甲酸脱氢酶用于辅酶NADH再生的研究进展

NADH依赖型氧化还原酶广泛应用于精细化学品和手性化合物的生物合成,其中辅酶NADH作为还原当量起着关键的作用,NADH的再生关系到生物氧化还原过程能否进行. 甲酸脱氢酶在辅酶NADH再生中的应用是目前代谢工程领域研究的热点之一. 本工作回顾了甲酸脱氢酶的来源和氨基酸序列、酶的理化性质和催化机理等方面的研究进展,从化学稳定性、热稳定性和成本等方面阐述了甲酸脱氢酶在辅酶再生系统中的应用,讨论了甲酸脱氢酶用于辅酶再生的代谢工程平台的发展趋势,并对研究发展方向提出了一些设想.     

Directed Evolution of a Formate Dehydrogenase for Increased Tolerance to Ionic Liquids Reveals a New Site for Increasing the Stability

The formate dehydrogenase (FDH) from Candida boidinii is a well‐known enzyme in biocatalysis for NADH regeneration. Nevertheless, it has low activity in a water‐miscible ionic liquid (1,3‐dimethylimidazolium dimethyl phosphate, [MMIm][Me₂PO₄]). In this work, this enzyme was subjected to directed evolution by using error‐prone PCR, and a mutant (N187S/T321S) displaying higher activity was obtained following selection based on the formazan‐based colorimetric assay. The mutation N187S is responsible for improved activity both in aqueous solution and in [MMIm][Me₂PO₄], through an enhancement of the k_cat value by a factor of 5.8. Fluorescence experiments performed in the presence of a quenching agent revealed that the mutant does not unfold in the presence of 50 % (v/v) [MMIm][Me₂PO₄] whereas the wild‐type enzyme does. Molecular modelling revealed that the mutation is located at the monomer–monomer interface and causes an increase in the pK_a of residue E163 from 4.8 to 5.5. Calculation of the pK_a of this residue in other microbial FDHs showed that thermostable FDHs have a highly basic glutamate at this position (pK_a up to 6.2). We have identified a new site for improving FDH thermostability and tolerance to ionic liquids, and it is linked to the local charge of the enzymes in this class.     

Engineering a Formate Dehydrogenase for NADPH Regeneration**

Nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) constitute major hydrogen donors for oxidative/reductive bio-transformations. NAD(P)H regeneration systems coupled with formate dehydrogenases (FDHs) represent a dreamful method. However, most of the native FDHs are NAD⁺-dependent and suffer from insufficient reactivity compared to other enzymatic tools, such as glucose dehydrogenase. An efficient and competitive NADP⁺-utilizing FDH necessitates the availability and robustness of NADPH regeneration systems. Herein, we report the engineering of a new FDH from Candida dubliniensis (CdFDH), which showed no strict NAD⁺ preference by a structure-guided rational/semi-rational design. A combinatorial mutant CdFDH-M4 (D197Q/Y198R/Q199N/A372S/K371T/▵Q375/K167R/H16L/K159R) exhibited 75-fold intensification of catalytic efficiency (k_cat/K_m). Moreover, CdFDH-M4 has been successfully employed in diverse asymmetric oxidative/reductive processes with cofactor total turnover numbers (TTNs) ranging from 135 to 986, making it potentially useful for NADPH-required biocatalytic transformations.     

The Evolution of an Amine Dehydrogenase Biocatalyst for the Asymmetric Production of Chiral Amines

The reductive amination of ketones to produce chiral amines is an important transformation in the production of pharmaceutical intermediates. Therefore, industrially applicable enzymatic methods that enable the selective synthesis of chiral amines could be very useful. Using a phenylalanine dehydrogenase scaffold devoid of amine dehydrogenase activity, a robust amine dehydrogenase has been evolved with a single two‐site library allowing for the direct production of (R)‐1‐(4‐fluorophenyl)‐propyl‐2‐amine from para‐fluorophenylacetone with a k_cat value of 6.85 s⁻¹ and a K_M value of 7.75 mM for the ketone substrate. This is the first example of a highly active amine dehydrogenase capable of accepting aliphatic and benzylic ketone substrates. The stereoselectivity of the evolved amine dehydrogenase was very high (>99.8% ee) showing that high selectivity of the wild‐type phenylalanine dehydrogenase was conserved in the evolution process. When paired with glucose/glucose dehydrogenase, NADH cofactor can be effficiently regenerated and the reaction driven to over 93% conversion. The broad specificity, high selectivity, and near complete conversion render this amine dehydrogenase an attractive target for further evolution toward pharmaceutical compounds and subsequent application.     

Cofactor Regeneration of NAD+ from NADH: Novel Water‐Forming NADH Oxidases

Dehydrogenases with their superb enantioselectivity can be employed advantageously to prepare enantiomerically pure alcohols, hydroxy acids, and amino acids. For economic syntheses, however, the co‐substrate of dehydrogenases, the NAD(P)(H) cofactor, has to be regenerated. Whereas the problem of regenerating NADH from NAD⁺ can be considered solved, the inverse problem of regenerating NAD⁺ from NADH still awaits a definitive and practical solution. A possible solution is the oxidation of NADH to NAD⁺ with concomitant reduction of oxygen catalyzed by NADH oxidase (E.C. 1.6.‐.‐) which can reduce O₂ either to undesirable H₂O₂ or to innocuous H₂O. We have found and cloned two novel genes from Borrelia burgdorferi and Lactobacillus sanfranciscensis with hitherto only machine‐annotated NADH oxidase function. We have overexpressed the corresponding proteins and could prove the annotated function to be correct. As demonstrated with a more sensitive assay than employed previously, the two novel NADH oxidases reduce O₂ to H₂O.     

Construction of Mutant Glucose Oxidases with Increased Dye-Mediated Dehydrogenase Activity

Mutagenesis studies on glucose oxidases (GOxs) were conducted to construct GOxs with reduced oxidase activity and increased dehydrogenase activity. We focused on two representative GOxs, of which crystal structures have already been reported—Penicillium amagasakiense GOx (PDB ID; 1gpe) and Aspergillus niger GOx (PDB ID; 1cf3). We constructed oxygen-interacting structural models for GOxs, and predicted the residues responsible for oxidative half reaction with oxygen on the basis of the crystal structure of cholesterol oxidase as well as on the fact that both enzymes are members of the glucose/methanol/choline (GMC) oxidoreductase family. Rational amino acid substitution resulted in the construction of an engineered GOx with drastically decreased oxidase activity and increased dehydrogenase activity, which was higher than that of the wild-type enzyme. As a result, the dehydrogenase/oxidase ratio of the engineered enzyme was more than 11-fold greater than that of the wild-type enzyme. These results indicate that alteration of the dehydrogenase/oxidase activity ratio of GOxs is possible by introducing a mutation into the putative functional residues responsible for oxidative half reaction with oxygen of these enzymes, resulting in a further increased dehydrogenase activity. This is the first study reporting the alteration of GOx electron acceptor preference from oxygen to an artificial electron acceptor.     

Synthesis,Characterization and Application of New Rhodium Complexes for Indirect Electrochemical Cofactor Regeneration

Electroenzymatic synthesis often suffers from electrochemical reaction steps which proceed slower than the coupled enzyme reaction. For indirect electrochemical cofactor regeneration, we here report two new mediators with superior properties compared to the established rhodium complex (2,2′‐bipyridyl)(pentamethylcyclopentadienyl)rhodium [Cp*Rh(2,2′‐bipyridine)]. After constructing a robotic system for fast and reliable cyclic voltammetry measurements, we screened twelve rhodium complexes with substituted 2,2′‐bipyridine ligands for their reduction potentials and catalytic activity towards the reduction of NADP. Promising complexes were investigated in more detail by cyclic voltammetry and under batch electrolysis conditions. The new complexes Cp*Rh(5,5′‐methyl‐2,2′‐bipyridine) and Cp*Rh(4,4′‐methoxy‐2,2′‐bipyridine) reduced NADP to NADPH three times faster than the established mediator, resulting in volumetric productivities of up to 136 mmol L⁻¹ d⁻¹ and turnover frequencies of up to 113 h⁻¹. This increased reaction rate of these new mediators makes indirect electrochemical approach significantly more competitive to other methods of cofactor regeneration. Abbreviations: ADH=alcohol dehydrogenase; Ag|AgCl=silver|silver chloride reference electrode; bpy=2,2′‐bipyridine; ci=current increase; Cp*=pentamethylcyclopentadienyl; CV=cyclic voltammetry; Ep=peak potential; equiv=equivalent; NADP/NADPH=nicotinamide adenine dinucleotide phosphate oxidised/reduced form.     

Directed Evolution of Enzymes for Industrial Biocatalysis

Enzymes have the potential to catalyse a wide variety of chemical reactions. They are increasingly being sought as environmentally friendly and cost‐effective alternatives to conventional catalysts used in industries ranging from bioremediation to applications in medicine and pharmaceutics. Despite the benefits, they are not without their limitations. Many naturally occurring enzymes are not suitable for use outside of their native cellular environments. However, protein engineering can be used to generate enzymes tailored for specific industrial applications. Directed evolution is particularly useful and can be employed even when lack of structural information impedes the use of rational design. The aim of this review is to provide an overview of current industrial applications of enzyme technology and to show how directed evolution can be used to modify and to enhance enzyme properties. This includes a brief discussion on library generation and a more detailed focus on library screening methods, which are critical to any directed evolution experiment.     

Improving the Stability and Catalyst Lifetime of the Halogenase RebH By Directed Evolution

We previously reported that the halogenase RebH catalyzes selective halogenation of several heterocycles and carbocycles, but product yields were limited by enzyme instability. Here, we use directed evolution to engineer an RebH variant, 3‐LR, with a T_opt over 5 °C higher than that of wild‐type, and 3‐LSR, with a T_m 18 °C higher than that of wild‐type. These enzymes provided significantly improved conversion (up to fourfold) for halogenation of tryptophan and several non‐natural substrates. This initial evolution of RebH not only provides improved enzymes for immediate synthetic applications, but also establishes a robust protocol for further halogenase evolution.     

Eosin Y‐Sensitized Artificial Photosynthesis by Highly Efficient Visible‐Light‐Driven Regeneration of Nicotinamide Cofactor

Dye‐sensitized photosynthesis : Eosin Y (EY), a dye photosensitizer, works efficiently as a molecular photoelectrode by catalyzing the visible‐light‐driven electron‐transfer reaction for efficient regeneration of NADH through a photosensitizer–electron relay dyad. Injection of the photosensitized electron resulted in highly accelerated regeneration of NADH, which can be used by glutamate dehydrogenase for the photosynthesis of L ‐glutamate.

     

Emerging Enzymes for ATP Regeneration in Biocatalytic Processes

Adenosine‐5′‐triphosphate‐dependent enzyme catalysed reactions are widespread in nature. Consequently, the enzymes involved have an intrinsic potential for use in syntheses of high value products. Although regeneration systems for ATP starting from adenosine‐5′‐diphosphate are available, certain limitations exist for both in vitro and in vivo applications requiring ATP regeneration from adenosine‐5′‐monophosphate, or adenosine. Following a short overview of the chemical and thermodynamic background, this Minireview focuses on emerging enzymes and methodologies for ATP regeneration. A large range of as yet unexploited reactions will be accessible with new, powerful, multistep ATP regeneration systems that use cheap phosphate donors and provide high longevity, compatibility, and robustness under process conditions. Their potential might go far beyond the direct use of ATP in enzymatic reactions; enzyme discovery, and engineering, as well as immobilisation strategies, will help to realise such systems.     

Guidelines for the Application of NAD(P)H Regenerating Glucose Dehydrogenase in Synthetic Processes

Glucose dehydrogenase (GDH) is frequently used for the reduction of NAD⁺ and NADP⁺ in bench‐ and industrial‐scale syntheses because the coenzyme regenerating system GDH is easy to apply, robust and relatively inexpensive. To optimize the application of this long known coenzyme regeneration system we investigated the commonly applied Bacillus GDH and characterized this enzyme by its kinetic features in the presence of substrates and products at pH 6.4 and 8.0. Three substrates/products were found to inhibit GDH considerably: (i) the reaction product glucono‐1,5‐lactone, (ii) the reduced coenzyme NAD(P)H and (iii) the oxidized coenzyme NAD(P)⁺. The inhibition of GDH under several process conditions was modeled using the determined kinetic constants. It was found that the GDH regeneration system is strongly inhibited by the usually applied conditions. This study provides the rate equation of the GDH reaction and simulations of this coenzyme regenerating system leading to an improved prediction and, thus, to a faster scale‐up and increased efficiency of NAD(P)H‐dependent synthetic processes.     

Methodology Development in Directed Evolution: Exploring Options when Applying Triple‐Code Saturation Mutagenesis

Directed evolution of stereo‐ or regioselective enzymes as catalysts in asymmetric transformations is of particular interest in organic synthesis. Upon evolving these biocatalysts, screening is the bottleneck. To beat the numbers problem most effectively, methods and strategies for building “small but smart” mutant libraries have been developed. Herein, we compared two different strategies regarding the application of triple‐code saturation mutagenesis (TCSM) at multiresidue sites of the Thermoanaerobacter brockii alcohol dehydrogenase by using distinct reduced amino‐acid alphabets. By using the synthetically difficult‐to‐reduce prochiral ketone tetrahydrofuran‐3‐one as a substrate, highly R‐ and S‐selective variants were obtained (92–99 % ee) with minimal screening. The origin of stereoselectivity was provided by molecular dynamics analyses, which is discussed in terms of the Bürgi–Dunitz trajectory.     

In Vitro Double Oxidation of n‐Heptane with Direct Cofactor Regeneration

A novel concept for the direct oxidation of cycloalkanes to the corresponding cyclic ketones in a one‐pot synthesis in water with molecular oxygen as sole oxidizing agent was reported recently. Based on this concept we have developed a new strategy for the double oxidation of n‐heptane to enable a biocatalytic resolution for the direct synthesis of heptanone and (R)‐heptanols in a one‐pot reaction. The bicatalytic cascade employs an NADH driven P450 BM3 monooxygenase variant (WT^NADH, 19A12^NADH or CM1^NADH) and an (S)‐enantioselective alcohol dehydrogenase (RE‐ADH). In the initial step n‐heptane is hydroxylated under consumption of NADH to produce (R/S)‐heptanol. In the second oxidation step the (S)‐heptanol enantiomers are transformed to the corresponding ketones, reducing and thereby regenerating the cofactor. Characterization of initial hydroxylation step revealed high turnover frequencies (TOF) of up to 600 min⁻¹, as well as high coupling efficiencies using NADH as cofactor (up to 44%). In the cascade reaction a nearly 2‐fold improved product formation was achieved, compared to the single hydroxylation reaction. The total product concentration reached 1.1 mM, corresponding to a total turnover number (TTN) of 2500. Implementation of an additional cofactor regeneration system (D ‐glucose/glucose dehydrogenase) enabled a further enhancement in product formation with a total product concentration of 1.8 mM and a TTN of 3500.     

Second‐Generation Engineering of a Thermostable Transketolase (TKGst) for Aliphatic Aldehyde Acceptors with Either Improved or Reversed Stereoselectivity

The transketolase from Geobacillus stearothermophilus (TK_Gst) is a thermostable enzyme with notable high activity and stability at elevated temperatures, but it accepts non‐α‐hydroxylated aldehydes only with low efficiency. Here we report a protein engineering study of TK_Gst based on double‐site saturation mutagenesis either at Leu191 or at Phe435 in combination with Asp470; these are the residues responsible for substrate binding in the active site. Screening of the mutagenesis libraries resulted in several positive variants with activity towards propanal up to 7.4 times higher than that of the wild type. Variants F435L/D470E and L191V/D470I exhibited improved (73 % ee, 3S) and inverted (74 % ee, 3R) stereoselectivity, respectively, for propanal. L191V, L382F/E, F435L, and D470/D470I were concluded to be positive mutations at Leu191, Leu382, Phe435, and Asp470 both for activity and for stereoselectivity improvement. These results should benefit further engineering of TK_Gst for various applications in asymmetric carboligation.     

A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase

Lactate dehydrogenase from Bacillus stearothermophilus is specific for NAD+. There have been several attempts to alter the cofactor specificity of this enzyme, but these have yielded enzymes with relatively low activities that still largely prefer NAD+. A modified consensus approach was used to create a library of phylogenetically preferred amino acids situated near the cofactor binding site, and variants were screened for their ability to utilize NMN+. A triple mutant (Mut31) was discovered that proved to be more catalytically efficient than wild-type. Mut31 was also better at utilizing NAD+ than the wild-type enzyme and was weakly active with NADP+ and NMN+. An analysis of single amino acid substitutions suggested that all three mutations worked in a concerted fashion to yield robust cofactor utilization. When two previously identified amino acid substitutions were introduced into the Mut31 background, the resultant quintuply substituted enzyme not only utilized NADP+ far better than the wild-type enzyme, it actually inverted its preference for NAD+ and NADP+.     

Halogenase Engineering for the Generation of New Natural Product Analogues

Halogenases catalyze the incorporation of halogen atoms into organic molecules. Given the importance that halogenation has on the biological activity of small molecules, these enzymes have been subjected to intense engineering efforts to make them more suitable for biotechnology applications. The ability to biohalogenate complex molecules provides, in principle, the opportunity for rapid generation of a series of analogues with new or improved properties. Here we discuss the potential and limitations of using halogenases as biocatalysts, including recent advances in engineering halogenases to generate halogenated natural product analogues.     

Orientated Immobilization of FAD-Dependent Glucose Dehydrogenase on Electrode by Carbohydrate-Binding Module Fusion for Efficient Glucose Assay

The discovery or engineering of fungus-derived FAD-dependent glucose 1-dehydrogenase (FAD-GDH) is especially important in the fabrication and performance of glucose biosensors. In this study, a novel FAD-GDH gene, phylogenetically distantly with other FAD-GDHs from Aspergillus species, was identified. Additionally, the wild-type GDH enzyme, and its fusion enzyme (GDH-NL-CBM2) with a carbohydrate binding module family 2 (CBM2) tag attached by a natural linker (NL), were successfully heterogeneously expressed. In addition, while the GDH was randomly immobilized on the electrode by conventional methods, the GDH-NL-CBM2 was orientationally immobilized on the nanocellulose-modified electrode by the CBM2 affinity adsorption tag through a simple one-step approach. A comparison of the performance of the two electrodes demonstrated that both electrodes responded linearly to glucose in the range of 0.12 to 40.7 mM with a coefficient of determination R² > 0.999, but the sensitivity of immobilized GDH-NL-CBM2 (2.1362 × 10⁻² A/(M*cm²)) was about 1-fold higher than that of GDH (1.2067 × 10⁻² A/(M*cm²)). Moreover, a lower detection limit (51 µM), better reproducibility (<5%) and stability, and shorter response time (≈18 s) and activation time were observed for the GDH-NL-CBM2-modified electrode. This facile and easy immobilization approach used in the preparation of a GDH biosensor may open up new avenues in the development of high-performance amperometric biosensors.