Structure-function relationships among the nickel-containing hydrogenases

Biohybrid Systems for Improved Bioinspired, Energy-Relevant Catalysis

Biomimetic catalysts, ranging from small-molecule metal complexes to supramolecular assembles, possess many exciting properties that could address salient challenges in industrial-scale manufacturing. Inspired by natural enzymes, these biohybrid catalytic systems demonstrate superior characteristics, including high activity, enantioselectivity, and enhanced aqueous solubility, over their fully synthetic counterparts. However, instability and limitations in the prediction of structure-function relationships are major drawbacks that often prevent the application of biomimetic catalysts outside of the laboratory. Despite these obstacles, recent advances in synthetic enzyme models have improved our understanding of complicated biological enzymatic processes and enabled the production of catalysts with increased efficiency. This review outlines important developments and future prospects for the design and application of bioinspired and biohybrid systems at multiple length scales for important, biologically relevant, clean energy transformations.

In vitro assessment of the impact of nickel on the viability and steroidogenesis in the human adrenocortical carcinoma (NCI-H295R) cell line

Nickel is a ubiquitous environmental pollutant, which has various effects on reproductive endocrinology. In this study, human adrenocortical carcinoma (NCI-H295R) cell line was used as an in vitro biological model to study the effect of nickel chloride (NiCl2) on the viability and steroidogenesis. The cells were exposed to different concentrations (3.90; 7.80; 15.60; 31.20; 62.50; 125; 250 and 500 microM) of NiCl2 and compared with control group (culture medium without NiCl2). The cell viability was measured by the metabolic activity assay. Production of sexual steroid hormones was quantified by enzyme linked immunosorbent assay. Following 48 h culture of the cells in the presence of NiCl2 a dose-dependent depletion of progesterone release was observed even at the lower concentrations. In fact, lower levels of progesterone were detected in groups with higher doses (>/=125 microM) of NiCl2 (P<0.01), which also elicited cytotoxic action. A more prominent decrease in testosterone production (P<0.01) was also noted in comparison to that of progesterone. On the other hand, the release of 17beta-estradiol was substantially increased at low concentrations (3.90 to 62.50 microM) of NiCl2. The cell viability remained relatively unaltered up to 125 microM (P>0.05) and slightly decreased from 250 microM of NiCl2 (P<0.05). Our results indicate endocrine disruptive effect of NiCl2 on the release of progesterone and testosterone in the NCI-H295R cell line. Although no detrimental effect of NiCl2 (</=62.50 microM) could be found on 17beta-estradiol production, its toxicity may reflect at other points of the steroidogenic pathway.

Catalytic H2 evolution/oxidation in [FeFe]-hydrogenase biomimetics: account from DFT on the interplay of related issues and proposed solutions

A DFT overview on selected issues regarding diiron catalysts related to [FeFe]-hydrogenase biomimetic research, with implications for both energy conversion and storage strategies.

Synthesis, Magnetic Properties, and Catalytic Properties of a Nickel(II)-Dependent Biomimetic of Metallohydrolases

A dinickel(II) complex of the ligand 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol (HL1) has been prepared and characterized to generate a functional model for nickel(II) phosphoesterase enzymes. The complex, [Ni2(L1)(μ-OAc)(H2O)2](ClO4)2·H2O, was characterized by microanalysis, X-ray crystallography, UV-visible, and IR absorption spectroscopy and solid state magnetic susceptibility measurements. Susceptibility studies show that the complex is antiferromagnetically coupled with the best fit parameters J = -27.4 cm-1, g = 2.29, D = 28.4 cm-1, comparable to corresponding values measured for the analogous dicobalt(II) complex [Co2(L1)(μ-OAc)](ClO4)2·0.5 H2O (J = -14.9 cm-1 and g = 2.16). Catalytic measurements with the diNi(II) complex using the substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) demonstrated activity toward hydrolysis of the phosphoester substrate with K m ~10 mM, and k cat ~0.025 s-1. The combination of structural and catalytic studies suggests that the likely mechanism involves a nucleophilic attack on the substrate by a terminal nucleophilic hydroxido moiety.

Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA

Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Thermococcus kodakarensis Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a β-strand adjacent to its N-terminal β-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.

CO-Bridged H-Cluster Intermediates in the Catalytic Mechanism of [FeFe]-Hydrogenase CaI

The [FeFe]-hydrogenases ([FeFe] H₂ases) catalyze reversible H₂ activation at the H-cluster, which is composed of a [4Fe-4S]_H subsite linked by a cysteine thiolate to a bridged, organometallic [2Fe-2S] ([2Fe]_H) subsite. Profoundly different geometric models of the H-cluster redox states that orchestrate the electron/proton transfer steps of H₂ bond activation have been proposed. We have examined this question in the [FeFe] H₂ase I from Clostridium acetobutylicum (CaI) by Fourier-transform infrared (FTIR) spectroscopy with temperature annealing and H/D isotope exchange to identify the relevant redox states and define catalytic transitions. One-electron reduction of H_ox led to formation of H_redH⁺ ([4Fe-4S]_H²⁺-Fe^I-Fe^I) and H_red' ([4Fe-4S]_H¹⁺-Fe^II-Fe^I), with both states characterized by low frequency μ-CO IR modes consistent with a fully bridged [2Fe]_H. Similar μ-CO IR modes were also identified for H_redH⁺ of the [FeFe] H₂ase from Chlamydomonas reinhardtii (CrHydA1). The CaI proton-transfer variant C298S showed enrichment of an H/D isotope-sensitive μ-CO mode, a component of the hydride bound H-cluster IR signal, H_hyd. Equilibrating CaI with increasing amounts of NaDT, and probed at cryogenic temperatures, showed H_redH⁺ was converted to H_hyd. Over an increasing temperature range from 10 to 260 K catalytic turnover led to loss of H_hyd and appearance of H_ox, consistent with enzymatic turnover and H₂ formation. The results show for CaI that the μ-CO of [2Fe]_H remains bridging for all of the "H_red" states and that H_redH⁺ is on pathway to H_hyd and H₂ evolution in the catalytic mechanism. These results provide a blueprint for designing small molecule catalytic analogs.

Anaerobic Formate and Hydrogen Metabolism

Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.

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

The assembly of multi-protein complexes requires the concerted synthesis and maturation of its components and subsequently their co-ordinated interaction. The membrane-bound 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.

Metal organic frameworks mimicking natural enzymes: a structural and functional analogy

In this review, we have portrayed the structure, synthesis and applications of a variety of biomimetic MOFs from an unprecedented angle.

[NiFe]-hydrogenase maturation in vitro: analysis of the roles of the HybG and HypD accessory proteins1

[NiFe]-hydrogenases (Hyd) bind a nickel-iron-based cofactor. The Fe ion of the cofactor is bound by two cyanide ligands and a single carbon monoxide ligand. Minimally six accessory proteins (HypA-HypF) are necessary for NiFe(CN)2CO cofactor biosynthesis in Escherichia coli. It has been shown that the anaerobically purified HypC-HypD-HypE scaffold complex carries the Fe(CN)2CO moiety of this cofactor. In the present study, we have purified the HybG-HypDE complex and used it to successfully reconstitute in vitro active Hyd from E. coli. HybG is a homologue of HypC that is specifically required for the maturation of Hyd-2 and also functions in the maturation of Hyd-1 of E. coli. Maturation of active Hyd-1 and Hyd-2 could be demonstrated in extracts derived from HybG- and HypD-deficient E. coli strains by adding anaerobically purified HybG-HypDE complex. In vitro maturation was dependent on ATP, carbamoylphosphate, nickel and reducing conditions. Hydrogenase maturation was prevented when the purified HybG-HypDE complex used in the maturation assay lacked a bound Fe(CN)2CO moiety. These findings demonstrate that it is possible to isolate incompletely processed intermediates on the maturation pathway and to use these to activate apo-forms of [NiFe]-hydrogenase large subunits.

Heterolytic activation of dihydrogen molecule by hydroxo-/sulfido-bridged ruthenium-germanium dinuclear complex. Theoretical insights

Heterolytic activation of dihydrogen molecule (H2) by hydroxo-/sulfido-bridged ruthenium-germanium dinuclear complex [Dmp(Dep)Ge(μ-S)(μ-OH)Ru(PPh3)](+) (1) (Dmp = 2,6-dimesitylphenyl, Dep = 2,6-diethylphenyl) is theoretically investigated with the ONIOM(DFT:MM) method. H2 approaches 1 to afford an intermediate [Dmp(Dep)(HO)Ge(μ-S)Ru(PPh3)](+)-(H2) (2). In 2, the Ru-OH coordinate bond is broken but H2 does not yet coordinate with the Ru center. Then, the H2 further approaches the Ru center through a transition state TS2-3 to afford a dihydrogen σ-complex [Dmp(Dep)(HO)Ge(μ-S)Ru(η(2)-H2)(PPh3)](+) (3). Starting from 3, the H-H σ-bond is cleaved by the Ru and Ge-OH moieties to form [Dmp(Dep)(H2O)Ge(μ-S)Ru(H)(PPh3)](+) (4). In 4, hydride and H2O coordinate with the Ru and Ge centers, respectively. Electron population changes clearly indicate that this H-H σ-bond cleavage occurs in a heterolytic manner like H2 activation by hydrogenase. Finally, the H2O dissociates from the Ge center to afford [Dmp(Dep)Ge(μ-S)Ru(H)(PPh3)](+) (PRD). This step is rate-determining. The activation energy of the backward reaction is moderately smaller than that of the forward reaction, which is consistent with the experimental result that PRD reacts with H2O to form 1 and H2. In the Si analogue [Dmp(Dep)Si(μ-S)(μ-OH)Ru(PPh3)](+) (1Si), the isomerization of 1Si to 2Si easily occurs with a small activation energy, while the dissociation of H2O from the Si center needs a considerably large activation energy. Based on these computational findings, it is emphasized that the reaction of 1 resembles well that of hydrogenase and the use of Ge in 1 is crucial for this heterolytic H-H σ-bond activation.

Genome-wide analysis of alternative splicing in Volvox carteri

Background

Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction.

Results

Here we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5′ (17.9%) and 3′ (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types (Mol Biol Evol 31:1402-1413, 2014). To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR.

Conclusions

The results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1117) contains supplementary material, which is available to authorized users.

External mitochondrial NADH-dependent reductase of redox cyclers: VDAC1 or Cyb5R3?

It was reported that VDAC1 possesses an NADH oxidoreductase activity and plays an important role in the activation of xenobiotics in the outer mitochondrial membrane. In the present work, we evaluated the participation of VDAC1 and Cyb5R3 in the NADH-dependent activation of various redox cyclers in mitochondria. We show that external NADH oxidoreductase caused the redox cycling of menadione ≫ lucigenin>nitrofurantoin. Paraquat was predominantly activated by internal mitochondria oxidoreductases. An increase in the ionic strength stimulated and suppressed the redox cycling of negatively and positively charged acceptors, as was expected for the Cyb5R3-mediated reduction. Antibodies against Cyb5R3 but not VDAC substantially inhibited the NADH-related oxidoreductase activities. The specific VDAC blockers G3139 and erastin, separately or in combination, in concentrations sufficient for the inhibition of substrate transport, exhibited minimal effects on the redox cycler-dependent NADH oxidation, ROS generation, and reduction of exogenous cytochrome c. In contrast, Cyb5R3 inhibitors (6-propyl-2-thiouracil, p-chloromercuriobenzoate, quercetin, mersalyl, and ebselen) showed similar patterns of inhibition of ROS generation and cytochrome c reduction. The analysis of the spectra of the endogenous cytochromes b5 and c in the presence of nitrofurantoin and the inhibitors of VDAC and Cyb5R3 demonstrated that the redox cycler can transfer electrons from Cyb5R3 to endogenous cytochrome c. This caused the oxidation of outer membrane-bound cytochrome b5, which is in redox balance with Cyb5R3. The data obtained argue against VDAC1 and in favor of Cyb5R3 involvement in the activation of redox cyclers in the outer mitochondrial membrane.

Pyridin-2-yl guanidine derivatives: conformational control induced by intramolecular hydrogen-bonding interactions

The synthesis and conformational analysis of a series of pyridin-2-yl guanidine derivatives using NMR, X-ray crystallography, and B3LYP/6-31+G** theoretical studies are reported. A remarkable difference was observed in the (1)H NMR spectra of the guanidinium salts as compared with their N,N'-di-Boc protected and neutral analogues. This difference corresponds to a 180° change in the dihedral angle between the guanidine/ium moiety and the pyridine ring in the salts as compared to the Boc-protected derivatives, a conclusion that was supported by theoretical studies, X-ray data, and NMR analysis. Moreover, our data sustain the existence of two intramolecular hydrogen-bonding systems: (i) between the pyridine N1 atom and the guanidinium protons in the salts and (ii) within the tert-butyl carbamate groups of the Boc-protected derivatives. To verify that the observed conformational control arises from these intramolecular interactions, a new series of N-Boc-N'-propyl-substituted pyridin-2-yl guanidines were also prepared and studied.

Site-selective fragmentation of peptides and proteins at quinone-modified cysteine residues investigated by ESI-MS

Described herein are several unique analytical applications utilizing mass spectrometry and the selective modification of the free thiol form of cysteine in both peptides and proteins by various quinones. This simple modification can be used to quantify the number of free or disulfide bound cysteines in a protein. In addition, quinone modification can also be used to easily probe the solvent accessibility of cysteine residues, which provides information about protein structure or folding state. Furthermore, the chromophoric properties of the quinone moiety can be leveraged for site specific photodissociation of the backbone. The photodissociation reveals both the presence and location of modified cysteine residues. For example, cleavage of the protein backbone of alpha-hemoglobin is observed selectively at a single cysteine out of 140 residues in the whole protein. This selective backbone fragmentation is accompanied by a parent ion mass loss, which is unique to the modifying quinone. When combined, this information can be used to determine both the presence and site of modification generated by naturally occurring molecules, such as dopamine, which can harness quinone chemistry to modify proteins.

Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina

Using a metagenomics approach, we have cloned a piece of environmental DNA from the Sargasso Sea that encodes an [NiFe] hydrogenase showing 60% identity to the large subunit and 64% to the small subunit of a Thiocapsa roseopersicina O2-tolerant [NiFe] hydrogenase. The DNA sequence of the hydrogenase identified by the metagenomic approach was subsequently found to be 99% identical to the hyaA and hyaB genes of an Alteromonas macleodii hydrogenase, indicating that it belongs to the Alteromonas clade. We were able to express our new Alteromonas hydrogenase in T. roseopersicina. Expression was accomplished by coexpressing only two accessory genes, hyaD and hupH, without the need to express any of the hyp accessory genes (hypABCDEF). These results suggest that the native accessory proteins in T. roseopersicina could substitute for the Alteromonas counterparts that are absent in the host to facilitate the assembly of a functional Alteromonas hydrogenase. To further compare the complex assembly machineries of these two [NiFe] hydrogenases, we performed complementation experiments by introducing the new Alteromonas hyaD gene into the T. roseopersicina hynD mutant. Interestingly, Alteromonas endopeptidase HyaD could complement T. roseopersicina HynD to cleave endoproteolytically the C-terminal end of the T. roseopersicina HynL hydrogenase large subunit and activate the enzyme. This study refines our knowledge on the selectivity and pleiotropy of the elements of the [NiFe] hydrogenase assembly machineries. It also provides a model for functionally analyzing novel enzymes from environmental microbes in a culture-independent manner.

Carbon Monoxide and Cyanide Ligands in the Active Site of [FeFe]-Hydrogenases

The [FeFe]-hydrogenases, although share common features when compared to other metal containing hydrogenases, clearly have independent evolutionary origins. Examples of [FeFe]-hydrogenases have been characterized in detail by biochemical and spectroscopic approaches and the high resolution structures of two examples have been determined. The active site H-cluster is a complex bridged metal assembly in which a [4Fe-4S] cubane is bridged to a 2Fe subcluster with unique non-protein ligands including carbon monoxide, cyanide, and a five carbon dithiolate. Carbon monoxide and cyanide ligands as a component of a native active metal center is a property unique to the metal containing hydrogenases and there has been considerable attention to the characterization of the H-cluster at the level of electronic structure and mechanism as well as to defining the biological means to synthesize such a unique metal cluster. The chapter describes the structural architecture of [FeFe]-hydrogenases and key spectroscopic observations that have afforded the field with a fundamental basis for understanding the relationship between structure and reactivity of the H-cluster. In addition, the results and ideas concerning the topic of H-cluster biosynthesis as an emerging and fascinating area of research, effectively reinforcing the potential linkage between iron-sulfur biochemistry to the role of iron-sulfur minerals in prebiotic chemistry and the origin of life.

Refining the active site structure of iron-iron hydrogenase using computational infrared spectroscopy

Iron-iron hydrogenases ([FeFe]H2ases) are exceptional natural catalysts for the reduction of protons to dihydrogen. Future biotechnological applications based on these enzymes require a precise understanding of their structures and properties. Although the [FeFe]H2ases have been characterized by single-crystal X-ray crystallography and a range of spectroscopic techniques, ambiguities remain regarding the details of the molecular structures of the spectroscopically observed forms. We use density functional theory (DFT) computations on small-molecule computational models of the [FeFe]H2ase active site to address this problem. Specifically, a series of structural candidates are geometry optimized and their infrared (IR) spectra are simulated using the computed C-O and C-N stretching frequencies and infrared intensities. Structural assignments are made by comparing these spectra to the experimentally determined IR spectra for each form. The H red form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide has been protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox(air)(ox) form is assigned as an Fe(II)Fe(II) redox level with OH(-) or OOH(-) bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker. Comparisons of the computed IR spectra of the (12)CO and (13)CO inhibited form with the experimental IR spectra show that exogenous CO binds terminally to the distal iron center.

Oriented nanostructures for energy conversion and storage

Recently, the role of nanostructured materials in addressing the challenges in energy and natural resources has attracted wide attention. In particular, oriented nanostructures demonstrate promising properties for energy harvesting, conversion, and storage. In this Review, we highlight the synthesis and application of oriented nanostructures in a few key areas of energy technologies, namely photovoltaics, batteries, supercapacitors, and thermoelectrics. Although the applications differ from field to field, a common fundamental challenge is to improve the generation and transport of electrons and ions. We highlight the role of high surface area to maximize the surface activity and discuss the importance of optimum dimension and architecture, controlled pore channels, and alignment of the nanocrystalline phase to optimize the transport of electrons and ions. Finally, we discuss the challenges in attaining integrated architectures to achieve the desired performance. Brief background information is provided for the relevant technologies, but the emphasis is focused mainly on the nanoscale effects of mostly inorganic-based materials and devices.

Hydrogen metabolism in Desulfovibrio desulfuricans strain New Jersey (NCIMB 8313)--comparative study with D. vulgaris and D. gigas species

This article aims to study hydrogen production/consumption in Desulfovibrio (D.) desulfuricans strain New Jersey, a sulfate reducer isolated from a medium undergoing active biocorrosion and to compare its hydrogen metabolism with two other Desulfovibrio species, D. gigas and D. vulgaris Hildenborough. Hydrogen production was followed during the growth of these three bacterial species under different growth conditions: no limitation of sulfate and lactate, sulfate limitation, lactate limitation, pyruvate/sulfate medium and in the presence of molybdate. Hydrogen production/consumption by D. desulfuricans shows a behavior similar to that of D. gigas but a different one from that of D. vulgaris, which produces higher quantities of hydrogen on lactate/sulfate medium. The three species are able to increase the hydrogen production when the sulfate became limiting. Moreover, in a pyruvate/sulfate medium hydrogen production was lower than on lactate/sulfate medium. Hydrogen production by D. desulfuricans in presence of molybdate is extremely high. Hydrogenases are key enzymes on production/consumption of hydrogen in sulfate reducing organisms. The specific activity, number and cellular localization of hydrogenases vary within the three Desulfovibrio species used in this work, which could explain the differences observed on hydrogen utilization.

Maturation of hydrogenases

Enzymes possessing the capacity to oxidize molecular hydrogen have developed convergently three class of enzymes leading to: [FeFe]-, [NiFe]-, and [FeS]-cluster-free hydrogenases. They differ in the composition and the structure of the active site metal centre and the sequence of the constituent structural polypeptides but they show one unifying feature, namely the existence of CN and/or CO ligands at the active site Fe. Recent developments in the analysis of the maturation of [FeFe]- and [NiFe]- hydrogenases have revealed a remarkably complex pattern of mostly novel biochemical reactions. Maturation of [FeFe]-hydrogenases requires a minimum of three auxiliary proteins, two of which belong to the class of Radical-SAM enzymes and other to the family of GTPases. They are sufficient to generate active enzyme when their genes are co-expressed with the structural genes in a heterologous host, otherwise deficient in [FeFe]-hydrogenase expression. Maturation of the large subunit of [NiFe]-hydrogenases depends on the activity of at least seven core proteins that catalyse the synthesis of the CN ligand, have a function in the coordination of the active site iron, the insertion of nickel and the proteolytic maturation of the large subunit. Whereas this core maturation machinery is sufficient to generate active hydrogenase in the cytoplasm, like that of hydrogenase 3 from Escherichia coli, additional proteins are involved in the export of the ready-assembled heterodimeric enzyme to the periplasm via the twin-arginine translocation system in the case of membrane-bound hydrogenases. A series of other gene products with intriguing putative functions indicate that the minimal pathway established for E. coli [NiFe]-hydrogenase maturation may possess even higher complexity in other organisms.

Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox

The 3561 m Vostok ice core sample originating from the subglacial Lake Vostok accretion (frozen lake water) ice with sediment inclusions was thoroughly studied by various means to confirm the presence of the thermophile bacterium Hydrogenophilus thermoluteolus reported earlier in the 3607 m accretion ice sample. PCR and molecular-phylogenetic analyses performed in two independent laboratories were made using different 16S rRNA gene (rrs) targeted primers. As a result, rrs-targeted PCR permitted to recover several very closely related clones with a small genetic distance to Hydrogenophilus thermoluteolus (< 1%). In addition, RubisCO (cbbL or rbcL) and NiFe-Hydrogenase (hoxV or hupL) targeted PCR have also allowed to recover sequences highly related to Hydrogenophilus thermoluteolus. All these results point to the presence of thermophilic chemoautotrophic microorganisms in Lake Vostok accretion ice. They presumably originate from deep faults in the bedrock cavity containing the lake in which episodes of seismotectonic activity would release debris along with microbial cells.

De Novo Design of Synthetic Di-Iron(I) Complexes as Structural Models of the Reduced Form of Iron−Iron Hydrogenase

Simple synthetic di-iron dithiolate complexes provide good models of the composition of the active site of the iron-iron hydrogenase enzymes. However, the formally Fe(I)Fe(I) complexes synthesized to date fail to reproduce the precise orientation of the diatomic ligands about the iron centers that is observed in the molecular structure of the reduced form of the enzyme active site. This structural difference is often used to explain the fact that the synthetic di-iron complexes are generally poor catalysts when compared to the enzyme. Herein, density functional theory computations are used for the rational design of synthetic complexes as structural models of the reduced form of the enzyme active site. These computations suggest several possible synthetic targets. The synthesis of complexes containing five-atom S-to-S linkers of the form S(CH2)2X(CH2)2S (X = CH2, NH, or O) or pendant functionalities attached to the three-carbon framework is one method. Another approach is the synthesis of asymmetrically substituted complexes, in which one iron center has strongly electron donating ligands and the adjacent iron center has strongly electron accepting ligands. The combination of a sterically demanding S-to-S linker and asymmetric substitution of the CO ligands is predicted to be a particularly effective synthetic target.

Cloning and characterization of hoxH genes from Arthrospira and Spirulina and application in phylogenetic study

Partial hoxH genes of 2 cyanobacterial genera, including 5 strains of Arthrospira and 2 strains of Spirulina, were cloned and characterized. This gene encodes the large subunit of nickel-iron hydrogenase. The results showed that these genes comprised 1349 nucleotides in Arthrospira and 1343 nucleotides in Spirulina, respectively. The GC contents of hoxH were 45.7% to 47.3% in Arthrospira and up to 50.4% to 50.9% in Spirulina. The hoxH gene was demonstrated to be single copy by Southern analysis, and its transcription was verified by reverse transcriptase polymerase chain reaction in Arthrospira platensis FACHB341. The similarities of nucleotide sequences among the 5 strains of Arthrospira ranged from 95.7% to 99.8%, which are higher than those between Arthrospira and Spirulina (72.9-77.0%). However, similarity between the 2 Spirulina strains was only 72.5%, slightly lower than that between the 2 genera. A phylogenetic tree based on hoxH was constructed. All 5 strains of Arthrospira formed a monophyletic clade, which was highly supported by bootstrap value, while the 2 strains of Spirulina were separated into 2 different clades.

The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective

The hydrogenase content of the genome of Geobacter sulfurreducens, a member of the family Geobacteraceae within the delta-subdivision of the Proteobacteria, was examined and found to be distinct from that of Desulfovibrio species, another family of delta-Proteobacteria on which extensive research concerning hydrogen metabolism has been conducted. Four [NiFe]-hydrogenases are encoded in the G. sulfurreducens genome: two periplasmically oriented, membrane-bound hydrogenases, Hya and Hyb, and two cytoplasmic hydrogenases, Mvh and Hox. None of these [NiFe]-hydrogenases has a counterpart in Desulfovibrio species. Furthermore, the large and small subunits of Mvh and Hox appear to be related to archaeal and cyanobacterial hydrogenases, respectively. Clusters encoding [Fe]-hydrogenases and periplasmic [NiFeSe]-hydrogenases, which are commonly found in the genomes of Desulfovibrio species, are not present in the genome of G. sulfurreducens. Hydrogen-evolving Ech hydrogenases, which are present in the genomes of at least two Desulfovibrio species, were also absent from the G. sulfurreducens genome, despite the fact that G. sulfurreducens is capable of hydrogen production. Instead, the G. sulfurreducens genome contained a cluster encoding a multimeric Ech hydrogenase related (Ehr) complex that was similar in content to operons encoding Ech hydrogenases, but did not appear to encode a hydrogenase. Phylogenetic analysis revealed that the G. sulfurreducens ehr cluster is part of a family of related clusters found in both the Archaea and Bacteria.