Characterization of an L-phosphinothricin resistant glutamine synthetase from Exiguobacterium sp. and its improvement

Identification of a novel thermostable transaminase and its application in L-phosphinothricin biosynthesis

Transaminase (TA) is a crucial biocatalyst for enantioselective production of the herbicide L-phosphinothricin (L-PPT). The use of enzymatic cascades has been shown to effectively overcome the unfavorable thermodynamic equilibrium of TA-catalyzed transamination reaction, also increasing demand for TA stability. In this work, a novel thermostable transaminase (PtTA) from Pseudomonas thermotolerans was mined and characterized. The PtTA showed a high specific activity (28.63 U/mg) towards 2-oxo-4-[(hydroxy)(methyl)phosphinoyl]butyric acid (PPO), with excellent thermostability and substrate tolerance. Two cascade systems driven by PtTA were developed for L-PPT biosynthesis, including asymmetric synthesis of L-PPT from PPO and deracemization of D, L-PPT. For the asymmetric synthesis of L-PPT from PPO, a three-enzyme cascade was constructed as a recombinant Escherichia coli (E. coli G), by co-expressing PtTA, glutamate dehydrogenase (GluDH) and D-glucose dehydrogenase (GDH). Complete conversion of 400 mM PPO was achieved using only 40 mM amino donor L-glutamate. Furthermore, by coupling D-amino acid aminotransferase (Ym DAAT) from Bacillus sp. YM-1 and PtTA, a two-transaminase cascade was developed for the one-pot deracemization of D, L-PPT. Under the highest reported substrate concentration (800 mM D, L-PPT), a 90.43% L-PPT yield was realized. The superior catalytic performance of the PtTA-driven cascade demonstrated that the thermodynamic limitation was overcome, highlighting its application prospect for L-PPT biosynthesis. KEY POINTS: • A novel thermostable transaminase was mined for L-phosphinothricin biosynthesis. • The asymmetric synthesis of L-phosphinothricin was achieved via a three-enzyme cascade. • Development of a two-transaminase cascade for D, L-phosphinothricin deracemization.

Nutritional stress induced intraspecies competition revealed by transcriptome analysis in Sphingomonas melonis TY

Bacteria have developed various mechanisms by which they can compete or cooperate with other bacteria. This study showed that in the cocultures of wild-type Sphingomonas melonis TY and its isogenic mutant TYΔndpD grow with nicotine, the former can outcompete the latter. TYΔndpD undergoes growth arrest after four days when cocultured with wild-type TY, whereas the coculture has just entered a stationary phase and the substrate was nearly depleted, and the interaction between the two related strains was revealed by transcriptomic analysis. Analysis of the differential expression genes indicated that wild-type TY inhibited the growth of TYΔndpD mainly through toxin-antitoxin (TA) systems. The four upregulated antitoxin coding genes belong to type II TA systems in which the bactericidal effect of the cognate toxin was mainly through inhibition of translation or DNA replication, whereas wild-type TY with upregulated antitoxin genes can regenerate cognate immunity protein continuously and thus prevent the lethal action of toxin to itself. In addition, colicin-mediated antibacterial activity against closely related species may also be involved in the competition between wild-type TY and TYΔndpD under nutritional stress. Moreover, upregulation of carbon and nitrogen catabolism related-, stress response related-, DNA repair related-, and DNA replication-related genes in wild-type TY showed that it triggered a series of response mechanisms when facing dual stress of competition from isogenic mutant cells and nutritional limitation. Thus, we proposed that S. melonis TY employed the TA systems and colicin to compete with TYΔndpD under nutritional stress, thereby maximally acquiring and exploiting finite resources. KEY POINTS: • Cross-feeding between isogenic mutants and the wild-type strain. • Nutrition stress caused a shift from cooperation to competition. • TYΔndpD undergo growth arrest by exogenous and endogenous toxins.

Emerging trends in environmental and industrial applications of marine carbonic anhydrase: a review

Biocatalytic conversion of greenhouse gases such as carbon dioxide into commercial products is one of the promising key approaches to solve the problem of climate change. Microbial enzymes, including carbonic anhydrase, NAD-dependent formate dehydrogenase, ribulose bisphosphate carboxylase, and methane monooxygenase, have been exploited to convert atmospheric gases into industrial products. Carbonic anhydrases are Zn²⁺-dependent metalloenzymes that catalyze the reversible conversion of CO₂ into bicarbonate. They are widespread in bacteria, algae, plants, and higher organisms. In higher organisms, they regulate the physiological pH and contribute to CO₂ transport in the blood. In plants, algae, and photosynthetic bacteria carbonic anhydrases are involved in photosynthesis. Converting CO₂ into bicarbonate by carbonic anhydrases can solidify gaseous CO2, thereby reducing global warming due to the burning of fossil fuels. This review discusses the three-dimensional structures of carbonic anhydrases, their physiological role in marine life, their catalytic mechanism, the types of inhibitors, and their medicine and industry applications.

Enhanced catalytic activity of recombinant transaminase by molecular modification to improve L-phosphinothricin production

Transaminases catalyze the transfer of an amino group from a donor to a keto group of an acceptor substrate and are applicable to the asymmetric synthesis of herbicide L-phosphinothricin (L-PPT). Here, the important residue sites (C390, I22, V52, R141, Y138 and D239) of transaminase from Salmonella enterica (SeTA) were modified at the adjacency of the substrate-binding pocket to improve the enzyme activity. Among the constructed mutant library, the SeTA-Y138F mutant displayed higher activity than the wild-type enzyme. Compared to the wild-type, SeTA-Y138F showed improved catalytic efficiency with a 4.36-fold increase. The K_m and k_cat of SeTA -Y138F toward 4-(hydroxy(methyl) phosphoryl)-2-oxobutanoic acid (PPO) were 26.39 mM and 34.28 s^-1, respectively. Subsequently, the three-enzyme co-expression system of E. coli BL21 (DE3)/pACYCDuet-SeTA-Y138F/pETDuet-AlaDH-BsGDH was developed by combining a alanine dehydrogenase (AlaDH) to recycle the byproduct of amino donor, a glucose dehydrogenase (BsGDH) for cofactor recycling. Under the optimized conditions, an excellent L-PPT yield of 90.8% was achieved by the whole-cell biotransformation with 500 mM PPO. It exhibited the tri-enzymatic coupling system was potential for effective production of target L-PPT.

Highly Efficient Chemoenzymatic Synthesis of l-Phosphinothricin from N-Phenylacetyl-d,l-phosphinothricin by a Robust Immobilized Amidase

A chemoenzymatic strategy was developed for the highly efficient synthesis of l-phosphinothricin employing a robust immobilized amidase. An enzymatic hydrolysis of 500 mM N-phenylacetyl-d,l-phosphinothricin resulted in 49.9% conversion and 99.9% ee of l-phosphinothricin within 6 h. To further evaluate the bioprocess for l-phosphinothricin production, the biotransformation was performed for 100 batches under a stirred tank reactor with an average productivity of 8.21 g L^-1 h^-1. Moreover, unreacted N-phenylacetyl-d-phosphinothricin was racemized and subjected to the enzymatic hydrolysis, giving l-phosphinothricin with a 22.3% yield. A total yield of 69.4% was achieved after one recycle of N-phenylacetyl-d-phosphinothricin. Significantly, this chemoenzymatic approach shows great potential in the industrial production of l-phosphinothricin.

Characterization and improved properties of Glutamine synthetase from Providencia vermicola by site-directed mutagenesis

In this study, a novel gene for Glutamine synthetase was cloned and characterized for its activities and stabilities from a marine bacterium Providencia vermicola (PveGS). A mutant S54A was generated by site directed mutagenesis, which showed significant increase in the activity and stabilities at a wide range of temperatures. The K_m values of PveGS against hydroxylamine, ADP-Na₂ and L-Glutamine were 15.7 ± 1.1, (25.2 ± 1.5) × 10^-5 and 32.6 ± 1.7 mM, and the k_cat were 17.0 ± 0.6, 9.14 ± 0.12 and 30.5 ± 1.0 s^-1 respectively. In-silico-analysis revealed that the replacement of Ser at 54th position with Ala increased the catalytic activity of PveGS. Therefore, catalytic efficiency of mutant S54A had increased by 3.1, 0.89 and 2.9-folds towards hydroxylamine, ADP-Na₂ and L-Glutamine respectively as compared to wild type. The structure prediction data indicated that the negatively charged pocket becomes enlarged and hydrogen bonding in Ser54 steadily promotes the product release. Interestingly, the residual activity of S54A mutant was increased by 10.7, 3.8 and 3.8 folds at 0, 10 and 50 °C as compared to WT. Structural analysis showed that S54A located on the loop near to the active site improved its flexibility due to the breaking of hydrogen bonds between product and enzyme. This also facilitated the enzyme to increase its cold adaptability as indicated by higher residual activity shown at 0 °C. Thus, replacement of Ala to Ser54 played a pivotal role to enhance the activities and stabilities at a wide range of temperatures.

Improved catalytic properties of a serine hydroxymethyl transferase from Idiomarina loihiensis by site directed mutagenesis

A novel glyA gene was screened from a marine bacterium, Idiomarina loihiensis encoding a thermo-stable serine hydroxymethyl transferase (SHMT; 418 AA; 45.4 kDa). The activities of wild type (WT) and mutants were analyzed against d-phenylserine using pyrodoxal-5-phosphate (PLP) as cofactor under optimized conditions. Based on homology modelling and molecular docking, several residues were found that may be able to improve the activity of WT-SHMT. Site directed mutagenesis was conducted. The activity and thermostability of the wild type SHMT was improved by two variants H61G and G132P, which showed a noteworthy change in the thermo-stability and activity as compared to WT. To investigate the mechanism of activity of mutants, we combined two residues into one mutant DUAL. WT showed the optimum activity at 50 °C, whereas H61G, G132P and DUAL had the temperature optima of 55, 60 and 60 °C, respectively. These mutants G132P, H61G and DUAL were quite stable at 45 and 55 °C as compared to WT. Dual mutant was relatively more stable at all tested pH(s) while WT loses its activity in alkaline pH(s). Kinetics studies indicated the 1.52, 2.42 and 4.54 folds increase in the k_cat value of H61G, G132P and Dual mutants as compared to WT respectively. The molecular docking indicated that hydrophobic interactions are more prominent than hydrogen-bonding and had more influence on ligand binding and active site cavity. The molecular dynamics showed the changed RMSD values for ligand and formation of new hydrogen bonds, hydrophobic interaction which considerably increased the activity and thermo-stability of the mutant proteins as compared to WT. Thus, increased stabilities at higher temperatures and activities can be attributed to new hydrogen bonding, altered active site geometry and increased ligand interactions.

Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam

Tabtoxinine-β-lactam (TβL), also known as wildfire toxin, is a time- and ATP-dependent inhibitor of glutamine synthetase produced by plant pathogenic strains of Pseudomonas syringae. Here we demonstrate that recombinant glutamine synthetase from Escherichia coli phosphorylates the C3-hydroxyl group of the TβL 3-(S)-hydroxy-β-lactam (3-HβL) warhead. Phosphorylation of TβL generates a stable, noncovalent enzyme-ADP-inhibitor complex that resembles the glutamine synthetase tetrahedral transition state. The TβL β-lactam ring remains intact during enzyme inhibition, making TβL mechanistically distinct from traditional β-lactam antibiotics such as penicillin. Our findings could enable the design of new 3-HβL transition state inhibitors targeting enzymes in the ATP-dependent carboxylate-amine ligase superfamily with broad therapeutic potential in many disease areas.