Structure, function and biosynthesis of O2-tolerant hydrogenases

Fully Oxidized State of the Oxygen-Tolerant [NiFe] Hydrogenase from Hydrogenophilus thermoluteolus SH: A Quantum Mechanics Cluster and Quantum Mechanics/Molecular Mechanics Study

The oxygen tolerance of some [NiFe] hydrogenase enzymes is crucial for designing efficient bioinspired catalysts for sustainable hydrogen production and advancing renewable energy technologies. To investigate this, we employed a quantum mechanical (QM) cluster model and quantum mechanics/molecular mechanics (QM/MM) calculations to study the fully oxidized state of the [NiFe]-hydrogenase from Hydrogenophilus thermoluteolus SH. Our analysis focused on the structural and electronic properties of the enzyme's active site across different spin states, including closed-shell singlet (CS, S = 0), high-spin triplet (HS, S = 1), and open-shell singlet broken symmetry (BS, S = 0). Using a comprehensive structural model (>300 atoms), we identified the ground state of the fully oxidized enzyme state to be a spin-coupled BS Ni(III)Fe(III) oxidation state, where residues beyond the first coordination sphere primarily contribute sterically. Notably, natural bond order calculations revealed an unusual three-center two-electron bond at the active site, which may enhance the open-shell ground state stability and the enzyme's resilience under oxidative conditions. Our comparative study of QM and QM/MM methods provides insights into their performance, facilitating and guiding the choice of suitable enzyme models when studying other metalloproteins.

A strong H-bond between a cysteine and the catalytic center of a [NiFe]-hydrogenase

Infrared spectroscopy at cryogenic temperatures was used to monitor protonation changes on an H+-accepting, nickel-coordinating active site cysteine of the H2/H+-cycling membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Surprisingly, we identified another cysteine in the outer coordination sphere forming a strong H-bond with a cysteine thiolate coordinating both nickel and iron of the catalytic center.

Conceptual Approach for Aerobic Autotrophic Gas Cultivation in Shake Flasks: Overcoming the Inhibitory Effects of Oxygen in Cupriavidus necator

This study conceptualizes the design of a small-scale system (250 mL-1 L) for the autotrophic cultivation of hydrogen-oxidizing bacteria, such as the representative strain Cupriavidus necator. The research aimed to systematically investigate the impact of bottle volume and gas composition, particularly oxygen concentration, on the growth and performance of C. necator during autotrophic cultivations. To this end, customized, pressure-tight, baffled glass bottles of various sizes (250, 500, and 1000 mL) and gas mixtures with varying oxygen concentrations (4%, 8%, and 12% v/v) were tested. Growth was monitored by measuring optical density. The maximum specific growth rate (µmax), the biomass production rate (BPR), the volumetric gas-liquid mass transfer coefficient (kLa), and the oxygen transfer rate were calculated. Among the various combinations, the 1000-mL bottles demonstrated the highest µmax (0.13 h-1) and the second-highest BPR (0.074 g L-1 h-1) at an oxygen concentration of 8%, without the need to refill the headspace. The proposed small-scale system offers a swift and replicable method for concurrently investigating multiple autotrophic cultivations. In this regard, increasing the size of the bottle flask proved to be an efficient strategy to minimize the periodicity for gas refilling. Due to the inhibitory effect of oxygen, changing the liquid-gas volume ratio in hydrogen-driven shake flask cultivation had so far strongly influenced the growth rate. Our results provide a solid foundation for the scaling and optimization of small-scale cultivation of chemolithotrophic bacteria and will facilitate future parallelization and, hence, optimization of metabolic aspects.

Reactivation and long-term stabilization of the [NiFe] Hox hydrogenase of Synechocystis sp. PCC6803 by glutathione after oxygen exposure

Hydrogenases are key enzymes forming or consuming hydrogen. The inactivation of these transition metal biocatalysts with oxygen limits their biotechnological applications. Oxygen-sensitive hydrogenases are distinguished from oxygen-insensitive (tolerant) ones by their initial hydrogen turnover rates influenced by oxygen. Several hydrogenases, such as the oxygen-sensitive bidirectional [NiFe] Hox hydrogenase (Hox) of the unicellular cyanobacterium Synechocystis sp. PCC6803, are reactivated after oxygen-induced deactivation by redox mechanisms. In cyanobacteria, the glutathione (GSH) redox buffer majorly controls intracellular redox potentials. The relationship between Hox turnover rates and the redox potential in its natural reaction environment is not fully understood. We thus determined hydrogen oxidation rates as activities of Hox in cell-free extracts of Synechocystis using benzyl viologen as artificial electron acceptor. We found that GSH modulates Hox hydrogen oxidation rates under oxygen-free conditions. After oxygen exposure, it influences the maximal turnover rate and aids in the reactivation of Hox. Moreover, GSH stabilizes the long-term Hox activity under anoxic conditions and attenuates oxygen-induced deactivation of Hox in a concentration-dependent manner, probably by fostering reactivation. Conversely, oxidized GSH (GSSG) negatively affects Hox activity and oxygen insensitivity. Using Blue Native PAGE followed by mass spectrometry, we showed that oxygen affects Hox complex integrity. The in silico predicted structure of the Hox complex and complexome analyses reveal the formation of various Hox subcomplexes under different conditions. Our findings refine our current classification of oxygen-hydrogenase interactions beyond sensitive and insensitive, which is particularly important for understanding hydrogenase function under physiological conditions in future.

A Strep-Tag Imprinted Polymer Platform for Heterogenous Bio(electro)catalysis

Molecularly imprinted polymers (MIPs) are artificial receptors equipped with selective recognition sites for target molecules. One of the most promising strategies for protein MIPs relies on the exploitation of short surface-exposed protein fragments, termed epitopes, as templates to imprint binding sites in a polymer scaffold for a desired protein. However, the lack of high-resolution structural data of flexible surface-exposed regions challenges the selection of suitable epitopes. Here, we addressed this drawback by developing a polyscopoletin-based MIP that recognizes recombinant proteins via imprinting of the widely used Strep-tag II affinity peptide (Strep-MIP). Electrochemistry, surface-sensitive IR spectroscopy, and molecular dynamics simulations were employed to ensure an utmost control of the Strep-MIP electrosynthesis. The functionality of this novel platform was verified with two Strep-tagged enzymes: an O2-tolerant [NiFe]-hydrogenase, and an alkaline phosphatase. The enzymes preserved their biocatalytic activities after multiple utilization confirming the efficiency of Strep-MIP as a general biocompatible platform to confine recombinant proteins for exploitation in biotechnology.

The energy metabolism of Cupriavidus necator in different trophic conditions

The "knallgas" bacterium Cupriavidus necator is attracting interest due to its extremely versatile metabolism. C. necator can use hydrogen or formic acid as an energy source, fixes CO2 via the Calvin-Benson-Bassham (CBB) cycle, and grows on organic acids and sugars. Its tripartite genome is notable for its size and duplications of key genes (CBB cycle, hydrogenases, and nitrate reductases). Little is known about which of these isoenzymes and their cofactors are actually utilized for growth on different substrates. Here, we investigated the energy metabolism of C. necator H16 by growing a barcoded transposon knockout library on succinate, fructose, hydrogen (H2/CO2), and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that (i) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. (ii) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. (iii) For hydrogenases, both soluble and membrane-bound enzymes were utilized for lithoautotrophic growth. (iv) Of the six terminal respiratory complexes in C. necator H16, only some are utilized, and utilization depends on the energy source. (v) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon. This study evaluates the contribution of each of C. necator's genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium and inspire future engineering strategies.IMPORTANCEThe soil bacterium Cupriavidus necator can grow on gas mixtures of CO2, H2, and O2. It also consumes formic acid as carbon and energy source and various other substrates. This metabolic flexibility comes at a price, for example, a comparatively large genome (6.6 Mb) and a significant background expression of lowly utilized genes. In this study, we mutated every non-essential gene in C. necator using barcoded transposons in order to determine their effect on fitness. We grew the mutant library in various trophic conditions including hydrogen and formate as the sole energy source. Fitness analysis revealed which of the various energy-generating iso-enzymes are actually utilized in which condition. For example, only a few of the six terminal respiratory complexes are used, and utilization depends on the substrate. We also show that the protein cost for the various lowly utilized enzymes represents a significant growth disadvantage in specific conditions, offering a route to rational engineering of the genome. All fitness data are available in an interactive app at https://m-jahn.shinyapps.io/ShinyLib/.

Ultrathin Film Antimony-Doped Tin Oxide Prevents [NiFe] Hydrogenase Inactivation at High Electrode Potentials

For hydrogenases to serve as effective electrocatalysts in hydrogen biotechnological devices, such as enzymatic fuel cells, it is imperative to design electrodes that facilitate stable and functional enzyme immobilization, efficient substrate accessibility, and effective interfacial electron transfer. Recent years have seen considerable advancements in this area, particularly concerning hydrogenases. However, a significant limitation remains: the inactivation of hydrogenases at high oxidative potentials across most developed electrodes. Addressing this issue necessitates a thorough understanding of the interactions between the enzyme and the electrode surface. In this study, we employ ATR-IR spectroscopy combined with electrochemistry in situ to investigate the interaction mechanisms, electrocatalytic behavior, and stability of the oxygen-tolerant membrane-bound [NiFe] hydrogenase from Cupriavidus necator (MBH), which features a His-tag on its small subunit C-terminus. Antimony-doped tin oxide (ATO) thin films were selected as electrodes due to their protein compatibility, suitable potential window, conductivity, and transparency, making them an ideal platform for spectroelectrochemical measurements. Our comprehensive examination of the physiological and electrochemical processes of [NiFe] MBH on ATO thin film electrodes demonstrates that by tuning the electron transport properties of the ATO thin film, we can prevent MBH inactivation at extended oxidative potentials while maintaining direct electron transfer between the enzyme and the electrode.

Strain and model development for auto- and heterotrophic 2,3-butanediol production using Cupriavidus necator H16

The production of platform chemicals from renewable energy sources is a crucial step towards a post-fossil economy. This study reports on the production of acetoin and 2,3-butanediol heterotrophically with fructose as substrate and autotrophically from CO2 as carbon source, H2 as electron donor and O2 as electron acceptor with Cupriavidus necator. In a previous study, the strain was developed for the production of acetoin with high carbon efficiency. Acetoin can serve as a precursor for the synthesis of 2,3-butanediol by the integration of a butanediol dehydrogenase. In this study, different plasmid backbones and butanediol dehydrogenases were evaluated regarding efficiency for CO2-based 2,3-butanediol production. The developed strain utilizes the pBBR1 plasmid bearing a 2,3-butanediol dehydrogenase from Enterobacter cloacae and is characterized by 2,3-butanediol as the main product and a heterotrophic total product yield of 88.11%, an autotrophic volumetric productivity of 39.45 mg L-1 h-1, a total product carbon yield of 81.6%, an H2 efficiency of 33.46%, and a specific productivity of 0.016 g product per gram of biomass per hour. In addition, a mathematical model was developed to simulate the processes under these conditions. With this model, it was possible to calculate productivities and substrate usage at distinct time points of the production processes and calculate productivities and substrate usage with high resolution which will be useful in future applications.

Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase

[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.

Unveiling the Low-Lying Spin States of [Fe3S4] Clusters via the Extended Broken-Symmetry Method

Photosynthetic water splitting, when synergized with hydrogen production catalyzed by hydrogenases, emerges as a promising avenue for clean and renewable energy. However, theoretical calculations have faced challenges in elucidating the low-lying spin states of iron-sulfur clusters, which are integral components of hydrogenases. To address this challenge, we employ the Extended Broken-Symmetry method for the computation of the cubane-[Fe3S4] cluster within the [FeNi] hydrogenase enzyme. This approach rectifies the error caused by spin contamination, allowing us to obtain the magnetic exchange coupling constant and the energy level of the low-lying state. We find that the Extended Broken-Symmetry method provides more accurate results for differences in bond length and the magnetic coupling constant. This accuracy assists in reconstructing the low-spin ground state force and determining the geometric structure of the ground state. By utilizing the Extended Broken-Symmetry method, we further highlight the significance of the geometric arrangement of metal centers in the cluster's properties and gain deeper insights into the magnetic properties of transition metal iron-sulfur clusters at the reaction centers of hydrogenases. This research illuminates the untapped potential of hydrogenases and their promising role in the future of photosynthesis and sustainable energy production.

Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion

The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.

Stepwise conversion of the Cys6[4Fe-3S] to a Cys4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase

The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O2-tolerant hydrogenase. It catalyzes the oxidation of H2 into 2e- and 2H+ in the presence of high O2 concentrations. This characteristic trait is intimately linked to the unique Cys6[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys5[4Fe-4S] or Cys4[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O2 tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O2 protection mechanism that detoxifies O2 to H2O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O2 binding under electron-deficient conditions.

Stepwise assembly of the active site of [NiFe]-hydrogenase

[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H₂ into 2e^- and 2H⁺ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)₂(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN^- molecules. Here, we investigated the sequential assembly of the [NiFe] cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O₂-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)₂(CO) fragment, a precursor that contained all cofactor components but remained redox inactive and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.

Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations

Background

O₂-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H₂-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks.

Results

In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L⁻¹ of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity.

Conclusions

This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01919-w.

Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal

Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H₂ and fix CO₂ to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO₂ capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli

Hydrogenases are biotechnologically relevant metalloenzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. The O2-tolerant [NiFe]-hydrogenases from Cupriavidus necator (formerly Ralstonia eutropha) are of particular interest as they maintain catalysis even in the presence of molecular oxygen. However, to meet the demands of biotechnological applications and scientific research, a heterologous production strategy is required to overcome the low production yields in their native host. We have previously used the regulatory hydrogenase (RH) from C. necator as a model for the development of such a heterologous hydrogenase production process in E. coli. Although high protein yields were obtained, the purified enzyme was inactive due to the lack of the catalytic center, which contains an inorganic nickel-iron cofactor. In the present study, we significantly improved the production process to obtain catalytically active RH. We optimized important factors such as O2 content, metal availability, production temperature and time as well as the co-expression of RH-specific maturase genes. The RH was successfully matured during aerobic cultivation of E. coli by co-production of seven hydrogenase-specific maturases and a nickel permease, which was confirmed by activity measurements and spectroscopic investigations of the purified enzyme. The improved production conditions resulted in a high yield of about 80 mg L–1 of catalytically active RH and an up to 160-fold space-time yield in E. coli compared to that in the native host C. necator [<0.1 U (L d) –1]. Our strategy has important implications for the use of E. coli K-12 and B strains in the recombinant production of complex metalloenzymes, and provides a blueprint for the production of catalytically active [NiFe]-hydrogenases in biotechnologically relevant quantities.

Molecular hydrogen is a promising therapeutic agent for pulmonary disease

Molecular hydrogen exerts biological effects on nearly all organs. It has anti-oxidative, anti-inflammatory, and anti-aging effects and contributes to the regulation of autophagy and cell death. As the primary organ for gas exchange, the lungs are constantly exposed to various harmful environmental irritants. Short- or long-term exposure to these harmful substances often results in lung injury, causing respiratory and lung diseases. Acute and chronic respiratory diseases have high rates of morbidity and mortality and have become a major public health concern worldwide. For example, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. An increasing number of studies have revealed that hydrogen may protect the lungs from diverse diseases, including acute lung injury, chronic obstructive pulmonary disease, asthma, lung cancer, pulmonary arterial hypertension, and pulmonary fibrosis. In this review, we highlight the multiple functions of hydrogen and the mechanisms underlying its protective effects in various lung diseases, with a focus on its roles in disease pathogenesis and clinical significance.

Rewiring cyanobacterial photosynthesis by the implementation of an oxygen-tolerant hydrogenase

Molecular hydrogen (H₂) is considered as an ideal energy carrier to replace fossil fuels in future. Biotechnological H₂ production driven by oxygenic photosynthesis appears highly promising, as biocatalyst and H₂ syntheses rely mainly on light, water, and CO₂ and not on rare metals. This biological process requires coupling of the photosynthetic water oxidizing apparatus to a H₂-producing hydrogenase. However, this strategy is impeded by the simultaneous release of oxygen (O₂) which is a strong inhibitor of most hydrogenases. Here, we addressed this challenge, by the introduction of an O₂-tolerant hydrogenase into phototrophic bacteria, namely the cyanobacterial model strain Synechocystis sp. PCC 6803. To this end, the gene cluster encoding the soluble, O₂-tolerant, and NAD(H)-dependent hydrogenase from Ralstonia eutropha (ReSH) was functionally transferred to a Synechocystis strain featuring a knockout of the native O₂ sensitive hydrogenase. Intriguingly, photosynthetically active cells produced the O₂ tolerant ReSH, and activity was confirmed in vitro and in vivo. Further, ReSH enabled the constructed strain Syn_ReSH⁺ to utilize H₂ as sole electron source to fix CO₂. Syn_ReSH⁺ also was able to produce H₂ under dark fermentative conditions as well as in presence of light, under conditions fostering intracellular NADH excess. These findings highlight a high level of interconnection between ReSH and cyanobacterial redox metabolism. This study lays a foundation for further engineering, e.g., of electron transfer to ReSH via NADPH or ferredoxin, to finally enable photosynthesis-driven H₂ production.

Optimization of Culture Conditions for Oxygen-Tolerant Regulatory [NiFe]-Hydrogenase Production from Ralstonia eutropha H16 in Escherichia coli

Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring many efforts and high costs for cultivation limiting their investigation. Heterologous production of these hydrogenases in a robust and genetically tractable expression host is an attractive strategy to make these enzymes more accessible. In the present study, we chose the oxygen-tolerant H2-sensing regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha H16 owing to its relatively simple architecture compared to other [NiFe]-hydrogenases as a model to develop a heterologous hydrogenase production system in Escherichia coli. Using screening experiments in 24 deep-well plates with 3 mL working volume, we investigated relevant cultivation parameters, including inducer concentration, expression temperature, and expression time. The RH yield could be increased from 14 mg/L up to >250 mg/L by switching from a batch to an EnPresso B-based fed-batch like cultivation in shake flasks. This yield exceeds the amount of RH purified from the homologous host R. eutropha by several 100-fold. Additionally, we report the successful overproduction of the RH single subunits HoxB and HoxC, suitable for biochemical and spectroscopic investigations. Even though both RH and HoxC proteins were isolated in an inactive, cofactor free apo-form, the proposed strategy may powerfully accelerate bioprocess development and structural studies for both basic research and applied studies. These results are discussed in the context of the regulation mechanisms governing the assembly of large and small hydrogenase subunits.

Direct Targets and Subsequent Pathways for Molecular Hydrogen to Exert Multiple Functions: Focusing on Interventions in Radical Reactions

Molecular hydrogen (H₂) was long regarded as non-functional in mammalian cells. We overturned the concept by demonstrating that H₂ exhibits antioxidant effects and protects cells against oxidative stress. Subsequently, it has been revealed that H₂ has multiple functions in addition to antioxidant effects, including antiinflammatory, anti-allergic functions, and as cell death and autophagy regulation. Additionally, H₂ stimulates energy metabolism. As H₂ does not readily react with most biomolecules without a catalyst, it is essential to identify the primary targets with which H₂ reacts or interacts directly. As a first event, H₂ may react directly with strong oxidants, such as hydroxyl radicals (•OH) in vivo. This review addresses the key issues related to this in vivo reaction. •OH may have a physiological role because it triggers a free radical chain reaction and may be involved in the regulation of Ca2+- or mitochondrial ATP-dependent K+-channeling. In the subsequent pathway, H₂ suppressed a free radical chain reaction, leading to decreases in lipid peroxide and its end products. Derived from the peroxides, 4-hydroxy-2-nonenal functions as a mediator that up-regulates multiple functional PGC-1α. As the other direct target in vitro and in vivo, H₂ intervenes in the free radical chain reaction to modify oxidized phospholipids, which may act as an antagonist of Ca2+-channels. The resulting suppression of Ca2+-signaling inactivates multiple functional NFAT and CREB transcription factors, which may explain H₂ multi-functionality. This review also addresses the involvement of NFAT in the beneficial role of H₂ in COVID-19, Alzheimer's disease and advanced cancer. We discuss some unsolved issues of H₂ action on lipopolysaccharide signaling, MAPK and NF-κB pathways and the Nrf2 paradox. Finally, as a novel idea for the direct targeting of H2, this review introduces the possibility that H₂ causes structural changes in proteins via hydrate water changes.

Application of Molecular Hydrogen as an Antioxidant in Responses to Ventilatory and Ergogenic Adjustments during Incremental Exercise in Humans

We investigated effects of molecular hydrogen (H₂) supplementation on acid-base status, pulmonary gas exchange responses, and local muscle oxygenation during incremental exercise. Eighteen healthy, trained subjects in a randomized, double-blind, crossover design received H₂-rich calcium powder (HCP) (1500 mg/day, containing 2.544 µg/day of H₂) or H₂-depleted placebo (1500 mg/day) for three consecutive days. They performed cycling incremental exercise starting at 20-watt work rate, increasing by 20 watts/2 min until exhaustion. Breath-by-breath pulmonary ventilation (V˙_E) and CO₂ output (V˙CO₂) were measured and muscle deoxygenation (deoxy[Hb + Mb]) was determined via time-resolved near-infrared spectroscopy in the vastus lateralis (VL) and rectus femoris (RF). Blood gases' pH, lactate, and bicarbonate (HCO₃^-) concentrations were measured at rest and 120-, 200-, and 240-watt work rates. At rest, the HCP group had significantly lower V˙_E, V˙CO₂, and higher HCO₃^-, partial pressures of CO₂ (PCO₂) versus placebo. During exercise, a significant pH decrease and greater HCO₃^- continued until 240-watt workload in HCP. The V˙_E was significantly lower in HCP versus placebo, but HCP did not affect the gas exchange status of V˙CO₂ or oxygen uptake (V˙O₂). HCP increased absolute values of deoxy[Hb + Mb] at the RF but not VL. Thus, HCP-induced hypoventilation would lead to lower pH and secondarily impaired balance between O₂ delivery and utilization in the local RF during exercise, suggesting that HCP supplementation, which increases the at-rest antioxidant potential, affects the lower ventilation and pH status during incremental exercise. HPC induced a significantly lower O₂ delivery/utilization ratio in the RF but not the VL, which may be because these regions possess inherently different vascular/metabolic control properties, perhaps related to fiber-type composition.

Deuteration mechanistic studies of hydrogenase mimics

The role of deuterium in disentangling key steps of the mechanisms of H₂ activation by mimics of hydrogenases is presented. These studies have allowed to a better understanding of the mode of action of the natural enzymes and their mimics.

Membrane Protein Modified Electrodes in Bioelectrocatalysis

Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.

In Vitro Assembly as a Tool to Investigate Catalytic Intermediates of [NiFe]-Hydrogenase

[NiFe]-hydrogenases catalyze the reversible reaction H2 ⇄ 2H+ + 2e-. Their basic module consists of a large subunit, coordinating the NiFe(CO)(CN)2 center, and a small subunit that carries electron-transferring iron-sulfur clusters. Here, we report the in vitro assembly of fully functional [NiFe]-hydrogenase starting from the isolated large and small subunits. Activity assays complemented by spectroscopic measurements revealed a native-like hydrogenase. This approach was used to label exclusively the NiFe(CO)(CN)2 center with 57Fe, enabling a clear view of the catalytic site by means of nuclear resonance vibrational spectroscopy. This strategy paves the way for in-depth studies of [NiFe]-hydrogenase catalytic intermediates.

A NiRhS fuel cell catalyst - lessons from hydrogenase

We present a novel fuel cell heterogeneous catalyst based on rhodium, nickel and sulfur with power densities 5-28% that of platinum. The NiRhS heterogeneous catalyst was developed via a homogeneous model complex of the [NiFe]hydrogenases (H₂ases) and can act as both the cathode and anode of a fuel cell.

Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen

Hydrogenases are metalloenzymes that catalyse both H₂ evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O₂-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O₂ molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.

Biosynthetic Approaches towards the Design of Artificial Hydrogen-Evolution Catalysts

Hydrogen is a clean and sustainable form of fuel that can minimize our heavy dependence on fossil fuels as the primary energy source. The need of finding greener ways to generate H₂ gas has ignited interest in the research community to synthesize catalysts that can produce H₂ by the reduction of H⁺ . The natural H₂ producing enzymes hydrogenases have served as an inspiration to produce catalytic metal centers akin to these native enzymes. In this article we describe recent advances in the design of a unique class of artificial hydrogen evolving catalysts that combine the features of the active site metal(s) surrounded by a polypeptide component. The examples of these biosynthetic catalysts discussed here include i) assemblies of synthetic cofactors with native proteins; ii) peptide-appended synthetic complexes; iii) substitution of native cofactors with non-native cofactors; iv) metal substitution from rubredoxin; and v) a reengineered Cu storage protein into a Ni binding protein. Aspects of key design considerations in the construction of these artificial biocatalysts and insights gained into their chemical reactivity are discussed.

Prospects of molecular hydrogen in perioperative neuroprotection from basic research to clinical application

PURPOSE OF REVIEW

The current systematic review summarizes recent, basic clinical achievements regarding the neuroprotective effects of molecular hydrogen in distinct central nervous system conditions.

RECENT FINDINGS

Perioperative neuroprotection remains a major topic of clinical anesthesia. Various gaseous molecules have previously been explored as a feasible therapeutic option in neurological disorders. Among them, molecular hydrogen, which has emerged as a novel and potential therapy for perioperative neuroprotection, has received much attention.

SUMMARY

Fundamental and clinical evidence supports the antioxidant, antiinflammation, antiapoptosis and mitochondrial protective effects of hydrogen in the pathophysiology of nervous system diseases. The clinically preventive and therapeutic effects of hydrogen on different neural diseases, however, remain uncertain, and the lack of support by large randomized controlled trials has delayed its clinical application.

Engineering Clostridium ljungdahlii as the gas-fermenting cell factory for the production of biofuels and biochemicals

Clostridium ljungdahlii is a representative autotrophic gas-fermenting acetogen capable of converting CO₂ and CO into biomass and multiple metabolites. The carbon fixation and conversion based on C. ljungdahlii have great potential for the sustainable production of bulk biochemicals and biofuels using industrial syngas and waste gases. With substantial recent advances in genetic manipulation tools, it has become possible to study and improve the metabolic capability of C. ljungdahlii in gas fermentation. The product scope of C. ljungdahlii has been expanded through the introduction of heterologous production pathways followed by the modification of native metabolic networks. In addition, progress has been made in understanding the physiological and metabolic mechanisms of this anaerobe, contributing to strain designs for expected phenotypes. In this review, we highlight the latest research progresses regarding C. ljungdahlii and discuss the next steps to comprehensively understand and engineer this bacterium for an improved bacterial gas bioconversion platform.

A membrane-bound [NiFe]-hydrogenase large subunit precursor whose C-terminal extension is not essential for cofactor incorporation but guarantees optimal maturation

[NiFe]‐hydrogenases catalyze the reversible conversion of molecular hydrogen into protons end electrons. This reaction takes place at a NiFe(CN)₂(CO) cofactor located in the large subunit of the bipartite hydrogenase module. The corresponding apo‐protein carries usually a C‐terminal extension that is cleaved off by a specific endopeptidase as soon as the cofactor insertion has been accomplished by the maturation machinery. This process triggers complex formation with the small, electron‐transferring subunit of the hydrogenase module, revealing catalytically active enzyme. The role of the C‐terminal extension in cofactor insertion, however, remains elusive. We have addressed this problem by using genetic engineering to remove the entire C‐terminal extension from the apo‐form of the large subunit of the membrane‐bound [NiFe]‐hydrogenase (MBH) from Ralstonia eutropha. Unexpectedly, the MBH holoenzyme derived from this precleaved large subunit was targeted to the cytoplasmic membrane, conferred H₂‐dependent growth of the host strain, and the purified protein showed exactly the same catalytic activity as native MBH. The only difference was a reduced hydrogenase content in the cytoplasmic membrane. These results suggest that in the case of the R. eutropha MBH, the C‐terminal extension is dispensable for cofactor insertion and seems to function only as a maturation facilitator.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

A Dithiolato and Hydrido Bridged (CO/CN)Fe-Ni Complex with Unprotected CN: A Model for the [Ni-R] State of the [Ni-Fe] Hydrogenase Active Site

A dithiolate/hydride bridged Fe-Ni complex, [(CN)(CO)₂Fe^II(μ-pdt)(μ-H)Ni^II(CN)(PCy₃)]^- (2, pdt = propane-1,3-dithiolate) has been synthesized by the reaction of [(CN)₂(CO)₂Fe^II(pdt)]^2- with [Ni^II(Cl)(H)(PCy₃)₂] as a synthetic analogue of the Ni-R state of the active site of the [Ni-Fe] hydrogenase. X-ray crystallography of this model complex suggests that the hydride unsymmetrically binds to Ni and Fe similar to natural [Ni-Fe] hydrogenases.

Selective Oxidation of H2 and CO by NiIr Catalyst in Aqueous Solution: A DFT Mechanistic Study

One of the challenges in utilizing hydrogen gas (H₂) as a sustainable fossil fuel alternative is the inhibition of H₂ oxidation by carbon monoxide (CO), which is involved in the industrial production of H₂ sources. To solve this problem, a catalyst that selectively oxidizes either CO or H₂ or one that co-oxidizes H₂ and CO is needed. Recently, a NiIr catalyst [Ni^IICl(X)Ir^IIICl(η⁵-C₅Me₅)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H₂ or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H₂ and CO oxidation catalyzed by this NiIr catalyst. During H₂ oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH₃COO^-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH^- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO₂ leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H₂, OH^-, H₂O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H₂O and H₂. These calculations indicate that H₂ oxidation is inhibited by CO and OH^- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH^- attack to a carbonyl-C and the binding of OH^- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H₂ and CO.

Application of Molecular Hydrogen as a Novel Antioxidant in Sports Science

Molecular hydrogen (H₂) is a colorless, tasteless, odorless, and minimal molecule with high flammability. Although H₂ has been thought to be an inert gas in living bodies for many years, an animal study reported that inhalation of H₂ gas decreased oxidative stress and suppressed brain injury caused by ischemia and reperfusion injury due to its antioxidant action. Since then, the antioxidant action of H₂ has attracted considerable attention and many studies have reported on its benefits. Most studies have reported the effects of H₂ on diseases such as cancer, diabetes, cerebral infarction, and Alzheimer's disease. However, little is known regarding its effects on healthy subjects and exercise. Thus far, including our study, only 6 studies have explored the effect of H₂ on exercise. H₂ is the smallest molecule and therefore can easily penetrate the cellular membrane and rapidly diffuse into organelles. H₂ is thought to be able to selectively reduce hydroxyl radicals and peroxynitrite and does not affect physiologically reactive species. H₂ can be supplied to the body through multiple routes of administration, such as oral intake of H₂ water and H₂ bathing. Therefore, H₂ may be a potential alternative strategy for conventional exogenous antioxidant interventions in sports science. The purpose of this review is to provide evidence regarding the effects of H₂ intake on changes in physiological and biochemical parameters, centering on exercise-induced oxidative stress, for each intake method. Furthermore, this review highlights possible future directions in this area of research.

X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases

[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H₂). However, structural determinants of efficient H₂ binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H₂‐binding [NiFe] intermediate. Using an F₄₂₀‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H₂ binding and conversion. The protein matrix also directs H₂ diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H₂‐conversion catalysts.

How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer

Hydrogenases are metalloenzymes that catalyze the conversion of protons and molecular hydrogen, H₂. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H₂ production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, our understanding of proton transfer is poor. Previously, residues were identified forming a hydrogen-bonding network between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ infrared difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon photoreduction. While proton transfer appears to be impaired in the oxidized state (Hox), the presented data support continuous proton transfer in the reduced state (Hred). Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of glutamic acid residue E141 and, most notably, arginine R148 facilitate bidirectional proton transfer in [FeFe]-hydrogenases.

O2 sensitivity and H2 production activity of hydrogenases-A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.

Inactivation of the uptake hydrogenase in the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS enables a biological water–gas shift platform for H2 production

Biological H2 production has potential to address energy security and environmental concerns if produced from renewable or waste sources. The purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS produces H2 while oxidizing CO, a component of synthesis gas (Syngas). CO-linked H2 production is facilitated by an energy-converting hydrogenase (Ech), while a subsequent H2 oxidation reaction is catalyzed by a membrane-bound hydrogenase (MBH). Both hydrogenases contain [NiFe] active sites requiring 6 maturation factors (HypA-F) for assembly, but it is unclear which of the two annotated sets of hyp genes are required for each in R. gelatinosus CBS. Herein, we report correlated expression of hyp1 genes with Ech genes and hyp2 expression with MBH genes. Moreover, we find that while Ech H2 evolving activity is only delayed when hyp1 is deleted, hyp2 deletion completely disrupts MBH H2 uptake, providing a platform for a biologically driven water–gas shift reaction to produce H2 from CO.

Proton Transfer Pathways between Active Sites and Proximal Clusters in the Membrane-Bound [NiFe] Hydrogenase

[NiFe] hydrogenases are enzymes that catalyze the splitting of molecular hydrogen according to the reaction H₂ → 2H⁺ + 2e^-. Most of these enzymes are inhibited even by low traces of O₂. However, a special group of O₂-tolerant hydrogenases exists. A member of this group is the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha ( ReMBH). The ReMBH harbors an unusual iron sulfur cluster with composition 4Fe3S(6Cys) that is able to undergo structural changes triggering the flow of two electrons to the [NiFe] active site. These electrons promote oxygen reduction at the active site, preventing, in this way, aerobic inactivation of the enzyme. In the superoxidized state, the [4Fe3S] cluster binds to a hydroxyl group that originates from either molecular oxygen or water reaching the site. Both reactions, oxygen reduction to water at the [NiFe]- or [4Fe3S]-centers and oxygen evolution from water at the proximal cluster, require the delivery of protons regulated by a subtle communication mechanism between these metal centers. In this work, we sequentially apply multiscale modeling techniques as quantum mechanical/molecular mechanics methods and classical molecular dynamics simulations to investigate the role of two distinct proton transfer pathways connecting the [NiFe] active site and the [4Fe3S] proximal cluster of ReMBH in the protection mechanism against an oxygen attack. Although the "glutamate" pathway is preferred by protons migrating toward the active site to avoid inactivation by O₂, the "histidine" pathway plays an essential role in delivering protons for O₂ reduction at the proximal cluster. The results obtained in this work not only provide new pieces to the puzzling catalytic mechanisms governing O₂-tolerant hydrogenases but also highlight the relevance of dynamics in the proper description of biochemical reactions in general.

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.