Surfactant-mediated permeabilization of Pseudomonas putida KT2440 and use of the immobilized permeabilized cells in biotransformation

Dual-function transaminases with hybrid nanoflower for the production of value-added chemicals from biobased levulinic acid

The U.S. Department of Energy has listed levulinic acid (LA) as one of the top 12 compounds derived from biomass. LA has gained much attention owing to its conversion into enantiopure 4-aminopentanoic acid through an amination reaction. Herein, we developed a coupled-enzyme recyclable cascade employing two transaminases (TAs) for the synthesis of (S)-4-aminopentanoic acid. TAs were first utilized to convert LA into (S)-4-aminopentanoic acid using (S)-α-Methylbenzylamine [(S)-α-MBA] as an amino donor. The deaminated (S)-α-MBA i.e., acetophenone was recycled back using a second TAs while using isopropyl amine (IPA) amino donor to generate easily removable acetone. Enzymatic reactions were carried out using different systems, with conversions ranging from 30% to 80%. Furthermore, the hybrid nanoflowers (HNF) of the fusion protein were constructed which afforded complete biocatalytic conversion of LA to the desired (S)-4-aminopentanoic acid. The created HNF demonstrated storage stability for over a month and can be reused for up to 7 sequential cycles. A preparative scale reaction (100 mL) achieved the complete conversion with an isolated yield of 62%. Furthermore, the applicability of this recycling system was tested with different β-keto ester substrates, wherein 18%-48% of corresponding β-amino acids were synthesized. Finally, this recycling system was applied for the biosynthesis of pharmaceutical important drug sitagliptin intermediate ((R)-3-amino-4-(2,4,5-triflurophenyl) butanoic acid) with an excellent conversion 82%.

Metabolic engineering of Pseudomonas putida KT2440 for medium-chain-length fatty alcohol and ester production from fatty acids

Medium-chain-length fatty alcohols have broad applications in the surfactant, lubricant, and cosmetic industries. Their acetate esters are widely used as flavoring and fragrance substances. Pseudomonas putida KT2440 is a promising chassis for fatty alcohol and ester production at the industrial scale due to its robustness, versatility, and high oxidative capacity. However, P. putida has also numerous native alcohol dehydrogenases, which lead to the degradation of these alcohols and thereby hinder its use as an effective biocatalyst. Therefore, to harness its capacity as a producer, we constructed two engineered strains (WTΔpedFΔadhP, GN346ΔadhP) incapable of growing on mcl-fatty alcohols by deleting either a cytochrome c oxidase PedF and a short-chain alcohol dehydrogenase AdhP in P. putida or AdhP in P. putida GN346. Carboxylic acid reductase, phosphopantetheinyl transferase, and alcohol acetyltransferase were expressed in the engineered P. putida strains to produce hexyl acetate. Overexpression of transporters further increased 1-hexanol and hexyl acetate production. The optimal strain G23E-MPAscTP produced 93.8 mg/L 1-hexanol and 160.5 mg/L hexyl acetate, with a yield of 63.1%. The engineered strain is applicable for C₆-C₁₀ fatty alcohols and their acetate ester production. This study lays a foundation for P. putida being used as a microbial cell factory for sustainable synthesis of a broad range of products based on medium-chain-length fatty alcohols.

Immobilization of transaminase from Bacillus licheniformis on copper phosphate nanoflowers and its potential application in the kinetic resolution of RS-α-methyl benzyl amine

This study reports the isolation and partial purification of transaminase from the wild species of Bacillus licheniformis. Semi-purified transaminase was immobilized on copper nanoflowers (NFs) synthesized through sonochemical method and explored it as a nanobiocatalyst. The conditions for the synthesis of transaminase NFs [TA@Cu3(PO4)2NF] were optimized. Synthesized NFs revealed the protein loading and activity yield-60 ± 5% and 70 ± 5%, respectively. The surface morphology of the synthesized hybrid NFs was examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), which revealed the average size to be around 1 ± 0.5 μm. Fourier-transform infrared (FTIR) was used to confirm the presence of the enzyme inside the immobilized matrix. In addition, circular dichroism and florescence spectroscopy were also used to confirm the integrity of the secondary and tertiary structures of the protein in the immobilized material. The transaminase hybrid NFs exhibited enhanced kinetic properties and stability over the free enzyme and revealed high reusability. Furthermore, the potential application of the immobilized transaminase hybrid NFs was demonstrated in the resolution of racemic α-methyl benzylamine.

Studies on antibacterial and chemotaxis properties of Pseudomonas aeruginosa TEN01 biomass-derived sustainable biosurfactant

Biosurfactant producing bacterial strains were isolated from oil-contaminated sites at Chennai Petroleum Corporation Limited, Chennai, the potential strain was selected and identified as Pseudomonas aeruginosa TEN01 by 16 S rRNA sequencing technique. Biosurfactant was produced from cassava solid waste from the sago industry. Further, it was extracted by solvent extraction and partially purified by column chromatography. The partially purified biosurfactant was qualitatively analyzed by Thin Layer Chromatography (TLC), quantitatively analyzed by anthrone assay and characterized by Fourier Transform Infra-Red Spectroscopy (FT-IR) and Gas Chromatography-Mass Spectrometry (GC-MS). R_f value and chemical groups confirm the presence of glycolipid in the partially purified biosurfactant. GC-MS results confirmed the presence of long-chain fatty acids and carbohydrate which is found to be mainly present in glycolipids. Biosurfactants are surface-active molecules which have been found to be the best alternative to chemical-based surfactants. The present study focuses on modifying the cell surface using a biosurfactant from P. aeruginosa TEN01 to enhance membrane permeabilization. Antibacterial and chemotaxis properties of biosurfactant from P. aeruginosa TEN01 were found to be better towards Xenorhabdus poinarii, a bio-pesticide producing microbial strain, X. poinarii exhibited 81.7% adhesion to hydrocarbons upon biosurfactant treatment as analyzed by Bacterial Adhesion to Hydrocarbon (BATH) assay. The alteration in the membrane permeability was tested in X. poinarii using biosurfactant and chemical surfactants viz. Sodium dodecyl sulfate (SDS) and toluene by estimating the amount of intracellular protein released. High protein recovery (51.55%) was achieved with a biosurfactant. Cell viability in the biosurfactant-treated cells was also high (93.98%) in comparison to cells treated with chemical surfactants. Increased recovery of intracellular protein along with high cell viability makes the biosurfactant a potential candidate for application in numerous environmental fields.

Effective immobilization of Bacillus subtilis in chitosan-sodium alginate composite carrier for ammonia removal from anaerobically digested swine wastewater

To overcome the easy loss of microorganism, the mass production of sludge and the consumption of aeration energy during biological treatment of anaerobically digested swine wastewater, this study used chitosan-sodium alginate composite carrier to prepare immobilized bacteria pellets. The heterotrophic bacteria tolerant to high concentrations of ammonia nitrogen were isolated and the conditions for immobilizing bacteria were optimized. The performance of immobilized bacteria pellets to remove ammonia nitrogen from ADSW was determined and the corresponding mechanism was investigated. Results showed that the isolated bacteria were Bacillus subtilis, and the optimal conditions to prepare the immobilized bacteria pellets by response surface methodology tests were sodium alginate of 0.84% (m/V), chitosan of 0.22% (m/V), embedding time of 32 min and embedding amount of 15% (V/V). In ADSW treatment, at pH 6, 20 g/L of the immobilized bacteria pellets removed 96.5% of ammonia nitrogen. Both adsorption and microbial action contributed to ammonia nitrogen removal, and their contributions were 54.3% and 42.2%, respectively. Compared with the immobilized bacteria pellets using chitosan-sodium alginate as carrier, the one using mono alginate as carrier had a weaker ability to remove ammonia nitrogen, with a removal efficiency of 67.4%. The main mechanism was the formation of polyelectrolyte membrane by the connection between amino groups of chitosan and carboxyl groups of sodium alginate, which stabilized the immobilized bacteria pellets and prolonged their service life. To sum up, the immobilized bacteria pellets using chitosan-sodium alginate as an embedding agent have a promising prospect in ammonia nitrogen removal from wastewater.

Optimization of medium composition to increase the expression of recombinant human interferon-β using the Plackett-Burman and central composite design in E. coli SE1

Recombinant human interferon-β (rhIFN-β) is therapeutically important and new commercially viable approaches are needed for its increased production. In this study, a codon-optimized gene encoding for rhIFN-β_(C17S) protein was designed and expressed in E. coli SE1. As a first step of medium optimization, growth of E. coli as a function of different media components was studied. Subsequently, to optimize the media composition, a response surface methodology (RSM) was used. Our results show that optimized medium (15.0 g/L tryptone, 12.3 g/L meat extract, 1.0 g/L MgSO₄ and 0.5 g/L thiamine along with minimal medium) obtained in this study provide better growth of recombinant cells and the expression level of recombinant protein was ~ 1.7-fold more than Luria-Bertani medium. The optimized medium may be utilized for the large-scale production of rhIFN-β.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

Permeabilization and immobilization of whole-cell Pseudomonas nitroreducens SP.001 to improve its l-glutaminase performance

BACKGROUND

L-Glutaminase is considered to be an important industrial enzyme in both the pharmaceutical and food industries, especially for producing functional glutamyl compounds, such as l-theanine. Pseudomonas nitroreducens SP.001 with intracellular l-glutaminase activity has been screened previously. In the present study, three physical permeabilization methods were used to improve l-glutaminase activity. Then, the whole-cell immobilization conditions of permeabilized cells using sodium alginate as an embedding agent were optimized to enhance the enzyme's stability and reusability. The characteristics of the immobilized cells were investigated in comparison with those of permeabilized cells.

RESULTS

The results obtained showed that cell permeabilization using osmotic shock with 155 g L^-1 sucrose markedly improved enzyme activity. Then, an effective procedure for immobilization of permeabilized P. nitroreducens cells was established. The optimum conditions for cell immobilization were: sodium alginate 40 g L^-1 , calcium chloride 30 g L^-1 , cell mass 100 g L^-1 and a curing time of 3 h. After successful immobilization, characterization studies revealed that the thermostability and pH resistance of l-glutaminase from immobilized cells were enhanced compared to those from permeabilized cells. Moreover, the immobilized biocatalyst could be reused up to 10 times and retained 80% of its activity.

CONCLUSION

The stability and reusability of the permeabilized cells were improved through the immobilization. These findings indicated that immobilized whole-cell l-glutaminase from P. nitroreducens SP.001 possesses more potential for various industrial biotechnological applications than free cells. © 2020 Society of Chemical Industry.

Production of 12-hydroxy dodecanoic acid methyl ester using a signal peptide sequence-optimized transporter AlkL and a novel monooxygenase

In this study, a signal peptide of AlkL was replaced with other signal peptides to improve the soluble expression and thereby facilitate the transport of dodecanoic acid methyl ester (DAME) substrate into the E. coli. Consequently, AlkL with signal peptide FadL (AlkL_f) showed higher transport activity toward DAME. Furthermore, the promoter optimization for the efficient heterologous expression of the transporter AlkL_f and alkane monooxygenase (AlkBGT) system was conducted and resulted in increased ω-oxygenation activity of AlkBGT system. Moreover, bioinformatic studies led to the identification of novel monooxygenase from Pseudomonas pelagia (Pel), which exhibited 20% higher activity towards DAME as substrate compared to AlkB. Finally, the construction of a chimeric transporter and the expression of newly identified monooxygenase enabled the production of 44.8 ± 7.5 mM of 12-hydroxy dodecanoic acid methyl ester (HADME) and 31.8 ± 1.7 mM of dodecanedioic acid monomethyl ester (DDAME) in a two-phase reaction system.

Pseudomonas putida KT2440 is HV1 certified, not GRAS

Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.

Machine learning modelling for the ultrasonication-mediated disruption of recombinant E. coli for the efficient release of nitrilase

The ultrasonication-mediated cell disruption of recombinant E. coli was modeled using three machine learning techniques namely Multiple linear regression (MLR), Multi-layer perceptron (MLP) and Sequential minimal optimization (SMO). The four attributes were cellmass concentration (g/L), acoustic power (A), duty cycle (%) and treatment time of sonication (min). For the three responses (nitrilase, total protein release and cell disruption) MLP model was found to be at par with RSM model in terms of generalization as well as prediction capability. Nitrilase release was significantly influenced by the cellmass concentration so was in case of total protein release. Fraction of cells disrupted was heavily influenced by acoustic power and sonication time. Almost 32 U/mL nitrilase could be released for 300 g/L cellmass concentration when sonicated at 225 W for 1 min with 20% duty cycle.

Kinetic Resolution of Racemic Amines to Enantiopure (S)-amines by a Biocatalytic Cascade Employing Amine Dehydrogenase and Alanine Dehydrogenase

Amine dehydrogenases (AmDHs) efficiently catalyze the NAD(P)H-dependent asymmetric reductive amination of prochiral carbonyl substrates with high enantioselectivity. AmDH-catalyzed oxidative deamination can also be used for the kinetic resolution of racemic amines to obtain enantiopure amines. In the present study, kinetic resolution was carried out using a coupled-enzyme cascade consisting of AmDH and alanine dehydrogenase (AlaDH). AlaDH efficiently catalyzed the conversion of pyruvate to alanine, thus recycling the nicotinamide cofactors and driving the reaction forward. The ee values obtained for the kinetic resolution of 25 and 50 mM rac-α-methylbenzylamine using the purified enzymatic systems were only 54 and 43%, respectively. The use of whole-cells apparently reduced the substrate/product inhibition, and the use of only 30 and 40 mgDCW/mL of whole-cells co-expressing AmDH and AlaDH efficiently resolved 100 mM of rac-2-aminoheptane and rac-α-methylbenzylamine into the corresponding enantiopure (S)-amines. Furthermore, the applicability of the reaction protocol demonstrated herein was also successfully tested for the efficient kinetic resolution of wide range of racemic amines.

Efficient acylation of gastrodin by Aspergillus oryzae whole-cells in non-aqueous media

Gastrodin, a bioactive compound extracted from the plant source of Gastrodia elata Blume, has a wide range of therapeutic effects on central nervous system (CNS) diseases, but suffers from poor brain permeability and short half-life in plasma. In this study, fatty acid esters of gastrodin were successfully synthesized by a whole cell-based biocatalytic method. Aspergillus oryzae cells showed different catalytic activities in the organic solvent systems tested. Tetrahydrofuran was confirmed as the most suitable pure organic solvent, with the highest substrate conversion of 98.0%. Addition of ionic liquids (ILs) into pyridine dramatically accelerated the reaction with conversion increased from 5.9% to 84.2%, and also changed the selectivity of the cells, mainly due to the use of IL-containing systems altering cell permeability and contact of the enzymes with solvent molecules possessing different polarities. The ester products were characterized by 13C-NMR and ESI-MS as gastrodin monoester and diester.

Biosynthesis of Nylon 12 Monomer, ω-Aminododecanoic Acid Using Artificial Self-Sufficient P450, AlkJ and ω-TA

ω-Aminododecanoic acid is considered as one of the potential monomers of Nylon 12, a high-performance member of the bioplastic family. The biosynthesis of ω-aminododecanoic acid from renewable sources is an attractive process in the polymer industry. Here, we constructed three artificial self-sufficient P450s (ArtssP450s) using CYP153A13 from Alcanivorax borkumensis and cytochrome P450 reductase (CPR) domains of natural self-sufficient P450s (CYP102A1, CYP102A5, and 102D1). Among them, artificial self-sufficient P450 (CYP153A13BM3CPR) with CYP102A1 CPR showed the highest catalytically activity for dodecanoic acid (DDA) substrate. This form of ArtssP450 was further co-expressed with ω-TA from Silicobacter pomeroyi and AlkJ from Pseudomonas putida GPo1. This single-cell system was used for the biotransformation of dodecanoic acid (DDA) to ω-aminododecanoic acid (ω-AmDDA), wherein we could successfully biosynthesize 1.48 mM ω-AmDDA from 10 mM DDA substrate in a one-pot reaction. The productivity achieved in the present study was five times higher than that achieved in our previously reported multistep biosynthesis method (0.3 mM).