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Determination of free cyanide (fCN) is required for various industrial, environmental, food, and clinical samples. Enzymatic methods are not widely used in this field despite their selectivity and mild conditions. Therefore, we present here a proof of concept for new spectrophotometric enzymatic assays of fCN. These are based on the hydrolysis of fCN affording the readily detectable NADH. fCN is hydrolyzed either in one step by cyanide dihydratase (CynD) or in two steps by cyanide hydratase (CynH) and formamidase (AmiF). An advantage of the latter route is the higher activity of CynH and AmiF compared to CynD. In both cases, the resulting formate is then transformed by an NAD-dependent formate dehydrogenase (FDH). The NADH thus formed is quantified colorimetrically using a known method based on a reduction of a tetrazolium salt (WST-8) with NADH. The developed assays of fCN are selective except for formic acid interference, proceed under mild conditions, and, moreover, fCN is detoxified during the reactions. The assays proceeded in a microtiter plate format. The limit of detection (LOD) and the limit of quantification (LOQ) were lower for the three-enzyme (CynH-AmiF-FDH) method (7.00 and 21.2 µmol/L, respectively) than for the two-enzyme (CynD-FDH) method (10.7 and 32.4 µmol/L, respectively). In conclusion, the new fCN assays presented in this work are selective, high-throughput, do not require harsh conditions, and use only small amounts of chemicals and enzymes. [ABSTRACT FROM AUTHOR]

Anaerobic digestion is a critical technology for pollution control, resource capacity enhancement, and sludge management, necessitating improvements in its efficiency. Formate serves as an electron carrier in syntrophic oxidation of volatile fatty acids (VFAs) during anaerobic digestion. The accumulation of formate can exert an inhibitory effect on the anaerobic digestion process. However, the stress concentration and the mechanism of the formate are not as simple as theoretical calculations based on thermodynamics. Thus, we investigated the response to different concentrations of formate in the syntrophic oxidation of propionate. The anaerobic sludge system and syntrophic co-culture system were applied. The propionate showed more stable degradation when formate dosage ranged from 5 to 10 mM. However, when the formate dosage reached 50 mM, the concentration of propionate was significantly higher than that of CK group, and the propionate metabolism was significantly inhibited. The reduction in functional flora and homogeneous metabolic pathways were found to be unfavorable for the stable progression of syntrophic propionate metabolism. Thus, the enhancement of homoacetogenesis can be a strategy adopted by the sludge system to alleviate formate stress. The methylmalonyl-CoA (MMC) pathway was inhibited under formate stress; the downregulation of RNA transcription of formate dehydrogenase (FDH) and hydrogenase (Hyd) related to MMC pathway may be the main reason for the inhibition of syntrophic propionate oxidation. The anaerobic sludge experiment and the co-culture experiment elucidated the mechanism of action of formate from both macroscopic rules and microscopic molecular mechanisms, respectively. [ABSTRACT FROM AUTHOR]

Abstract Formate dehydrogenase (FDH) is widely applied in regeneration of redox cofactors. There are continuing interests to engineer FDH for improved catalytic activity and cofactor preference. In the crystal structure of FDH from Pseudomonas sp. 101 (pseFDH), the C terminus with 9 amino acid residues cannot be resolved. However, our earlier work showed mutations at C terminus led pseFDH variants to favor a non-natural cofactor nicotinamide cytosine dinucleotide (NCD). Here, we investigated the role of C-terminal residues on cofactor preference by truncating their corresponding C terminus of pseFDH variants. Sequence comparison analysis showed that C-terminal residues were barely conservative among different FDHs. pseFDH and mutants with their C termini truncated were constructed, and the resulted variants showed improved preference to NCD mainly because NAD-dependent activity dropped more substantially. Further structure analysis showed that these pseFDH variants had their cofactor binding domains reconstructed to favor molecular interactions with NCD. Our work indicated that C-terminal residues of pseFDH affected enzyme activity and cofactor preference, which provides a new approach for ameliorating the performance of redox enzymes.

Sophisticated enzymatic systems have evolved in nature to efficiently couple distinct biochemical reactions in form of cascades. As such, they serve as reference models to understand the indirect interactions of catalytic centers. Herein, we studied, in solution, the coupling of the reactions from membrane‐bound [NiFe] hydrogenase (MBH) from Cupriavidus necator (reversible H2 splitting into H+ and e−) and the molybdenum‐dependent formate dehydrogenase from Rhodobacter capsulatus (reversible formate to CO2 interconversion). To follow their interplay via the characteristic absorptions from the MBH's active site or the respective substrate and product bands of FDH, we utilized in situ IR spectrocopy and GC(‐MS), in the absence and presence of soluble redox mediators. Coarse‐grained molecular dynamics (CGMD) computations revealed the lack of productive enzyme complexes for direct electron transfer (ET). Thus, the observed minor amounts of H2 or formate were produced from transient interactions between the two enzymes. On the contrary, the significantly increased product formation in the presence of methyl viologen can be related to the putative multiple interaction sites of the redox mediator with FDH identified by CGMD. Our study represents a proof‐of‐concept approach that can be used in the future to develop novel coupled biocatalytic systems by identifying potential ET pathways. [ABSTRACT FROM AUTHOR]

Enzyme engineering is a powerful tool for improving or altering the properties of biocatalysts for industrial, research, and therapeutic applications. Fast and accurate screening of variant libraries is often the bottleneck of enzyme engineering and may be overcome by growth-based screening strategies with simple processes to enable high throughput. The currently available growth-based screening strategies have been widely employed for enzymes but not yet for catalytically potent and oxygen-sensitive metalloenzymes. Here, we present a screening system that couples the activity of an oxygen-sensitive formate dehydrogenase to the growth of Escherichia coli. This system relies on the complementation of the E. coli formate hydrogenlyase (FHL) complex by Mo-dependent formate dehydrogenase H (EcFDH-H). Using an EcFDH-Hdeficient strain, we demonstrate that growth inhibition by acidic glucose fermentation products can be alleviated by FHL complementation. This allows the identification of catalytically active EcFDH-H variants at a readily measurable cell density readout, reduced handling efforts, and a low risk of oxygen contamination. Furthermore, a good correlation between cell density and formate oxidation activity was established using EcFDH-H variants with variable catalytic activities. As proof of concept, the growth assay was employed to screen a library of 1,032 EcFDH-H variants and reduced the library size to 96 clones. During the subsequent colorimetric screening of these clones, the variant A12G exhibiting an 82.4% enhanced formate oxidation rate was identified. Since many metal-dependent formate dehydrogenases and hydrogenases form functional complexes resembling E. coli FHL, the demonstrated growth-based screening strategy may be adapted to components of such electron-transferring complexes. [ABSTRACT FROM AUTHOR]

The present energy demand of the world is increasing but the fossil fuels are gradually depleting. As a result, the need for alternative fuels and energy sources is growing. Fuel cells could be one alternative to address the challenge. The fuel cell can convert CO2 to value-added chemicals. The potential of bio-fuel cells, specifically enzymatic fuel cells and microbial fuel cells, and the importance of immobilization technology in bio-fuel cells are highlighted. The review paper also includes a detailed explanation of the microbial electrosynthesis system to reduce CO2 and the value-added products during microbial electrosynthesis. Future research in bio-electrochemical synthesis for CO2 conversion is expected to prioritize enhancing biocatalyst efficiency, refining reactor design, exploring novel electrode materials, understanding microbial interactions, integrating renewable energy sources, and investigating electrochemical processes for carbon capture and selective CO2 reduction. The challenges and perspectives of bio-electrochemical systems in the application of CO2 conversion are also discussed. Overall, this review paper provides valuable insights into the latest developments and criteria for effective research and implementation in bio-fuel cells, immobilization technology, and microbial electro-synthesis systems. [ABSTRACT FROM AUTHOR]

The nature of air-inactivation of the formate dehydrogenase FdsDABG from Cupriavidus necator has been investigated. It is found that superoxide, generated in the reaction of reduced enzyme with oxygen, is responsible for the loss of activity and that superoxide dismutase protects the enzyme from air-inactivation. Inhibition appears to be due to the reaction of superoxide with the catalytically essential MoS group of the enzyme's molybdenum center in such a way that generates sulfite. SYNOPSIS: Superoxide generated in the reaction of reduced formate dehydrogenase FdsDABG from Cupriavidus necator with O2 is found to be responsible for the loss of activity. Catalytic amounts of superoxide dismutase are found to protect FdsDABG just as well as more generally used stabilizing inhibitors such as nitrate.

Post synthetic modification of a hydrophilic metal–organic framework (MOF), HKUST-1, with stearic acid (SA) was carried out to enhance the stability of HKUST-1 in aqueous solution to be used as a support for formate dehydrogenase (FDH) used for CO2 conversion to formate. SA modification improved the hydrophobicity without affecting the morphology and crystal structure of MOF. Adsorption of FDH on the modified MOF (SA@HKUST-1) was compared to that of the native HKUST-1 and ZIF-L. The adsorption kinetics on all MOFs was found to follow pseudo-second order kinetics and the isotherm was best described by Freundlich model. The high stability of SA@HKUST-1 and enhanced hydrophobic interaction between support and CO2 resulted in high catalytic efficiency and stability of FDH@SA@HKUST-1. The immobilized enzyme retained 95.1% of its initial activity after 4 cycles of repeated use. It was also shown that FDH@SA@HKUST-1 retained morphology and crystal structure after repeated use. Results of the present work provide novel insight into the influence of hydrophobic MOFs on the activity and stability of immobilized FDH. These findings are expected to assist in developing highly active and stable biocatalysts for CO2 hydrogenation at commercial level.

Pichia pastoris (P. pastoris) is one of the most popular cell factories for expressing exogenous proteins and producing useful chemicals. The alcohol oxidase 1 promoter (PAOX1) is the most commonly used strong promoter in P. pastoris and has the characteristic of biphasic expression. However, the inducer for PAOX1, methanol, has toxicity and poses risks in industrial settings. In the present study, analyzing transcriptomic data of cells collected at different stages of growth found that the formate dehydrogenase (FDH) gene ranked 4960th in relative expression among 5032 genes during the early logarithmic growth phase but rose to the 10th and 1st during the middle and late logarithmic growth phases, respectively, displaying a strict biphasic expression characteristic. The unique transcriptional regulatory profile of the FDH gene prompted us to investigate the properties of its promoter (PFDH800). Under single-copy conditions, when a green fluorescent protein variant was used as the expression target, the PFDH800 achieved 119% and 69% of the activity of the glyceraldehyde-3-phosphate dehydrogenase promoter and PAOX1, respectively. After increasing the copy number of the expression cassette in the strain to approximately four copies, the expression level of GFPuv driven by PFDH800 increased to approximately 2.5 times that of the strain containing GFPuv driven by a single copy of PAOX1. Our PFDH800-based expression system exhibited precise biphasic expression, ease of construction, minimal impact on normal cellular metabolism, and high strength. Therefore, it has the potential to serve as a new expression system to replace the PAOX1 promoter. [ABSTRACT FROM AUTHOR]

The formate dehydrogenase (FDH) is regarded as a universal stress protein involved in various plant abiotic stress responses. This study aims to ascertain GmFDH function in conferring tolerance to aluminum (Al) stress. The bioinformatics analysis demonstrates that GmFDH from Tamba black soybean (TBS) encodes FDH. Quantitative reverse transcription-PCR (qRT-PCR) showed that GmFDH expression was induced by Al stress with a concentration-time-specific pattern. Moreover, Al stress promotes formate content and activates FDH activity. Further studies revealed that GmFDH overexpression alleviated root growth of tobacco under Al stress inhibition and reduced Al and ROS accumulation in roots. In addition, transgenic tobacco had much more root citrate exudation and much higher activity of antioxidant enzymes than wild type. Moreover, under Al stress, NtMATE and NtALS3 expression showed no changes in wild type and overexpression lines, suggesting that here the known Al-resistant mechanisms are not involved. However citrate synthase activity is higher in transgenic tobaccos than that of wild type, which might be the reason for citrate secretion increase. Thus, the increased Al tolerance of GmFDH overexpression lines is likely attributable to enhanced activities of antioxidant enzymes and promoting citrate secretion. Taken together, our findings advance understanding of higher plant Al toxicity mechanisms and suggest a possible new route towards the improvement of plant growth under Al stress. [ABSTRACT FROM AUTHOR]

It has been reported that the frhAGB-encoded hydrogenase from Thermococcus onnurineus NA1 is homologous to the F420-reducing hydrogenase from methanogens and can reduce thioredoxin reductase (TrxR) via direct electron transfer from H2 oxidation. In this study, to find other interaction targets of frhAGB-encoded hydrogenase, we searched for structural homologs of TrxR using the Position-Specific Iterative Basic Local Alignment Search Tool (PSI-BLAST) protein database search program and AlphaFold Protein Structure Database. Fdh3B (TON_0542), a subunit of the formate dehydrogenase 3 (Fdh3), showed the most similar structure to TrxR in its domains. The interaction potential of Fdh3B with frhAGB-encoded hydrogenase was demonstrated by measuring H2-dependent NADP+ reduction by a mixture of purified proteins. Similarly, the H2-dependent NADP+ -reducing activity of Fdh3 whole complex and two other TrxR homologs encoded by TON_0702 and TON_1376 was determined. It was also demonstrated that the Fdh3 complex could reduce CO2 to formate in the presence of the frhAGB-encoded hydrogenase and H2, as shown for the H2-dependent CO2 reductase (HDCR) of acetogen. The in vivo contribution of the frhAGB-encoded hydrogenase and Fdh3 to H2-dependent CO2 reduction was investigated using a resting cell assay, and formate production was significantly decreased in fdh3A or frhA deletion mutants. In conclusion, the frhAGB-encoded hydrogenase was identified to directly transfer electrons to Fdh3 without an electron carrier, similar to the mechanism observed for TrxR. These results expand our understanding of the functional role of the frhAGB-encoded hydrogenase in non-methanogenic Thermococcus species. IMPORTANCE The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the frhAGBencoded hydrogenase of Thermococcus onnurineus NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)+ is significant in that the enzyme can function to supply reducing equivalents, just as F420-reducing hydrogenases in methanogens use coenzyme F420 as an electron carrier. Additionally, it was identified that T. onnurineus NA1 could produce formate from H2 and CO2 by the concerted action of frhAGB-encoded hydrogenase and formate dehydrogenase Fdh3. [ABSTRACT FROM AUTHOR]

The urgent need to reduce CO2 emissions has motivated the development of CO2 capture and utilization technologies. An emerging application is CO2 transformation into storage chemicals for clean energy carriers. Formic acid (FA), a valuable product of CO2 reduction, is an excellent hydrogen carrier. CO2 conversion to FA, followed by H2 release from FA, are conventionally chemically catalyzed. Biocatalysts offer a highly specific and less energy‐intensive alternative. CO2 conversion to formate is catalyzed by formate dehydrogenase (FDH), which usually requires a cofactor to function. Several FDHs have been incorporated in bioelectrochemical systems where formate is produced by the biocathode and the cofactor is electrochemically regenerated. H2 production from formate is also catalyzed by several microorganisms possessing either formate hydrogenlyase or hydrogen‐dependent CO2 reductase complexes. Combination of these two processes can lead to a CO2‐recycling cycle for H2 production, storage, and release with potentially lower environmental impact than conventional methods. [ABSTRACT FROM AUTHOR]

Formate dehydrogenases (Fdhs) mediate the oxidation of formate to carbon dioxide and concomitant reduction of nicotinamide adenine dinucleotide (NAD+). The low cost of the substrate formate and importance of the product NADH as a cellular source of reducing power make this reaction attractive for biotechnological applications. However, the majority of Fdhs are sensitive to inactivation by thiol‐modifying reagents. In this study, we report a chemically resistant Fdh (FdhSNO) from the soil bacterium Starkeya novella strictly specific for NAD+. We present its recombinant overproduction, purification and biochemical characterization. The mechanistic basis of chemical resistance was found to be a valine in position 255 (rather than a cysteine as in other Fdhs) preventing the inactivation by thiol‐modifying compounds. To further improve the usefulness of FdhSNO as for generating reducing power, we rationally engineered the protein to reduce the coenzyme nicotinamide adenine dinucleotide phosphate (NADP+) with better catalytic efficiency than NAD+. The single mutation D221Q enabled the reduction of NADP+ with a catalytic efficiency kCAT/KM of 0.4 s−1·mm−1 at 200 mm formate, while a quadruple mutant (A198G/D221Q/H379K/S380V) resulted in a fivefold increase in catalytic efficiency for NADP+ compared with the single mutant. We determined the cofactor‐bound structure of the quadruple mutant to gain mechanistic evidence behind the improved specificity for NADP+. Our efforts to unravel the key residues for the chemical resistance and cofactor specificity of FdhSNO may lead to wider use of this enzymatic group in a more sustainable (bio)manufacture of value‐added chemicals, as for instance the biosynthesis of chiral compounds. [ABSTRACT FROM AUTHOR]

Previously, the gene of formate dehydrogenase (FDH, EC 1.2.1.2) from the thermotolerant methylotrophic yeast Ogataea parapolymorpha DL 1 (OpaFDH) was cloned in our laboratory. Recombinant enzyme with additional glycine amino acid residue (OpaFDH_GK) was obtained in Escherichia coli cells in active and soluble form with a yield of more than 1 g per liter of the medium. In the present work, a detailed comparison of this enzyme with FDHs from other sources was carried out. Among eukaryotic formate dehydrogenases, OpaFDH has the highest thermal stability. To elucidate effect of N-terminal residue on the properties of the enzyme, OpaFDH_K (identical to natural) and OpaFDH_AK variants containing an additional Ala residue at the N-terminus were also obtained. It was shown that addition of an Ala residue to the N-terminus reduces four-fold the rate constant of thermal inactivation compared with the addition of a Gly residue. Addition of six more histidine residues to the N-terminus of OpaFDH_AK leads to acceleration of purification, practically does not affect kinetic parameters, but somewhat reduces thermal stability, which, however, can be restored to the level of OpaFDH_AK stability by adding 0.5 M NaCl. [ABSTRACT FROM AUTHOR]

Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH-, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases.

Metal-dependent formate dehydrogenases (Me-FDHs) are highly active CO2-reducing enzymes operating at low redox potentials and employ either molybdenum or tungsten to reduce the bound substrate. This makes them suitable for electrochemical applications such as fossil-free production of commodity chemicals utilizing renewable energy. Electrocatalytic CO2 reduction by cathode-immobilized Me-FDHs has been recently demonstrated and rational protein engineering can be used to optimize Me-FDHs for various carbon reduction reactions. In the present study, CO2 reduction by soluble monomeric Escherichia coli formate dehydrogenase H (EcFDH-H) was demonstrated and the function of its nucleophilic selenocysteine residue as a transient ligand of a centrally bound molybdenum atom was investigated. Kinetic analysis of the wildtype enzyme revealed maximum CO2 reduction rates of 44 ± 6 s−1 at pH 5.8 that was decreased to 19% and 0% in the case of selenocysteine substitution with the structural homologues cysteine and serine, respectively. Further selenocysteine-to-cysteine substitution effects included an increased acid tolerance as well as stronger inhibition by nitrate and azide indicating a shift of the Mo oxidation state from IV to VI. Conversely, a destabilizing effect on the oxidized Mo(VI) center could be assigned to the native selenocysteine residue that may facilitate the observed efficient CO2 reduction by rapid transition between Mo oxidation states. Taken together, the performed characterization of EcFDH-H as a catalyst for CO2 reduction and the selenocysteine substitution analysis furthers the understanding of the active-site structure of Me-FDHs and thereby supports the development of more efficient biocatalysts for CO2 reduction.

The enzymatic reduction of carbon dioxide presents limited applicability due to denaturation and the impossibility of biocatalyst recovery; disadvantages that can be minimized by its immobilization. Here, a recyclable bio‐composed system was constructed by in‐situ encapsulation under mild conditions using formate dehydrogenase in a ZIF‐8 metalorganic framework (MOF) in the presence of magnetite. The partial dissolution of ZIF‐8 in the enzyme's operation medium can be relatively inhibited if the concentration of magnetic support used exceeds 10 mg mL−1. The bio‐friendly environment for immobilization does not harm the integrity of the biocatalyst, and the production of formic acid is improved 3.4‐fold compared to the free enzyme because the MOFs act as concentrators of the enzymatic cofactor. Furthermore, the bio‐composed system retains 86 % of its activity after a long time of five cycles, thus indicating an excellent magnetic recovery and a good reusability. [ABSTRACT FROM AUTHOR]

NAD(P)+-dependent formate dehydrogenase (FDH, EC 1.2.1.2.) catalyzes the oxidation of formate ion with the coupled reduction of NAD(P)+ to NAD(P)H. Previously, in our laboratory, a genetic construct was obtained with the soyfdh2 gene encoding isoenzyme 2 of formate dehydrogenase from soybean Glycine max (SoyFDH). In this construct the nucleotide sequence encoding the signal peptide responsible for the transport of the pro-enzyme into the mitochondria of plant cells (the SoyFDH_L enzyme) was deleted. In this work, a second variant of SoyFDH_S was obtained, in which, compared to SoyFDH_L, the sequence at the N-terminus was reduced and changed to mimic the N-terminus sequence in FDH from Pseudomonas sp.101 bacterium. Next, a sequence of six histidine residues (His-tag) was added to the N-terminus of the long and short forms of SoyFDH. All four SoyFDH variants were expressed in E. coli BL21(DE3)CodonPlus cells. These enzymes were purified, their kinetic parameters were determined, and thermal stability was studied. In the case of SoyFDH_L, which is similar to the natural form of the enzyme, both variants, with and without His-tag, the expression level is two times higher compared to the truncated variant. The addition of His-tag to the N-terminus of enzymes reduces the level of expression. Changing the sequence of the N-terminus, as well as introducing the His-tag sequence to the N-terminus, does not significantly affect thermal stability of the enzymes at temperatures of 50–56°C. However, due to the higher values of the activation enthalpy ΔH≠ of the thermal inactivation process, the shortened form at normal temperatures is 3 times more stable than the natural one. A comparison of the kinetic parameters of the two SoyFDH variants shows that the catalytic constants are the same, but the long version SoyFDH_L has lower values , and the short version SoyFDH_S has lower values. The introduction of His-tag into the N-terminus of enzymes does not affect their kinetic parameters. [ABSTRACT FROM AUTHOR]

NAD(P)+-dependent formate dehydrogenase (EC 1.2.1.2, FDH) catalyzes the simplest reaction from chemical and biological points of view, oxidation of formate-ion to carbon dioxide coupled to NAD(P)+ reduction to yield NAD(P)H. Advances in the life sciences have shown that this reaction plays an extremely important role in a wide variety of organisms. The areas and types of practical applications of FDH are also permanently expanding. The review analyzes the key steps in the development of our knowledge on the role of formate dehydrogenase in living systems. Achievements in creation of highly efficient catalysts based on FDH for classic biotechnology as well as for new areas are also considered. The importance of a correct selection of the starting FDH form for the purpose of a biocatalyst design with required properties with minimal costs is demonstrated. The prospects for the use of FDH for CO2 fixation of CO2 are discussed. [ABSTRACT FROM AUTHOR]

It is challenging to capture carbon dioxide (CO2), a major greenhouse gas in the atmosphere, due to its high chemical stability. One potential practical solution to eliminate CO2 is to convert CO2 into formate using hydrogen (H2) (CO2 hydrogenation), which can be accomplished with inexpensive hydrogen from sustainable sources. While industrial flue gas could provide an adequate source of hydrogen, a suitable catalyst is needed that can tolerate other gas components, such as carbon monoxide (CO) and oxygen (O2), potential inhibitors. Our proposed CO2 hydrogenation system uses the hydrogenase derived from Ralstonia eutropha H16 (ReSH) and formate dehydrogenase derived from Methylobacterium extorquens AM1 (MeFDH1). Both enzymes are tolerant to CO and O2, which are typical inhibitors of metalloenzymes found in flue gas. We have successfully demonstrated that combining ReSH- and MeFDH1-immobilized resins can convert H2 and CO2 in real flue gas to formate via a nicotinamide adenine dinucleotide-dependent cascade reaction. We anticipated that this enzyme system would enable the utilization of diverse H2 and CO2 sources, including waste gases, biomass, and gasified plastics.

Promoting the activity of biological enzymes under in vitro environment is a promising technique for bioelectrocatalytic reactions, such as the conversion of carbon dioxide (CO2) into valuable chemicals, which is a promising strategy to address the environmental issue of CO2 in the atmosphere; however, this technique remains challenging. Herein, a nanocage structure for enzyme confinement is synthesized to enable the in situ encapsulation of formate dehydrogenase (FDH) in a porous metal–organic framework, which acts as a coenzyme and boosts the hybrid synergistic catalysis using enzymes. This study reveals that the synthesized FDH@ZIF‐8 nanocage‐structured hybrid (CSH) catalyst exhibits an improved catalytic ability of the enzymes and increases the hydrophobicity of the electrode and its affinity to CO2. Thus, CSH can trap CO2 and control its microenvironments. The CSH catalyst boosts the conversion rate of CO2 to formic acid (HCOOH) to 28 times higher than that when using pure FDH. The in situ attenuated total reflectance surface‐enhanced infrared absorption spectroscopy (ATR‐SEIRAS) spectra indicates that OCHO* is the key intermediate. Density functional theory (DFT) calculations show that CSH has extremely low overpotential and is particularly effective for producing formate. This protection architecture for enzymes considerably promotes their biological application under in vitro environments. [ABSTRACT FROM AUTHOR]

Direct biocatalytic processes for CO2 capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO2 uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO2 into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C1-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO2 uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes. [ABSTRACT FROM AUTHOR]

Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium–carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions. [ABSTRACT FROM AUTHOR]

Photosynthesis as one of the most fascinating natural processes uses sunlight and CO2 for the preparation of various organic substances. Taking nature as inspiration the present work applies two proteins in an artificial matrix for constructing a biohybrid system allowing light-to-chemical photocataysis. Thus, the protein complexes photosystem I (PSI) and formate dehydrogenase (FDH) are combined with a porous three-dimensional indium tin oxide structure. Direct electron transfer takes place between the electrode material and PSI resulting in cathodic photocurrents. Instead of maximizing the current output, the study focuses on the usage of the excited electrons to drive FDH catalysis. At the enzyme carbon dioxide is reduced to formate with an efficiency of about 15% relative to the number of enhanced photoelectrons. The arrangement is favorable since it enables the conversion of CO2 at rather small applied potential of −0.2 V vs Ag/AgCl and over a longer period of illumination. Conversion efficiency and stability provide a good starting point for further investigations. The reported ITO/PSI/FDH electrode represents a system that combines photocatalysis with enzymatic catalysis allowing the storage of light energy in chemical energy.

Here, we report recent progress our laboratories have made in understanding the maturation and reaction mechanism of the cytosolic and NAD+-dependent formate dehydrogenase from Cupriavidus necator. Our recent work has established that the enzyme is fully capable of catalyzing the reverse of the physiological reaction, namely, the reduction of CO2 to formate using NADH as a source of reducing equivalents. The steady-state kinetic parameters in the forward and reverse directions are consistent with the expected Haldane relationship. The addition of an NADH-regenerating system consisting of glucose and glucose dehydrogenase increases the yield of formate approximately 10-fold. This work points to possible ways of optimizing the reverse of the enzyme's physiological reaction with commercial potential as an effective means of CO2 remediation. New insight into the maturation of the enzyme comes from the recently reported structure of the FdhD sulfurase. In E. coli, FdhD transfers a catalytically essential sulfur to the maturing molybdenum cofactor prior to insertion into the apoenzyme of formate dehydrogenase FdhF, which has high sequence similarity to the molybdenum-containing domain of the C. necator FdsA. The FdhD structure suggests that the molybdenum cofactor may first be transferred from the sulfurase to the C-terminal cap domain of apo formate dehydrogenase, rather than being transferred directly to the body of the apoenzyme. Closing of the cap domain over the body of the enzymes delivers the Mo-cofactor into the active site, completing the maturation of formate dehydrogenase. The structural and kinetic characterization of the NADH reduction of the FdsBG subcomplex of the enzyme provides further insights in reversing of the formate dehydrogenase reaction. Most notably, we observe the transient formation of a neutral semiquinone FMNH, a species that has not been observed previously with holoenzyme. After initial reduction of the FMN of FdsB byNADHto the hydroquinone (with a kred of 680 s-1 and Kd of 190 μM), one electron is rapidly transferred to the Fe2S2 cluster of FdsG, leaving FMNH. The Fe4S4 cluster of FdsB does not become reduced in the process. These results provide insight into the function not only of the C. necator formate dehydrogenase but also of other members of the NADH dehydrogenase superfamily of enzymes to which it belongs.

Rising global greenhouse gas emissions and the impacts of resultant climate change necessitate development and deployment of carbon capture and conversion technologies. Amongst the myriad of bio-based conversion approaches under evaluation, a formate bio-economy has recently been proposed, wherein CO2-derived formate serves as a substrate for concurrent carbon and energy delivery to microbial systems. To date, this approach has been explored in chemolithotrophic and heterotrophic organisms via native or engineered formatotrophy. However, utilization of this concept in phototrophic organisms has yet to be reported. Herein, we have taken the first steps to establish formate utilization in Picochlorum renovo, a recently characterized eukaryotic microalga with facile genetic tools and promising applied biotechnology traits. Plastidial heterologous expression of a formate dehydrogenase (FDH) enabled P. renovo growth on formate as a carbon and energy source. Further, FDH expression enhanced cultivation capacity on ambient CO2, underscoring the potential for bypass of conventional CO2 capture and concentration limitations. This work establishes a photoformatotrophic cultivation regime that leverages light energy-driven formate utilization. The resultant photosynthetic formate platform has widespread implications for applied phototrophic cultivation systems and the bio-economy at large.

Biohydrogen is mainly produced by anaerobic bacteria, anaerobic fungi, and algae under anaerobic conditions. In higher eukaryotes, it is thought that molecular hydrogen (H2) functions as a signaling molecule for physiological processes such as stress responses. Here, it is demonstrated that white-rot fungi produce H2 during wood decay. The white-rot fungus Trametes versicolor produces H2 from wood under aerobic conditions, and H2 production is completely suppressed under hypoxic conditions. Additionally, oxalate and formate supplementation of the wood culture increased the level of H2 evolution. RNA-seq analyses revealed that T. versicolor oxalate production from the TCA/glyoxylate cycle was down-regulated, and conversely, genes encoding oxalate and formate metabolism enzymes were up-regulated. Although the involvement in H2 production of a gene annotated as an iron hydrogenase was uncertain, the results of organic acid supplementation, gene expression, and self-recombination experiments strongly suggest that formate metabolism plays a role in the mechanism of H2 production by this fungus. It is expected that this novel finding of aerobic H2 production from wood biomass by a white-rot fungus will open new fields in biohydrogen research.

The conversion of CO2 into fuels and valuable chemicals is one of the central topics to combat climate change and meet the growing demand for renewable energy. Herein, we show that the formate dehydrogenase from Clostridium ljungdahlii (ClFDH) adsorbed on electrodes displays clear characteristic voltammetric signals that can be assigned to the reduction and oxidation potential of the [4Fe‐4S]2+/+ cluster under nonturnover conditions. Upon adding substrates, the signals transform into a specific redox center that engages in catalytic electron transport. ClFDH catalyzes rapid and efficient reversible interconversion between CO2 and formate in the presence of substrates. The turnover frequency of electrochemical CO2 reduction is determined as 1210 s−1 at 25 °C and pH 7.0, which can be further enhanced up to 1786 s−1 at 50°C. The Faradaic efficiency at −0.6 V (vs. standard hydrogen electrode) is recorded as 99.3% in a 2‐h reaction. Inhibition experiments and theoretical modeling disclose interesting pathways for CO2 entry, formate exit, and OCN− competition, suggesting an oxidation‐state‐dependent binding mechanism of catalysis. Our results provide a different perspective for understanding the catalytic mechanism of FDH and original insights into the design of synthetic catalysts. [ABSTRACT FROM AUTHOR]

This study was carried out in a tissue culture medium using two salt stress-tolerant varieties (Oryza sativa L. cv. Dhan47 and Kızıltan mutant8) and two stress resistance varieties (Oryza sativa L. cv. Maraş Yellow Rice and Kızıltan) at 50 mM, 100 mM and 200 mM NaCl concentrations in two different periods (fifteen and thirty days). In this study, we analysed root and stem length, antioxidant enzyme activities and gene expressions. Among the varieties, the highest size was observed in the maraş variety, and the least length was observed in the dhan47 rice varieties in the 30-day stem length results. While there was no adverse effect on root lengths as much as 100 mm, it was observed that it had a negative impact on a 200 mM medium. In the 30-day results, it was observed that the SOD activity in the leaves of the Kızıltan variety decreased compared to the control, while it was observed that the activity increased up to 100 mM salt concentration in the roots. It was determined that CAT activity increased in leaves and roots at all concentrations compared to the control at increasing salt concentrations over a 15-day period. At the same time, it was observed that CAT activity was the highest at 100 mM salt concentration on the leaves of dhan 47 plant. In the 30-day results, it was observed that FDH activity increased in leaves and roots in all rice varieties compared to the control. In gene expression analyses, the highest (7 times) gene expression in roots was observed on Kızıltan100 mM salt concentration. The highest relative expression (14 times) in leaves was on the Kiziltan mutant leaf at 200 mM salt concentration. The results showed different responses in physiological effects, antioxidant activities and gene expression analyses as salt concentrations of all rice varieties. With the results obtained in this study, it is expected that different rice varieties that are sensitive and resistant to salt stress will contribute to the usability of agricultural lands where salinity is gradually increasing. [ABSTRACT FROM AUTHOR]

Herein, a Zr‐based dual‐ligand MOFs with pre‐installed Rh complex was employed for NADH regeneration in situ and also used for immobilization of formic acid dehydrogenase (FDH) in order to realize a highly efficient CO2 fixation system. Then, based on the detailed investigations into the photochemical and electrochemical properties, it is demonstrated that the introduction of the photosensitive meso‐tetra(4‐carboxyphenyl) porphin (TCPP) ligands increased the catalytic active sites and improved photoelectric properties. Furthermore, the electron mediator Rh complex, anchored on the zirconium‐based dual‐ligand MOFs, enhanced the efficiency of electron transfer efficiency and facilitated the separation of photogenerated electrons and holes. Compared with UiO‐66‐NH2, Rh‐H2TCPP‐UiO‐66‐NH2 exhibits an optimized valence band structure and significantly improved photocatalytic activity for NAD+ reduction, resulting the synthesis of formic acid from CO2 increased from 150 μg mL−1 (UiO‐66‐NH2) to 254 μg mL−1 (Rh‐H2TCPP‐UiO‐66‐NH2). Moreover, the assembled photocatalyst‐enzyme coupled system also allows facile recycling of expensive electron mediator, enzyme, and photocatalyst. [ABSTRACT FROM AUTHOR]

Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated. [ABSTRACT FROM AUTHOR]

Schematic representing the influence of non-native graphite-specific peptide (Gr; IMVTESSDYSSY) as molecular binder on NAD+/NADH-dependent CO 2 reductase (CR) immobilization to assess the influence of site-specific fusion on graphite electrode towards electrocatalyzed CO 2 reduction to formate. [Display omitted] • NAD+/NADH-dependent CO 2 reductase for catalytic CO 2 to formate inter-conversion. • Solid-binding peptide enabled direct electron transfer towards effective CO 2 reduction. • Graphite surface characteristics benefitted in capacitive enzyme-electrode interfacing. • Amino-acids position in peptide inserts impact CO 2 -specific binding for redox catalysis. • Graphite in enzyme-electrode system include low-costs for bioelectronics upscaling. NAD+/NADH-dependent CO 2 reductase (CR) adapted from Candida methylica (E.C. 1.17.1.9) was introduced with a non-native graphite-specific peptide (Gr; IMVTESSDYSSY) as molecular binder to modify the native enzyme (CR-WT) with peptide insertion at N, C and NC terminus (CR-GrN, CR-GrC and CR-GrNC) to assess the influence of site-specific fusion on electrode binding. Graphite surface-binding activity relative to the electrode topography was evaluated for both native and synthetic CRs to establish the enzyme-electrode interfacing potentiality for efficient electron channelling. Impact of site-specific peptide fusion and amino-acids positioning was assessed for the active site binding availability and adsorption/desorption capability towards competent CO 2 -based redox catalysis. Solid-binding peptide and graphite surface interactive ability on direct electron transfer was studied with structural, enzymatic and electrochemical characterizations for efficient CO 2 electrosynthesis. Overall, enzymatic CO 2 reduction to formate based on interactive potentiality of enzyme-electrode complex with peptide modifications and graphite surface towards possibility of bioelectronics upscaling was depicted. [ABSTRACT FROM AUTHOR]

An overview is provided of the molybdenum- and tungsten-containing enzymes that catalyze the interconversion of formate and CO2 , focusing on common structural and mechanistic themes, as well as a consideration of the manner in which the mature Mo- or W-containing cofactor is inserted into apoprotein.

Abstract The conversion of CO2 into fuels and valuable chemicals is one of the central topics to combat climate change and meet the growing demand for renewable energy. Herein, we show that the formate dehydrogenase from Clostridium ljungdahlii (ClFDH) adsorbed on electrodes displays clear characteristic voltammetric signals that can be assigned to the reduction and oxidation potential of the [4Fe‐4S]2+/+ cluster under nonturnover conditions. Upon adding substrates, the signals transform into a specific redox center that engages in catalytic electron transport. ClFDH catalyzes rapid and efficient reversible interconversion between CO2 and formate in the presence of substrates. The turnover frequency of electrochemical CO2 reduction is determined as 1210 s−1 at 25 °C and pH 7.0, which can be further enhanced up to 1786 s−1 at 50°C. The Faradaic efficiency at −0.6 V (vs. standard hydrogen electrode) is recorded as 99.3% in a 2‐h reaction. Inhibition experiments and theoretical modeling disclose interesting pathways for CO2 entry, formate exit, and OCN− competition, suggesting an oxidation‐state‐dependent binding mechanism of catalysis. Our results provide a different perspective for understanding the catalytic mechanism of FDH and original insights into the design of synthetic catalysts.

Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.

Mo/W-containing formate dehydrogenases (FDH) catalyzed the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. While in the reaction of formate oxidation, the product is CO2, which exits the active site via a hydrophobic channel; bicarbonate is formed as the first intermediate during the reaction at the active site. Other than what has been previously reported, bicarbonate is formed after an oxygen atom transfer reaction, transferring the oxygen from water to formate and a subsequent proton-coupled electron transfer or hydride transfer reaction involving the sulfido ligand as acceptor. [ABSTRACT FROM AUTHOR]

NAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) from methylotrophic bacterium Pseudomonas sp.101 (PseFDH) has one of the highest thermal stability among all known enzymes of this group. The introduction of a number of amino acid substitutions into PseFDH made it possible to obtain a multipoint mutant PseFDH SM4S enzyme with even higher temperature and chemical stability. Previously, we showed that the introduction of additional single point replacements S131A, or S160A, or E170D into PseFDH SM4S led to further stabilization of the enzyme. In this work, based on the PseFDH SM4S S131A mutant, new mutant FDHs obtained, in which, compared to PseFDH SM4S, we added double S131A/E170D (M2), triple S131A/S160A/E170D (M3) and quadruple S131A/S160A/E170D/S145A (PseFDH SM4A M3) amino acids replacements. The new PseFDH mutants were overexpressed in E. coli cells, purified and characterized. The S131A/E170D and S131A/S160A/E170D changes provided further improving thermal stability. The introduction of the S145A substitution into PseFDH SM4A M3 leads to a significant decrease in and while maintaining the catalytic constant at the same level. This mutant form can be successfully used in NADH regeneration systems, as well as for the detection of NAD+ and formate in biological systems. [ABSTRACT FROM AUTHOR]

SUMMARY: Formate dehydrogenase (FDH; EC 1.2.1.2.) has been implicated in plant responses to a variety of stresses, including aluminum (Al) stress in acidic soils. However, the role of this enzyme in Al tolerance is not yet fully understood, and how FDH gene expression is regulated is unknown. Here, we report the identification and functional characterization of the tomato (Solanum lycopersicum) SlFDH gene. SlFDH encodes a mitochondria‐localized FDH with Km values of 2.087 mm formate and 29.1 μm NAD+. Al induced the expression of SlFDH in tomato root tips, but other metals did not, as determined by quantitative reverse transcriptase‐polymerase chain reaction. CRISPR/Cas9‐generated SlFDH knockout lines were more sensitive to Al stress and formate than wild‐type plants. Formate failed to induce SlFDH expression in the tomato root apex, but NAD+ accumulated in response to Al stress. Co‐expression network analysis and interaction analysis between genomic DNA and transcription factors (TFs) using PlantRegMap identified seven TFs that might regulate SlFDH expression. One of these TFs, SlSTOP1, positively regulated SlFDH expression by directly binding to its promoter, as demonstrated by a dual‐luciferase reporter assay and electrophoretic mobility shift assay. The Al‐induced expression of SlFDH was completely abolished in Slstop1 mutants, indicating that SlSTOP1 is a core regulator of SlFDH expression under Al stress. Taken together, our findings demonstrate that SlFDH plays a role in Al tolerance and reveal the transcriptional regulatory mechanism of SlFDH expression in response to Al stress in tomato. Significance Statement: Formate dehydrogenase (FDH; EC 1.2.1.2.) catalyzes the degradation of formate and the reduction of NAD+ to NADH. Here, we demonstrate that the FDH gene SlFDH is induced by aluminum stress in tomato, which relies on the transcription factor SlSTOP1, to enhance tolerance to aluminum stress via SlFDH‐catalyzed reduction of NAD+. [ABSTRACT FROM AUTHOR]

Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies. [ABSTRACT FROM AUTHOR]

Oxidoreductases catalyze essential redox reactions, and many require a diffusible cofactor for electron transport, such as NAD(H). Non-canonical cofactor analogs have been explored as a means to create enzymatic reactions that operate orthogonally to existing metabolism. Here, we aimed to engineer the formate dehydrogenase from Candid boidinii (CbFDH) for activity with the non-canonical cofactor nicotinamide adenine dinucleotide 3′-phosphate (3′-NADP(H)). We used PyRosetta, the Cofactor Specificity Reversal Structural Analysis and Library Design (CSR-SALAD), and structure-guided saturation mutagenesis to identify mutations that enable CbFDH to use 3′-NADP+. Two single mutants, D195A and D195G, had the highest activities with 3′-NADP+, while the double mutant D195G/Y196S exhibited the highest cofactor selectivity reversal behavior. Steady state kinetic analyses were performed; the D195A mutant exhibited the highest KTS value with 3′-NADP+. This work compares the utility of computational approaches for cofactor specificity engineering while demonstrating the engineering of an important enzyme for novel non-canonical cofactor selectivity. [ABSTRACT FROM AUTHOR]

Methanosarcinales are versatile methanogens, capable of regulating most types of methanogenic pathways. Despite the versatile metabolic flexibility of Methanosarcinales, no member of this order has been shown to use formate for methanogenesis. In the present study, we identified a cytosolic formate dehydrogenase (FdhAB) present in several Methanosarcinales, likely acquired by independent horizontal gene transfers after an early evolutionary loss, encouraging re-evaluation of our understanding of formate utilization in Methanosarcinales. To explore whether formate-dependent (methyl-reducing or CO 2 -reducing) methanogenesis can occur in Methanosarcinales, we engineered two different strains of Methanosarcina acetivorans by functionally expressing FdhAB from Methanosarcina barkeri in M. acetivorans. In the first strain, fdhAB was integrated into the N 5 -methyl- tetrahydrosarcinapterin:coenzyme M methyltransferase (mtr) operon, making it capable of growing by reducing methanol with electrons from formate. In the second strain, fdhAB was integrated into the F 420 -reducing hydrogenase (frh) operon, instead of the mtr operon, enabling its growth with formate as the only source of carbon and energy after adaptive laboratory evolution. In this strain, one CO 2 is reduced to one methane with electrons from oxidizing four formate to four CO 2 , a metabolism reported only in methanogens without cytochromes. Although methanogens without cytochromes typically utilize flavin-based electron bifurcation to generate the ferredoxins needed for CO 2 activation, we hypothesize that, in our engineered strains, reduced ferredoxins are obtained via the Rhodobacter nitrogen fixation complex complex running in reverse. Our work demonstrates formate-dependent methyl-reducing and CO 2 -reducing methanogenesis in M. acetivorans that is enabled by the flexible nature of the microbe working in tandem with the nurturing provided., (© 2025 Federation of European Biochemical Societies.)

Enzymatic asymmetric synthesis of l-phenylglycine by amino acid dehydrogenases has potential for industrial applications; however, this is hindered by their low catalytic efficiency toward high-concentration substrates. We identified and characterized a novel leucine dehydrogenase ( Ms LeuDH) with a high catalytic efficiency for benzoylformic acid via directed metagenomic approaches. Further, we obtained a triple-point mutant Ms LeuDH-EER (D332E/G333E/L334R) with improved stability and catalytic efficiency through the rational design of distal loop 13. A coexpression system of Ms LeuDH-EER and formate dehydrogenase completely converted a 300 mM substrate within 4 h with >99.9% enantiomeric excess. Molecular dynamics simulations revealed that mutations on loop 13 enhanced the overall structural rigidity of the protein to improve its stability but also stabilized the "closed" conformation through rigidifying the hinge region loop by distant modulation. Our results show that distal loop 13 can serve as a new hotspot region for enhancing the catalytic performance of leucine dehydrogenases.

Formic acid is an important source of reductant and energy for many microorganisms. Formate is also produced as a fermentation product, e.g., by enterobacteria like Escherichia coli . As such, formic acid shares many features in common with dihydrogen, explaining perhaps why their metabolism and physiology show considerable overlap. At physiological pH, formic acid is mainly present as the dissociated formate anion and therefore cannot diffuse freely across the cytoplasmic membrane. Specific and bidirectional translocation of formate across the cytoplasmic membrane is, however, achieved in E. coli by the homopentameric membrane protein, FocA. Formic acid translocation from the cytoplasm into the periplasm (efflux) serves to maintain a near-neutral cytosolic pH and to deliver formate to the periplasmically-oriented respiratory formate dehydrogenases, Fdh-N and Fdh-O. These enzymes oxidize formate, with the electrons being used to reduce nitrate, oxygen, or other acceptors. In the absence of exogenous electron acceptors, formate is re-imported into the cytoplasm by FocA, where it is sensed by the transcriptional regulator FhlA, resulting in induction of the formate regulon. The genes and operons of the formate regulon encode enzymes necessary to assemble the formate hydrogenlyase complex, which disproportionates formic acid into H 2 and CO 2 . Combined, these mechanisms of dealing with formate help to maintain cellular pH homeostasis and are suggested to maintain the proton gradient during growth and in stationary phase cells. This review highlights our current understanding of how formate metabolism helps balance cellular pH, how it responds to the redox status, and how it helps conserve energy.