Efficient CO2-reducing activity of NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA for formate production from CO2 gas

Theoretical study on CO2 reduction catalyzed by formate dehydrogenase using the cation radical of a bipyridinium salt with an ionic substituent as a co-enzyme

Mechanism for formate dehydrogenase from Candida boidinii catalyzed CO₂ reduction to formate with the cation radical of a 4,4′-bipyridinium salt with an ionic substituent as a co-enzyme was clarified by theoretical studies.

Artificial co-enzyme based on carbamoyl-modified viologen derivative cation radical for formate dehydrogenase in the catalytic CO2 reduction to formate

The interaction between the single-electron reduced carbamoyl-modified-4,4-bipyridinium salt and CbFDH in the CO₂ reduction to formate is elucidated by enzymatic kinetic analysis, the docking simulation and density functional theory calculation.

Trivalent metal ions promote the malic enzyme-catalyzed building of carbon–carbon bonds from CO2and pyruvate

ME is an attractive biocatalyst for building carbon–carbon bonds through carboxylation of pyruvate with CO₂. The carboxylation of pyruvate with CO₂was promoted by adding a trivalent metal ion. In particular, Al³⁺accelerates ME-catalyzed carboxylation of pyruvate with CO₂.

High-Level Production of 4-Hydroxyvalerate from Levulinic Acid via Whole-Cell Biotransformation Decoupled from Cell Metabolism

γ-Hydroxyvalerate (4HV) is an important monomer used to produce various valuable polymers and products. In this study, an engineered 3-hydroxybutyrate dehydrogenase that can convert levulinic acid (LA) into 4HV was co-expressed with a cofactor (NADH) regeneration system mediated by an NAD⁺-dependent formate dehydrogenase (CbFDH) in the Escherichia coli strain, MG1655. The resulting strain produced 23-fold more 4HV in a shake flask. The 4HV production was not dependent on ATP and required low aeration; all of these are considered beneficial characteristics for the production of target compounds, especially at an industrial scale. Under optimized conditions in a 5 L fermenter, the titer, productivity, and molar conversion efficiency for 4HV reached 100 g/L, 4.2 g/L/h, and 92%, respectively. Our system could prove to be a promising method for the large-scale production of 4HV from LA at low-cost and using a renewable biomass source.

Stabilization of Formate Dehydrogenase in a Metal-Organic Framework for Bioelectrocatalytic Reduction of CO2

The efficient fixation of excess CO₂ from the atmosphere to yield value-added chemicals remains crucial in response to the increasing levels of carbon emission. Coupling enzymatic reactions with electrochemical regeneration of cofactors is a promising technique for fixing CO₂ , while producing biomass which can be further transformed into biofuels. Herein, a bioelectrocatalytic system was established by depositing crystallites of a mesoporous metal-organic framework (MOF), termed NU-1006, containing formate dehydrogenase, on a fluorine-doped tin oxide glass electrode modified with Cp*Rh(2,2'-bipyridyl-5,5'-dicarboxylic acid)Cl₂ complex. This system converts CO₂ into formic acid at a rate of 79±3.4 mm h^-1 with electrochemical regeneration of the nicotinamide adenine dinucleotide cofactor. The MOF-enzyme composite exhibited significantly higher catalyst stability when subjected to non-native conditions compared to the free enzyme, doubling the formic acid yield.

Synthesis of Formate from CO2 Gas Catalyzed by an O2-Tolerant NAD-Dependent Formate Dehydrogenase and Glucose Dehydrogenase

Direct biocatalytic conversion of CO₂ to formic acid is an attractive means of reversibly storing energy in chemical bonds. Formate dehydrogenases (FDHs) are a heterogeneous group of enzymes that catalyze the oxidation of formic acid to carbon dioxide, generating two protons and two electrons. Several FDHs have recently been reported to catalyze the reverse reaction, i.e., the reduction of carbon dioxide to formic acid, under appropriate conditions. The main challenges with these enzymes are relatively low rates of CO₂ reduction and high oxygen sensitivity. Our earlier studies (Yu et al. (2017) J. Biol. Chem. 292, 16872-16879) have shown that the FdsABG formate dehydrogenase from Cupriavidus necator is able to effectively catalyze the reduction of CO₂, using NADH as a source of reducing equivalents, with a good oxygen tolerance. On the basis of this result, we have developed a highly thermodynamically efficient and cost-effective biocatalytic process for the transformation of CO₂ to formic acid using FdsABG. We have  cloned the full-length soluble formate dehydrogenase (FdsABG) from C. necator and expressed it in Escherichia coli with a His-tag fused to the N terminus of the FdsG subunit; this overexpression system has greatly simplified the FdsABG purification process. Importantly, we have also combined this recombinant C. necator FdsABG with another enzyme, glucose dehydrogenase, for continuous regeneration of NADH for CO₂ reduction and demonstrated that the combined system is highly effective in reducing CO₂ to formate. The results indicate that this system shows significant promise for the future development of an enzyme-based system for the industrial reduction of CO₂.

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

BACKGROUND

The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members.

RESULTS

We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase.

CONCLUSIONS

The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.

Photobiocatalysis: Activating Redox Enzymes by Direct or Indirect Transfer of Photoinduced Electrons

Biocatalytic transformation has received increasing attention in the green synthesis of chemicals because of the diversity of enzymes, their high catalytic activities and specificities, and mild reaction conditions. The idea of solar energy utilization in chemical synthesis through the combination of photocatalysis and biocatalysis provides an opportunity to make the "green" process greener. Oxidoreductases catalyze redox transformation of substrates by exchanging electrons at the enzyme's active site, often with the aid of electron mediator(s) as a counterpart. Recent progress indicates that photoinduced electron transfer using organic (or inorganic) photosensitizers can activate a wide spectrum of redox enzymes to catalyze fuel-forming reactions (e.g., H₂ evolution, CO₂ reduction) and synthetically useful reductions (e.g., asymmetric reduction, oxygenation, hydroxylation, epoxidation, Baeyer-Villiger oxidation). This Review provides an overview of recent advances in light-driven activation of redox enzymes through direct or indirect transfer of photoinduced electrons.

Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii

Over the next decades, with the growing concern of rising atmospheric carbon dioxide (CO₂) levels, the importance of investigating new approaches for its reduction becomes crucial. Reclamation of CO₂ for conversion into biofuels represents an alternative and attractive production method that has been studied in recent years, now with enzymatic methods gaining more attention. Formate dehydrogenases (FDHs) are NAD(P)H-dependent oxidoreductases that catalyze the conversion of formate into CO₂ and have been extensively used for cofactor recycling in chemoenzymatic processes. A new FDH from Clostridium ljungdahlii (ClFDH) has been recently shown to possess activity in the reverse reaction: the mineralization of CO₂ into formate. In this study, we show the successful homologous expression of ClFDH in Escherichia coli. Biochemical and kinetic characterization of the enzyme revealed that this homologue also demonstrates activity toward CO₂ reduction. Structural analysis of the enzyme through homology modeling is also presented.

Emerging platforms for co-utilization of one-carbon substrates by photosynthetic organisms

One-carbon substrates have generated increasing attention as long-term sustainable feedstocks for biobased production of fuels and chemicals. However, their physicochemical properties present significant biological and operational challenges for commercial bioprocesses including kinetically slower substrate activation, high energetic cost of assimilation, low mass transfer, substrate toxicity, and low productivity titers. Several different routes including optimization of native pathways, synthetic pathways, and hybrid methods are being explored to overcome these challenges. Integration of emerging biological solutions with process improvements is enabling faster bioprocess development for cost-effective conversion of one-carbon substrates into fuels and chemicals.

Characterization of a novel thermotolerant NAD+-dependent formate dehydrogenase from hot climate plant cotton (Gossypium hirsutum L.)

NAD+-dependent formate dehydrogenases (FDH, EC 1.2.1.2), providing energy to the cell in methylotrophic microorganisms, are stress proteins in higher plants and the level of FDH expression increases under several abiotic and biotic stress conditions. They are biotechnologically important enzymes in NAD(P)H regeneration as well as CO2 reduction. Here, the truncated form of the Gossypium hirsutum fdh1 cDNA was cloned into pQE-2 vector, and overexpressed in Escherichia coli DH5α-T1 cells. Recombinant GhFDH1 was purified 26.3-fold with a yield of 87.3%. Optimum activity was observed at pH 7.0, when substrate is formate. Kinetic analyses suggest that GhFDH1 has considerably high affinity to formate (0.76 ± 0.07 mM) and NAD+ (0.06 ± 0.01 mM). At the same time, the affinity (1.98 ± 0.4 mM) and catalytic efficiency (0.0041) values of the enzyme for NADP+ show that GhFDH1 is a valuable enzyme for protein engineering studies that is trying to change the coenzyme preference from NAD to NADP which has a much higher cost than that of NAD. Improving the NADP specificity is important for NADPH regeneration which is an important coenzyme used in many biotechnological production processes. The Tm value of GhFDH1 is 53.3 °C and the highest enzyme activity is measured at 30 °C with a half-life of 61 h. Whilst further improvements are still required, the obtained results show that GhFDH1 is a promising enzyme for NAD(P)H regeneration for its prominent thermostability and NADP+ specificity.

Activation of the catalytic function of formaldehyde dehydrogenase for formate reduction by single-electron reduced methylviologen

The kinetic properties of formate reduction to formaldehyde with formaldehyde dehydrogenase (FldDH) using single-electron reduced methylviologen (MV˙) as a co-enzyme were clarified.

Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other.

Specific and sustainable bioelectro-reduction of carbon dioxide to formate on a novel enzymatic cathode

To specifically convert waste CO2 into renewable chemicals, enzymatic electrosynthesis (EES) of formate from CO2 reduction was investigated in a bioelectrochemical system (BES). A novel cathode with immobilized enzyme and electropolymerized mediator-regenerator was fabricated for such bioelectrocatalytic EES. Formate dehydrogenase from Candida boidinii (CbFDH) was set as a new model enzyme in BES. Modified Nafion micelles with appropriate pore size were found to be suitable for immobilization of CbFDH and protection of its enzymatic activity and lifetime at optimal pH of 6.0. The enzymatic electrosynthesis activity of immobilized CbFDH was characterized systematically. Quite a small overpotential was required in the bioelectrochemical EES reaction. A two-electron transfer process was confirmed in the CbFDH-catalyzed reduction of bicarbonate to formate. With electro-polymerized neutral red (PolyNR) as a NADH (mediator)-regenerator, efficient formate production could be achieved at a maximum rate of 159.89 mg L(-1) h(-1) under poised potential of -0.80 V (vs. SHE). The immobilized CbFDH and electropolymerized PolyNR on an enzymatic cathode contributed greatly to sustainable EES, giving energy-rich formate as the only catalysis product.

Sunlight-assisted, biocatalytic formate synthesis from CO2 and water using silicon-based photoelectrochemical cells

A silicon-based photoelectrochemical cell is developed to convert CO₂ to formate with water as an electron donor by using formate dehydrogenase from Thiobacillus sp.

A review of harvesting clean fuels from enzymatic CO2 reduction

This review has summarised single enzyme, multi enzymatic and semiconducting nanomaterial integrated enzymatic systems for CO₂ conversion to clean fuels.

Biocatalysis for the application of CO2 as a chemical feedstock

Biocatalysts, capable of efficiently transforming CO2 into other more reduced forms of carbon, offer sustainable alternatives to current oxidative technologies that rely on diminishing natural fossil-fuel deposits. Enzymes that catalyse CO2 fixation steps in carbon assimilation pathways are promising catalysts for the sustainable transformation of this safe and renewable feedstock into central metabolites. These may be further converted into a wide range of fuels and commodity chemicals, through the multitude of known enzymatic reactions. The required reducing equivalents for the net carbon reductions may be drawn from solar energy, electricity or chemical oxidation, and delivered in vitro or through cellular mechanisms, while enzyme catalysis lowers the activation barriers of the CO2 transformations to make them more energy efficient. The development of technologies that treat CO2-transforming enzymes and other cellular components as modules that may be assembled into synthetic reaction circuits will facilitate the use of CO2 as a renewable chemical feedstock, greatly enabling a sustainable carbon bio-economy.

Electro-biocatalytic production of formate from carbon dioxide using an oxygen-stable whole cell biocatalyst

The use of biocatalysts to convert CO2 into useful chemicals is a promising alternative to chemical conversion. In this study, the electro-biocatalytic conversion of CO2 to formate was attempted with a whole cell biocatalyst. Eight species of Methylobacteria were tested for CO2 reduction, and one of them, Methylobacterium extorquens AM1, exhibited an exceptionally higher capability to synthesize formate from CO2 by supplying electrons with electrodes, which produced formate concentrations of up to 60mM. The oxygen stability of the biocatalyst was investigated, and the results indicated that the whole cell catalyst still exhibited CO2 reduction activity even after being exposed to oxygen gas. From the results, we could demonstrate the electro-biocatalytic conversion of CO2 to formate using an obligate aerobe, M. extorquens AM1, as a whole cell biocatalyst without providing extra cofactors or hydrogen gas. This electro-biocatalytic process suggests a promising approach toward feasible way of CO2 conversion to formate.

Site-specific bioconjugation of an organometallic electron mediator to an enzyme with retained photocatalytic cofactor regenerating capacity and enzymatic activity

Photosynthesis consists of a series of reactions catalyzed by redox enzymes to synthesize carbohydrates using solar energy. In order to take the advantage of solar energy, many researchers have investigated artificial photosynthesis systems mimicking the natural photosynthetic enzymatic redox reactions. These redox reactions usually require cofactors, which due to their high cost become a key issue when constructing an artificial photosynthesis system. Combining a photosensitizer and an Rh-based electron mediator (RhM) has been shown to photocatalytically regenerate cofactors. However, maintaining the high concentration of cofactors available for efficient enzymatic reactions requires a high concentration of the expensive RhM; making this process cost prohibitive. We hypothesized that conjugation of an electron mediator to a redox enzyme will reduce the amount of electron mediators necessary for efficient enzymatic reactions. This is due to photocatalytically regenerated NAD(P)H being readily available to a redox enzyme, when the local NAD(P)H concentration near the enzyme becomes higher. However, conventional random conjugation of RhM to a redox enzyme will likely lead to a substantial loss of cofactor regenerating capacity and enzymatic activity. In order to avoid this issue, we investigated whether bioconjugation of RhM to a permissive site of a redox enzyme retains cofactor regenerating capacity and enzymatic activity. As a model system, a RhM was conjugated to a redox enzyme, formate dehydrogenase obtained from Thiobacillus sp. KNK65MA (TsFDH). A RhM-containing azide group was site-specifically conjugated to p-azidophenylalanine introduced to a permissive site of TsFDH via a bioorthogonal strain-promoted azide-alkyne cycloaddition and an appropriate linker. The TsFDH-RhM conjugate exhibited retained cofactor regenerating capacity and enzymatic activity.

Structural insights into the efficient CO2-reducing activity of an NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA

CO2 fixation is thought to be one of the key factors in mitigating global warming. Of the various methods for removing CO2, the NAD-dependent formate dehydrogenase from Candida boidinii (CbFDH) has been widely used in various biological CO2-reduction systems; however, practical applications of CbFDH have often been impeded owing to its low CO2-reducing activity. It has recently been demonstrated that the NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA (TsFDH) has a higher CO2-reducing activity compared with CbFDH. The crystal structure of TsFDH revealed that the biological unit in the asymmetric unit has two conformations, i.e. open (NAD(+)-unbound) and closed (NAD(+)-bound) forms. Three major differences are observed in the crystal structures of TsFDH and CbFDH. Firstly, hole 2 in TsFDH is blocked by helix α20, whereas it is not blocked in CbFDH. Secondly, the sizes of holes 1 and 2 are larger in TsFDH than in CbFDH. Thirdly, Lys287 in TsFDH, which is crucial for the capture of formate and its subsequent delivery to the active site, is an alanine in CbFDH. A computational simulation suggested that the higher CO2-reducing activity of TsFDH is owing to its lower free-energy barrier to CO2 reduction than in CbFDH.

Liposomes as chaperone mimics with controllable affinity toward heat-denatured formate dehydrogenase from Candida boidinii

Chaperone machinery in living systems can catch denatured enzymes and induce their reactivation. Chaperone mimics are beneficial for applying enzymatic reactions in vitro. In this work, the affinity between liposomes and thermally denatured enzymes was controlled to stabilize the enzyme activity. The model enzyme is formate dehydrogenase from Candida boidinii (CbFDH) which is a homodimer and negatively charged in the phosphate buffer solution (pH 7.2) used. The activity of free CbFDH readily decreased at 58 °C following the first-order kinetics with the half-life t1/2 of 27 min. The turbidity measurements showed that the denatured enzyme molecules formed aggregates. The liposomes composed of zwitterionic phosphatidylcholines (PCs) stabilized the CbFDH activity at 58 °C, as revealed with six different PCs. The PC liposomes were indicated to bind to the aggregate-prone enzyme molecules, allowing reactivation at 25 °C. The cofactor β-reduced nicotinamide adenine dinucleotide (NADH) also stabilized the enzyme activity. The affinity between liposomes and denatured CbFDH could be modulated by incorporating cationic 1,2-dioleoyloxy-3-trimethylammonium propane chloride (DOTAP) in PC membranes. The t1/2 values significantly increased in the presence of liposomes ([lipid] = 1.5 mM) composed of PC and DOTAP at the mole fraction f(D) of 0.1. On the other hand, the DOTAP-rich liposomes (f(D) ≥ 0.7) showed strong affinity toward denatured CbFDH, accelerating its deactivation. The liposomes with low charge density function as chaperone mimics that can efficiently catch the denatured enzymes without interfering with their intramolecular interaction for reactivation.

Double clicking for site-specific coupling of multiple enzymes

Herein, we report a novel strategy to site-specifically couple multiple enzymes using two compatible click chemistries and site-specific incorporation of a clickable non-natural amino acid.