Overproduction of the prismane protein from Desulfovibrio desulfuricans ATCC 27774 in Desulfovibrio vulgaris (Hildenborough) and EPR spectroscopy of the [6Fe-6S] cluster in different redox states

Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon

Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.

A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold

Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-VCh . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-VCh catalyzes neither CO oxidation, nor CO2 reduction. The active site of CooS-VCh undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H2 O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-VCh , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.

Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion

Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.

Hybrid cluster proteins in a photosynthetic microalga

Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.

Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part IV. Canonical, non-canonical and hybrid iron-sulfur proteins

A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)₄}, {[Fe₂S₂](Cys)₄}, {[Fe₂S₂](Cys)₃(X)} (X = Asp, Arg, His), {[Fe₂S₂](Cys)₂(His)₂}, {[Fe₃S₄](Cys)₃}, {[Fe₄S₄](Cys)₄} and {[Fe₄S₄](Cys)₃(nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters. Our target is now to review structure and electrochemistry of proteins harboring canonical, non-canonical and hybrid iron-sulfur proteins.

Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio

Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H₂ with CO₂ during sulfate reduction are exhibited by some strains. The ability to produce or consume H₂ provides Desulfovibrio strains the capacity to participate as either partner in interspecies H₂ transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c₃ (Tp1-c₃), or the Type 1 cytochrome c₃:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration.

A thermostable hybrid cluster protein from Pyrococcus furiosus: effects of the loss of a three helix bundle subdomain

Pyrococcus furiosus hybrid cluster protein (HCP) was expressed in Escherichia coli, purified, and characterized. This is the first archaeal and thermostable HCP to be isolated. Compared with the protein sequences of previously characterized HCPs from mesophiles, the protein sequence of P. furiosus HCP exhibits a deletion of approximately 13 kDa as a single amino acid stretch just after the N-terminal cysteine motif, characteristic for class-III HCPs from (hyper)thermophilic archaea and bacteria. The protein was expressed as a thermostable, soluble homodimeric protein. Hydroxylamine reductase activity of P. furiosus HCP showed a K_m value of 0.40 mM and a k_cat value of 3.8 s⁻¹ at 70 °C and pH 9.0. Electron paramagnetic resonance spectroscopy showed evidence for the presence of a spin-admixed, S = 3/2 [4Fe–4S]⁺ cubane cluster and of the hybrid cluster. The cubane cluster of P. furiosus HCP is presumably coordinated by a CXXC–X₇–C–X₅–C motif close to the N-terminus, which is similar to the CXXC–X₈–C–X₅–C motif of the Desulfovibrio desulfuricans and Desulfovibrio vulgaris HCPs. Amino acid sequence alignment and homology modeling of P. furiosus HCP reveal that the deletion results in a loss of one of the two three-helix bundles of domain 1. Clearly the loss of one of the three-helix bundles of domain 1 does not diminish the hydroxylamine reduction activity and the incorporation of the iron–sulfur clusters.

The Role of the Hybrid Cluster Protein in Oxidative Stress Defense

Hybrid cluster proteins (HCP) contain two types of Fe/S clusters, namely a [4Fe-4S](2+/1+) or [2Fe-2S](2+/1+) cluster and a novel type of hybrid cluster, [4Fe-2S-2O], in the as-isolated state. Although first isolated from anaerobic sulfate-reducing bacteria, the analysis of the genomic sequences reveals that genes encoding putative hybrid cluster proteins are present in a wide range of organisms, aerobic, anaerobic, or facultative, from the Bacteria, Archaea, and Eukarya domains. Despite a detailed spectroscopic and structural characterization, the precise physiological function of these proteins remained unknown. The present work shows that the transcription of the Escherichia coli hcp gene is induced by hydrogen peroxide, and this induction is regulated by the redox-sensitive transcriptional activator, OxyR. The E. coli hcp mutant strain exhibits higher sensitivity to hydrogen peroxide, a behavior that reverts to the wild type phenotype once a plasmid carrying the hcp gene is reintroduced. Furthermore, the purified HCPs from E. coli and Desulfovibrio desulfuricans ATCC 27774 show an alternative enzymatic activity, which under physiological conditions exhibited K(m) values for hydrogen peroxide (approximately 0.3 mM) within the range of other peroxidases. Altogether, the results reveal that HCP is involved in oxidative stress protection.

Transcriptional regulation of a hybrid cluster (prismane) protein

HCP (hybrid-cluster protein) contains two Fe/S clusters, one of which is a hybrid [4Fe-2S-2O] cluster. Despite intensive study, its physiological function has not been reported. The Escherichia coli hcp gene is located in a two-gene operon with hcr, which encodes an NADH-dependent HCP reductase. E. coli HCP is detected after anaerobic growth with nitrate or nitrite: possible roles for it in hydroxylamine or nitric oxide reduction have been proposed. To study the regulation and role of HCP, an hcp::lacZ fusion was constructed and transformed into fnr, arcA and norR mutant strains of E. coli. Transcription from the hcp promoter was induced during anaerobic growth. Only the fnr mutant was defective in hcp expression. Nitrate- and nitrite-induced transcription from the hcp promoter was activated by the response regulator proteins NarL and NarP. Gel retardation assays were used to show that FNR (fumarate-nitrate regulation) and NarL form a complex with the hcp promoter. Transcription of the hcp-hcr operon initiates at a thymine nucleotide located 31 bp upstream of the translation-initiation codon. HCP has been overexpressed from a recombinant plasmid for physiological studies.

Hydroxylamine Assimilation by Rhodobacter capsulatus E1F1

Rhodobacter capsulatus E1F1 grows phototrophically with nitrate as nitrogen source. Using primers designed for conserved motifs in bacterial assimilatory nitrate reductases, a 450-bp DNA was amplified by PCR and used for the screening of a genomic library. A cosmid carrying an insert with four SalI fragments of 2.8, 4.1, 4.5, and 5.8 kb was isolated, and DNA sequencing revealed that it contains a nitrate assimilation (nas) gene region, including the hcp gene coding for a hybrid cluster protein (HCP). Expression of hcp is probably regulated by a nitrite-sensitive repressor encoded by the adjacent nsrR gene. A His(6)-HCP was overproduced in Escherichia coli and purified. HCP contained about 6 iron and 4 labile sulfide atoms per molecule, in agreement with the presence of both [2Fe-2S] and [4Fe-2S-2O] clusters, and showed hydroxylamine reductase activity, forming ammonia in vitro with methyl viologen as reductant. The apparent K(m) values for NH(2)OH and methyl viologen were 1 mM and 7 microM, respectively, at the pH and temperature optima (9.3 and 40 degrees C). The activity was oxygen-sensitive and was inhibited by sulfide and iron reagents. R. capsulatus E1F1 grew phototrophically, but not heterotrophically, with 1 mM NH(2)OH as nitrogen source, and up to 10 mM NH(2)OH was taken up by anaerobic resting cells. Ammonium was transiently accumulated in the media, and its assimilation was prevented by L-methionine-D,L-sulfoximine, a glutamine synthetase inhibitor. In addition, hydroxylamine- or nitrite-grown cells showed the higher hydroxylamine reductase activities. However, R. capsulatus B10S, a strain lacking the whole hcp-nas region, did not grow with 1 mM NH(2)OH. Also, E. coli cells overproducing HCP tolerate hydroxyl-amine better during anaerobic growth. These results suggest that HCP is involved in assimilation of NH(2)OH, a toxic product that could be formed during nitrate assimilation, probably in the nitrite reduction step.

Cloning, sequencing and expression of the tetraheme cytochrome c(3) from Desulfovibrio gigas

The gene encoding the tetraheme cytochrome c(3) from Desulfovibrio gigas was cloned and sequenced from a 2.7-kb EcoRI-PstI insert of D. gigas DNA. The derived amino acid sequence showed that the D. gigas cytochrome c(3) is synthesized as a precursor protein with an N-terminal signal peptide sequence of 25 residues and allowed the correction of the previous reported amino acid sequence (Matias et al. Protein Science 5 (1996) 1342-1354). Expression in D. vulgaris (Hildenborough) was possible by conjugal transfer of a recombinant broad-host-range vector pSUP104 containing a SmaI fragment of the D. gigas cytochrome c(3) gene. Biochemical, immunological and spectroscopic analysis of the purified protein showed that the recombinant cytochrome is identical to that isolated from D. gigas.

The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]

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 degrees C, pH 7.5) for the Fe/S clusters in both proteins indicate that electrons derived from the oxidation of NADH (Em NADH/NAD+ couple: -320 mV) are transferred along the [2Fe-2S] cluster of the NADH oxidoreductase (Em = -220 mV) and the [2Fe-2S] cluster of the hybrid-cluster protein (Em = -35 mV) to the hybrid cluster (Em = -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.

Carbon monoxide dehydrogenase from Methanosarcina frisia Gö1. Characterization of the enzyme and the regulated expression of two operon-like cdh gene clusters

Carbon monoxide dehydrogenase (Cdh) has been anaerobically purified from Methanosarcina frisia Gö1. The enzyme is a Ni2+-, Fe2+-, and S2--containing alpha2beta2 heterotetramer of 214 kDa with a pI of 5.2 and subunits of 94 and 19 kDa. It has a Vmax of 0.3 mmol of CO min-1 mg-1 and Km values for CO and methyl viologen of approximately 0.9 mM and 0.12 mM, respectively. EPR spectroscopy on the reduced enzyme showed two overlapping signals: one indicative for 2 (4Fe-4S)+ clusters and a second signal that is atypical for standard Fe/S clusters. The latter was, together with high-spin EPR signals of the oxidized enzyme tentatively assigned to an Fe/S cluster of high nuclearity.

Reversible super-reduction of the cubane [4Fe-4S](3+;2+;1+) in the high-potential iron-sulfur protein under non-denaturing conditions. EPR spectroscopic and electrochemical studies

The reversible 2 x 1 e- reduction of the cubane cluster from oxidized to reduced to super-reduced states ([4Fe-4S]3+<-->[4Fe-4S]2+<-->[4Fe-4S]1+) was studied in high-potential iron-sulfur proteins (HiPIPs). Super-reduction to the 1+ state was not observed in any of the seven HiPIPs tested during cyclic voltammetry (down to -0.95 V). However, equilibration at low potential (pH 7.5) of Rhodopila globiformis HiPIP yields a transient peak around -0.47 V due to the oxidation of super-reduced HiPIP adsorbed at the electrode. The peak area depends on the equilibration potential according to a one-electron Nernst curve with a half-wave potential at -0.91 V. Reduction of R. globiformis HiPIP with titanium (III)citrate at pH 9.5 is very slow [pseudo-first-order half-life of 23 min with a 100-fold excess Ti(III)] but is reversible, and the EPR spectrum with g values of 2.04 and 1.92 is similar to that of reduced [4Fe-4S]1+ ferredoxins. Chemical or electrochemical reoxidation of the super-reduced form resulted in an EPR spectrum with g parallel = 2.12 and g perpendicular = 2.03, i.e. identical to that of oxidized HiPIP. From the equilibrium concentration of super-reduced HiPIP at a low concentration of Ti(III), a reduction potential of -0.64 V can be estimated. Super-reduction of the large HiPIP (iso-2) from Rhodospirillum salinarum is also possible with Ti(III)(gz = 2.05) but the super-reduced state is unstable. No super-reduction with Ti(III) was observed for the other HiPIPs. The difference between the electrochemically observed reduction potential and oxidation potential is explained by a fast and reversible conformational change upon super-reduction. The rate of super-reduction with Ti(III) is limited by the small amount (0.1%) of HiPIP in the 2+ state with the super-reduced conformation.

Characterization of the prismane protein from Desulfovibrio vulgaris (Hildenborough) by low-temperature magnetic circular dichroic spectroscopy

The prismane protein of Desulfovibrio vulgaris (Hildenborough) contains a putative [6Fe-6S] cluster. This novel iron-sulfur cluster has been characterized here by magnetic circular dichroism (MCD) spectroscopy. Three paramagnetic redox states of the cluster, [6Fe-6S]5+, [6Fe-6S]4+ and [6Fe-6S]3+, each show a distinctive low-temperature MCD spectrum which is unlike that observed for any other iron-sulfur clusters. Magnetization data for the prismane protein in these three redox states indicate ground state spins that are in accordance with previous EPR assignments. For the protein as isolated, with the [6Fe-6S]5+ form of the cluster, magnetizations show an exceptionally steep initial slope that can be fit to a ground state of spin S = 9/2. For the semi-reduced protein, the cluster in the [6Fe-6S]4+ form, magnetizations show an initial slope characteristic for a ground state of spin S = 4. For the dithionite-reduced protein, with the [6Fe-6S]3+ form of the cluster, magnetizations are typical for a ground state of spin S = 1/2.

Electrochemical study of the redox properties of [2Fe-2S] ferredoxins. Evidence for superreduction of the Rieske [2Fe-2S] cluster

Direct, unmediated electrochemistry has been used to compare the redox properties of [2Fe-2S] clusters in spinach ferredoxin, Spirulina platensis ferredoxin and the water soluble fragment of the Rieske protein. The use of electrochemistry enabled, for the first time, the observation of the second reduction step, [Fe(III), Fe(II)] to [Fe(II), Fe(II)], in a biological [2Fe-2S] system. A water-soluble fragment of the Rieske protein from bovine heart bc1 complex exhibits two subsequent quasi-reversible responses in cyclic voltammetry on activated glassy carbon. In contrast the ferredoxins from spinach and Spirulina platensis only show one single reduction potential. These results support a seniority scheme for biological iron-sulfur clusters related cluster size to electron transfer versatility. Electrochemical reduction of spinach ferredoxin in the presence of NADP+ and ferredoxin: NADP+ oxidoreductase results in the generation of NADPH. The second order rate constant for the reaction between the ferredoxin and the reductase was estimated from cyclic voltammetry experiments to be > 3.10(5) M-1.s-1.