Engineering Isopropanol Dehydrogenase for Efficient Regeneration of Nicotinamide Cofactors

Advances in aldo-keto reductases immobilization for biocatalytic synthesis of chiral alcohols

Chiral alcohols are essential building blocks of numerous pharmaceuticals and fine chemicals. Aldo-keto reductases (AKRs) constitute a superfamily of oxidoreductases that catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NAD(P)H as a coenzyme. Knowledge about the crucial roles of AKRs immobilization in the biocatalytic synthesis of chiral alcohols is expanding. Herein, we reviewed the characteristics of various AKRs immobilization approaches, the applications of different immobilization materials, and the prospects of continuous flow bioreactor construction by employing these immobilized biocatalysts for synthesizing chiral alcohols. Finally, the opportunities and ongoing challenges for AKR immobilization are discussed and the outlook for this emerging area is analyzed.

Evolving ω-amine transaminase AtATA guided by substrate-enzyme binding free energy for enhancing activity and stability against non-natural substrates

In the field of chiral amine synthesis, ω-amine transaminase (ω-ATA) is one of the most established enzymes capable of asymmetric amination under optimal conditions. However, the applicability of ω-ATA toward more non-natural complex molecules remains limited due to its low transamination activity, thermostability, and narrow substrate scope. Here, by employing a combined approach of computational virtual screening strategy and combinatorial active-site saturation test/iterative saturation mutagenesis strategy, we have constructed the best variant M14C3-V5 (M14C3-V62A-V116S-E117I-L118I-V147F) with improved ω-ATA from Aspergillus terreus (AtATA) activity and thermostability toward non-natural substrate 1-acetylnaphthalene, which is the ketone precursor for producing the intermediate (R)-(+)-1-(1-naphthyl)ethylamine [(R)-NEA] of cinacalcet hydrochloride, showing activity enhancement of up to 3.4-fold compared to parent enzyme M14C3 (AtATA-F115L-M150C-H210N-M280C-V149A-L182F-L187F). The computational tools YASARA, Discovery Studio, Amber, and FoldX were applied for predicting mutation hotspots based on substrate-enzyme binding free energies and to show the possible mechanism with features related to AtATA structure, catalytic activity, and stability in silico analyses. M14C3-V5 achieved 71.8% conversion toward 50 mM 1-acetylnaphthalene in a 50 mL preparative-scale reaction for preparing (R)-NEA. Moreover, M14C3-V5 expanded the substrate scope toward aromatic ketone compounds. The generated virtual screening strategy based on the changes in binding free energies has successfully predicted the AtATA activity toward 1-acetylnaphthalene and related substrates. Together with experimental data, these approaches can serve as a gateway to explore desirable performances, expand enzyme-substrate scope, and accelerate biocatalysis.IMPORTANCEChiral amine is a crucial compound with many valuable applications. Their asymmetric synthesis employing ω-amine transaminases (ω-ATAs) is considered an attractive method. However, most ω-ATAs exhibit low activity and stability toward various non-natural substrates, which limits their industrial application. In this work, protein engineering strategy and computer-aided design are performed to evolve the activity and stability of ω-ATA from Aspergillus terreus toward non-natural substrates. After five rounds of mutations, the best variant, M14C3-V5, is obtained, showing better catalytic efficiency toward 1-acetylnaphthalene and higher thermostability than the original enzyme, M14C3. The robust combinational variant acquired displayed significant application value for pushing the asymmetric synthesis of aromatic chiral amines to a higher level.

Influence of deep eutectic solvents on redox biocatalysis involving alcohol dehydrogenases

Redox biocatalysis plays an increasingly important role in modern organic synthesis. The recent integration of novel media such as deep eutectic solvents (DESs) has significantly impacted this field of chemical biology. Alcohol dehydrogenases (ADHs) are important biocatalysts where their unique specificity is used for enantioselective synthesis. This review explores aspects of redox biocatalysis in the presence of DES both with whole cells and with isolated ADHs. In both cases, the presence of DES has a significant influence on the outcome of reactions albeit via different mechanisms. For whole cells, DES was shown to be a useful tool to direct product formation or configuration - a process of solvent engineering. Whole cells can tolerate DES as media components for the solubilization of hydrophobic substrates. In some cases, DES in the growth medium altered the enantioselectivity of whole cell transformations by solvent control. For isolated enzymes, on the other hand, the presence of DES promotes substrate solubility as well as enhancing enzyme stability and activity. DES can be employed as a smart solvent or smart cosubstrate particularly for cofactor regeneration purposes. From the literatures examined, it is suggested that DES based on choline chloride (ChCl) such as ChCl:Glycerol (Gly), ChCl:Glucose (Glu), and ChCl:1,4-butanediol (1,4-BD) are useful starting points for ADH-based redox biocatalysis. However, each specific reaction will require optimisation due to the influence of several factors on biocatalysis in DES. These include solvent composition, enzyme source, temperature, pH and ionic strength as well as the substrates and products under investigation.

Classification and functional origins of stereocomplementary alcohol dehydrogenases for asymmetric synthesis of chiral secondary alcohols: A review

Alcohol dehydrogenases (ADHs) mediated biocatalytic asymmetric reduction of ketones have been widely applied in the synthesis of optically active secondary alcohols with highly reactive hydroxyl groups ligated to the stereogenic carbon and divided into (R)- and (S)-configurations. Stereocomplementary ADHs could be applied in the synthesis of both enantiomers and are increasingly accepted as the "first of choice" in green chemistry due to the high atomic economy, low environmental factor, 100 % theoretical yield, and high environmentally friendliness. Due to the equal importance of complementary alcohols, development of stereocomplementary ADHs draws increasing attention. This review is committed to summarize recent advance in discovery of naturally evolved and tailor-made stereocomplementary ADHs, unveil the molecular mechanism of stereoselective catalysis in views of classification and functional basis, and provide guidance for further engineering the stereoselectivity of ADHs for the industrial biosynthesis of chiral secondary alcohol of industrial relevance.

Isopropanol production using engineered Corynebacterium glutamicum from waste rice straw biomass

Isopropanol, a well-known biofuel, is a widely used precursor for chemical products that can replace nonrenewable petroleum energy. Here, engineered Corynebacterium glutamicum that can effectively utilize all xylose and glucose in agricultural waste rice straw to produce isopropanol was described. First, codon mutations were introduced into transporters and glycolytic-related genes to decrease the glucose preference of C. glutamicum. A more energetically favorable xylose oxidative pathway was constructed that replaced traditional xylose isomerization pathways, saving twice the number of enzymatic steps. A succinate auxiliary module was incorporated into the tricarboxylic acid cycle (TCA), connecting the xylose-utilized pathway with the isopropanol pathway to maximize xylose orientation towards the product. The final engineered strain successfully consumed 100 % of the xylose from NaOH-pretreated, enzyme-hydrolyzed rice straw and effectively synthesized 4.91 g/L isopropanol. This study showcases the successful conversion of agricultural waste into renewable energy, unveiling new possibilities for advancing biological fermentation technology.

Characterization of the Pro101Gln mutation that enhances the catalytic performance of T. indicus NADH-dependent d-lactate dehydrogenase

NADH-dependent d-lactate dehydrogenases (d-LDH) are important for the industrial production of d-lactic acid. Here, we identify and characterize an improved d-lactate dehydrogenase mutant (d-LDH1) that contains the Pro101Gln mutation. The specific enzyme activities of d-LDH1 toward pyruvate and NADH are 21.8- and 11.0-fold greater compared to the wild-type enzyme. We determined the crystal structure of Apo-d-LDH1 at 2.65 Å resolution. Based on our structural analysis and docking studies, we explain the differences in activity with an altered binding conformation of NADH in d-LDH1. The role of the conserved residue Pro101 in d-LDH was further probed in site-directed mutagenesis experiments. We introduced d-LDH1 into Bacillus licheniformis yielding a d-lactic acid production of 145.9 g L-1 within 60 h at 50°C, which was three times higher than that of the wild-type enzyme. The discovery of d-LDH1 will pave the way for the efficient production of d-lactic acid by thermophilic bacteria.

Insights into the Unusual Activity of a Novel Homospermidine Synthase with a Promising Application to Produce Spermidine

Spermidine is a naturally occurring polyamine with multiple biological activities and potential food and agricultural applications. However, sustainable and scalable spermidine production has not yet been attained. In this study, a homospermidine synthase (HSS) from Pseudomonas frederiksbergensis (PfHSS) capable of catalyzing the synthesis of spermidine from 1,3-diaminopropane and putrescine was identified based on multiple sequence alignment using Blastochloris viridis HSS (BvHSS) as a template. The optimal reaction pH and temperature for purified PfHSS were determined to be 8.5 and 45 °C, respectively, and K+ was able to promote the enzyme activity. Further analysis of the structural and functional relationships through molecular docking and molecular dynamics simulation indicates that glutamic acid at position 359 is the essential residue for the enzyme-catalyzed synthesis of spermidine. The whole-cell catalytic reaction yielded 1321.4 mg/L spermidine and 678.2 mg/L of homospermidine. This study presents a novel, promising, and sustainable biological method for producing spermidine.

Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology

Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.

Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification

Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.

Directed reconstruction of a novel ancestral alcohol dehydrogenase featuring shifted pH-profile, enhanced thermostability and expanded substrate spectrum

Ancestral enzymes are promising for industrial biotechnology due to high stability and catalytic promiscuity. An effective protocol was developed for the directed resurrection of ancestral enzymes. Employing genome mining with diaryl alcohol dehydrogenase KpADH as the probe, descendant enzymes D10 and D11 were firstly identified. Then through ancestral sequence reconstruction, A64 was resurrected with a specific activity of 4.3 U·mg^-1. The optimum pH of A64 was 7.5, distinct from 5.5 of D10. The T15 50 and T_m values of A64 were 57.5 °C and 61.7 °C, significantly higher than those of the descendant counterpart. Substrate spectrum of A64 was quantitively characterized with a Shannon-Wiener index of 2.38, more expanded than D10, especially, towards bulky ketones in Group A and B. A64 also exhibited higher enantioselectivity. This study provides an effective protocol for constructing of ancestral enzymes and an efficient ancestral enzyme of industrial relevance for asymmetric synthesis of chiral alcohols.