Special Issue "Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing"

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: 31 July 2021.

Special Issue Editors

Prof. Dr. Anwar Sunna
E-Mail Website1 Website2
Guest Editor
Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Interests: biocatalysis; synthetic biology; bioengineering: proteins; nanoparticles
Special Issues and Collections in MDPI journals
Prof. Dr. Richard Daniellou
E-Mail Website
Guest Editor
Institut de Chimie Organique et Analytique (ICOA), Université d’Orléans UMR-CNRS 7311, BP 6759, rue de Chartres, 45067 Orléans CEDEX 2, France
Interests: biocatalysts; enzymology; glycobiochemistry; glycosyltransferases; glycosidases
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Enzyme technology and biocatalysis has become a prominent field in synthetic biology and “green” organic synthesis of chemicals due to the increased demand for environmentally friendly biomanufacturing. Global trends towards sustainability, the reduction of organic waste, and landfill avoidance are driving the demand for greener products with improved properties. Accordingly, the field of enzyme technology and biocatalysis (multi-enzymes and whole-cells) has become a primary focus for the synthesis of bio-based chemicals and high-value compounds. In this Special Issue of Catalysts, we would like to highlight these current advances with special emphasis on the following areas:

  1. Structure–function analysis and enzyme optimization;
  2. Enzymatic and whole-cell biotransformation;
  3. Cascade reactions and co-immobilization of enzymes;
  4. Strategies for enzyme stabilization and biocatalytic applications;
  5. Design of novel biocatalytic modules for enhanced transformation of biological waste products;
  6. Assembly of functional multi-enzyme pathways.

Prof. Dr. Anwar Sunna
Prof. Dr. Richard Daniellou
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chemo-enzymatic synthesis
  • protein engineering
  • biocatalysis
  • synthetic biology
  • industrial enzymes
  • enzyme stabilization
  • cell-free biocatalysis
  • natural and non-natural multi-enzyme pathways
  • bio-based chemicals
  • cascade reactions
  • biocatalytic modules

Published Papers (6 papers)

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Research

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Article
Biocatalytic Transformation of 5-Hydroxymethylfurfural into 2,5-di(hydroxymethyl)furan by a Newly Isolated Fusarium striatum Strain
Catalysts 2021, 11(2), 216; https://doi.org/10.3390/catal11020216 - 06 Feb 2021
Viewed by 554
Abstract
The compound 2,5-di(hydroxymethyl)furan (DHMF) is a high-value chemical block that can be synthesized from 5-hydroxymethylfurfural (HMF), a platform chemical that results from the dehydration of biomass-derived carbohydrates. In this work, the HMF biotransformation capability of different Fusarium species was evaluated, and F. striatum [...] Read more.
The compound 2,5-di(hydroxymethyl)furan (DHMF) is a high-value chemical block that can be synthesized from 5-hydroxymethylfurfural (HMF), a platform chemical that results from the dehydration of biomass-derived carbohydrates. In this work, the HMF biotransformation capability of different Fusarium species was evaluated, and F. striatum was selected to produce DHMF. The effects of the inoculum size, glucose concentration and pH of the media over DHMF production were evaluated by a 23 factorial design. A substrate feeding approach was found suitable to overcome the toxicity effect of HMF towards the cells when added at high concentrations (>75 mM). The process was successfully scaled-up at bioreactor scale (1.3 L working volume) with excellent DHMF production yields (95%) and selectivity (98%). DHMF was purified from the reaction media with high recovery and purity by organic solvent extraction with ethyl acetate. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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Article
Optimizing the Production of Recombinant Hydroperoxide Lyase in Escherichia coli Using Statistical Design
Catalysts 2021, 11(2), 176; https://doi.org/10.3390/catal11020176 - 28 Jan 2021
Viewed by 433
Abstract
Hydroperoxide lyase (HPL) catalyzes the synthesis of volatiles C6 or C9 aldehydes from fatty acid hydroperoxides. These short carbon chain aldehydes, known as green leaf volatiles (GLV), are widely used in cosmetic industries and as food additives because of their “fresh green” aroma. [...] Read more.
Hydroperoxide lyase (HPL) catalyzes the synthesis of volatiles C6 or C9 aldehydes from fatty acid hydroperoxides. These short carbon chain aldehydes, known as green leaf volatiles (GLV), are widely used in cosmetic industries and as food additives because of their “fresh green” aroma. To meet the growing demand for natural GLVs, the use of recombinant HPL as a biocatalyst in enzyme-catalyzed processes appears to be an interesting application. Previously, we cloned and expressed a 13-HPL from olive fruit in Escherichia coli and showed high conversion rates (up to 94%) during the synthesis of C6 aldehydes. To consider a scale-up of this process, optimization of the recombinant enzyme production is necessary. In this study, four host-vector combinations were tested. Experimental design and response surface methodology (RSM) were used to optimize the expression conditions. Three factors were considered, i.e., temperature, inducer concentration and induction duration. The Box–Behnken design consisted of 45 assays for each expression system performed in deep-well microplates. The regression models were built and fitted well to the experimental data (R2 coefficient > 97%). The best response (production level of the soluble enzyme) was obtained with E. coli BL21 DE3 cells. Using the optimal conditions, 2277 U L−1of culture of the soluble enzyme was produced in microliter plates and 21,920 U L−1of culture in an Erlenmeyer flask, which represents a 79-fold increase compared to the production levels previously reported. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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Article
Spirogyra Oil-Based Biodiesel: Response Surface Optimization of Chemical and Enzymatic Transesterification and Exhaust Emission Behavior
Catalysts 2020, 10(10), 1214; https://doi.org/10.3390/catal10101214 - 20 Oct 2020
Viewed by 664
Abstract
Algae are emerging as a major and reliable source of renewable biodiesel that could meet the energy requirements of the world. Like plants, algae produce and store oils in their cells. Algal samples were collected from Gujrat District, Pakistan, their oil content was [...] Read more.
Algae are emerging as a major and reliable source of renewable biodiesel that could meet the energy requirements of the world. Like plants, algae produce and store oils in their cells. Algal samples were collected from Gujrat District, Pakistan, their oil content was analyzed, and the best oil producing alga was identified as Spirogyra crassa. After collecting sample, oil was extracted using the Soxhlet extraction method. Spirogyra oil was characterized physico-chemically for the evaluation of its quality. Acid value, density, saponification value, peroxide value, as well as viscosity and iodine values were determined and their values were 16.67 ± 3.53 mg KOH/g, 0.859 ± 0.050 g/cm3, 165.33 ± 13.20 mg KOH/g, 4.633 ± 0.252 meq/kg, 5.63 ± 0.833 mm2/mL, and 117.67 ± 13.01 mg I2/g, respectively. Chemical as well as enzymatic transesterification protocols were employed for biodiesel production using NaOCH3 and NOVOZYME-435, respectively. Different reactions parameters involved in transesterification were optimized by the response surface methodology. The optimized yield of biodiesel (77.3 ± 1.27%) by the chemical transesterification of algal oil (spirogyra) was observed by carrying out the reaction for 90 minutes at a reaction temperature of 45 °C using 1.13% catalyst (NaOCH3) concentration and 6:1 methanol:oil. Meanwhile, for enzymatic transesterification, the optimized yield (93.2 ± 1.27%) was obtained by conducting the reaction for 42.5 h at the temperature of 35 °C using 1% enzyme concentration and 4.5:1 methanol:oil. Fuel properties, including flash point, pour point, cloud point, fire point, kinematic viscosity, and density, were determined and their values are 125.67 ± 2.11 °C, −19.67 ± 0.8 °C, −13 ± 1 °C, 138.667 ± 2.52 °C, 5.87 ± 2.20 mm2/mL, and 0.85 6 ± 0.03 g/cm3, respectively. Fourier transfer infrared spectroscopic (FTIR) and Gas chromatography with flame ionization detector (GC-FID) analysis were performed for the monitoring of the transesterification process and fatty acid methyl acid (FAME) profiling, respectively. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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Article
Discovery and Engineering of an Aldehyde Tolerant 2-deoxy-D-ribose 5-phosphate Aldolase (DERA) from Pectobacterium atrosepticum
Catalysts 2020, 10(8), 883; https://doi.org/10.3390/catal10080883 - 05 Aug 2020
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Abstract
DERA (2-Deoxy-D-ribose 5-phosphate aldolase) is the only known aldolase that accepts two aldehyde substrates, which makes it an attractive catalyst for the synthesis of a chiral polyol motif that is present in several pharmaceuticals, such as atorvastatin and pravastatin. However, inactivation of the [...] Read more.
DERA (2-Deoxy-D-ribose 5-phosphate aldolase) is the only known aldolase that accepts two aldehyde substrates, which makes it an attractive catalyst for the synthesis of a chiral polyol motif that is present in several pharmaceuticals, such as atorvastatin and pravastatin. However, inactivation of the enzyme in the presence of aldehydes hinders its practical application. Whole cells of Pectobacterium atrosepticum were reported to exhibit good tolerance toward acetaldehyde and to afford 2-deoxyribose 5-phosphate with good yields. The DERA gene (PaDERA) was identified, and both the wild-type and a C49M mutant were heterologously expressed in Escherichia coli. The purification protocol was optimized and an initial biochemical characterization was conducted. Unlike other DERAs, which show a maximal activity between pH 4.0 and 7.5, PaDERA presented an optimum pH in the alkaline range between 8.0 and 9.0. This could warrant its use for specific syntheses in the future. PaDERA also displayed fourfold higher specific activity than DERA from E. coli (EcDERA) and displayed a promising acetaldehyde resistance outside the whole-cell environment. The C49M mutation, which was previously identified to increase acetaldehyde tolerance in EcDERA, also led to significant improvements in the acetaldehyde tolerance of PaDERA. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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Review

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Review
Organizing Multi-Enzyme Systems into Programmable Materials for Biocatalysis
Catalysts 2021, 11(4), 409; https://doi.org/10.3390/catal11040409 - 24 Mar 2021
Viewed by 678
Abstract
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of [...] Read more.
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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Review
Enzymology of Alternative Carbohydrate Catabolic Pathways
Catalysts 2020, 10(11), 1231; https://doi.org/10.3390/catal10111231 - 23 Oct 2020
Viewed by 877
Abstract
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in [...] Read more.
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria. Full article
(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)
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