Highly stereoselective biosynthesis of (R)-α-hydroxy carboxylic acids through rationally re-designed mutation of D-lactate dehydrogenase

A two-enzyme system in an amorphous metal-organic framework for the synthesis of D-phenyllactic acid

In this study, we synthesized an amorphous metal-organic framework by adjusting the concentration of precursors, and established a two-enzyme system consisting of lactate dehydrogenase (LDH) and glucose dehydrogenase (GDH), which successfully achieved coenzyme recycling, and applied it to the synthesis of D-phenyllactic acid (D-PLA). The prepared two-enzyme-MOF hybrid material was characterized using XRD, SEM/EDS, XPS, FT-IR, TGA, CLSM, etc. In addition, reaction kinetic studies indicated that the MOF-encapsulated two-enzyme system exhibited faster initial reaction velocities than free enzymes due to its amorphous ZIF-generated mesoporous structure. Furthermore, the pH stability and temperature stability of the biocatalyst were evaluated, and the results indicated a significant improvement compared to the free enzymes. Moreover, the amorphous structure of the mesopores still maintained the shielding effect and protected the enzyme structure from damage by proteinase K and organic solvents. Finally, the remaining activity of the biocatalyst for the synthesis of D-PLA reached 77% after 6 cycles of use, and the coenzyme regeneration still maintained at 63%, while the biocatalyst also retained 70% and 68% residual activity for the synthesis of D-PLA after 12 days of storage at 4 °C and 25 °C, respectively. This study provides a reference for the design of MOF-based multi-enzyme biocatalysts.

Enantioselective Biosynthesis of L-Phenyllactic Acid From Phenylpyruvic Acid In Vitro by L-Lactate Dehydrogenase Coupling With Glucose Dehydrogenase

As a valuable versatile building block, L-phenyllactic acid (L-PLA) has numerous applications in the fields of agriculture, pharmaceuticals, and biodegradable plastics. However, both normally chemically synthesized and naturally occurring PLA are racemic, and the production titer of L-PLA is not satisfactory. To improve L-PLA production and reduce the high cost of NADH, an in vitro coenzyme regeneration system of NADH was achieved using the glucose dehydrogenase variant LsGDHD255C and introduced into the L-PLA production process. Here an NADH-dependent L-lactate dehydrogenase-encoding variant gene (L-Lcldh1Q88A/I229A) was expressed in Pichia pastoris GS115. The specific activity of L-LcLDH1Q88A/I229A (Pp) was as high as 447.6 U/mg at the optimum temperature and pH of 40°C and 5.0, which was 38.26-fold higher than that of wild-type L-LcLDH1 (Pp). The catalytic efficiency (kcat/Km) of L-LcLDH1Q88A/I229A (Pp) was 94.3 mM−1 s−1, which was 67.4- and 25.5-fold higher than that of L-LcLDH1(Pp) and L-LcLDH1Q88A/I229A (Ec) expressed in Escherichia coli, respectively. Optimum reactions of L-PLA production by dual-enzyme catalysis were at 40°C and pH 5.0 with 10.0 U/ml L-LcLDH1Q88A/I229A (Pp) and 4.0 U/ml LsGDHD255C. Using 0.1 mM NAD+, 400 mM (65.66 g/L) phenylpyruvic acid was completely hydrolyzed by fed-batch process within 6 h, affording L-PLA with 90.0% yield and over 99.9% eep. This work would be a promising technical strategy for the preparation of L-PLA at an industrial scale.

Improvement in the catalytic performance of a phenylpyruvate reductase from Lactobacillus plantarum by site-directed and saturation mutagenesis based on the computer-aided design

To enhance the specific activity and catalytic efficiency (k _cat/K _m) of an NADH-dependent LpPPR, its directed modification was performed based on the computer-aided design using molecular docking simulation and multiple sequence alignment. Firstly, five single-site variants of an LpPPR-encoding gene (lpppr) were amplified and expressed in E. coli BL21 (DE3). The asymmetric reduction of 20 mM phenylpyruvic acid (PPA) was carried out using 50 mg/mL E. coli/lpppr ^R53Q or /lpppr ^A79V whole wet cells at 37 °C for 20 min, giving d-phenyllactic acid (PLA) with 41.1 or 44.3% yield, being 1.17- or 1.26-fold that by E. coli/lpppr. Secondly, double-site variants were obtained by saturation mutagenesis of Ala79 in LpPPR^R53Q. Among all tested E. coli transformants, E. coli/lpppr ^R53Q/A79V exhibited the highest d-PLA yield of 85.3%. The specific activity and k _cat/K _m of the purified LpPPR^R53Q/A79V increased to 67.5 U/mg and 169.8 mM^-1 s^-1, which were 3.0- and 13.2-fold those of LpPPR, respectively. Finally, the catalytic mechanism analysis of LpPPR^R53Q/A79V by molecular docking simulation indicated that the replacement of Arg53 in LpPPR with Gln expanded its substrate-binding pocket, while that Ala79 with Val formed an additional π-sigma interaction with phenyl group of PPA.

SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s13205-020-02633-3) contains supplementary material, which is available to authorized users.

Enzymological characterization of a novel d-lactate dehydrogenase from Lactobacillus rossiae and its application in d-phenyllactic acid synthesis

A novel lactate dehydrogenase gene, named lrldh, was cloned from Lactobacillus rossiae and heterologously expressed in Escherichia coli. The lactate dehydrogenase LrLDH is NADH-dependent with a molecular weight of approximately 39 kDa. It is active at 40 °C and pH 6.5 and stable in a neutral to alkaline environment below 35 °C. The kinetic constants, including maximal reaction rate (V _max), apparent Michaelis-Menten constant (K _m), turnover number (K _cat) and catalytic efficiency (K _cat/K _m) for phenylpyruvic acid were 1.95 U mg^-1, 2.83 mM, 12.29 s^-1, and 4.34 mM^-1 s^-1, respectively. Using whole cells of recombinant E. coli/pET28a-lrldh, without coexpression of a cofactor regeneration system, 20.5 g l^-1 d-phenyllactic acid with ee above 99% was produced from phenylpyruvic acid in a fed-batch biotransformation process, with a productivity of 49.2 g l^-1 d^-1. Moreover, LrLDH has broad substrate specificity to a range of ketones, keto acids and ketonic esters. Taken together, LrLDH is a promising biocatalyst for the efficient synthesis of d-phenyllactic acid and other fine chemicals.

Efficient synthesis of d-phenyllactic acid by a whole-cell biocatalyst co-expressing glucose dehydrogenase and a novel d-lactate dehydrogenase from Lactobacillus rossiae

d-Phenyllactic acid is a versatile natural organic acid, which is used as an antiseptic agent, monomer of the biodegradable material poly-phenyllactic acid and in the synthesis chiral intermediate of pharmaceuticals. In this report, the novel NADH-dependent d-lactate dehydrogenase LrLDH was identified by screening a shotgun genome of Lactobacillus rossiae. To improve cofactor regeneration, the Exiguobacterium sibiricum glucose dehydrogenase EsGDH was overexpressed together with LrLDH in E. coli BL21(DE3)-pCDFDuet-1-gdh-ldh. The total enzyme activity in the fermentation broth of E. coli BL 21(DE3)-pCDFDuet-1-gdh-ldh peaked at 2359.0 U l-1 when induced by 10 g l-1 lactose at 28 °C and 150 rpm for 14 h. The biocatalytic reduction of sodium phenylpyruvate to d-phenyllactic acid was successfully carried out using whole cells of the engineered E. coli. Under the optimized biocatalysis conditions, 50 g l-1 sodium phenylpyruvate was completely converted to d-phenyllactic acid with a space-time yield and enantiomeric excess of 262.8 g l-1 day-1 and > 99.5%, respectively. To our best knowledge, it is the highest productivity reported to date, with great potential for the mass production of d-phenyllactic acid.

Engineering D-Lactate Dehydrogenase from Pediococcus acidilactici for Improved Activity on 2-Hydroxy Acids with Bulky C3 Functional Group

Engineering D-lactic acid dehydrogenases for higher activity on various 2-oxo acids is important for the synthesis of 2-hydroxy acids that can be utilized in a wide range of industrial fields including the production of biopolymers, pharmaceuticals, and cosmetic compounds. Although there are many D-lactate dehydrogenases (D-LDH) available from a diverse range of sources, there is a lack of biocatalysts with high activities for 2-oxo acids with large functional group at C₃. In this study, the D-LDH from Pediococcus acidilactici was rationally designed and further engineered by controlling the intermolecular interactions between substrates and the surrounding residues via analysis of the active site structure of D-LDH. As a result, Y51L mutant with the catalytic efficiency on phenylpyruvate of 2200 s^-1 mM^-1 and Y51F mutant on 2-oxobutryate and 3-methyl-2-oxobutyrate of 37.2 and 23.2 s^-1 mM^-1 were found, which were 138-, 8.5-, and 26-fold increases than the wild type on the substrates, respectively. Structural analysis revealed that the distance and the nature of the interactions between the side chain of residue 51 and the substrate C₃ substituent group significantly affected the kinetic parameters. Bioconversion of phenyllactate as a practical example of production of the 2-hydroxy acids was investigated, and the Y51F mutant presented the highest productivity in in vitro conversion of D-PLA.

Engineering of a keto acid reductase through reconstructing the substrate binding pocket to improve its activity

Enzyme–substrate docking-guided point mutation of the substrate-binding pocket to generate mutant L244G/A250G/L245R with superior activity in the synthesis of (R)-2-hydroxy-4-phenylbutyric acid.

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

BACKGROUND

The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members.

RESULTS

We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase.

CONCLUSIONS

The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.

Efficient production of (R)-(-)-2-hydroxy-4-phenylbutyric acid by recombinant Pichia pastoris expressing engineered D-lactate dehydrogenase from Lactobacillus plantarum with a single-site mutation

(R)-2-hydroxy-4-phenylbutyric acid (R-HPBA) is a valuable intermediate for the synthesis of angiotensin-converting enzyme inhibitors. The asymmetric reduction of 2-oxo-4-phenylbutyric acid (OPBA) by oxidoreductases is an efficient approach for its synthesis. Here, we report a novel biocatalytic approach for asymmetric synthesis of R-HPBA using recombinant Pichia pastoris expressing the Tyr52Leu variant of D-lactate dehydrogenase (D-LDH) from Lactobacillus plantarum. The recombinant yeast cells showed impressive catalytic activity at a high concentration of NaOPBA (380 mM, 76 g/L) and achieved full conversion starting with 40 g/L NaOPBA or even at higher concentration. Under optimized reaction conditions (pH 7.5, 37 °C, and 2% glucose), a full conversion with > 95% reaction yield and ~ 100% product enantiomeric excess (ee) was achieved for the preparation of R-HPBA on a 2-g scale. The findings of this study promote both the biotransformation of R-HPBA and an extension of the application of recombinant yeast as biocatalysts.

Efficient production of enantiomerically pure D-phenyllactate from phenylpyruvate by structure-guided design of an engineered D-lactate dehydrogenase

3-Phenyllactic acid (PLA) is an antimicrobial compound with broad-spectrum activity against bacteria and fungi that could be widely used in the food industry and livestock feeds. Notably, D-PLA exhibits higher antibacterial activity, which gains more attention than L-PLA. In this report, the D-lactate dehydrogenase DLDH744 from Sporolactobacillus inulinus CASD was engineered to increase the enzymatic activities toward phenylpyruvate by protein structure-guided modeling analysis. The phenylpyruvate molecule was first docked in the active center of DLDH744. The residues that might tightly pack around the benzene ring of phenylpyruvate were all selected for mutation. The single site mutant M307L showed the highest increased activity toward bulkier substrate phenylpyruvate than the wild type. By using the engineered D-lactate dehydrogenase M307L expressed in Escherichia coli strains, without coexpression of the cofactor regeneration system, 21.43 g/L D-PLA was produced from phenylpyruvate with a productivity of 1.58 g/L/h in the fed-batch biotransformation process, which ranked in the list as the highest production titer of D-PLA by D-lactate dehydrogenase. The enantiomeric excess value of produced D-PLA in the broth was higher than 99.7 %. Additionally, the structure-guided design of this enzyme will also provide referential information for further engineering other 2-hydroxyacid dehydrogenases, which are useful for a wide range of fine chemical synthesis.

Enzymatic preparation of D-phenyllactic acid at high space-time yield with a novel phenylpyruvate reductase identified from Lactobacillus sp. CGMCC 9967

An NADH-dependent phenylpyruvate reductase (LaPPR) was identified through screening the shotgun library of Lactobacillus sp. CGMCC 9967. It belongs to D-3-phosphoglycerate dehydrogenase (PGDH) subfamily of 2-hydroxy acid dehydrogenase superfamily. LaPPR was stable at pH 6.5 and 30 °C, with a half-life of 152 h. LaPPR has a substrate preference towards aromatic to aliphatic keto acids, and various keto acids could be reduced into D-hydroxy acids with excellent enantioselectivity (>99%). By construction the coexpression system with glucose dehydrogenase, as much as 100 g L(-1) phenylpyruvic acid was asymmetrically reduced into D-phenyllactic acid with 91.3% isolation yield and 243 g L(-1) d(-1) productivity. The results suggest that LaPPR is a promising biocatalyst for the efficient synthesis of optically pure D-phenyllactic acid.

Metabolic mechanism of phenyllactic acid naturally occurring in Chinese pickles

Phenyllactic acid, a phenolic acid phytochemical with the antimicrobial activity, was rarely reported in food besides honey and sourdough. This study evidenced a new food source of phenyllactic acid and elucidated its metabolic mechanism. Phenyllactic acid naturally occurred in Chinese pickles with concentrations ranged from 0.02 to 0.30 mM in 23 pickle samples including homemade and commercial ones. Then, lactic acid bacteria capable of metabolizing phenyllactic acid were screened from each homemade pickle and a promising strain was characterized as Lactobacillus plantarum. Moreover, the investigation of the metabolic mechanism of phenyllactic acid in pickles suggested that the yield of phenyllactic acid was positively related to the content of phenylalanine in food, and the addition of phenylalanine as precursor substance could significantly promote the production of phenyllactic acid. This investigation could provide some insights into the accumulation of phenyllactic acid in pickle for long storage life.

Efficient production of (R)-2-hydroxy-4-phenylbutyric acid by using a coupled reconstructed D-lactate dehydrogenase and formate dehydrogenase system

Background

(R)-2-Hydroxy-4-phenylbutyric acid [(R)-HPBA] is a key precursor for the production of angiotensin-converting enzyme inhibitors. However, the product yield and concentration of reported (R)-HPBA synthetic processes remain unsatisfactory.

Methodology/Principal Findings

The Y52L/F299Y mutant of NAD-dependent d-lactate dehydrogenase (d-nLDH) in Lactobacillus bulgaricus ATCC 11842 was found to have high bio-reduction activity toward 2-oxo-4-phenylbutyric acid (OPBA). The mutant d-nLDH^Y52L/F299Y was then coexpressed with formate dehydrogenase in Escherichia coli BL21 (DE3) to construct a novel biocatalyst E. coli DF. Thus, a novel bio-reduction process utilizing whole cells of E. coli DF as the biocatalyst and formate as the co-substrate for cofactor regeneration was developed for the production of (R)-HPBA from OPBA. The biocatalysis conditions were then optimized.

Conclusions/Significance

Under the optimum conditions, 73.4 mM OPBA was reduced to 71.8 mM (R)-HPBA in 90 min. Given its high product enantiomeric excess (>99%) and productivity (47.9 mM h⁻¹), the constructed coupling biocatalysis system is a promising alternative for (R)-HPBA production.