The primary structure of a protein containing a putative [6Fe‐6S] prismane cluster from <i>Desulfovibrio vulgaris</i> (Hildenborough)

Stokkermans, J.P.W.G.; Pierik, Antonio J.; Wolbert, R.B.G.; Hagen, Wilfred R.; Dongen, W.M.A.M. van; Veeger, C.

doi:10.1111/j.1432-1033.1992.tb17205.x

Cited by 43 publications

(18 citation statements)

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“…HCP and the gene encoding this protein have previously been isolated from D. vulgaris (Hildenborough) and D. desulfuricans ATCC 27774 [1–4,8,21,22]. Cross‐reactivity with antibodies and hybridization with nucleic acid probes indicated that proteins and DNA sequences with similarity to D. vulgaris HCP and the hcp gene, respectively, also occur in other strictly anaerobic sulfate‐reducing bacteria [2,22]. However, screening of recent sequence databases suggests a much wider distribution of the hcp gene within the bacterial and archaeal kingdoms.…”

Section: Resultsmentioning

confidence: 99%

The hybrid‐cluster protein (‘prismane protein’) from Escherichia coli

Berg

Hagen

Dongen

2000

European Journal of Biochemistry

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Hybrid-cluster proteins (`prismane proteins') have previously been isolated and characterized from strictly anaerobic sulfate-reducing bacteria. These proteins contain two types of Fe/S clusters unique in biological systems: a [4Fe±4S] cubane cluster with spin-admixed S = 3/2 ground-state paramagnetism and a novel type of hybrid [4Fe±2S±2O] cluster, which can attain four redox states.Genomic sequencing reveals that genes encoding putative hybrid-cluster proteins are present in a range of bacterial and archaeal species. In this paper we describe the isolation and spectroscopic characterization of the hybrid-cluster protein from Escherichia coli. EPR spectroscopy shows the presence of a hybrid cluster in the E. coli protein with characteristics similar to those in the proteins of anaerobic sulfate reducers. EPR spectra of the reduced E. coli hybrid-cluster protein, however, give evidence for the presence of a [2Fe±2S] cluster instead of a [4Fe±4S] cluster. The hcp gene encoding the hybrid-cluster protein in E. coli and other facultative anaerobes occurs, in contrast with hcp genes in obligate anaerobic bacteria and archaea, in a small operon with a gene encoding a putative NADH oxidoreductase. This NADH oxidoreductase was also isolated and shown to contain FAD and a [2Fe±2S] cluster as cofactors. It catalysed the reduction of the hybrid-cluster protein with NADH as an electron donor. Midpoint potentials (25 8C, pH 7.5) for the Fe/S clusters in both proteins indicate that electrons derived from the oxidation of NADH (E m NADH/NAD + couple: 2320 mV) are transferred along the [2Fe±2S] cluster of the NADH oxidoreductase (E m = ±220 mV) and the [2Fe±2S] cluster of the hybrid-cluster protein (E m = ±35 mV) to the hybrid cluster (E m = ±50, +85 and +365 mV for the three redox transitions).The physiological function of the hybrid-cluster protein has not yet been elucidated. The protein is only detected in the facultative anaerobes E. coli and Morganella morganii after cultivation under anaerobic conditions in the presence of nitrate or nitrite, suggesting a role in nitrate-and/or nitrite respiration.Keywords: EPR; hybrid-cluster protein (`prismane protein'); NAD(H) oxidoreductase; nitrate regulation; redox titration.The`hybrid-cluster protein' (HCP, formerly named`prismane protein') was initially purified from species of the strictly anaerobic sulfate-reducing bacterial genus Desulfovibrio: D. vulgaris (Hildenborough) [1,2] and D. desulfuricans ATCC 27774 [3,4]. This soluble cytoplasmic protein has been extensively studied because of the unusual properties of its redox-active iron clusters. Initial characterization with EPR and Mo Èssbauer spectroscopy suggested the presence of an Fe/S cluster with magnetic properties similar to those of synthetic [6Fe±6S] model compounds (`prismane' clusters; hence the name`prismane protein' was initially proposed for this protein) [1,5].Recently, the three-dimensional structure of the D. vulgaris HCP' at 1.7 A Ê resolution was obtained by X-ray crystallography [6]. The structure reveal...

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Section: Resultsmentioning

confidence: 99%

The hybrid‐cluster protein (‘prismane protein’) from Escherichia coli

Berg

Hagen

Dongen

2000

European Journal of Biochemistry

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“…We have found no homology to the E. coli region of fur. However, no consensus promoter sequence has yet emerged from the known D. vulgaris gene sequences (48,51,54). Therefore, based on our present results, the 0.8-kb band could represent either an independent rbr-rdl transcript or a processed (or degraded) version of the fur-rbr-rdl transcript.…”

Section: Resultsmentioning

confidence: 99%

A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough)

et al. 1997

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Rubrerythrin is a nonheme iron protein of unknown function isolated from Desulfovibrio vulgaris (Hildenborough). We have sequenced a 3.3-kbp SalI fragment of D. vulgaris chromosomal DNA containing the rubrerythrin gene, rbr, identified additional open reading frames (ORFs) adjacent to rbr, and shown that these ORFs are part of a transcriptional unit containing rbr. One ORF, designated fur, lies just upstream of rbr and encodes a 128-amino-acid-residue protein which shows homology to Fur (ferric uptake regulatory) proteins from other purple bacteria. The other ORF, designated rdl, lies just downstream of rbr and encodes a 74-residue protein with significant sequence homology to rubredoxins but with a different number and spacing of cysteine residues. Overexpression of rdl in Escherichia coli yielded a protein, Rdl, which has spectroscopic properties and iron content consistent with one Fe 3؉ (SCys) 4 site per polypeptide but is clearly distinct from both rubrerythrin and a related protein, nigerythrin. Northern analysis indicated that fur, rbr, and rdl were each present on a transcript of 1.3 kb; i.e., these three genes are cotranscribed. Because D. vulgaris nigerythrin appears to be closely related to rubrerythrin, and its function is also unknown, we cloned and sequenced the gene encoding nigerythrin, ngr. The amino acid sequence of nigerythrin is 33% identical to that of rubrerythrin, and all residues which furnish iron ligands to both the FeS 4 and diiron-oxo sites in rubrerythrin are conserved in nigerythrin. Despite the close resemblance of these two proteins, ngr was found to be no closer than 7 kb to rbr on the D. vulgaris chromosome, and Northern analysis showed that, in contrast to rbr, ngr is not cotranscribed with other genes. Possible redox-linked functions for rubrerythrin and nigerythrin in iron homeostasis are proposed.Rubrerythrin (Rr) is one of a large number of nonheme iron proteins found in anaerobic sulfate-reducing bacteria (16,28). Rr was isolated from Desulfovibrio vulgaris (Hildenborough) as a 44-kDa homodimer which exhibited spectroscopic signatures characteristic of two distinct types of iron sites: one rubredoxin-like FeS 4 site and one nonsulfur, oxo-bridged diiron site. The crystal structure of recombinant D. vulgaris Rr (10) revealed that each subunit is folded into two domains: an Nterminal four-helix bundle surrounding the oxo-bridged diiron site, and a smaller C-terminal rubredoxin-like protein fold surrounding the FeS 4 site. Rr can be structurally classified as a member of a continually expanding class of so-called diironoxo proteins (20,30). This class of proteins contains an oxo-or hydroxo-bridged diiron site connected to the protein by carboxylate and histidine ligands and embedded within a fourhelix bundle protein fold. Other members of this class utilize O 2 for functions ranging from tyrosyl radical generation and hydrocarbon hydroxylation in prokaryotes, fatty acyl desaturation in plants, and reversible O 2 binding in invertebrates (20). The iron storage proteins ferriti...

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“…2B). The D. vulgaris genome sequence indicated the presence of hcp2 in addition to hcp1, encoding hybrid cluster protein 1, previously referred to as prismane protein (23). Hcps are induced by nitrate, nitrite, nitric oxide, and/or hydrogen peroxide, suggesting a role in nitrogen metabolism and/or oxidative stress defense (2,3,10).…”

Section: Discussionmentioning

confidence: 99%

Physiological and Gene Expression Analysis of Inhibition of Desulfovibrio vulgaris Hildenborough by Nitrite

et al. 2004

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A Desulfovibrio vulgaris Hildenborough mutant lacking the nrfA gene for the catalytic subunit of periplasmic cytochrome c nitrite reductase (NrfHA) was constructed. In mid-log phase, growth of the wild type in medium containing lactate and sulfate was inhibited by 10 mM nitrite, whereas 0.6 mM nitrite inhibited the nrfA mutant. Lower concentrations (0.04 mM) inhibited the growth of both mutant and wild-type cells on plates. Macroarray hybridization indicated that nitrite upregulates the nrfHA genes and downregulates genes for sulfate reduction enzymes catalyzing steps preceding the reduction of sulfite to sulfide by dissimilatory sulfite reductase (DsrAB), for two membrane-bound electron transport complexes (qmoABC and dsrMKJOP) and for ATP synthase (atp). DsrAB is known to bind and slowly reduce nitrite. The data support a model in which nitrite inhibits DsrAB (apparent dissociation constant K m for nitrite ‫؍‬ 0.03 mM), and in which NrfHA (K m for nitrite ‫؍‬ 1.4 mM) limits nitrite entry by reducing it to ammonia when nitrite concentrations are at millimolar levels. The gene expression data and consideration of relative gene locations suggest that QmoABC and DsrMKJOP donate electrons to adenosine phosphosulfate reductase and DsrAB, respectively. Downregulation of atp genes, as well as the recorded cell death following addition of inhibitory nitrite concentrations, suggests that the proton gradient collapses when electrons are diverted from cytoplasmic sulfate to periplasmic nitrite reduction.Sulfate-reducing bacteria are frequently exposed to nitrite by interaction with nitrate-reducing, sulfide-oxidizing bacteria in anoxic environments. Because sulfate is often the predominant electron acceptor in anoxic environments (e.g., marine sediments), sulfate-reducing bacteria are primarily responsible for organic carbon oxidation. The sulfide produced is then targeted by nitrate-reducing, sulfide-oxidizing bacteria, which generally use CO 2 as their sole carbon source (4). Thus, sulfate-reducing bacteria and nitrate-reducing, sulfide-oxidizing bacteria symbiotically catalyze the oxidation of organic matter with nitrate through a sulfide intermediate. This symbiosis can potentially be stalled by production of nitrite by the nitratereducing, sulfide-oxidizing bacteria, which is a powerful inhibitor of sulfate-reducing bacteria. Some sulfate-reducing bacteria have a periplasmic nitrite reductase to prevent and/or overcome this inhibition. Cocultures of a Desulfovibrio sp. and the nitrate-reducing, sulfide-oxidizing bacterium Thiomicrospira sp. strain CVO were strongly or transiently inhibited, depending on the absence or presence of nitrite reductase activity in the Desulfovibrio sp. (6). Desulfovibrio vulgaris Hildenborough was very resistant to inhibition by either nitrite or strain CVO and nitrate and had high nitrite reductase activity through the presence of a periplasmic cytochrome c nitrite reductase (NrfHA) that reduces nitrite to ammonium. This reaction is purely detoxifying; no cell growth is associated with t...

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The primary structure of a protein containing a putative [6Fe‐6S] prismane cluster from Desulfovibrio vulgaris (Hildenborough)

Cited by 43 publications

References 58 publications

The hybrid‐cluster protein (‘prismane protein’) from Escherichia coli

The hybrid‐cluster protein (‘prismane protein’) from Escherichia coli

A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough)

Physiological and Gene Expression Analysis of Inhibition of Desulfovibrio vulgaris Hildenborough by Nitrite

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