Engineering of Biocatalysts and Biocatalytic Processes

Bioconversion of Mushroom Chitin-Rich Waste into Valuable Chitin Oligosaccharides Using a Combined Approach of Biocatalysis and Precision Fermentation

The shift toward a circular economy has increased efforts to derive valuable chemicals from renewable resources, including chitin-rich waste. Mushroom cultivation generates significant waste, particularly the stalks left behind on breeding beds, which contain a substantial amount of chitin with untapped potential. This research establishes a proof of concept for valorizing this waste stream by converting it into valuable chitin oligosaccharides, which have applications across food, feed, agriculture, and pharmaceuticals. Using a combined approach of enzymatic saccharification with five chitinolytic enzymes, followed by precision fermentation of the resulting N-acetyl-d-glucosamine (GlcNAc), we successfully produced defined chitinpentaose. Chitin extracted from Agaricus bisporus brown demonstrated the highest saccharification efficiency, achieving a GlcNAc conversion of 31 ± 1% (w/w). Our findings highlight the necessity of purifying the saccharification product to ensure product specificity during fermentation, although the production strain's growth remained suboptimal compared to commercially available GlcNAc. Using an engineered E. coli strain, we achieved pure chitinpentaose, with a yield of 0.0327 g/L at a 10 mL scale and production levels (g/OD600) comparable to those obtained with HPLC-grade commercial GlcNAc. This study provides a foundation for further research aimed at improving biocatalyst recycling and optimizing the growth phase, thereby enhancing the cost-efficiency and scalability of this sustainable bioconversion process.

Toward scalable biocatalytic conversion of 5-hydroxymethylfurfural by galactose oxidase using coordinated reaction and enzyme engineering

5-Hydroxymethylfurfural (HMF) has emerged as a crucial bio-based chemical building block in the drive towards developing materials from renewable resources, due to its direct preparation from sugars and its readily diversifiable scaffold. A key obstacle in transitioning to bio-based plastic production lies in meeting the necessary industrial production efficiency, particularly in the cost-effective conversion of HMF to valuable intermediates. Toward addressing the challenge of developing scalable technology for oxidizing crude HMF to more valuable chemicals, here we report coordinated reaction and enzyme engineering to provide a galactose oxidase (GOase) variant with remarkably high activity toward HMF, improved O₂ binding and excellent productivity (>1,000,000 TTN). The biocatalyst and reaction conditions presented here for GOase catalysed selective oxidation of HMF to 2,5-diformylfuran offers a productive blueprint for further development, giving hope for the creation of a biocatalytic route to scalable production of furan-based chemical building blocks from sustainable feedstocks.

5-Hydroxymethylfurfural (HMF) can be transformed to a range of industrially useful derivatives, such as 2,5-diformylfuran (DFF), but the reactions needed for efficient industrial production are hindered by several issues. Here, the authors perform reaction and enzyme engineering resulting in a galactose oxidase variant with high activity towards HMF, improved oxygen binding and high productivity.

Three-level hybrid modeling for systematic optimization of biocatalytic synthesis: α-glucosyl glycerol production by enzymatic trans-glycosylation from sucrose

Mechanism-based kinetic models are rigorous tools to analyze enzymatic reactions, but their extension to actual conditions of the biocatalytic synthesis can be difficult. Here, we demonstrate (mechanistic-empirical) hybrid modeling for systematic optimization of the sucrose phosphorylase-catalyzed glycosylation of glycerol from sucrose, to synthesize the cosmetic ingredient α-glucosyl glycerol (GG). The empirical model part was developed to capture nonspecific effects of high sucrose concentrations (up to 1.5 M) on microscopic steps of the enzymatic trans-glycosylation mechanism. Based on verified predictions of the enzyme performance under initial rate conditions (Level 1), the hybrid model was expanded by microscopic terms of the reverse reaction to account for the full-time course of GG synthesis (Level 2). Lastly (Level 3), the application of the hybrid model for comprehensive window-of-operation analysis and constrained optimization of the GG production (~250 g/L) was demonstrated. Using two candidate sucrose phosphorylases (from Leuconostoc mesenteroides and Bifidobacterium adolescentis), we reveal the hybrid model as a powerful tool of "process decision making" to guide rational selection of the best-suited enzyme catalyst. Our study exemplifies a closing of the gap between enzyme kinetic models considered for mechanistic research and applicable in technologically relevant reaction conditions; and it highlights the important benefit thus realizable for biocatalytic process development.

Sustainable synthesis of branched-chain diesters

Esters from branched alcohols and dicarboxylic linear acids are widely used as lube bases due to their good performance at low temperatures. This work proposes a new process to synthesize bis(2-ethylbutyl) adipate and bis(2-ethylbutyl) sebacate by using the lipase-based catalyst Novozym® 435 in a solvent-free system. Different reaction strategies have been tested in order to minimize 2-ethyl-1-butanol losses due to its evaporation and optimum operation conditions have been determined: 2.5 % of biocatalyst, 50 °C and a molar excess of alcohol of 15 % for the adipic diester and of 25 % for the sebacic one. It has also been proven that the immobilized enzyme can be reused in seven successive reaction cycles, achieving high yields without an appreciable reduction of activity. This biocatalytic pathway is a promising basis for the development of a more sustainable large scale process for obtaining biodegradable lubricants, as it is pointed out by productivity, economic and green metrics calculations.

Efficient production of (S)-1-phenyl-1,2-ethanediol using xylan as co-substrate by a coupled multi-enzyme Escherichia coli system

Background

(S)-1-phenyl-1,2-ethanediol is an important chiral intermediate in the synthesis of liquid crystals and chiral biphosphines. (S)-carbonyl reductase II from Candida parapsilosis catalyzes the conversion of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol with NADPH as a cofactor. Glucose dehydrogenase with a Ala258Phe mutation is able to catalyze the oxidation of xylose with concomitant reduction of NADP⁺ to NADPH, while endo-β-1,4-xylanase 2 catalyzes the conversion of xylan to xylose. In the present work, the Ala258Phe glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 were introduced into the (S)-carbonyl reductase II-mediated chiral pathway to strengthen cofactor regeneration by using xylan as a naturally abundant co-substrate.

Results

We constructed several coupled multi-enzyme systems by introducing (S)-carbonyl reductase II, the A258F glucose dehydrogenase mutant and endo-β-1,4-xylanase 2 into Escherichia coli. Different strains were produced by altering the location of the encoding genes on the plasmid. Only recombinant E. coli/pET-G-S-2 expressed all three enzymes, and this strain produced (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone as a substrate and xylan as a co-substrate. The optical purity was 100% and the yield was 98.3% (6 g/L 2-HAP) under optimal conditions of 35 °C, pH 6.5 and a 2:1 substrate-co-substrate ratio. The introduction of A258F glucose dehydrogenase and endo-β-1,4-xylanase 2 into the (S)-carbonyl reductase II-mediated chiral pathway caused a 54.6% increase in yield, and simultaneously reduced the reaction time from 48 to 28 h.

Conclusions

This study demonstrates efficient chiral synthesis using a pentose as a co-substrate to enhance cofactor regeneration. This provides a new approach for enantiomeric catalysis through the inclusion of naturally abundant materials.

Mixed-trophies biofilm cultivation in capillary reactors

The biocatalytic application of photoautotrophic organisms is a promising alternative for the production of biofuels and value-added compounds as they do not rely on carbohydrates as a source of carbon, electrons, and energy. Although the photoautotrophic organisms hold potential for the development of sustainable processes, suitable reactor concepts that allow high cell density (HCD) cultivation of photoautotrophic microorganisms are limited. Such reactors need a high surface to volume ratio to enhance light availability. Furthermore, the accumulation of high oxygen concentrations as a consequence of oxygenic photosynthesis, and its inhibitory effect on cell growth needs to be prevented. Here, we present a method for HCD cultivation of oxygenic phototrophs based on the co-cultivation of different trophies in a biofilm format to avoid high oxygen partial-pressure and attain HCDs of up to 51.8 g_BDW L⁻¹ on a lab scale. In this article, we show:

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A robust method for mixed trophies biofilm cultivation in capillary reactors

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Set-up and operation of a biofilm capillary reactor

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A method to quantify oxygen in the continuous biofilm capillary reactor

Ionic liquids and protein folding-old tricks for new solvents

One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. In this short note, we briefly outline the nature of the parameters associated with different empirical and model-based characterization procedures and point out factors which affect their interpretation when using a base solvent different from water. This review principally describes arguments developed by Wakayama et al., Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry, 2019, edited by Y. Kuroda and F. Arisaka; CMC Publishing House. Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.

Reactor Selection for Effective Continuous Biocatalytic Production of Pharmaceuticals

Enzyme catalyzed reactions are rapidly becoming an invaluable tool for the synthesis of many active pharmaceutical ingredients. These reactions are commonly performed in batch, but continuous biocatalysis is gaining interest in industry because it would allow seamless integration of chemical and enzymatic reaction steps. However, because this is an emerging field, little attention has been paid towards the suitability of different reactor types for continuous biocatalytic reactions. Two types of continuous flow reactor are possible: continuous stirred tank and continuous plug-flow. These reactor types differ in a number of ways, but in this contribution, we focus on residence time distribution and how enzyme kinetics are affected by the unique mass balance of each reactor. For the first time, we present a tool to facilitate reactor selection for continuous biocatalytic production of pharmaceuticals. From this analysis, it was found that plug-flow reactors should generally be the system of choice. However, there are particular cases where they may need to be coupled with a continuous stirred tank reactor or replaced entirely by a series of continuous stirred tank reactors, which can approximate plug-flow behavior. This systematic approach should accelerate the implementation of biocatalysis for continuous pharmaceutical production.

Characterization and application of chemical-resistant polyurethane-based enzyme and whole cell compartments

This study presents the preparation and physical-chemical characterization of chemical resistant polyurethane-based compartments for biocatalytic application. The artificial compartments were prepared from an emulsion of polymer precursor and an aqueous phase that includes a biocatalytic reaction system. After curing, highly dispersed aqueous domains were obtained, which still contain the entire biocatalytic reaction system and remain fixed in the solid polymer preparation. The tensile and compression behavior of the prepared polymeric material is not significantly affected by the incorporation and facilitates excellent stability against various organic solvents and acid solutions. Thereby, the compartments can be used not only for enantioselective alcohol-dehydrogenase catalyzed reduction but also for a whole cell catalyzed hydrolysis of esters. Moreover, the compartmented whole-cell system was considerably stable to allow multiple reuses without a noticeable loss of catalytic activity of the incorporated whole cell catalytic reaction system.

Influence of Three Commercial Graphene Derivatives on the Catalytic Properties of a Lactobacillus plantarum α-l-Rhamnosidase When Used as Immobilization Matrices

The modification of carbon nanomaterials with biological molecules paves the way toward their use in biomedical and biotechnological applications, such as next-generation biocatalytic processes, development of biosensors, implantable electronic devices, or drug delivery. In this study, different commercial graphene derivatives, namely, monolayer graphene oxide (GO), graphene oxide nanocolloids (GOCs), and polycarboxylate-functionalized graphene nanoplatelets (GNs), were compared as biomolecule carrier matrices. Detailed spectroscopic analyses showed that GO and GOC were similar in composition and functional group content and very different from GN, whereas divergent morphological characteristics were observed for each nanomaterial through microscopy analyses. The commercial α-l-rhamnosidase RhaB1 from the probiotic bacterium Lactobacillus plantarum, selected as a model biomolecule for its relevant role in the pharma and food industries, was directly immobilized on the different materials. The binding efficiency and biochemical properties of RhaB1-GO, RhaB1-GOC, and RhaB1-GN composites were analyzed. RhaB1-GO and RhaB1-GOC showed high binding efficiency, whereas the enzyme loading on GN, not tested in previous enzyme immobilization studies, was low. The enzyme showed contrasting changes when immobilized on the different material supports. The effect of pH on the activity of the three RhaB1-immobilized versions was similar to that observed for the free enzyme, whereas the activity-temperature profiles and the response to the presence of inhibitors varied significantly between the RhaB1 versions. In addition, the apparent K_m for the immobilized and soluble enzymes did not change. Finally, the free RhaB1 and the immobilized enzyme in GOC showed the best storage and reutilization stability, keeping most of their initial activity after 8 weeks of storage at 4 °C and 10 reutilization cycles, respectively. This study shows, for the first time, that distinct commercial graphene derivatives can influence differently the catalytic properties of an enzyme during its immobilization.

Computational redesign of enzymes for regio- and enantioselective hydroamination

Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.

Integrating protein engineering with process design for biocatalysis

Biocatalysis uses enzymes for chemical synthesis and production, offering selective, safe and sustainable catalysis. While today the majority of applications are in the pharmaceutical sector, new opportunities are arising every day in other industry sectors, where production costs become a more important driver. In the early applications of the technology, it was necessary to design processes to match the properties of the biocatalyst. With the advent of protein engineering, organic chemists started to develop and improve enzymes to suit their needs. Likewise in industry, although not widespread, a new paradigm was already implemented several years ago to engineer enzymes to suit process needs. Today, a new era is entered, where the effectiveness with which such integrated protein and process engineering is achieved becomes critical to implementation. In this paper, the development of a tool to improve the effectiveness of this approach is discussed, namely the use of target-setting based on process requirements, to guide the necessary protein engineering.This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.

Overcoming "speed limits" in high throughput chromatographic analysis

The combination of high speed autosampler technology and ultrafast chromatographic separations enables faster high throughput analysis. With an injection cycle time of 10.6 s, MISER (Multiple Injection in a Single Experimental Run) HPLC-MS analysis of a 96 well microplate can be completed in only 17min. As chromatographic separations in the sub 5s range become increasingly common, even faster autosamplers will be needed to realize further speed improvements in high throughput LC-MS analysis. Indeed with proper hardware sampling approaches, chromatographic analysis of microplates could approach speeds of spectrophotometric plate readers while maintaining the advantage of multicomponent detection and monitoring.

Computational tools for enzyme improvement: why everyone can - and should - use them

This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists. These methods guide efficient experimental planning and allow the enzyme engineer to rationalize time and resources. Computational tools nevertheless face challenges in the realm of transient modern technology.

Progress in biocatalysis with immobilized viable whole cells: systems development, reaction engineering and applications

Viable microbial cells are important biocatalysts in the production of fine chemicals and biofuels, in environmental applications and also in emerging applications such as biosensors or medicine. Their increasing significance is driven mainly by the intensive development of high performance recombinant strains supplying multienzyme cascade reaction pathways, and by advances in preservation of the native state and stability of whole-cell biocatalysts throughout their application. In many cases, the stability and performance of whole-cell biocatalysts can be highly improved by controlled immobilization techniques. This review summarizes the current progress in the development of immobilized whole-cell biocatalysts, the immobilization methods as well as in the bioreaction engineering aspects and economical aspects of their biocatalytic applications.

Stereo- and region-specific biotransformation of physapubescin by four fungal strains

Biotransformations of physapubescin (1) were performed by four fungal strains-Mucor subtilissimus AS 3.2454, Mucor polymorphosporus AS 3.3443, Aspergillus niger AS 3.795, and Syncephalastrum racemosum AS 3.264. Four metabolites were prepared in the biotransformation process of 1, and their structures were elucidated as 15α-acetoxy-5,6β:22,26:24,25-triepoxy-26α-hydroxy-3β-methoxy 4β-hydroxyergost-1-one (2), 15α-acetoxy-5,6β:22,26-diepoxy-4β,24β,25α,26(α, β)-tetrahydroxyergost-3β-methoxy-1-one (3a/3b), 15α-acetoxy-5,6β:22,26-diepoxy-4β,24β,25α,26(α, β)-tetrahydroxyergost-2-en-1-one (4a/4b), and physapubescin D (5), by spectroscopic data analysis. Among them, metabolites 2 and 3 are new. All of these fungal strains showed the ability to be highly stereo- and region-specific for the bioconversion of substrate (1). Our research provides a reference for the structural derivatization of withanolides or possibly even other natural products.

Novel eco-friendly biocatalyst: soybean peroxidase immobilized onto activated carbon obtained from agricultural waste

Closed cycle of immobilized biocatalyst production with maximum biomass use applicable in several areas.

The application of reaction engineering to biocatalysis

Biocatalysis is a growing area of synthetic and process chemistry with the ability to deliver not only improved processes for the synthesis of existing compounds, but also new routes to new compounds.

Biotransformation of Curcumenol by Mucor polymorphosporus

Biocatalysis of curcumenol (1) was performed by Mucor polymorphosporus AS 3.3443. Six metabolites including five new compounds were obtained, and their structures were elucidated as 10β-hydroxy-9,10-dihydrocurcumenol (2), 2β-hydroxycurcumenol (3), 15-hydroxycurcumenol (4), 12-hydroxycurcumenol (5), 1-hydroxy-4αH-guai-1,6,9-triene-2,8-dione (6), and 5-hydroxycarbonyl-1-oxo-3,7-dimethylindane (7) by spectroscopic analysis. M. polymorphosporus catalyzed unusual degradation and rearrangement reactions to generate a ring-contracted metabolite (7) of curcumenol (1). Curcumenol (1) and metabolites 4-7 exhibited inhibitory activities against lipopolysaccharide-induced nitric oxide production in RAW 264.7 macrophages, with 7 exhibiting more potent activity than curcumenol.

Guiding efficient microbial synthesis of non-natural chemicals by physicochemical properties of reactants

The recent progress in sustainable chemistry and in synthetic biology increased the interest of chemical and pharmaceutical industries to implement microbial processes for chemical synthesis. However, most organisms used in biotechnological applications are not evolved by Nature for the production of hydrophobic, non-charged, volatile, or toxic compounds. In order to overcome this discrepancy, bioprocess design should consist of an integrated approach addressing pathway, cellular, reaction, and process engineering. Highlighting selected examples, we show that surprisingly often Nature provides conceptual solutions to enable chemical synthesis. Complemented by established methods from (bio)chemical and metabolic engineering, these concepts offer potential strategies yet to be explored and translated into innovative technical solutions enabling sustainable microbial production of non-natural chemicals.