Whole-cell biotransformation systems for reduction of prochiral carbonyl compounds to chiral alcohol in Escherichia coli

Biosynthesis of Halogenated Tryptophans for Protein Engineering Using Genetic Code Expansion

Genetic Code Expansion technology offers significant potential in incorporating noncanonical amino acids into proteins at precise locations, allowing for the modulation of protein structures and functions. However, this technology is often limited by the need for costly and challenging-to-synthesize external noncanonical amino acid sources. In this study, we address this limitation by developing autonomous cells capable of biosynthesizing halogenated tryptophan derivatives and introducing them into proteins using Genetic Code Expansion technology. By utilizing inexpensive halide salts and different halogenases, we successfully achieve the selective biosynthesis of 6-chloro-tryptophan, 7-chloro-tryptophan, 6-bromo-tryptophan, and 7-bromo-tryptophan. These derivatives are introduced at specific positions with corresponding bioorthogonal aminoacyl-tRNA synthetase/tRNA pairs in response to the amber codon. Following optimization, we demonstrate the robust expression of proteins containing halogenated tryptophan residues in cells with the ability to biosynthesize these tryptophan derivatives. This study establishes a versatile platform for engineering proteins with various halogenated tryptophans.

Identification, Characterization, and Computer-Aided Rational Design of a Novel Thermophilic Esterase from Geobacillus subterraneus, and Application in the Synthesis of Cinnamyl Acetate

Investigation of a novel thermophilic esterase gene from Geobacillus subterraneus DSMZ 13552 indicated a high amino acid sequence similarity of 25.9% to a reported esterase from Geobacillus sp. A strategy that integrated computer-aided rational design tools was developed to select mutation sites. Six mutants were selected from four criteria based on the simulated saturation mutation (including 19 amino acid residues) results. Of these, the mutants Q78Y and G119A were found to retain 87% and 27% activity after incubation at 70 °C for 20 min, compared with the 19% activity for the wild type. Subsequently, a double-point mutant (Q78Y/G119A) was obtained and identified with optimal temperature increase from 65 to 70 °C and a 41.51% decrease in Km. The obtained T1/2 values of 42.2 min (70 °C) and 16.9 min (75 °C) for Q78Y/G119A showed increases of 340% and 412% compared with that in the wild type. Q78Y/G119A was then employed as a biocatalyst to synthesize cinnamyl acetate, for which the conversion rate reached 99.40% with 0.3 M cinnamyl alcohol at 60 °C. The results validated the enhanced enzymatic properties of the mutant and indicated better prospects for industrial application as compared to that in the wild type. This study reported a method by which an enzyme could evolve to achieve enhanced thermostability, thereby increasing its potential for industrial applications, which could also be expanded to other esterases.

Rational Design of l-Threonine Transaldolase-Mediated System for Enhanced Florfenicol Intermediate Production

l-threo-p-methylsulfonylphenylserine (compound 1b) is the main intermediate of florfenicol, and its efficient synthesis has been the subject of current research. Herein, Burkholderia diffusa l-threonine transaldolase (BuLTTA) was rationally designed based on the sequence-structure-function relationship. A mutant M4 (Asn35Ser/Thr352Asn) could produce 35.5 mM 1b with 88.8% conversion and 93.8% diastereoselectivity, 314 and 129% of the values observed for wild-type BuLTTA. Molecular dynamics simulations indicated that the shortened distance between key active site residues and the transition state (PLP-1b) and the improved hydrogen bond force enhanced the catalytic performance of the M4 variant. Then, the mutant M4 was combined with K. kurtzmanii alcohol dehydrogenase (KkADH) to eliminate the BuLTTA-inhibiting byproduct acetaldehyde, and a cosubstrate was added to regenerate the ADH cofactor NADH. Under optimized conditions, the yield of 1b reached 115.2 mM with a conversion of 96% and a diastereoselectivity of 95.5%. This work provides a new strategy for the efficient and sustainable production of 1b.

Electroenzymatic Reduction of Furfural to Furfuryl Alcohol by an Electron Mediator and Enzyme Orderly Assembled Biocathode

The electroenzymatic valorization of biomass derivatives into valuable biochemicals has a promising outlook. However, bottlenecks including poor electron transfer between the electrode surface and oxidoreductase, inefficient regeneration of cofactors, and high cost of enzymes and electron mediators hindered the realistic applications of the technique. Herein, to address the above technical barriers, a novel bio-electrocatalytic system that integrates the electrochemical NADH regeneration and enzymatic reaction was constructed, using an orderly assembled composite bioelectrode consisting of an outer immobilized enzyme layer and a sandwiched redox mediator rhodium complex layer. The as-prepared composite bioelectrode was further applied for the highly selective hydrogenation of furfural into furfural alcohol. Results indicated that the enzyme activity was significantly improved, while the furfural valorization was promoted by effective interfacial electron transition and co-factor regeneration on the composite bioelectrode. Considerable high furfural conversion (96.4%) can be achieved accompanied by a furfural alcohol selectivity of 90.0% at -1.2 V (vs Ag/AgCl). The novel composite bioelectrode also showed good stability and reusability. Up to 85.1% of the original furfural alcohol selectivity can be preserved after 10 times of recycling. This work presents a promising green alternative for the valorization of furfural, which also shows great potential extending to the valorization of other biomass compounds.

Selective Furfuryl Alcohol Production from Furfural via Bio-Electrocatalysis

The catalytic reduction of renewable furfural into furfuryl alcohol for various applications is in the ascendant. Nonetheless, the conventional chemo-catalysis hydrogenation of furfural always suffers from poor selectivity, harsh conditions, and expensive catalysts. Herein, to overcome the serious technical barriers of conventional furfuryl alcohol production, an alternative bio-electrocatalytic hydrogenation system was established under mild and neutral conditions, where the dissolved cofactor (NADH) and the alcohol dehydrogenase (ADH) participated in a tandem reaction driven by the electron from a novel Rh (III) complex fixed cathode. Under the optimized conditions, 81.5% of furfural alcohol selectivity can be realized at −0.43 V vs. RHE. This contribution presents a ‘green’ and promising route for the valorization of furfural and other biomass compounds.

Production of Tyrian purple indigoid dye from tryptophan in Escherichia coli

Tyrian purple, mainly composed of 6,6'-dibromoindigo (6BrIG), is an ancient dye extracted from sea snails and was recently demonstrated as a biocompatible semiconductor material. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and the difficulty of regiospecific bromination. Here, we introduce an effective 6BrIG production strategy in Escherichia coli using tryptophan 6-halogenase SttH, tryptophanase TnaA and flavin-containing monooxygenase MaFMO. Since tryptophan halogenases are expressed in highly insoluble forms in E. coli, a flavin reductase (Fre) that regenerates FADH₂ for the halogenase reaction was used as an N-terminal soluble tag of SttH. A consecutive two-cell reaction system was designed to overproduce regiospecifically brominated precursors of 6BrIG by spatiotemporal separation of bromination and bromotryptophan degradation. These approaches led to 315.0 mg l^-1 6BrIG production from tryptophan and successful synthesis of regiospecifically dihalogenated indigos. Furthermore, it was demonstrated that 6BrIG overproducing cells can be directly used as a bacterial dye.

Characterization and Catalytic-Site-Analysis of an Aldo-Keto Reductase with Excellent Solvent Tolerance

Aldo-keto reductases (AKRs) mediated stereoselective reduction of prochiral carbonyl compounds is an efficient way of preparing single enantiomers of chiral alcohols due to their high chemo-, enantio-, and regio-selectivity. To date, the application of AKRs in the asymmetric synthesis of chiral alcohols has been limited, due to the challenges of cloning and purifying. In this work, the aldo-keto reductase (AKR3-2-9) from Bacillus sp. was obtained, purified and proved to be NADPH-dependent. It exhibits good bioactivity and stability at 37 °C, pH 6.0. AKR3-2-9 is catalytically active on 11 pairs of substrates such as 3-methylcyclohexanone and methyl pyruvate, among which it showed the highest catalytic activity for acetylacetone. In addition, AKR3-2-9 was able to be resistant to five common organic solvents such as methanol and ethanol, it retained high catalytic activity even in a reaction system containing 10% v/v organic solvent for 6 h, which indicates its broad substrate spectrum and exceptional organic solvent tolerance. Furthermore, its three-dimensional structure was constructed and catalytic-site-analysis of the enzyme was conducted. Notably, it was capable of catalyzing the reaction of the key intermediates of duloxetine. The extensive substrate spectrum and predominant organic solvents resistance makes AK3-2-9 a promising enzyme which can be potentially applied in medicine synthesis.

Multi-enzyme cascade for improving β-hydroxy-α-amino acids production by engineering L-threonine transaldolase and combining acetaldehyde elimination system

L-threonine transaldolase(PsLTTA) could asymmetric synthesize β-hydroxy-α-amino acids (HAAs) with excellentstereoselectivity, while the poor yield limited its further application. Here we provided a combinatorial strategy to improve HAAs production, by directed evolution of PsLTTA towards enhanced activity and introducing an acetaldehyde elimination system to avoid acetaldehyde over-accumulation. A novel high throughput screening (HTS) method for evaluating PsLTTA activity was developed andapplied for directed evolution of PsLTTA. Subsequently, we co-expressedalcohol dehydrogenase andformate dehydrogenase to construct an acetaldehyde elimination system toremove acetaldehyde inhibition.Moreover, the above positive strategies were integrated. As a result,the (2S,3R)-p-methylsulfonyl phenylserine yield reached 154.0 mM andwith 94.6% devalue, the highest productivity and stereoselectivity of (2S,3R)-HAAs reported by enzymatic synthesis so far. Taken together, our studies provided an efficient and green route for chiral synthesis of (2S,3R)-HAAs, which might contribute to the industrialization production of these useful building blocks.

Characterization and Application of a Robust Glucose Dehydrogenase from Paenibacillus pini for Cofactor Regeneration in Biocatalysis

Glucose dehydrogenases are important auxiliary enzymes in biocatalysis, employed in the regeneration of reduced nicotinamide cofactors for oxidoreductase catalysed reactions. Here we report the identification and characterization of a novel glucose-1-dehydrogenase (GDH) from Paenibacillus pini that prefers NAD⁺ as cofactor over NADP⁺. The purified recombinant P. pini GDH displayed a specific activity of 247.5 U/mg. The enzyme was stable in the pH range 4-8.5 and exhibited excellent thermostability till 50 °C for 24 h, even in the absence of NaCl or glycerol. Paenibacillus pini GDH was also tolerant to organic solvents, demonstrating its potential for recycling cofactors for biotransformation. The potential application of the enzyme was evaluated by coupling with a NAD⁺-dependent alcohol dehydrogenase for the reduction of acetophenone and ethyl-4-chloro-3-oxo-butanoate. Conversions higher than 95% were achieved within 2 h with low enzyme loading using lyophilized cell lysate, suggesting that P. pini GDH could be highly effective for recycling NADH in redox biocatalysis.

Highly Efficient Biosynthesis of Heliotropin by Engineered Escherichia coli Coexpressing Trans-Anethole Oxygenase and Formate Dehydrogenase

Heliotropin, a compound with important roles in the spice and fragrance industries and broad application prospects, is mainly produced through chemical methods. Here, we established a novel process for the synthesis of heliotropin by Escherichia coli whole cells through biotransformation of isosafrole. Directed evolution and high-throughput screening based on 2,4-dinitrophenylhydrazine were used to improve the activity of trans-anethole oxygenase toward isosafrole, and a mutant (TAO_3G2) was obtained that had a high ability to oxidize isosafrole. Formate dehydrogenase (FDH) and TAO_3G2 were coexpressed in E. coli, significantly increasing the catalytic efficiency by regenerating more NADH to promote isosafrole oxidation. Furthermore, after optimizing the molar ratio of isosafrole to the auxiliary substrate, the final concentration of heliotropin was increased from 9.15 to 19.45 g/L, and the maximum yield and space-time yield reached 96.02% and 3.89 g/L/h, respectively. These results suggest that the biosynthesis of heliotropin should have excellent industrial application value.

Biocatalysis Fueled by Light: On the Versatile Combination of Photocatalysis and Enzymes

Enzymes catalyze a plethora of highly specific transformations under mild and environmentally benign reaction conditions. Their fascinating performances attest to high synthetic potential that is often hampered by operational obstacles such as in vitro cofactor supply and regeneration. Exploiting light and combining it with biocatalysis not only helps in overcoming these drawbacks, but the fruitful liaison of these two fields of "green chemistry" also offers opportunities to unlock new synthetic reactivities. In this review we provide an overview of the wide variety of photo-biocatalysis, ranging from the photochemical delivery of electrons required in redox biocatalysis and photochemical cofactor and reagent (re)generation to direct photoactivation of enzymes enabling reactions unknown in nature. We highlight synthetically relevant transformations such as asymmetric reactions facilitated by the combination of light as energy source and enzymes' catalytic power.

Enzyme Fusions in Biocatalysis: Coupling Reactions by Pairing Enzymes

One approach to bringing enzymes together for multienzyme biocatalysis is genetic fusion. This enables the production of multifunctional enzymes that can be used for whole-cell biotransformations or for in vitro (cascade) reactions. In some cases and in some aspects, such as expression and conversions, the fused enzymes outperform a combination of the individual enzymes. In contrast, some enzyme fusions are greatly compromised in activity and/or expression. In this Minireview, we give an overview of studies on fusions between two or more enzymes that were used for biocatalytic applications, with a focus on oxidative enzymes. Typically, the enzymes are paired to facilitate cofactor recycling or cosubstrate supply. In addition, different linker designs are briefly discussed. Although enzyme fusion is a promising tool for some biocatalytic applications, future studies could benefit from integrating the findings of previous studies in order to improve reliability and effectiveness.

The effect of CO2 in enhancing photosynthetic cofactor recycling for alcohol dehydrogenase mediated chiral synthesis in cyanobacteria

The light harvesting photosystem in cyanobacteria offers a potential pathway for the regeneration of the nicotinamide cofactor NADPH, thereby facilitating the application of cyanobacteria as excellent whole cell biocatalysts in oxidoreductase-mediated biotransformation. The use of cyanobacterial metabolism for cofactor recycling improves the atom economy of the process compared to the commonly employed enzyme-coupled cofactor recycling using enzymes such as glucose dehydrogenase. Here we report the asymmetric conversion of acetophenone to chiral 1-phenylethanol by recombinant Synechococcus elongatus PCC 7942 whole cell biocatalyst that expresses the NADPH dependent L. kefir alcohol dehydrogenase. Besides light, it was observed that carbon dioxide levels play a critical role in improving the bioconversion efficiency possibly due to the enhanced growth rate and improved cofactor availability at elevated CO₂ levels. Complete reduction of acetophenone to optically pure (R)-1-phenylethanol at 99% enantiomeric excess was achieved within 6 h with a relatively low cell density of 0.66 g/l by coupling optimum light and CO₂ levels and without the need for a co-substrate.

Enzymatic characterization of a recombinant carbonyl reductase from Acetobacter sp. CCTCC M209061

Background

Acetobacter sp. CCTCC M209061 could catalyze carbonyl compounds to chiral alcohols following anti-Prelog rule with excellent enantioselectivity. Therefore, the enzymatic characterization of carbonyl reductase (CR) from Acetobacter sp. CCTCC M209061 needs to be investigated.

Results

A CR from Acetobacter sp. CCTCC M209061 (AcCR) was cloned and expressed in E. coli. AcCR was purified and characterized, finding that AcCR as a dual coenzyme-dependent short-chain dehydrogenase/reductase (SDR) was more preferred to NADH for biocatalytic reactions. The AcCR was activated and stable when the temperature was under 35 °C and the pH range was from 6.0 to 8.0 for the reduction of 4′-chloroacetophenone with NADH as coenzyme, and the optimal temperature and pH were 45 °C and 8.5, respectively, for the oxidation reaction of isopropanol with NAD⁺. The enzyme showed moderate thermostability with half-lives of 25.75 h at 35 °C and 13.93 h at 45 °C, respectively. Moreover, the AcCR has broad substrate specificity to a range of ketones and ketoesters, and could catalyze to produce chiral alcohol with e.e. >99% for the majority of tested substrates following the anti-Prelog rule.

Conclusions

The recombinant AcCR exhibited excellent enantioselectivity, broad substrate spectrum, and highly stereoselective anti-Prelog reduction of prochiral ketones. These results suggest that AcCR is a powerful catalyst for the production of anti-Prelog alcohols.Graphical abstract

Engineering bi-functional enzyme complex of formate dehydrogenase and leucine dehydrogenase by peptide linker mediated fusion for accelerating cofactor regeneration

This study reports the application of peptide linker in the construction of bi-functional formate dehydrogenase (FDH) and leucine dehydrogenase (LeuDH) enzymatic complex for efficient cofactor regeneration and L-tert leucine (L-tle) biotransformation. Seven FDH-LeuDH fusion enzymes with different peptide linker were successfully developed and displayed both parental enzyme activities. The incorporation order of FDH and LeuDH was investigated by predicting three-dimensional structures of LeuDH-FDH and FDH-LeuDH models using the I-TASSER server. The enzymatic characterization showed that insertion of rigid peptide linker obtained better activity and thermal stability in comparison with flexible peptide linker. The production rate of fusion enzymatic complex with suitable flexible peptide linker was increased by 1.2 times compared with free enzyme mixture. Moreover, structural analysis of FDH and LeuDH suggested the secondary structure of the N-, C-terminal domain and their relative positions to functional domains was also greatly relevant to the catalytic properties of the fusion enzymatic complex. The results show that rigid peptide linker could ensure the independent folding of moieties and stabilized enzyme structure, while the flexible peptide linker was likely to bring enzyme moieties in close proximity for superior cofactor channeling.

A review of harvesting clean fuels from enzymatic CO2 reduction

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

Whole-Cell Biocatalysts for Stereoselective C-H Amination Reactions

Enantiomerically pure chiral amines are ubiquitous chemical building blocks in bioactive pharmaceutical products and their synthesis from simple starting materials is of great interest. One of the most attractive strategies is the stereoselective installation of a chiral amine through C-H amination, which is a challenging chemical transformation. Herein we report the application of a multienzyme cascade, generated in a single bacterial whole-cell system, which is able to catalyze stereoselective benzylic aminations with ee values of 97.5%. The cascade uses four heterologously expressed recombinant enzymes with cofactors provided by the host cell and isopropyl amine added as the amine donor. The cascade presents the first example of the successful de novo design of a single whole-cell biocatalyst for formal stereoselective C-H amination.