hydrogenases predominant. We subsequently analyzed the hydrogenase gene content of stools from 20 healthy human subjects. The hydrogenase gene content of all samples was overwhelmingly dominated by fermentative and electron-bifurcating [FeFe]-hydrogenases emerging from the Bacteroidetes and Firmicutes. This study supports that H 2 metabolism in the human gut is driven by fermentative H 2 production and interspecies H 2 transfer. However, it suggests that electron-bifurcation rather than respiration is the dominant mechanism of H 2 reoxidation in the human colon, generating reduced ferredoxin to sustain carbon-fixation (e.g. acetogenesis) and respiration (via the Rnf complex). This work provides the first comprehensive bioinformatic insight into the mechanisms of H 2 metabolism in the human colon.

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“…How this is achieved in C. jejuni is largely unknown. In E. coli, which expresses at least three distinct NiFe hydrogenases (Lukey et al, 2010) plus the nickel enzyme glyoxylase I (Clugston et al, 1998), expression of the nikABCDE operon is under dual control. Firstly, the global regulator FNR induces the nik operon under low-oxygen conditions, and mutations in fnr abolish nik expression (Wu et al, 1989).…”

Section: Discussionmentioning

confidence: 99%

Hydrogenase activity in the foodborne pathogen Campylobacter jejuni depends upon a novel ABC-type nickel transporter (NikZYXWV) and is SlyD-independent

et al. 2012

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Campylobacter jejuni is a human pathogen of worldwide significance. It is commensal in the gut of many birds and mammals, where hydrogen is a readily available electron donor. The bacterium possesses a single membrane-bound, periplasmic-facing NiFe uptake hydrogenase that depends on the acquisition of environmental nickel for activity. The periplasmic binding protein Cj1584 (NikZ) of the ATP binding cassette (ABC) transporter encoded by the cj1584c-cj1580c (nikZYXWV) operon in C. jejuni strain NCTC 11168 was found to be nickel-repressed and to bind free nickel ions with a submicromolar K d value, as measured by fluorescence spectroscopy. Unlike the Escherichia coli NikA protein, NikZ did not bind EDTA-chelated nickel and lacks key conserved residues implicated in metallophore interaction. A C. jejuni cj1584c null mutant strain showed an approximately 22-fold decrease in intracellular nickel content compared with the wildtype strain and a decreased rate of uptake of 63 NiCl 2 . The inhibition of residual nickel uptake at higher nickel concentrations in this mutant by hexa-ammine cobalt (III) chloride or magnesium ions suggests that low-affinity uptake occurs partly through the CorA magnesium transporter. Hydrogenase activity was completely abolished in the cj1584c mutant after growth in unsupplemented media, but was fully restored after growth with 0.5 mM nickel chloride. Mutation of the putative metallochaperone gene slyD (cj0115) had no effect on either intracellular nickel accumulation or hydrogenase activity. Our data reveal a strict dependence of hydrogenase activity in C. jejuni on high-affinity nickel uptake through an ABC transporter that has distinct properties compared with the E. coli Nik system.

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How Escherichia coli is equipped to oxidize hydrogen under different redox conditions.

Cited by 57 publications

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[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

H₂metabolism is widespread and diverse among human colonic microbes

Hydrogenase activity in the foodborne pathogen Campylobacter jejuni depends upon a novel ABC-type nickel transporter (NikZYXWV) and is SlyD-independent

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How Escherichia coli is equipped to oxidize hydrogen under different redox conditions.

Cited by 57 publications

References 0 publications

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage

H2metabolism is widespread and diverse among human colonic microbes

Hydrogenase activity in the foodborne pathogen Campylobacter jejuni depends upon a novel ABC-type nickel transporter (NikZYXWV) and is SlyD-independent

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[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

[NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O₂-Tolerant H₂ Cleavage

H₂metabolism is widespread and diverse among human colonic microbes