Vht hydrogenase is required for hydrogen cycling during nitrogen fixation by the non-hydrogenotrophic methanogen Methanosarcina acetivorans.

Methanosarcina acetivorans is the primary model to understand the physiology of methanogens that do not use hydrogenase to consume or produce hydrogen (H2) during methanogenesis. The genome of M. acetivorans encodes putative methanophenazine-reducing hydrogenases (Vht and Vhx), F420-reducing hydrogenase (Frh), and hydrogenase maturation machinery (Hyp), yet cells lack significant hydrogenase activity under all growth conditions tested to date. Thus, the importance of hydrogenase to the physiology of M. acetivorans has remained a mystery. M. acetivorans can fix dinitrogen (N2) using nitrogenase that is documented in bacteria to produce H2 during the reduction of N2 to ammonia. Therefore, we hypothesized that M. acetivorans uses hydrogenase to recycle H2 produced by nitrogenase during N2 fixation. Results demonstrate that hydrogenase expression and activity is higher in N2-grown cells compared to cells grown with fixed nitrogen (NH4Cl). To test the importance of each hydrogenase and the maturation machinery, the CRISPRi-dCas9 system was used to generate separate M. acetivorans strains where transcription of the vht, frh, vhx, or hyp operons is repressed. Repression of vhx and frh does not alter growth with either NH4Cl or N2 and has no effect on H2 metabolism. However, repression of vht or hyp results in impaired growth with N2 but not NH4Cl. Importantly, H2 produced endogenously by nitrogenase is detected in the headspace of culture tubes containing the vht or hyp repression strains. Overall, the results reveal that Vht hydrogenase recycles H2 produced by nitrogenase that is required for optimal growth of M. acetivorans during N2 fixation.

A Voltammetric Perspective of Multi-Electron and Proton Transfer in Protein Redox Chemistry: Insights From Computational Analysis of Escherichia coli HypD Fourier Transformed Alternating Current Voltammetry

This paper explores the impact of pH on the mechanism of reversible disulfide bond (CysS-SCys) reductive breaking and oxidative formation in Escherichia coli hydrogenase maturation factor HypD, a protein which forms a highly stable adsorbed film on a graphite electrode. To achieve this, low frequency (8.96 Hz) Fourier transformed alternating current voltammetric (FTACV) experimental data was used in combination with modelling approaches based on Butler-Volmer theory with a dual polynomial capacitance model, utilizing an automated two-step fitting process conducted within a Bayesian framework. We previously showed that at pH 6.0 the protein data is best modelled by a redox reaction of two separate, stepwise one-electron, one-proton transfers with slightly “crossed” apparent reduction potentials that incorporate electron and proton transfer terms (Eapp20 > Eapp10). Remarkably, rather than collapsing to a concerted two-electron redox reaction at more extreme pH, the same two-stepwise one-electron transfer model with Eapp20 > Eapp10 continues to provide the best fit to FTACV data measured across a proton concentration range from pH 4.0 to pH 9.0. A similar, small level of crossover in reversible potentials is also displayed in overall two-electron transitions in other proteins and enzymes, and this provides access to a small but finite amount of the one electron reduced intermediate state.

HydG, the “Dangler” Iron, and Catalytic Production of Free CO and CN−: Implications for [FeFe]-Hydrogenase Maturation

The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN–, and dithiomethylamine (DTMA) ligands. The H-cluster...

Hydroxy-bridged Active Site States of [NiFe]-Hydrogenase Unraveled by Cryogenic Vibrational Spectroscopy and DFT Computations

The catalytic mechanism of H₂ conversion by [NiFe]-hydrogenase is subject of extensive research. Apart from at least four reaction intermediates of H₂/H⁺ cycling, there is also a number of resting states, which are formed under oxidizing conditions. While not directly involved in the catalytic cycle, knowledge of their molecular structure and reactivity is important, because these states usually accumulate in the course of hydrogenase purification, and they may also play a role <i>in vivo</i> during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit, HoxC, of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from <i>Ralstonia eutropha</i>. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, ⁵⁷Fe labeled HoxC granted an unprecedented view onto the active site modes, including those obscured by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data allow the structural description of two hydroxy-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. <br>

Hydroxy-bridged Active Site States of [NiFe]-Hydrogenase Unraveled by Cryogenic Vibrational Spectroscopy and DFT Computations

The catalytic mechanism of H₂ conversion by [NiFe]-hydrogenase is subject of extensive research. Apart from at least four reaction intermediates of H₂/H⁺ cycling, there is also a number of resting states, which are formed under oxidizing conditions. While not directly involved in the catalytic cycle, knowledge of their molecular structure and reactivity is important, because these states usually accumulate in the course of hydrogenase purification, and they may also play a role <i>in vivo</i> during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit, HoxC, of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from <i>Ralstonia eutropha</i>. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, ⁵⁷Fe labeled HoxC granted an unprecedented view onto the active site modes, including those obscured by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data allow the structural description of two hydroxy-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. <br>

Heterologous Hydrogenase Overproduction Systems for Biotechnology—An Overview

Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.

[FeFe]-Hydrogenase Maturation: H-Cluster Assembly Intermediates Tracked by Electron Paramagnetic Resonance, Infrared, and X-Ray Absorption Spectroscopy

[FeFe]-hydrogenase enzymes employ a unique organometallic cofactor for efficient and reversible hydrogen conversion. This so-called H-cluster consists of a [4Fe-4S] cubane cysteine-linked to a diiron complex coordinated by carbon monoxide and cyanide ligands and an azadithiolate ligand (adt = NH(CH2S)2). [FeFe]-hydrogenase apo-protein binding only the [4Fe-4S] sub-complex can be fully activated in vitro by the addition of a synthetic diiron site precursor complex ([2Fe]adt,). Elucidation of the mechanism of cofactor assembly will aid in the design of improved hydrogen processing synthetic catalysts. We combined in situ electron paramagnetic resonance, Fourier-transform infrared, and X-ray absorption spectroscopy to characterize intermediates of H-cluster assembly as initiated by mixing of the apo-protein (HydA1) from the green alga Chlamydomonas reinhardtii with [2Fe]adt. The three methods consistently show rapid formation of a complete H-cluster in the oxidized, CO-inhibited state (Hox-CO) already within seconds after the mixing. Moreover, FTIR spectroscopy support a model in which Hox-CO formation is preceded by a short-lived Hred´-CO like intermediate. Accumulation of Hox-CO was followed by CO release resulting in the slower conversion to the catalytically active state (Hox) as well as formation of reduced states of the H-cluster.

[FeFe]-Hydrogenase Maturation: H-Cluster Assembly Intermediates Tracked by Electron Paramagnetic Resonance, Infrared, and X-Ray Absorption Spectroscopy

[FeFe]-hydrogenase enzymes employ a unique organometallic cofactor for efficient and reversible hydrogen conversion. This so-called H-cluster consists of a [4Fe-4S] cubane cysteine-linked to a diiron complex coordinated by carbon monoxide and cyanide ligands and an azadithiolate ligand (adt = NH(CH2S)2). [FeFe]-hydrogenase apo-protein binding only the [4Fe-4S] sub-complex can be fully activated in vitro by the addition of a synthetic diiron site precursor complex ([2Fe]adt,). Elucidation of the mechanism of cofactor assembly will aid in the design of improved hydrogen processing synthetic catalysts. We combined in situ electron paramagnetic resonance, Fourier-transform infrared, and X-ray absorption spectroscopy to characterize intermediates of H-cluster assembly as initiated by mixing of the apo-protein (HydA1) from the green alga Chlamydomonas reinhardtii with [2Fe]adt. The three methods consistently show rapid formation of a complete H-cluster in the oxidized, CO-inhibited state (Hox-CO) already within seconds after the mixing. Moreover, FTIR spectroscopy support a model in which Hox-CO formation is preceded by a short-lived Hred´-CO like intermediate. Accumulation of Hox-CO was followed by CO release resulting in the slower conversion to the catalytically active state (Hox) as well as formation of reduced states of the H-cluster.