Hydrogenase Reaction Research Articles

13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions

Carbon dioxide-fixing acetogenic bacteria (acetogens) utilizing the Wood-Ljungdahl Pathway (WLP) play an important role in CO2 fixation in the biosphere and in the development of biological processes – alone or in cocultures, under both autotrophic and mixotrophic conditions – for production of chemicals and fuels. To date, limited work has been reported in experimentally validating and quantifying reaction fluxes of their core metabolic pathways. Here, the core metabolic model of the acetogen Clostridium ljungdahlii was interrogated using 13C-metabolic flux analysis (13C-MFA), which required the development of a new defined culture medium. Autotrophic, heterotrophic, and mixotrophic growth in defined medium was possible by adding 1 mM methionine to replace yeast extract. Our 13C-MFA found an incomplete TCA cycle and inactive core pathways/reactions, notably those of the oxidative pentose phosphate pathway, Entner-Doudoroff pathway, and malate dehydrogenase. 13C-MFA during mixotrophic growth using the parallel tracers [1–13C]fructose, [1,2–13C]fructose, [1,2,3–13C]fructose, and [U–13C]asparagine found that externally supplied CO2 contributed the majority of carbon consumed. All internally-produced CO2 from the catabolism of asparagine and fructose was consumed by the WLP. While glycolysis of fructose was active, it was not a major contributor to overall production of ATP, NADH, and acetyl-CoA. Gluconeogenic reactions were active despite the availability of organic carbon. Asparagine was catabolized equally via conversion to threonine and subsequent cleavage to produce acetaldehyde and glycine, and via deamination to fumarate and then the anaplerotic conversion of malate to pyruvate. Both pathways for asparagine catabolism produced acetyl-CoA, either directly via pyruvate or indirectly via the WLP. Cofactor stoichiometry based on our data predicted an essentially zero flux through the ferredoxin-dependent transhydrogenase (Nfn) reaction. Instead, nearly all of NADPH generated from the hydrogenase reaction was consumed by the WLP. Reduced ferredoxin produced by the hydrogenase reaction and glycolysis was mostly used for ATP generation via the RNF/ATPase system, with the remainder consumed by the WLP. NADH produced by RNF/ATPase was entirely consumed via the WLP.

Diversifying Metal-Ligand Cooperative Catalysis in Semi-Synthetic [Mn]-Hydrogenases.

The reconstitution of [Mn]‐hydrogenases using a series of MnI complexes is described. These complexes are designed to have an internal base or pro‐base that may participate in metal–ligand cooperative catalysis or have no internal base or pro‐base. Only MnI complexes with an internal base or pro‐base are active for H2 activation; only [Mn]‐hydrogenases incorporating such complexes are active for hydrogenase reactions. These results confirm the essential role of metal–ligand cooperation for H2 activation by the MnI complexes alone and by [Mn]‐hydrogenases. Owing to the nature and position of the internal base or pro‐base, the mode of metal–ligand cooperation in two active [Mn]‐hydrogenases is different from that of the native [Fe]‐hydrogenase. One [Mn]‐hydrogenase has the highest specific activity of semi‐synthetic [Mn]‐ and [Fe]‐hydrogenases. This work demonstrates reconstitution of active artificial hydrogenases using synthetic complexes differing greatly from the native active site.

Diversifying Metal–Ligand Cooperative Catalysis in Semi‐Synthetic [Mn]‐Hydrogenases

A series of [Mn]-hydrogenases were reconstituted using specifically designed MnI complexes. In two catalytically active [Mn]-hydrogenases, the mode of metal–ligand cooperation is different from that of the native [Fe]-hydrogenase. One such [Mn]-hydrogenase exhibits the highest specific activity among all known semi-synthetic [Mn]- and [Fe]-hydrogenases.

Diatom-inspired multiscale mineralization of patterned protein-polysaccharide complex structures.

Marine diatoms construct their hierarchically ordered, three-dimensional (3D) external structures called frustules through precise biomineralization processes. Recapitulating the remarkable architectures and functions of diatom frustules in artificial materials is a major challenge that has important technological implications for hierarchically ordered composites. Here, we report the construction of highly ordered, mineralized composites based on fabrication of complex self-supporting porous structures—made of genetically engineered amyloid fusion proteins and the natural polysaccharide chitin—and performing in situ multiscale protein-mediated mineralization with diverse inorganic materials, including SiO2, TiO2 and Ga2O3. Subsequently, using sugar cubes as templates, we demonstrate that 3D fabricated porous structures can become colonized by engineered bacteria and can be functionalized with highly photoreactive minerals, thereby enabling co-localization of the photocatalytic units with a bacteria-based hydrogenase reaction for a successful semi-solid artificial photosynthesis system for hydrogen evolution. Our study thus highlights the power of coupling genetically engineered proteins and polysaccharides with biofabrication techniques to generate hierarchically organized mineralized porous structures inspired by nature.

Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H2 production

Electron bifurcating, [FeFe]-hydrogenases are recently described members of the hydrogenase family and catalyze a combination of exergonic and endergonic electron exchanges between three carriers (2 ferredoxinred− + NAD(P)H + 3 H+ = 2 ferredoxinox + NAD(P)+ + 2 H2). A thermodynamic analysis of the bifurcating, [FeFe]-hydrogenase reaction, using electron path-independent variables, quantified potential biological roles of the reaction without requiring enzyme details. The bifurcating [FeFe]-hydrogenase reaction, like all bifurcating reactions, can be written as a sum of two non-bifurcating reactions. Therefore, the thermodynamic properties of the bifurcating reaction can never exceed the properties of the individual, non-bifurcating, reactions. The bifurcating [FeFe]-hydrogenase reaction has three competitive properties: 1) enabling NAD(P)H-driven proton reduction at pH2 higher than the concurrent operation of the two, non-bifurcating reactions, 2) oxidation of NAD(P)H and ferredoxin simultaneously in a 1:1 ratio, both are produced during typical glucose fermentations, and 3) enhanced energy conservation (~10 kJ mol−1 H2) relative to concurrent operation of the two, non-bifurcating reactions. Our analysis demonstrated ferredoxin E°′ largely determines the sensitivity of the bifurcating reaction to pH2, modulation of the reduced/oxidized electron carrier ratios contributed less to equilibria shifts. Hydrogenase thermodynamics data were integrated with typical and non-typical glycolysis pathways to evaluate achieving the ‘Thauer limit’ (4 H2 per glucose) as a function of temperature and pH2. For instance, the bifurcating [FeFe]-hydrogenase reaction permits the Thauer limit at 60 °C if pH 2 ≤ ~10 mbar. The results also predict Archaea, expressing a non-typical glycolysis pathway, would not benefit from a bifurcating [FeFe]-hydrogenase reaction; interestingly, no Archaea have been observed experimentally with a [FeFe]-hydrogenase enzyme.

H2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki.

We determined 2H stable isotope fractionation at natural abundances associated with hydrogenase activity by whole cells of Desulfovibrio vulgaris strain Miyazaki F expressing a NiFe(Se) hydrogenase. Inhibition of sulfate reduction by molybdate inhibited the overall oxidation of hydrogen but still facilitated an equilibrium isotope exchange reaction with water. The theoretical equilibrium isotope exchange δ2H-values of the chemical exchange reaction were identical to the hydrogenase reaction, as confirmed using three isotopically different waters with δ2H-values of – 62, +461, and + 1533‰. Expected kinetic isotope fractionation of hydrogen oxidation by non-inhibited cells was also superimposed by an equilibrium isotope exchange. The isotope effects were solely catalyzed biotically as hydrogen isotope signatures did not change in control experiments without cells of D. vulgaris Miyazaki.

A fully protected hydrogenase/polymer-based bioanode for high-performance hydrogen/glucose biofuel cells

Hydrogenases with Ni- and/or Fe-based active sites are highly active hydrogen oxidation catalysts with activities similar to those of noble metal catalysts. However, the activity is connected to a sensitivity towards high-potential deactivation and oxygen damage. Here we report a fully protected polymer multilayer/hydrogenase-based bioanode in which the sensitive hydrogen oxidation catalyst is protected from high-potential deactivation and from oxygen damage by using a polymer multilayer architecture. The active catalyst is embedded in a low-potential polymer (protection from high-potential deactivation) and covered with a polymer-supported bienzymatic oxygen removal system. In contrast to previously reported polymer-based protection systems, the proposed strategy fully decouples the hydrogenase reaction form the protection process. Incorporation of the bioanode into a hydrogen/glucose biofuel cell provides a benchmark open circuit voltage of 1.15 V and power densities of up to 530 µW cm−2 at 0.85 V.

Reaction fronts of the autocatalytic hydrogenase reaction.

We have built a model to describe the hydrogenase catalyzed, autocatalytic, reversible hydrogen oxidation reaction where one of the enzyme forms is the autocatalyst. The model not only reproduces the experimentally observed front properties, but also explains the found hydrogen ion dependence. Furthermore, by linear stability analysis, two different front types are found in good agreement with the experiments.

Dioxygen Sensitivity of [Fe]‐Hydrogenase in the Presence of Reducing Substrates

AbstractMono‐iron hydrogenase ([Fe]‐hydrogenase) reversibly catalyzes the transfer of a hydride ion from H2 to methenyltetrahydromethanopterin (methenyl‐H4MPT+) to form methylene‐H4MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H2 activation. Evidence is presented for O2 sensitivity of [Fe]‐hydrogenase under turnover conditions in the presence of reducing substrates, methylene‐H4MPT or methenyl‐H4MPT+/H2. Only then, H2O2 is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O2 reduction to H2O2 requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]‐hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.

Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates.

Mono-iron hydrogenase ([Fe]-hydrogenase) reversibly catalyzes the transfer of a hydride ion from H2 to methenyltetrahydromethanopterin (methenyl-H4 MPT+ ) to form methylene-H4 MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H2 activation. Evidence is presented for O2 sensitivity of [Fe]-hydrogenase under turnover conditions in the presence of reducing substrates, methylene-H4 MPT or methenyl-H4 MPT+ /H2 . Only then, H2 O2 is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O2 reduction to H2 O2 requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]-hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.

How does the ([NiFe]) hydrogenase enzyme work?

Previous experimental results and theoretical considerations led to the conclusion that there are two autocatalytic reaction steps in the H2-oxidizing reaction of hydrogenase. One autocatalytic reaction occurs when the enzyme is mainly in inactive forms (Ni-A and/or Ni-B). This finding is supported by the special patterns of H2 oxidation in a thin-layer reaction chamber, and by the special, long lag phase observed. The autocatalytic step takes place between two enzyme forms, one of which also interacts directly with the terminal electron acceptor, i.e. the autocatalyst is an enzyme form in which [FeS]distal is reduced. During the autocatalytic interaction, an electron is passed from the autocatalyst to the other enzyme form. Inactive hydrogenase is used as a substrate in this autocatalytic step for another, activated hydrogenase molecule.The second autocatalytic step is located in the enzyme cycle. Its presence is supported by the facts that the Ni-R form is exclusively diamagnetic and that the steady-state concentration of the product of the H2-oxidizing reaction (i.e. reduced benzyl viologen) displays a strong enzyme concentration dependence. This enzyme concentration dependence does not depend on the “active-inactive” states of the enzyme and remains valid in consecutive H2-oxidizing - proton-reducing reaction series performed on the same sample. This autocatalytic step involves an enzyme–enzyme interaction; both interacting enzyme forms should participate in the catalytic cycle of the enzyme. Since the reduction of all [FeS] clusters would also be possible in a non-autocatalytic reaction, we hypothesize a small conformational change in the enzyme, catalyzed by the autocatalyst, which removes a block in the electron flow in either the [NiFe]/[FeS]proximal or the [FeS]proximal/[FeS]distal reaction step, or removes a blockade of the penetration of gaseous H2 from the surface to the [NiFe] cluster. As far as we are aware, this is the first experimental observation of such a phenomenon on an enzyme. The interaction of two protein forms and the conformation change as a result of the interaction between the two enzyme forms resembles those in prion reactions.

Hydrogen-driven asymmetric reduction of hydroxyacetone to (R)-1,2-propanediol by Ralstonia eutropha transformant expressing alcohol dehydrogenase from Kluyveromyces lactis.

BackgroundConversion of industrial processes to more nature-friendly modes is a crucial subject for achieving sustainable development. Utilization of hydrogen-oxidation reactions by hydrogenase as a driving force of bioprocess reaction can be an environmentally ideal method because the reaction creates no pollutants. We expressed NAD-dependent alcohol dehydrogenase from Kluyveromyces lactis in a hydrogen-oxidizing bacterium: Ralstonia eutropha. This is the first report of hydrogen-driven in vivo coupling reaction of the alcohol dehydrogenase and indigenous soluble NAD-reducing hydrogenase. Asymmetric reduction of hydroxyacetone to (R)-1,2-propanediol, which is a commercial building block for antibacterial agents, was performed using the transformant as the microbial cell catalyst.ResultsThe two enzymes coupled in vitro in vials without a marked decrease of reactivity during the 20 hr reaction because of the hydrogenase reaction, which generates no by-product that affects enzymes. Alcohol dehydrogenase was expressed functionally in R. eutropha in an activity level equivalent to that of indigenous NAD-reducing hydrogenase under the hydrogenase promoter. The hydrogen-driven in vivo coupling reaction proceeded only by the transformant cell without exogenous addition of a cofactor. The decrease of reaction velocity at higher concentration of hydroxyacetone was markedly reduced by application of an in vivo coupling system. Production of (R)-1,2-propanediol (99.8% e.e.) reached 67.7 g/l in 76 hr with almost a constant rate using a jar fermenter. The reaction velocity under 10% PH2 was almost equivalent to that under 100% hydrogen, indicating the availability of crude hydrogen gas from various sources. The in vivo coupling system enabled cell-recycling as catalysts.ConclusionsAsymmetric reduction of hydroxyacetone by a coupling reaction of the two enzymes continued in both in vitro and in vivo systems in the presence of hydrogen. The in vivo reaction system using R. eutropha transformant expressing heterologous alcohol dehydrogenase showed advantages for practical usage relative to the in vitro coupling system. The results suggest a hopeful perspective of the hydrogen-driven bioprocess as an environmentally outstanding method to achieve industrial green innovation. Hydrogen-oxidizing bacteria can be useful hosts for the development of hydrogen-driven microbial cell factories.

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

BackgroundSolventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications.ResultsWe present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed.ConclusionsMicrobial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production.

Direct electron transfer to hydrogenase for catalytic hydrogen production using a single-walled carbon nanotube forest

The production of hydrogen through the direct electron transfer from electrode to hydrogenase was successfully performed using hydrogenase combined with a single-walled carbon nanotube forest (SWNT-forest). The SWNT-forest has a unique structure comprising dense and vertically aligned SWNTs with millimeter-scale height. The vertically aligned SWNTs became rearranged into a wall-like architecture after immersing in water. Hydrogenase was spontaneously incorporated within the SWNT-forest and confined on the sidewall of the rearranged architecture. The SWNT-forest was a very stable protein carrier in aqueous solution, and an SWNT-forest integrated with hydrogenase could easily be constructed. With a hydrogenase assembled SWNT-forest we were able to electrochemically produce hydrogen with an electron transfer efficiency exceeding 30% without the use of any chemical mediator. Furthermore, a reverse oxidative reaction of hydrogen was also successfully performed using the same device. Thus, the SWNT-forest can work as an effective and direct electron mediator for the oxidation/reduction reaction of hydrogenase. The usefulness of the SWNT-forest as a beneficial material for electrochemistry was demonstrated, underlining the potential of protein assembled SWNT-forests in fabricating highly efficient biofuel cell devices.

Acclimation of green algae to sulfur deficiency: underlying mechanisms and application for hydrogen production

Hydrogen is definitely one of the most acceptable fuels in the future. Some photosynthetic microorganisms, such as green algae and cyanobacteria, can produce hydrogen gas from water by using solar energy. In green algae, hydrogen evolution is coupled to the photosynthetic electron transport in thylakoid membranes via reaction catalyzed by the specific enzyme, (FeFe)-hydrogenase. However, this enzyme is highly sensitive to oxygen and can be quickly inhibited when water splitting is active. A problem of incompatibility between the water splitting and hydrogenase reaction can be overcome by depletion of algal cells of sulfur which is essential element for life. In this review the mechanisms underlying sustained hydrogen photoproduction in sulfur deprived C. reinhardtii and the recent achievements in studying of this process are discussed. The attention is focused on the biophysical and physiological aspects of photosynthetic response to sulfur deficiency in green algae.

Hydrogen production by Chlamydomonas reinhardtii under light driven sulfur deprived condition

This article explores the possibility of demonstrating sustainable photohydrogen production using Chlamydomonas reinhardtii when grown in sulfur deprived photoautotrophic condition. The hydrogen evolving capability of the algal species was monitored based on alternating light and dark period. Investigation was carried out during the day time in order to exploit the solar energy for meeting the demand of the light period. The results showed that when the reactor was operated at varying photoperiod namely 2, 3 and 4 h of alternating light and dark period, the gas generation was found to be 32 ± 4, 63 ± 7 and 52 ± 5 mL/h, while the corresponding hydrogen content was 47, 86 and 87% respectively. Functional components of hydrogen generation reaction centers were also analyzed, which showed that the PS(I) reaction centers were involved in hydrogen production pathway, as the light absorption by PS(I) was prerequisite for hydrogen generation under sulfur deprived photoautotrophic condition. The findings showed a higher gas yield and hydrogen content under dark period, whereas under light period the gas content was below detectable level for hydrogen due to the reversible hydrogenase reaction.

Concentration-Dependent Front Velocity of the Autocatalytic Hydrogenase Reaction

HynSL hydrogenase from Thiocapsa roseopersicina was applied to catalyze the oxidation of molecular hydrogen in a new, improved, thin-layer reaction chamber. Investigation of the nature of this catalysis via the development of reduced benzyl viologen showed clearly the typical characteristics of an autocatalytic reaction: propagation of a reaction front originating from a single point, with a constant velocity of front propagation. The dependence of the reaction velocity on enzyme concentration was a power function with a positive enzyme concentration threshold, with an exponent of 0.4 ± 0.05. This indicates that the autocatalyst is an enzyme form. The front velocity decreased on increase of the electron acceptor concentration, as a sign that the autocatalyst interacts directly with the final electron acceptor. Overall, it may be concluded that the autocatalyst is an enzyme form in which [FeS] distal is reduced. Model calculations corroborate this. Because the reduction of all [FeS] clusters would be possible in a nonautocatalytic reaction, we hypothesize a small conformational change in the enzyme, catalyzed by the autocatalyst, which removes a block in the electron flow in either [NiFe] → [FeS] proximal or the [FeS] proximal → [FeS] distal reaction step, or removes a block of the penetration of gaseous hydrogen from the surface to the [NiFe] cluster.

Johnson Matthey: interim management statement

Previous experimental results and theoretical considerations led to the conclusion that there are two autocatalytic reaction steps in the H2-oxidizing reaction of hydrogenase. One autocatalytic reaction occurs when the enzyme is mainly in inactive forms (Ni-A and/or Ni-B). This finding is supported by the special patterns of H2 oxidation in a thin-layer reaction chamber, and by the special, long lag phase observed. The autocatalytic step takes place between two enzyme forms, one of which also interacts directly with the terminal electron acceptor, i.e. the autocatalyst is an enzyme form in which [FeS]distal is reduced. During the autocatalytic interaction, an electron is passed from the autocatalyst to the other enzyme form. Inactive hydrogenase is used as a substrate in this autocatalytic step for another, activated hydrogenase molecule.The second autocatalytic step is located in the enzyme cycle. Its presence is supported by the facts that the Ni-R form is exclusively diamagnetic and that the steady-state concentration of the product of the H2-oxidizing reaction (i.e. reduced benzyl viologen) displays a strong enzyme concentration dependence. This enzyme concentration dependence does not depend on the “active-inactive” states of the enzyme and remains valid in consecutive H2-oxidizing - proton-reducing reaction series performed on the same sample. This autocatalytic step involves an enzyme–enzyme interaction; both interacting enzyme forms should participate in the catalytic cycle of the enzyme. Since the reduction of all [FeS] clusters would also be possible in a non-autocatalytic reaction, we hypothesize a small conformational change in the enzyme, catalyzed by the autocatalyst, which removes a block in the electron flow in either the [NiFe]/[FeS]proximal or the [FeS]proximal/[FeS]distal reaction step, or removes a blockade of the penetration of gaseous H2 from the surface to the [NiFe] cluster. As far as we are aware, this is the first experimental observation of such a phenomenon on an enzyme. The interaction of two protein forms and the conformation change as a result of the interaction between the two enzyme forms resembles those in prion reactions.

Modeling methanogenesis with a genome‐scale metabolic reconstruction of Methanosarcina barkeri

We present a genome-scale metabolic model for the archaeal methanogen Methanosarcina barkeri. We characterize the metabolic network and compare it to reconstructions from the prokaryotic, eukaryotic and archaeal domains. Using the model in conjunction with constraint-based methods, we simulate the metabolic fluxes and resulting phenotypes induced by different environmental and genetic conditions. This represents the first large-scale simulation of either a methanogen or an archaeal species. Model predictions are validated by comparison to experimental growth measurements and phenotypes of M. barkeri on different substrates. The predicted growth phenotypes for wild type and mutants of the methanogenic pathway have a high level of agreement with experimental findings. We further examine the efficiency of the energy-conserving reactions in the methanogenic pathway, specifically the Ech hydrogenase reaction, and determine a stoichiometry for the nitrogenase reaction. This work demonstrates that a reconstructed metabolic network can serve as an analysis platform to predict cellular phenotypes, characterize methanogenic growth, improve the genome annotation and further uncover the metabolic characteristics of methanogenesis.

Theoretical Calculations on Hydrogenase Kinetics: Explanation of the Lag Phase and the Enzyme Concentration Dependence of the Activity of Hydrogenase Uptake

Two models of the hydrogenase reaction cycle were investigated by means of theoretical calculations and model simulations. The first model is the widely accepted triangular hydrogenase reaction cycle with minor modifications; the second is a modified triangular model, where we have introduced an autocatalytic step into the reaction cycle. Both models include a one-step activation reaction. The theoretical calculations and model simulations corroborate the assumed autocatalytic reaction step concluded from the experimental characteristics of the hydrogenase reaction.