Industrial biocatalysis today and tomorrow

Rapid Assembly of Ultrafine Palladium Nanoparticle-Decorated HOF-101 Triggered by Guest Enzyme Encapsulation

Rapid enzyme immobilization is essential for enzyme catalysis and sensing applications, yet constructing effective immobilization systems is challenging due to the need to balance enzyme activity with the properties of the surrounding framework. Herein, taking glucose oxidase (GOx) as a model, a rapid and straightforward approach was presented for synthesizing palladium nanoparticles (PdNPs)-decorated GOx encapsulated in HOF-101 nanocomposite materials (designated as PdNPs/GOx@HOF-101) through an in situ photoreduction and enzyme-triggering HOF-101 encapsulation. The enzyme's surface residues trigger the nucleation of HOF-101 around it through the hydrogen-bonded bio interface, completing the self-assembly of HOF-101 in 0.5 h. Furthermore, the biocomposites loaded with ultrafine PdNPs show satisfactory photoelectrochemical (PEC) properties. As a proof-of-concept, a PEC biosensor was constructed by utilizing PdNPs/GOx@HOF-101 as a photoactive probe, which can quickly and sensitively detect glucose and simultaneously remain stable within the circumstance of 30-60 °C and pH 4-8. These attributes pave the way for diverse applications, including improved enzyme immobilization techniques, advanced biosensors, and more efficient biocatalytic processes.

In Situ Biomineralization and Citric Acid Etching Strategy for Enhancing Activity of Immobilized Acetylcholinesterase

Enhancing the structural stability of an enzyme and maintaining its catalytic activity are effective ways to improve enzyme utilization and reduce the cost of drug screening. However, immobilized enzyme activity tends to decrease in existing immobilization techniques due to conformational changes and microenvironmental restrictions. In this paper, we present a facile approach to prepare immobilized acetylcholinesterase (AChE) with high activity by a ZIF-8 in situ immobilization and citric acid (CA) etching strategy. CA breaks the coordination bond of ZIF-8 and produces defects, expanding the pore space, improving substrate accessibility, and fully exposing the active site of the enzyme. The enhancement of the catalytic activity of AChE@ZIF-8-CA was about 6.10-fold compared with the free enzyme. In addition, AChE@ZIF-8-CA exhibited an excellent encapsulation efficiency and good tolerance to temperature, pH, and organic solvents. The relative activity remains at the initial 83.77% even in five repeated experiments. The strategy provides a novel and efficient way to quickly construct highly active immobilized enzymes under mild conditions.

Optimizing the activation of agarose beads with divinyl sulfone for enzyme immobilization and stabilization

The focus of the present work is to find the optimal conditions for the activation of agarose beads with divinyl sulfone (DVS). The reactivity of the vinyl sulfone groups in the support was checked by the support capacity to react with ethylamine; via elemental analysis. In addition, trypsin was used as a model enzyme to test the immobilization and stabilization capabilities of the different supports. The higher the pH, the more vinyl sulfone groups are incorporated into the support, but lower reactivity versus ethylamine is observed. Too long activation times led to similar results. A N/S ratio of 1 means that all vinyl sulfone groups were reactive, and it was always lower than tis figure. The N in the support was 50 % of the amount observed for glyoxyl supports activated with ethylenediamine, suggesting the VS polymerization may be a likely explanation for this result. The higher N/S ratio in the support (modified with ethylamine), the higher the obtained stabilization, very likely by the lower polymerization of the vinyl sulfone on the support. We propose 360 mM divinyl sulfone, at pH 11.5 and 2 h as optimal conditions to reach the highest enzyme stabilization by immobilization in this support.

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

Ceria nanoparticles immobilized with self-assembling peptide for biocatalytic applications

Peptide-based artificial enzymes exhibit structure and catalytic mechanisms comparable to natural enzymes but they suffer from limited reusability due to their existence in homogenous solutions. Immobilization of self-assembling peptides on the surface of nanoparticles can be used to overcome limitations associated with artificial enzymes. A high, local density of peptides can be obtained on nanoparticles to exert cooperative or synergistic effects, resulting in an accelerated rate of reaction, distinct catalytic properties, and excellent biocompatibility. In this work, we have immobilized a branched, self-assembled, and nanofibrous catalytic peptide, (C12-SHD)2KK(Alloc)-NH2, onto thiolated ceria nanoparticles to generate a heterogeneous catalyst with an enhanced number of catalytic sites. This artificial enzyme mimics the activities of esterase, phosphatase, and haloperoxidase enzymes and the catalytic efficiency remains nearly unaltered when reused. The enzyme-mimicking property is investigated for pesticide detection, bone regeneration, and antibiofouling applications. Overall, this work presents a facile approach to develop a multifunctional heterogeneous biocatalyst that addresses the challenges associated with unstable peptide-based homogeneous catalysts and, thus, shows a strong potential for industrial applications.

Bioconversion of L-Tyrosine into p-Coumaric Acid by Tyrosine Ammonia-Lyase Heterologue of Rhodobacter sphaeroides Produced in Pseudomonas putida KT2440

p-Coumaric acid (p-CA) is a valuable compound with applications in food additives, cosmetics, and pharmaceuticals. However, traditional production methods are often inefficient and unsustainable. This study focuses on enhancing p-CA production efficiency through the heterologous expression of tyrosine ammonia-lyase (TAL) from Rhodobacter sphaeroides in Pseudomonas putida KT2440. TAL catalyzes the conversion of L-tyrosine into p-CA and ammonia. We engineered P. putida KT2440 to express TAL in a fed-batch fermentation system. Our results demonstrate the following: (i) successful integration of the TAL gene into P. putida KT2440 and (ii) efficient bioconversion of L-tyrosine into p-CA (1381 mg/L) by implementing a pH shift from 7.0 to 8.5 during fed-batch fermentation. This approach highlights the viability of P. putida KT2440 as a host for TAL expression and the successful coupling of fermentation with the pH-shift-mediated bioconversion of L-tyrosine. Our findings underscore the potential of genetically modified P. putida for sustainable p-CA production and encourage further research to optimize bioconversion steps and fermentation conditions.

Size-dependent ability of AtaA to immobilize cells in Acinetobacter sp. Tol 5

Microbial cells serve as efficient and environmentally friendly biocatalysts, but their stability and reusability in practical applications must often be improved through immobilization. Acinetobacter sp. Tol 5 shows high adhesiveness to materials due to its large cell surface protein AtaA, which consists of 3630 amino acids (aa). Previously, we developed a method for immobilizing bacteria using AtaA. Herein, we investigated the cell immobilization ability of in-frame deletion (IFD) mutants of AtaA with different sizes in Tol 5. Mini-AtaA, which consists of 775 aa and is functional in Escherichia coli, was produced and present on the cell surface; however, mini-AtaA showed no immobilization ability in Tol 5. A cell immobilization assay was performed with cells expressing 16 IFD mutants of AtaA with different sizes, revealing that a length of at least 1417 aa was required for the sufficient immobilization of Tol 5 cells; thus, the minimum length needed to achieve the adhesive function of AtaA varies among bacterial species. The constructed mutant library of AtaA ranging from 3630 to 775 aa will allow researchers to quickly and easily explore the optimal size of AtaA, even for bacteria newly introduced to AtaA.

NGS-Based Metagenomics Depicting Taxonomic and Functional Insights into North-Western Himalayan Hot Springs

Hot springs have tremendous significance due to their divulging physiochemical features. In the recent past, metagenomics has emerged as a unique methodology to explore microbiota as well as new biocatalysts possessing advantageous biochemical properties from hot springs. In the present study, metagenomics has been employed for microbial diversity exploration and identification of genes involved in various metabolic pathways among two hot springs, Manikaran and Tatapani, located in Himachal Pradesh, India. Taxonomic analysis of both metagenomes revealed the dominance of the Proteobacteria phylum. Genomic signatures of other bacterial phyla such as Chloroflexi, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Firmicutes were also found in significant abundance in both the metagenomes. The abundance of microorganisms belonging to genera, especially Nitrospira, Thauera, Meiothermus, Thiobacillus, Massilia, and Anaerolinea, was reported to be prevalent in the hot springs. A significant amount of metagenomic data remained taxonomically unclassified, which indeed emphasizes the scientific importance of these thermoaquatic niches. The functional potential analysis of both metagenomes revealed pathways related to carbohydrate metabolism, followed by amino acid metabolism, energy metabolism, genetic information processing, metabolism of cofactors and vitamins, membrane transporter, and signal transduction. Exploration of biomass-modifying biocatalysts enumerated the presence of glycoside hydrolases, glycosyl transferases, polysaccharide lyases, and carbohydrate esterases in the metagenomic data. Together, these findings offer an in-depth understanding of the microbial inhabitants in North-Western Himalayan hot springs and their underlying potential for various biotechnological and industrial applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01248-z.

A Hydrophilic Metal Azolate Coordination Polymer for In Situ Encapsulation of Haloalkane Dehalogenase with Enhanced Enzymatic Performance

Encapsulating enzymes within metal-organic frameworks such as zeolitic imidazolate framework-8 (ZIF-8) has been demonstrated to enhance enzymatic performance under harsh conditions. However, by computer-aided analysis, we revealed that highly hydrophobic organic ligands and unfavorable metal ions could greatly impair the activity of haloalkane dehalogenase DhaA by directly interacting with the catalytic sites, causing an extremely low activity of DhaA after encapsulating within ZIF-8. We also found that the presence of a protecting polymer could protect DhaA from the damage of organic ligands and metal ions and that a positively charged amino acid could increase the DhaA activity. Based on the simulations and experimental observations, we have designed to coencapsulate DhaA with poly(vinylpyrrolidone) (PVP) and lysine (Lys) within the amorphous Co-based metal azolate coordination polymer (CoCP). The as-prepared immobilized enzyme (DhaA/PVP/Lys@CoCP) exhibited significantly increased activity (91.5 times higher than that of DhaA@ZIF-8), dramatically enhanced thermostability at 50-70 °C, greatly improved catalytic performance in several organic solvent solutions, and good recyclability (over 75% of the initial activity after 10 cycles). The superiority of the immobilized enzyme was also demonstrated with a substrate frequently detected in the real world. In addition to the protective effect of PVP and positive effect of Lys, experimental and computational investigations unveiled other two favorable aspects that contributed to the enhanced enzymatic performance: (1) high hydrophilicity of the immobilization material and (2) the use of Co2+ with a minimal negative effect on DhaA. The research has thus provided a promising immobilized DhaA with favorable catalytic performance and great potential in industrial applications.

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

Termostable and effective immobilized invertase for sucrose determination in fruit juices

In this study, immobilization of invertase enzyme was performed on a previously synthesized and characterized poly(N-vinylpyrrolidone-co-butylacrylate-co-N hydroxymethylacrylamide) terpolymer membranes by covalent bonding method. Glutaraldehyde(GA) was used as the crosslinker and Bovine Serum Albumin(BSA) was used as the binding agent. Optimum pH, temperature, amount of polymer, substrate concentration, amount of BSA and amount of GA values were determined for both free and immobilized enzyme. Optimum pH and temperature values were found as pH = 5.0, T = 55 °C, pH = 7.0 and T = 80 °C for free and immobilized enzyme, respectively. In particular, the optimum temperature of 80 °C for the immobilized enzyme provides its potential to be used commercially. The kinetic parameters of the free enzyme and the immobilized enzyme were determined using the well known Lineweaver-Burk method. The Vmax values for free (13.4 μM/min) and immobilized enzyme (12.2 μM/min) were found as close to each other, while the Km value of the immobilized enzyme (8.33 mM) was much lower than that of the free enzyme (29.41 mM). In reuse studies conducted with peach and orange juices, it was determined that the immobilized enzyme retained approximately 90% of its activity even after 30 reuses within 1 month.

Simple Sol-Gel Protein Stabilization toward Rainbow and White Lighting Devices

Fluorescent proteins (FPs) are heralded as a paradigm of sustainable materials for photonics/optoelectronics. However, their stabilization under non-physiological environments and/or harsh operation conditions is the major challenge. Among the FP-stabilization methods, classical sol-gel is the most effective, but less versatile, as most of the proteins/enzymes are easily degraded due to the need of multi-step processes, surfactants, and mixed water/organic solvents in extreme pH. Herein, sol-gel chemistry with archetypal FPs (mGreenLantern; mCherry) is revisited, simplifying the method by one-pot, surfactant-free, and aqueous media (phosphate buffer saline pH = 7.4). The synthesis mechanism involves the direct reaction of the carboxylic groups at the FP surface with the silica precursor, generating a positively charged FP intermediate that acts as a seed for the formation of size-controlled mesoporous FP@SiO2 nanoparticles. Green-/red-emissive (single-FP component) and dual-emissive (multi-FPs component; kinetic studies not required) FP@SiO2 are prepared without affecting the FP photoluminescence and stabilities (>6 months) under dry storage and organic solvent suspensions. Finally, FP@SiO2 color filters are applied to rainbow and white bio-hybrid light-emitting diodes featuring up to 15-fold enhanced stabilities without reducing luminous efficacy compared to references with native FPs. Overall, an easy, versatile, and effective FP-stabilization method is demonstrated in FP@SiO2 toward sustainable protein lighting.

Co-Immobilization of ADH and GDH on Metal-Organic-Framework: An Effective Biocatalyst for Asymmetric Reduction of Ketones

Chiral alcohols are not only important building blocks of various bioactive natural compounds and pharmaceuticals, but can serve as synthetic precursors for other valuable organic chemicals, thus the synthesis of these products is of great importance. Bio-catalysis represents one effective way to obtain these molecules, however, the weak stability and high cost of enzymes often hinder its broad application. In this work, we designed a biological nanoreactor by embedding alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) in metal-organic-framework ZIF-8. The biocatalyst ADH&GDH@ZIF-8 could be applied to the asymmetric reduction of a series of ketones to give chiral alcohols in high yields (up to 99 %) and with excellent enantioselectivities (>99 %). In addition, the heterogeneous biocatalyst could be recycled and reused at least four times with slight activity decline. Moreover, E. coli containing ADH and GDH was immobilized by ZIF-8 to form biocatalyst E. coli@ZIF-8, which also exhibits good catalytic behaviours. Finally, the chiral alcohols are further converted to marketed drugs (R)-Fendiline, (S)-Rivastigmine and NPS R-568 respectively.

Current status and emerging frontiers in enzyme engineering: An industrial perspective

Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.

Droplet-based microfluidics and enzyme evolution

Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.

Progress in the Preparation and Application of Inulin-Based Hydrogels

Inulin, a natural polysaccharide, has emerged as a promising precursor for the preparation of hydrogels due to its biocompatibility, biodegradability, and structural versatility. This review provides a comprehensive overview of the recent progress in the preparation, characterization, and diverse applications of inulin-based hydrogels. Different synthesis strategies, including physical methods (thermal induction and non-thermal induction), chemical methods (free-radical polymerization and chemical crosslinking), and enzymatic approaches, are discussed in detail. The unique properties of inulin-based hydrogels, such as stimuli-responsiveness, antibacterial activity, and their potential as fat replacers, are highlighted. Special emphasis is given to their promising applications in drug delivery systems, especially for colon-targeted delivery, due to the selective degradation of inulin via colonic microflora. The ability to incorporate both hydrophilic and hydrophobic drugs further expands their therapeutic potential. In addition, the applications of inulin-based hydrogels in responsive materials, the food industry, wound dressings, and tissue engineering are discussed. While significant progress has been achieved, challenges and prospects in optimizing synthesis, improving mechanical properties, and exploring new functionalities are discussed. Overall, this review highlights the remarkable properties of inulin-based hydrogels as a promising class of biomaterials with immense potential in the biomedical, pharmaceutical, and materials science fields.

Site-Specific Conjugation of Bottlebrush Polymers to Therapeutic Protein via Bioorthogonal Chemistry

Achieving efficient and site-specific conjugation of therapeutic protein to polymer is crucial to augment their applicability in the realms of biomedicine by improving their stability and enzymatic activity. In this study, we exploited tetrazine bioorthogonal chemistry to achieve the site-specific conjugation of bottlebrush polymers to urate oxidase (UOX), a therapeutic protein for gout treatment. An azido-functionalized zwitterionic bottlebrush polymer (N3-ZBP) using a "grafting-from" strategy involving RAFT and ATRP methods was synthesized, and a trans-cyclooctene (TCO) moiety was introduced at the polymer end through the strain-promoted azide-alkyne click (SPAAC) reaction. The subsequent coupling between TCO-incorporated bottlebrush polymer and tetrazine-labeled UOX using a fast and safe bioorthogonal reaction, inverse electron demand Diels-Alder (IEDDA), led to the formation of UOX-ZBP conjugates with a 52% yield. Importantly, the enzymatic activity of UOX remained unaffected following polymer conjugation, suggesting a minimal change in the folded structure of UOX. Moreover, UOX-ZBP conjugates exhibited enhanced proteolytic resistance and reduced antibody binding, compared to UOX-wild type. Overall, the present findings reveal an efficient and straightforward route for synthesizing protein-bottlebrush polymer conjugates without compromising the enzymatic activity while substantially reducing proteolytic degradation and antibody binding.

Sustainable combination of ionic liquid and deep eutectic solvent for protecting and preserving of the protein structure: The synergistic interaction of enzymes and eco-friendly hybrid ionic fluids

Hybrid ionic fluids (HIFs) are one of the emerging and fascinating sustainable solvent media, a novel environment-friendly solvent for biomolecules. The HIFs have been synthesized by combining a deep eutectic solvent (DES), an ionic liquid (IL) having a common ion. The stability and activity of hen's egg white lysozyme (Lyz) in the presence of a recently designed new class of biocompatible solvents, HIFs have been explored by UV-visible, steady-state fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) along with dynamic light scattering (DLS) measurements. This work emphasizes the effect of DES synthesized by using 1:2 choline chloride and glycerol [Glyn], ILs (1-butly-3-methylimidazolium chloride [BMIM]Cl and choline acetate [Chn][Ac]) and their corresponding HIFs on the structure and functionality of Lyz. Moving forward, we also studied the secondary structure, thermal stability and enzymatic activity and thermodynamic profile of Lyz at pH = 7 in the presence of varying concentrations (0.1 to 0.5) M of [BMIM]Cl, [Chn][Ac] ILs, [Glyn] DES and [Glyn][BMIM]Cl (hybrid ionic fluid1) as well as [Glyn][Chn][Ac] (hybrid ionic fluid2). Spectroscopic results elucidate that ILs affect the activity and structural stability of Lyz, whereas the stability and activity are increased by DES and are maintained by HIFs at all the studied concentrations. Overall, the experimental results studied elucidate expressly that the properties of Lyz are maintained in the presence of hybrid ionic fluid1 while these properties are intensified in hybrid ionic fluid2. This work has elucidated expressly biocompatible green solvents in protein stability and functionality due to the alluring properties of DES, which can counteract the negative effect of ILs in HIFs.

Attachment of Fibrinogen on Ion Beam Treated Polyurethane

Protein-stable coverage of the artificial implant is a key problem for biocompatibility. In the present study, a protein layer was attached covalently to a polyurethane surface treated by an ion beam. A plasma system consisting of a vacuum chamber (0.8 Pa pressure) with a high voltage electrode powered by a short pulse (20 μS pulse duration and 200 Hz pulse repetition) generator was designed. Polyurethane with a formulation certified as a material for medical implants was treated by nitrogen ions with an energy of 20 keV and 5 × 1014-1016 ions/cm2 fluence range. Wettability measurements, X-ray photoelectron, Raman, Fourier transform infrared attenuated total reflection, and ellipsometry spectra showed a significant change in the structure of the surface layer of the treated polyurethane. The surface of the treated polyurethane contained a carbonised layer containing condensed aromatic clusters with terminal free radicals. The surface energy of polyurethane surface increased from 33 to 65 mJ/m2. The treated polyurethane surface became capable of adsorbing and chemically binding protein (fibrinogen). The designed system for ion beam treatment can be used for surface activation of biomedical polymer devices, where a total protein coverage is required.

Ratiometric fluorescence sensing NADH using AIE-dots transducers at the point of care

Reduced nicotinamide adenine dinucleotide (NADH) has a strong impact on physiological metabolism, and its concentration is related to metabolic and neurodegenerative diseases. A more reliable and accurate detection method for NADH quantitation is needed for early disease diagnosis and point-of-care testing. Aggregation-induced emission (AIE) materials are widely used to improve the sensitivity in analytes assays due to their anti-aggregation-caused quenching property. Here we developed TPA-BQD-Py AIE-dots transducers and evaluated its performance in NADH detection. The NADH concentration-dependent ratiometric sensing was based on electron transfer from TPA-BQD-Py AIE-dots to NADH with variable fluorescence intensity at 584 nm and 470 nm, resulting in high sensitivity (limit of detection at 110 nM), photostability, selectivity, and a rapid and reversible response. We further developed the application of TPA-BQD-Py AIE-dots transducers in in vivo NADH imaging using a smartphone and digital camera, respectively, demonstrating the potential for NADH point-of-care testing.

Arylacetonitrilases: Potential Biocatalysts for Green Chemistry

Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.

Biocatalysis: landmark discoveries and applications in chemical synthesis

Biocatalysis has become an important tool in chemical synthesis, allowing access to complex molecules with high levels of activity and selectivity and with low environmental impact. Key discoveries in protein engineering, bioinformatics, recombinant technology and DNA sequencing have contributed towards the rapid acceleration of the field. This tutorial review explores enzyme engineering strategies and high-throughput screening approaches that have been applied for the discovery and development of enzymes for synthetic application. Landmark developments in the field are discussed and have been carefully selected to highlight the diverse synthetic applications of enzymes within the pharmaceutical, agricultural, food and chemical industries. The design and development of artificial biocatalytic cascades is also examined. This tutorial review will give readers an insight into the landmark discoveries and milestones that have helped shape and grow this branch of catalysis since the discovery of the first enzyme.

Peanut oil odor enhances the immunomodulatory effect on immunosuppressed mice by regulating the cAMP signaling pathway via the brain-spleen axis

The role of sniffing relative to immune function has attracted considerable attention. The present study investigated the immunomodulatory effects of peanut oil odor on cyclophosphamide (CTX)-induced immunosuppressed mice. The subset of mice subjected to prolonged (8 h) sniffing peanut oil odor (PL) demonstrated significantly elevated levels of agouti-related peptide, neuropeptide Y, and glutamate (p < 0.05), whereas it significantly down-regulated the level of γ-aminobutyric acid in the brain (p < 0.05). Furthermore, immunohistochemistry results indicated significantly increased expression of mGluR1/5 and decreased expression of GABABR in the hippocampus and hypothalamus (p < 0.05) of the PL group. Additionally, the PL group had significantly up-regulated expression levels of cAMP, Epac, Rap1, ERK1/2 and PKA (p < 0.05) and remarkably increased phosphorylation of CREB in the cAMP signaling pathway (p < 0.05), which influenced the central nervous system. Moreover, compared with CTX-induced mice, the percentages of peripheral blood T lymphocytes (CD3+CD4+ and CD3+CD8+) and the levels of splenic cytokines (IL-2, IL-4, and TNF-α) were significantly increased following PL treatment (p < 0.05). The PL group also showed significantly up-regulated expression levels of cAMP, p-p65, and p-IκBα in the spleen (p < 0.05) by western blot analysis. In summary, PL intervention significantly up-regulated the expression levels of cAMP in the brain (p < 0.05), with subsequent transfer of cAMP to the spleen which promoted phosphorylation of p65 and IκBα. This series of events enhanced the immunity of mice, which confirmed the regulatory effect of PL on the cAMP signaling pathway, thereby enhancing immune function via the brain-spleen axis.

Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity

While enzymes are potentially useful in various applications, their limited operational stability and production costs have led to an extensive search for stable catalytic agents that will retain the efficiency, specificity, and environmental-friendliness of natural enzymes. Despite extensive efforts, there is still an unmet need for improved enzyme mimics and novel concepts to discover and optimize such agents. Inspired by the catalytic activity of amyloids and the formation of amyloid-like assemblies by metabolites, our group pioneered the development of novel metabolite-metal co-assemblies (bio-nanozymes) that produce nanomaterials mimicking the catalytic function of common metalloenzymes that are being used for various technological applications. In addition to their notable activity, bio-nanozymes are remarkably safe as they are purely composed of amino acids and minerals that are harmless to the environment. The bio-nanozymes exhibit high efficiency and exceptional robustness, even under extreme conditions of temperature, pH, and salinity that are impractical for enzymes. Our group has recently also demonstrated the formation of ordered amino acid co-assemblies showing selective and preferential interactions comparable to the organization of residues in folded proteins. The identified bio-nanozymes can be used in various applications including environmental remediation, synthesis of new materials, and green energy.

Two-substrate enzyme engineering using small libraries that combine the substrate preferences from two different variant lineages

Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in kcat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.

Microbial alcohol dehydrogenases: recent developments and applications in asymmetric synthesis

Alcohol dehydrogenases are a well-known group of enzymes in the class of oxidoreductases that use electron transfer cofactors such as NAD(P)+/NAD(P)H for oxidation or reduction reactions of alcohols or carbonyl compounds respectively. These enzymes are utilized mainly as purified enzymes and offer some advantages in terms of green chemistry. They are environmentally friendly and a sustainable alternative to traditional chemical synthesis of bulk and fine chemicals. Industry has implemented several whole-cell biocatalytic processes to synthesize pharmaceutically active ingredients by exploring the high selectivity of enzymes. Unlike the whole cell system where cofactor regeneration is well conserved within the cellular environment, purified enzymes require additional cofactors or a cofactor recycling system in the reaction, even though cleaner reactions can be carried out with fewer downstream work-up problems. The challenge of producing purified enzymes in large quantities has been solved in large part by the use of recombinant enzymes. Most importantly, recombinant enzymes find applications in many cascade biotransformations to produce several important chiral precursors. Inevitably, several dehydrogenases were engineered as mere recombinant enzymes could not meet the industrial requirements for substrate and stereoselectivity. In recent years, a significant number of engineered alcohol dehydrogenases have been employed in asymmetric synthesis in industry. In a parallel development, several enzymatic and non-enzymatic methods have been established for regenerating expensive cofactors (NAD+/NADP+) to make the overall enzymatic process more efficient and economically viable. In this review article, recent developments and applications of microbial alcohol dehydrogenases are summarized by emphasizing notable examples.

Proteases immobilized on nanomaterials for biocatalytic, environmental and biomedical applications: Advantages and drawbacks

Proteases have gained significant scientific and industrial interest due to their unique biocatalytic characteristics and broad-spectrum applications in different industries. The development of robust nanobiocatalytic systems by attaching proteases onto various nanostructured materials as fascinating and novel nanocarriers has demonstrated exceptional biocatalytic performance, substantial stability, and ease of recyclability over multiple reaction cycles under different chemical and physical conditions. Proteases immobilized on nanocarriers may be much more resistant to denaturation caused by extreme temperatures or pH values, detergents, organic solvents, and other protein denaturants than free enzymes. Immobilized proteases may present a lower inhibition. The use of non-porous materials in the immobilization prevents diffusion and steric hindrances during the binding of the substrate to the active sites of enzymes compared to immobilization onto porous materials; when using very large or solid substrates, orientation of the enzyme must always be adequate. The advantages and problems of the immobilization of proteases on nanoparticles are discussed in this review. The continuous and batch reactor operations of nanocarrier-immobilized proteases have been successfully investigated for a variety of applications in the leather, detergent, biomedical, food, and pharmaceutical industries. Information about immobilized proteases on various nanocarriers and nanomaterials has been systematically compiled here. Furthermore, different industrial applications of immobilized proteases have also been highlighted in this review.

Magnetic macroporous chitin microsphere as a support for covalent enzyme immobilization

In this study, a novel magnetic macroporous chitin microsphere (MMCM) was developed for enzyme immobilization. Chitin nanofibers were prepared and subsequently subjected to self-assembly with magnetic nanoparticles and PMMA (polymethyl methacrylate). Following this, microspheres were formed through spray drying, achieving a porous structure through etching. The MMCM serves as an effective support for immobilizing enzymes, allowing for their covalent immobilization both on the microsphere's surface and within its pores. The substantial surface area resulting from the porous structure leads to a 2.1-fold increase in enzyme loading capacity compared to non-porous microspheres. The MMCM enhances stability of the immobilized enzymes under various pH and temperature conditions. Furthermore, after 20 days of storage at 4 °C, the residual activity of the immobilized enzyme was 2.93 times that of the free enzyme. Even after being recycled 10 times, the immobilized enzyme retained 56.7 % of its initial activity. It's noteworthy that the active sites of the enzymes remained unchanged after immobilization using the MMCM, and kinetic analysis revealed that the affinity of the immobilized enzymes rivals that of the free enzymes.

Efficiency aspects of regioselective testosterone hydroxylation with highly active CYP450-based whole-cell biocatalysts

Steroid hydroxylations belong to the industrially most relevant reactions catalysed by cytochrome P450 monooxygenases (CYP450s) due to the pharmacological relevance of hydroxylated derivatives. The implementation of respective bioprocesses at an industrial scale still suffers from several limitations commonly found in CYP450 catalysis, that is low turnover rates, enzyme instability, inhibition and toxicity related to the substrate(s) and/or product(s). Recently, we achieved a new level of steroid hydroxylation rates by introducing highly active testosterone-hydroxylating CYP450 BM3 variants together with the hydrophobic outer membrane protein AlkL into Escherichia coli-based whole-cell biocatalysts. However, the activity tended to decrease, which possibly impedes overall productivities and final product titres. In this study, a considerable instability was confirmed and subject to a systematic investigation regarding possible causes. In-depth evaluation of whole-cell biocatalyst kinetics and stability revealed a limitation in substrate availability due to poor testosterone solubility as well as inhibition by the main product 15β-hydroxytestosterone. Instability of CYP450 BM3 variants was disclosed as another critical factor, which is of general significance for CYP450-based biocatalysis. Presented results reveal biocatalyst, reaction and process engineering strategies auguring well for industrial implementation of the developed steroid hydroxylation platform.

Hydrolytic nanozymes: Preparation, properties, and applications

Hydrolytic nanozymes, as promising alternatives to hydrolytic enzymes, can efficiently catalyze the hydrolysis reactions and overcome the operating window limitations of natural enzymes. Moreover, they exhibit several merits such as relatively low cost, easier recovery and reuse, improved operating stability, and adjustable catalytic properties. Consequently, they have found relevance in practical applications such as organic synthesis, chemical weapon degradation, and biosensing. In this review, we highlight recent works addressing the broad topic of the development of hydrolytic nanozymes. We review the preparation, properties, and applications of six types of hydrolytic nanozymes, including AuNP-based nanozymes, polymeric nanozymes, surfactant assemblies, peptide assemblies, metal and metal oxide nanoparticles, and MOFs. Last, we discuss the remaining challenges and future directions. This review will stimulate the development and application of hydrolytic nanozymes.

Agar plate-based activity assay for easy and fast screening of recombinant Pichia pastoris expressing unspecific peroxygenases

Unspecific peroxygenases (UPOs) are promising biocatalysts that catalyze oxyfunctionalization reactions without the need for costly cofactors. Pichia pastoris (reclassified as Komagataella phaffii) is considered an attractive host for heterologous expression of UPOs. However, integration of UPO-expression cassettes into the genome via a single cross-over yields recombinant Pichia transformants with different UPO gene copy numbers resulting in different expression levels. Selection of the most productive Pichia transformants by a commonly used screening in liquid medium in 96-well plates is laborious and lasts up to 5 days. In this work, we developed a simple two-step agar plate-based assay to screen P. pastoris transformants for UPO activity with less effort, within shorter time, and without automated screening devices. After cell growth and protein expression on agar plates supplemented with methanol and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), an additional top agar layer supplemented with ABTS and peroxide is added. UPO activity is visualized within 15 min by formation of green zones around UPO-secreting P. pastoris transformants. The assay was validated with two UPOs, AbrUPO from Aspergillus brasiliensis and evolved PaDa-I from Agrocybe aegerita. The assay results were confirmed in a quantitative 96-deep well plate screening in liquid medium.

Biomimetic Metal-Pyrimidine Nanoflowers: Enzyme Immobilization Platforms with Boosted Activity

For the enzyme immobilization platform, enhancing enzyme activity retention while improving enzyme stability remains a challenge for sensitive sensing analysis. Herein, an in situ biomimetic immobilized enzyme carrier (metal-pyrimidine nanoflowers, MPNFs) synthesized by the coordination of DNA base derivative (2-aminopyrimidine) with Zn2+ in the aqueous phase at room temperature is developed. The biocompatibility of 2-aminopyrimidine and the hydrophilicity and green synthetic conditions of MPNFs allows the immobilized enzymes to retain above 91.2% catalytic activity. On this basis, a cascade catalytic platform is constructed by simultaneously immobilizing acetylcholinesterase (AChE), choline oxidase (CHO), and horseradish peroxidase (HRP) in MPNFs (AChE/CHO/HRP@MPNFs) for organophosphorus pesticides (OPs) colorimetric biosensing detection. The assay could specifically detect parathion-methyl within 13 min with a wider linear range (0.1-1000.0 nm) and a lower limit of detection (LOD) (0.032 nm). The remarkable stability of the immobilized enzymes is also achieved under harsh environments, room temperature storage, and recycling. Furthermore, a portable and cost-effective biosensing platform is developed by integrating AChE/CHO/HRP@MPNFs with a smartphone-assisted paper device for the on-site detection of OPs. Overall, the high catalytic activity retention and the enhanced detection performance demonstrate that MPNF is a robust carrier in enzyme immobilization and holds great promise in biosensing and other field applications.

Recent advances in metal-organic frameworks: Synthesis, application and toxicity

Metal-organic frameworks (MOFs) are a new class of crystalline porous hybrid materials with high porosity, large specific surface area and adjustable channel structure and biocompatibility, which are being investigated with increasing interest for energy storage and conversion, gas adsorption/separation, catalysis, sensing and biomedicine. However, the practical applications of MOFs make them release into the environment inevitable, posing a threat to humans and organisms. In this article, we cover advances in the currently available MOFs synthesis methods and the emerging applications of MOFs, especially in the biomedical field (therapeutic agents and bioimaging). Additionally, after evaluating the current status of main exposure routes and affecting factors in the field of MOFs-toxicity, the molecular mechanism is also clarified and identified. Knowledge gaps are identified from such a summarization and frontier development are explored for MOFs. Afterwards, we also present the limitations, challenges, and future perspectives in the study of the entire life cycle of MOFs. This review emphasizes the need for a more targeted discussion of the latest, widely used and effective versatile material class in order to exploit the full potential of high-performance and non-toxicity MOFs in the future.

Bioelectrocatalytic Synthesis: Concepts and Applications

Bioelectrocatalytic synthesis is the conversion of electrical energy into value-added products using biocatalysts. These methods merge the specificity and selectivity of biocatalysis and energy-related electrocatalysis to address challenges in the sustainable synthesis of pharmaceuticals, commodity chemicals, fuels, feedstocks and fertilizers. However, the specialized experimental setups and domain knowledge for bioelectrocatalysis pose a significant barrier to adoption. This review introduces key concepts of bioelectrosynthetic systems. We provide a tutorial on the methods of biocatalyst utilization, the setup of bioelectrosynthetic cells, and the analytical methods for assessing bioelectrocatalysts. Key applications of bioelectrosynthesis in ammonia production and small-molecule synthesis are outlined for both enzymatic and microbial systems. This review serves as a necessary introduction and resource for the non-specialist interested in bioelectrosynthetic research.

Growth-coupled high throughput selection for directed enzyme evolution

Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.

Modernized Machine Learning Approach to Illuminate Enzyme Immobilization for Biocatalysis

Biocatalysis is an established technology with significant application in the pharmaceutical industry. Immobilization of enzymes offers significant benefits for commercial and practical purposes to enhance the stability and recyclability of biocatalysts. Determination of the spatial and chemical distributions of immobilized enzymes on solid support materials is essential for an optimal catalytic performance. However, current analytical methodologies often fall short of rapidly identifying and characterizing immobilized enzyme systems. Herein, we present a new analytical methodology that combines non-negative matrix factorization (NMF)-an unsupervised machine learning tool-with Raman hyperspectral imaging to simultaneously resolve the spatial and spectral characteristics of all individual species involved in enzyme immobilization. Our novel approach facilitates the determination of the optimal NMF model using new data-driven, quantitative selection criteria that fully resolve all chemical species present, offering a robust methodology for analyzing immobilized enzymes. Specifically, we demonstrate the ability of NMF with Raman hyperspectral imaging to resolve the spatial and spectral profiles of an engineered pantothenate kinase immobilized on two different commercial microporous resins. Our results demonstrate that this approach can accurately identify and spatially resolve all species within this enzyme immobilization process. To the best of our knowledge, this is the first report of NMF within hyperspectral imaging for enzyme immobilization analysis, and as such, our methodology can now provide a new powerful tool to streamline biocatalytic process development within the pharmaceutical industry.

Semi-rational engineering an aldo-keto reductase for stereocomplementary reduction of α-keto amide compounds

Enantio-pure α-hydroxy amides are valuable intermediates for the synthesis of chiral pharmaceuticals. The asymmetric reduction of α-keto amides to generate chiral α-hydroxy amides is a difficult and challenging task in biocatalysis. In this study, iolS, an aldo-keto reductase from Bacillus subtilis 168 was exhibited as a potential biocatalyst, which could catalyze the reduction of diaryl α-keto amide such as 2-oxo-N, 2-diphenyl-acetamide (ONDPA) with moderate S-selectivity (76.1%, ee) and 60.5% conversion. Through semi-rational engineering, two stereocomplementary variants (I57F/F126L and N21A/F126A) were obtained with ee value of 97.6% (S) and 99.9% (R) toward ONDPA (1a), respectively, delivering chiral α-hydroxy amide with > 98% conversions. Moreover, the excellent S- and R-preference variants displayed improved stereoselectivities toward the other α-keto amide compounds. Molecular dynamic and docking analysis revealed that the two key residues at 21 and 126 were identified as the "switch", which specifically controlled the stereopreference of iolS by regulating the shape of substrate binding pocket as well as the substrate orientation. Our results offer an effective strategy to obtain α-hydroxy amides with high optical purity and provide structural insights into altering the stereoselectivity of AKRs.

Co-Immobilization of a Multi-Enzyme Cascade: (S)-Selective Amine Transaminases, l-Amino Acid Oxidase and Catalase

An enzyme cascade was established previously consisting of a recycling system with an l-amino acid oxidase (hcLAAO4) and a catalase (hCAT) for different α-keto acid co-substrates of (S)-selective amine transaminases (ATAs) in kinetic resolutions of racemic amines. Only 1 mol % of the co-substrate was required and l-amino acids instead of α-keto acids could be applied. However, soluble enzymes cannot be reused easily. Immobilization of hcLAAO4, hCAT and the (S)-selective ATA from Vibrio fluvialis (ATA-Vfl) was addressed here. Immobilization of the enzymes together rather than on separate beads showed higher reaction rates most likely due to fast co-substrate channeling between ATA-Vfl and hcLAAO4 due to their close proximity. Co-immobilization allowed further reduction of the co-substrate amount to 0.1 mol % most likely due to a more efficient H2 O2 -removal caused by the stabilized hCAT and its proximity to hcLAAO4. Finally, the co-immobilized enzyme cascade was reused in 3 cycles of preparative kinetic resolutions to produce (R)-1-PEA with high enantiomeric purity (97.3 %ee). Further recycling was inefficient due to the instability of ATA-Vfl, while hcLAAO4 and hCAT revealed high stability. An engineered ATA-Vfl-8M was used in the co-immobilized enzyme cascade to produce (R)-1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethanamine, an apremilast-intermediate, with a 1,000 fold lower input of the co-substrate.

Microalgae-material hybrid for enhanced photosynthetic energy conversion: a promising path towards carbon neutrality

Photosynthetic energy conversion for high-energy chemicals generation is one of the most viable solutions in the quest for sustainable energy towards carbon neutrality. Microalgae are fascinating photosynthetic organisms, which can directly convert solar energy into chemical energy and electrical energy. However, microalgal photosynthetic energy has not yet been applied on a large scale due to the limitation of their own characteristics. Researchers have been inspired to couple microalgae with synthetic materials via biomimetic assembly and the resulting microalgae-material hybrids have become more robust and even perform new functions. In the past decade, great progress has been made in microalgae-material hybrids, such as photosynthetic carbon dioxide fixation, photosynthetic hydrogen production, photoelectrochemical energy conversion and even biochemical energy conversion for biomedical therapy. The microalgae-material hybrid offers opportunities to promote artificially enhanced photosynthesis research and synchronously inspires investigation of biotic-abiotic interface manipulation. This review summarizes current construction methods of microalgae-material hybrids and highlights their implication in energy and health. Moreover, we discuss the current problems and future challenges for microalgae-material hybrids and the outlook for their development and applications. This review will provide inspiration for the rational design of the microalgae-based semi-natural biohybrid and further promote the disciplinary fusion of material science and biological science.

LibGENiE - A bioinformatic pipeline for the design of information-enriched enzyme libraries

Enzymes are potent catalysts with high specificity and selectivity. To leverage nature's synthetic potential for industrial applications, various protein engineering techniques have emerged which allow to tailor the catalytic, biophysical, and molecular recognition properties of enzymes. However, the many possible ways a protein can be altered forces researchers to carefully balance between the exhaustiveness of an enzyme screening campaign and the required resources. Consequently, the optimal engineering strategy is often defined on a case-by-case basis. Strikingly, while predicting mutations that lead to an improved target function is challenging, here we show that the prediction and exclusion of deleterious mutations is a much more straightforward task as analyzed for an engineered carbonic acid anhydrase, a transaminase, a squalene-hopene cyclase and a Kemp eliminase. Combining such a pre-selection of allowed residues with advanced gene synthesis methods opens a path toward an efficient and generalizable library construction approach for protein engineering. To give researchers easy access to this methodology, we provide the website LibGENiE containing the bioinformatic tools for the library design workflow.

Glutaraldehyde modification of lipases immobilized on octyl agarose beads: Roles of the support enzyme loading and chemical amination of the enzyme on the final enzyme features

Lipase B from Candida antarctica (CALB) and lipase from Thermomyces lanuginosus (TLL) have been immobilized on octyl agarose at low loading and at a loading exceeding the maximum support capacity. Then, the enzymes have been treated with glutaraldehyde and inactivated at pH 7.0 in Tris-HCl, sodium phosphate and HEPES, giving different stabilities. Stabilization (depending on the buffer) of the highly loaded biocatalysts was found, very likely as a consequence of the detected intermolecular crosslinkings. This did not occur for the lowly loaded biocatalysts. Next, the enzymes were chemically aminated and then treated with glutaraldehyde. In the case of TLL, the intramolecular crosslinkings (visible by the apparent reduction of the protein size) increased enzyme stability of the lowly loaded biocatalysts, an effect that was further increased for the highly loaded biocatalysts due to intermolecular crosslinkings. Using CALB, the intramolecular crosslinkings were less intense, and the stabilization was lower, even though the intermolecular crosslinkings were quite intense for the highly loaded biocatalyst. The stabilization detected depended on the inactivation buffer. The interactions between enzyme loading and inactivating buffer on the effects of the chemical modifications suggest that the modification and inactivation studies must be performed under the target biocatalysts and conditions.

Charting the Evolution of Chemoenzymatic Strategies in the Syntheses of Complex Natural Products

Bolstered by recent advances in bioinformatics, genetics, and enzyme engineering, the field of chemoenzymatic synthesis has enjoyed a rapid increase in popularity and utility. This Perspective explores the integration of enzymes into multistep chemical syntheses, highlighting the unique potential of biocatalytic transformations to streamline the synthesis of complex natural products. In particular, we identify four primary conceptual approaches to chemoenzymatic synthesis and illustrate each with a number of landmark case studies. Future opportunities and challenges are also discussed.

A novel salt- and organic solvent-tolerant phosphite dehydrogenase from Cyanothece sp. ATCC 51142

Phosphite dehydrogenase (PtxD) is a promising enzyme for NAD(P)H regeneration. To expand the usability of PtxD, we cloned, expressed, and analyzed PtxD from the marine cyanobacterium Cyanothece sp. ATCC 51142 (Ct-PtxD). Ct-PtxD exhibited maximum activity at pH 9.0°C and 50°C and high stability over a wide pH range of 6.0-10.0. Compared to previously reported PtxDs, Ct-PtxD showed increased resistance to salt ions such as Na+, K+, and NH4 +. It also exhibited high tolerance to organic solvents such as ethanol, dimethylformamide, and methanol when bound to its preferred cofactor, NAD+. Remarkably, these organic solvents enhanced the Ct-PtxD activity while inhibiting the PtxD activity of Ralstonia sp. 4506 (Rs-PtxD) at concentrations ranging from 10% to 30%. Molecular electrostatic potential analysis showed that the NAD+-binding site of Ct-PtxD was rich in positively charged residues, which may attract the negatively charged pyrophosphate group of NAD+ under high-salt conditions. Amino acid composition analysis revealed that Ct-PtxD contained fewer hydrophobic amino acids than other PtxD enzymes, which reduced the hydrophobicity and increased the hydration of protein surface under low water activity. We also demonstrated that the NADH regeneration system using Ct-PtxD is useful for the coupled chiral conversion of trimethylpyruvic acid into L-tert-leucine using leucine dehydrogenase under high ammonium conditions, which is less supported by the Rs-PtxD enzyme. These results imply that Ct-PtxD might be a potential candidate for NAD(P)H regeneration in industrial applications under the reaction conditions containing salt and organic solvent.

Hierarchical covalent organic framework-foam for multi-enzyme tandem catalysis

Covalent organic frameworks (COFs) are ideal host matrices for biomolecule immobilization and biocatalysis due to their high porosity, various functionalities, and structural robustness. However, the porosity of COFs is limited to the micropore dimension, which restricts the immobilization of enzymes with large volumes and obstructs substrate flow during enzyme catalysis. A hierarchical 3D nanostructure possessing micro-, meso-, and macroporosity could be a beneficial host matrix for such enzyme catalysis. In this study, we employed an in situ CO2 gas effervescence technique to induce disordered macropores in the ordered 2D COF nanostructure, synthesizing hierarchical TpAzo COF-foam. The resulting TpAzo foam matrix facilitates the immobilization of multiple enzymes with higher immobilization efficiency (approximately 1.5 to 4-fold) than the COF. The immobilized cellulolytic enzymes, namely β-glucosidase (BGL), cellobiohydrolase (CBH), and endoglucanase (EG), remain active inside the TpAzo foam. The immobilized BGL exhibited activity in organic solvents and stability at room temperature (25 °C). The enzyme-immobilized TpAzo foam exhibited significant activity towards the hydrolysis of p-nitrophenyl-β-d-glucopyranoside (BGL@TpAzo-foam: Km and Vmax = 23.5 ± 3.5 mM and 497.7 ± 28.0 μM min-1) and carboxymethylcellulose (CBH@TpAzo-foam: Km and Vmax = 18.3 ± 4.0 mg mL-1 and 85.2 ± 9.6 μM min-1 and EG@TpAzo-foam: Km and Vmax = 13.2 ± 2.0 mg mL-1 and 102.2 ± 7.1 μM min-1). Subsequently, the multi-enzyme immobilized TpAzo foams were utilized to perform a one-pot tandem conversion from carboxymethylcellulose (CMC) to glucose with high recyclability (10 cycles). This work opens up the possibility of synthesizing enzymes immobilized in TpAzo foam for tandem catalysis.

Encapsulating and stabilizing enzymes using hydrogen-bonded organic frameworks

Enzymes are outstanding natural catalysts with exquisite 3D structures, initiating countless life-sustaining biotransformations in living systems. The flexible structure of an enzyme, however, is highly susceptible to non-physiological environments, which greatly limits its large-scale industrial applications. Seeking suitable supports to immobilize fragile enzymes is one of the most efficient routes to ameliorate the stability problem. This protocol imparts a new bottom-up strategy for enzyme encapsulation using a hydrogen-bonded organic framework (HOF-101). In short, the surface residues of the enzyme can trigger the nucleation of HOF-101 around its surface through the hydrogen-bonded biointerface. As a result, a series of enzymes with different surface chemistries are able to be encapsulated within a highly crystalline HOF-101 scaffold, which has long-range ordered mesochannels. The details of experimental procedures are described in this protocol, which involve the encapsulating method, characterizations of materials and biocatalytic performance tests. Compared with other immobilization methods, this enzyme-triggering HOF-101 encapsulation is easy to operate and affords higher loading efficiency. The formed HOF-101 scaffold has an unambiguous structure and well-arranged mesochannels, favoring mass transfer and understanding of the biocatalytic process. It takes ~13.5 h for successful synthesis of enzyme-encapsulated HOF-101, 3-4 d for characterizations of materials and ~4 h for the biocatalytic performance tests. In addition, no specific expertise is necessary for the preparation of this biocomposite, although the high-resolution imaging requires a low-electron-dose microscope technology. This protocol can provide a useful methodology to efficiently encapsulate enzymes and design biocatalytic HOF materials.

Assessment of New and Genome-Reduced Pseudomonas Strains Regarding Their Robustness as Chassis in Biotechnological Applications

Organic olvent-tolerant strains of the Gram-negative bacterial genus Pseudomonas are discussed as potential biocatalysts for the biotechnological production of various chemicals. However, many current strains with the highest tolerance are belonging to the species P. putida and are classified as biosafety level 2 strains, which makes them uninteresting for the biotechnological industry. Therefore, it is necessary to identify other biosafety level 1 Pseudomonas strains with high tolerance towards solvents and other forms of stress, which are suitable for establishing production platforms of biotechnological processes. In order to exploit the native potential of Pseudomonas as a microbial cell factory, the biosafety level 1 strain P. taiwanensis VLB120 and its genome-reduced chassis (GRC) variants as well as the plastic-degrading strain P. capeferrum TDA1 were assessed regarding their tolerance towards different n-alkanols (1-butanol, 1-hexanol, 1-octanol, 1-decanol). Toxicity of the solvents was investigated by their effects on bacterial growth rates given as the EC50 concentrations. Hereby, both toxicities as well as the adaptive responses of P. taiwanensis GRC3 and P. capeferrum TDA1 showed EC50 values up to two-fold higher than those previously detected for P. putida DOT-T1E (biosafety level 2), one of the best described solvent-tolerant bacteria. Furthermore, in two-phase solvent systems, all the evaluated strains were adapted to 1-decanol as a second organic phase (i.e., OD560 was at least 0.5 after 24 h of incubation with 1% (v/v) 1-decanol), which shows the potential use of these strains as platforms for the bio-production of a wide variety of chemicals at industrial level.

Controlled Self-Assembly of the Catalytic Core of Hydrolases Using DNA Scaffolds

Precisely organizing functional molecules of the catalytic cores in natural enzymes to promote catalytic performance is a challenging goal in respect to artificial enzyme construction. In this work, we report a DNA-scaffolded mimicry of the catalytic cores of hydrolases, which showed a controllable and hierarchical acceleration of the hydrolysis of fluorescein diacetate (FDA). The results revealed that the efficiency of hydrolysis was greatly increased by the DNA-scaffold-induced proximity of catalytic amino acid residues (histidine and arginine) with up to 4-fold improvement relative to the free amino acids. In addition, DNA-scaffolded one-dimensional and two-dimensional assemblies of multiple catalytic cores could further accelerate the hydrolysis. This work demonstrated that the DNA-guided assembly could be used as a promising platform to build enzyme mimics in a programmable and hierarchical way.

Magnetic metal-organic frameworks immobilized enzyme-based nano-biocatalytic systems for sustainable biotechnology

Nanobiocatalysts, in which enzyme molecules are integrated into/onto multifunctional materials, such as metal-organic frameworks (MOFs), have been fascinating and appeared as a new interface of nanobiocatalysis with multi-oriented applications. Among various nano-support matrices, functionalized MOFs with magnetic attributes have gained supreme interest as versatile nano-biocatalytic systems for organic bio-transformations. From the design (fabrication) to deployment (application), magnetic MOFs have manifested notable efficacy in manipulating the enzyme microenvironment for robust biocatalysis and thus assure requisite applications in several areas of enzyme engineering at large and nano-biocatalytic transformations, in particular. Magnetic MOFs-linked enzyme-based nano-biocatalytic systems offer chemo-regio- and stereo-selectivities, specificities, and resistivities under fine-tuned enzyme microenvironments. Considering the current sustainable bioprocesses demands and green chemistry needs, we reviewed synthesis chemistry and application prospects of magnetic MOFs-immobilized enzyme-based nano-biocatalytic systems for exploitability in different industrial and biotechnological sectors. More specifically, following a thorough introductory background, the first half of the review discusses various approaches to effectively developed magnetic MOFs. The second half mainly focuses on MOFs-assisted biocatalytic transformation applications, including biodegradation of phenolic compounds, removal of endocrine disrupting compounds, dye decolorization, green biosynthesis of sweeteners, biodiesel production, detection of herbicides and screening of ligands and inhibitors.