The challenges of using NAD+-dependent formate dehydrogenases for CO2 conversion

Metabolic engineering strategies to enable microbial electrosynthesis utilization of CO2: recent progress and challenges

Microbial electrosynthesis (MES) is a promising technology that mainly utilizes microbial cells to convert CO2 into value-added chemicals using electrons provided by the cathode. However, the low electron transfer rate is a solid bottleneck hindering the further application of MES. Thus, as an effective strategy, genetic tools play a key role in MES for enhancing the electron transfer rate and diversity of production. We describe a set of genetic strategies based on fundamental characteristics and current successes and discuss their functional mechanisms in driving microbial electrocatalytic reactions to fully comprehend the roles and uses of genetic tools in MES. This paper also analyzes the process of nanomaterial application in extracellular electron transfer (EET). It provides a technique that combines nanomaterials and genetic tools to increase MES efficiency, because nanoparticles have a role in the production of functional genes in EET although genetic tools can subvert MES, it still has issues with difficult transformation and low expression levels. Genetic tools remain one of the most promising future strategies for advancing the MES process despite these challenges.

Highly Efficient Carbon Dioxide Electroreduction via DNA-Directed Catalyst Immobilization

Electrochemical reduction of carbon dioxide (CO2) is a promising route to up-convert this industrial byproduct. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize molecular catalysts on electrodes have been stymied by the need to optimize the immobilization chemistries on a case-by-case basis. Taking inspiration from nature, we applied DNA as a molecular-scale "Velcro" to investigate the tethering of three porphyrin-based catalysts to electrodes. This tethering strategy improved both the stability of the catalysts and their Faradaic efficiencies (FEs). DNA-catalyst conjugates were immobilized on screen-printed carbon and carbon paper electrodes via DNA hybridization with nearly 100% efficiency. Following immobilization, a higher catalyst stability at relevant potentials is observed. Additionally, lower overpotentials are required for the generation of carbon monoxide (CO). Finally, high FE for CO generation was observed with the DNA-immobilized catalysts as compared to the unmodified small-molecule systems, as high as 79.1% FE for CO at -0.95 V vs SHE using a DNA-tethered catalyst. This work demonstrates the potential of DNA "Velcro" as a powerful strategy for catalyst immobilization. Here, we demonstrated improved catalytic characteristics of molecular catalysts for CO2 valorization, but this strategy is anticipated to be generalizable to any reaction that proceeds in aqueous solutions.

Identification of a novel growth-associated promoter for biphasic expression of heterogenous proteins in Pichia pastoris

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.IMPORTANCEThe alcohol oxidase 1 promoter (PAOX1) expression system has the characteristics of biphasic expression and high expression levels, making it the most widely used promoter in the yeast Pichia pastoris. However, PAOX1 requires methanol induction, which can be toxic and poses a fire hazard in large quantities. Our research has found that the activity of PFDH800 is closely related to the growth state of cells and can achieve biphasic expression without the need for an inducer. Compared to other reported non-methanol-induced biphasic expression systems, the system based on the PFDH800 offers several advantages, including high expression levels, simple construction, minimal impact on cellular metabolism, no need for an inducer, and the ability to fine-tune expression.

NADH-dependent formate dehydrogenase mutants for efficient carbon dioxide fixation

Bioconversion of CO2 to high-valuable products is a globally pursued sustainable technology for carbon neutrality. However, low CO2 activation with formate dehydrogenase (FDH) remains a major challenge for further upcycling due to the poor CO2 affinity, reduction activity and stability of currently used FDHs. Here, we present two recombined mutants, ΔFDHPa48 and ΔFDHPa4814, which exhibit high CO2 reduction activity and antioxidative activity. Compared to FDHPa, the reduction activity of ΔFDHPa48 was increased up to 743 % and the yield in the reduction of CO2 to methanol was increased by 3.16-fold. Molecular dynamics identified that increasing the width of the substrate pocket of ΔFDHPa48 could improve the enzyme reduction activity. Meanwhile, the enhanced rigidity of C-terminal residues effectively protected the active center. These results fundamentally advanced our understanding of the CO2 activation process and efficient FDH for enzymatic CO2 activation and conversion.

Direct Biocatalytic Processes for CO2 Capture as a Green Tool to Produce Value-Added Chemicals

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.

Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats

Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO₂ and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO₂ reduction to formate as the first step of methyl branch of WLP may have evolved independently.

Strategies for overcoming the limitations of enzymatic carbon dioxide reduction

The overexploitation of fossil fuels has led to a significant increase in atmospheric carbon dioxide (CO₂) concentrations, thereby causing problems, such as the greenhouse effect. Rapid global climate change has caused researchers to focus on utilizing CO₂ in a green and efficient manner. One of the ways to achieve this is by converting CO₂ into valuable chemicals via chemical, photochemical, electrochemical, or enzymatic methods. Among these, the enzymatic method is advantageous because of its high specificity and selectivity as well as the mild reaction conditions required. The reduction of CO₂ to formate, formaldehyde, and methanol using formate dehydrogenase (FDH), formaldehyde dehydrogenase (F_aldDH), and alcohol dehydrogenase (ADH) are attractive routes, respectively. In this review, strategies for overcoming the common limitations of enzymatic CO₂ reduction are discussed. First, we present a brief background on the importance of minimizing of CO₂ emissions and introduce the three bottlenecks limiting enzymatic CO₂ reduction. Thereafter, we explore the different strategies for enzyme immobilization on various support materials. To solve the problem of cofactor consumption, different state-of-the-art cofactor regeneration strategies as well as research on the development of cofactor substitutes and cofactor-free systems are extensively discussed. Moreover, aiming at improving CO₂ solubility, biological, physical, and engineering measures are reviewed. Finally, conclusions and future perspectives are presented.

Optimized Operating Conditions for a Biological Treatment Process of Industrial Residual Process Brine Using a Halophilic Mixed Culture

Residual process brine is a sustainable raw material for chlor-alkali electrolysis processes. This study investigates the influence of critical process parameters on the performance of a continuous treatment process for residual process brine using halophilic microorganisms. The goal of the bioprocess is an efficient degradation of the organic impurities formate, aniline, phenol, and 4,4′-methylenedianline from this residual stream. It was shown that formate could be degraded with high efficiencies (89–98%) during the treatment process. It was observed that formate degradation was influenced by the co-substrate glycerol. The lowest residual formate concentrations were achieved with specific glycerol uptake rates of 8.0–16.0 × 10−3 g L−1 h−1 OD600−1. Moreover, a triple-nutrient limitation for glycerol, ammonium, and phosphate was successfully applied for continuous cultivations. Furthermore, it was shown that all aromatic impurities were degraded with an efficiency of 100%. Ultimately, this study proposed optimized operating conditions, allowing the efficient degradation of organics in the residual process brine under various process conditions. Future optimization steps will require a strategy to prevent the accumulation of potential intermediate degradation products formed at high aniline feed concentrations and increase the liquid dilution rates of the system to achieve a higher throughput of brines.

Efficient Assay and Marker Significance of NAD+ in Human Blood

Oxidized nicotinamide adenine dinucleotide (NAD+) is a biological molecule of systemic importance. Essential role of NAD+ in cellular metabolism relies on the substrate action in various redox reactions and cellular signaling. This work introduces an efficient enzymatic assay of NAD+ content in human blood using recombinant formate dehydrogenase (FDH, EC 1.2.1.2), and demonstrates its diagnostic potential, comparing NAD+ content in the whole blood of control subjects and patients with cardiac or neurological pathologies. In the control group (n = 22, 25–70 years old), our quantification of the blood concentration of NAD+ (18 μM, minimum 15, max 23) corresponds well to NAD+ quantifications reported in literature. In patients with demyelinating neurological diseases (n = 10, 18–55 years old), the NAD+ levels significantly (p < 0.0001) decrease (to 14 μM, min 13, max 16), compared to the control group. In cardiac patients with the heart failure of stage II and III according to the New York Heart Association (NYHA) functional classification (n = 24, 42–83 years old), the blood levels of NAD+ (13 μM, min 9, max 18) are lower than those in the control subjects (p < 0.0001) or neurological patients (p = 0.1). A better discrimination of the cardiac and neurological patients is achieved when the ratios of NAD+ to the blood creatinine levels, mean corpuscular volume or potassium ions are compared. The proposed NAD+ assay provides an easy and robust tool for clinical analyses of an important metabolic indicator in the human blood.