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Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing

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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 34816

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Special Issue Editors

Prof. Dr. Anwar Sunna

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Guest Editor

Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Interests: biocatalysis; synthetic biology; bioengineering: proteins; nanoparticles
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Richard Daniellou

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Guest Editor

Institut de Chimie Organique et Analytique (ICOA), Université d’Orléans, UMR-CNRS 7311, BP 6759, Rue de Chartres, CEDEX 2, 45067 Orléans, France
Interests: biocatalysts; enzymology; glycobiochemistry; glycosyltransferases; glycosidases
Special Issues, Collections and Topics 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:

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

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

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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 (13 papers)

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13 pages, 4235 KiB

Open AccessArticle

Efficient Biosynthesis of (S)-1-chloro-2-heptanol Catalyzed by a Newly Isolated Fungi Curvularia hominis B-36

by Shenpeng Xu, Qinzhe Lin, Wentian Chen, Ruoyu Lin, Yikai Shen, Pinchuan Tang, Sisi Yu, Wenting Du and Jun Li

Catalysts 2023, 13(1), 52; https://doi.org/10.3390/catal13010052 - 27 Dec 2022

Cited by 1 | Viewed by 1251

Abstract

(S)-1-chloro-2-heptanol is an enantiopure chemical of great value that can synthesize Treprostinil for treating primary pulmonary hypertension. In this work, a new strain B-36, capable of asymmetric reduction of 1-chloro-2-heptanone to (S)-1-chloro-2-heptanol, was screened and identified as Curvularia hominis B-36 (CCTCC M 2017654) based on the morphological and internally transcribed spacer (ITS) sequence. The reductive capacity of Curvularia hominis B-36 was investigated as a whole-cell biocatalyst in the bioreduction, and the excellent yield (97.2%) and enantiomeric excess (ee) value (99.9%) were achieved under the optimal conditions as follows: 75 mM 1-chloro-2-heptanone, K₂HPO₄-KH₂PO₄ (100 mM, pH 6.0), 50 g L⁻¹ resting cells (dry cell weight; DCW), 15% (v/v) isopropanol as co-substrate, 200 rpm, 30 °C, 20 h. The scaled-up biocatalytic process was accomplished at a bioreactor in a 1.5 L working volume, showing superb yield (~97%) and selectivity (99.9%). The product (S)-1-chloro-2-heptanol was purified and characterized by NMR. Curvularia hominis B-36 is a novel catalyst and the asymmetric synthesis route is benign and eco-friendly. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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13 pages, 3027 KiB

Open AccessArticle

Optimization and Determination of Kinetic Parameters of the Synthesis of 5-Lauryl-hydroxymethylfurfural Catalyzed by Lipases

by Jorge Uribe, María Elena Lienqueo and Nadia Guajardo

Catalysts 2023, 13(1), 19; https://doi.org/10.3390/catal13010019 - 23 Dec 2022

Cited by 3 | Viewed by 1356

Abstract

Hydroxymethylfurfural esters (HMF-esters) have great potential for additive development; for this reason, the goal of this work was to study the optimization of the esterification conversion of HFM and lauric acid using two lipases: the Novozym 435^® biocatalyst and immobilized lipase from Thermomyces lanuginosus (TL). For the optimization of conversion, a three-level three-factorial Box–Behnken experimental design was used. The models achieved a good fit (R² over 90%) for reactions catalyzed with Novozym 435^® and immobilized TL lipase. The best conversion, 78.4%, was achieved with immobilized TL lipase using 30 mM HMF, 16 U of biocatalytic activity, and 50 °C. The kinetic parameters without inhibition by the substrate were determined using the Michaelis–Menten mechanism, whereby

V_{Max}

for both biocatalysts reached the highest values at 50 °C, and the highest enzyme–substrate affinities (low

K_{m}

) were reached at temperatures of 30 °C and 40 °C. It can be concluded that immobilized TL lipase has the potential to catalyze this reaction since, under optimal reaction conditions, an 80.6% conversion (value predicted) could be achieved. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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19 pages, 1491 KiB

Open AccessArticle

Untargeted Metabolomics Exploration of the Growth Stage-Dependent Chemical Space of the Sclareol-Converting Biocatalyst Hyphozyma roseonigra

by Efficient N. Ncube, Lungile Sitole, Paul A. Steenkamp, Lucia H. Steenkamp and Ian A. Dubery

Catalysts 2022, 12(10), 1225; https://doi.org/10.3390/catal12101225 - 13 Oct 2022

Viewed by 1210

Abstract

Hyphozyma roseonigra is a dimorphic yeast used as a biocatalyst to convert sclareol, a plant diterpenoid to ambradiol. The latter is an intermediate in the synthesis of ambrafuran, a high-value chemical in the fragrance industry. Unfortunately, little is known about the underlying biochemistry of this microorganism. In this study, the integration of multi-platform-based metabolomics was used to better comprehend H. roseonigra from a biochemical perspective. The focus on metabolomic changes during growth and development was accomplished using untargeted LC–MS and NMR analyses. Cell suspensions were grown in batch culture over a 14-day period, and cells from the early-, log-, and stationary phases were harvested every second day using platform-compatible extraction procedures. Following chemometric analysis of LC–MS and NMR data acquired from both intra- and extracellular extracts, the identified discriminatory ions annotated from the endo- and exometabolomes (metabo-fingerprinting and metabo-footprinting) were found to fall predominantly in the primary metabolism class. Pathway mapping and feature-based network correlation analysis assisted in gaining insights into the active metabolic pathways during growth and development and did not flag terpene synthesis. This study provides novel insights into the basic metabolic capabilities of H. roseonigra and suggests that sclareol is metabolized as the detoxification of a hydrophobic xenobiotic compound. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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9 pages, 2099 KiB

Open AccessArticle

Production of Taxifolin from Astilbin by Fungal Biotransformation

by Jianfeng Mei, Xiang Chen, Pingya Wang, Yichun Wu, Yu Yi and Guoqing Ying

Catalysts 2022, 12(9), 1037; https://doi.org/10.3390/catal12091037 - 12 Sep 2022

Viewed by 1552

Abstract

Taxifolin is known to have multiple biological functions. It has been widely used as a multifunctional food additive, and consequently, the global demand for taxifolin is increasing. The main method for taxifolin production is an extraction from larch wood, but the global resources of larch are limited. Astilbin, taxifolin-3-o-rhamnoside, is abundant in many plants and much more readily available, meaning taxifolin can be obtained by deglycosylation of astilbin. In this study, a fungal strain, Aspergillus fumigatus SQH4, was isolated from an enrichment culture of Smilax glabra rhizome to achieve the deglycosylation reaction. A culture of SQH4, adjusted to pH 6.5, with 5 g/L astilbin achieved a yield of taxifolin of 91.3% after biotransformation for 14 h at 35 °C. These findings offer an alternative method for the production of taxifolin. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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14 pages, 1653 KiB

Open AccessArticle

Enhancing Soluble Expression of Phospholipase B for Efficient Catalytic Synthesis of L-Alpha-Glycerylphosphorylcholine

by Jiao Feng, Wenjing Yang, Yuanyuan Lu, Hui Li, Sheng Xu, Xin Wang and Kequan Chen

Catalysts 2022, 12(6), 650; https://doi.org/10.3390/catal12060650 - 13 Jun 2022

Cited by 3 | Viewed by 1866

Abstract

Phospholipase B (PLB) harbors three distinct activities with broad substrate specificities and application fields. Its hydrolyzing of sn-1 and sn-2 acyl ester bonds enables it to catalyze the production of L-alpha-glycerylphosphorylcholine (L-α-GPC) from phosphatidylcholine (PC) without speed-limiting acyl migration. This work was intended to obtain high-level active PLB and apply it to establish an efficient system for L-α-GPC synthesis. PLB from Pseudomonas fluorescens was co-expressed with five different molecular chaperones, including trigger factor (Tf), GroEL-GroES (GroELS), DnaK-DnaJ-GrpE (DnaKJE), GroELS and DnaKJE, or GroELS and Tf or fused with maltose binding protein (MBP) in Escherichia coli BL21(DE3) to improve PLB expression. PLB with DnaKJE-assisted expression exhibited the highest catalytic activity. Further optimization of the expression conditions identified an optimal induction OD₆₀₀ of 0.8, IPTG concentration of 0.3 mmol/L, induction time of 9 h, and temperature of 25 °C. The PLB activity reached a maximum of 524.64 ± 3.28 U/mg under optimal conditions. Subsequently, to establish an efficient PLB-catalyzed system for L-α-GPC synthesis, a series of organic-aqueous mixed systems and surfactant-supplemented aqueous systems were designed and constructed. Furthermore, the factors of temperature, reaction pH, metal ions, and substrate concentration were further systematically identified. Finally, a high yield of 90.50 ± 2.21% was obtained in a Span 60-supplemented aqueous system at 40 °C and pH 6.0 with 0.1 mmol/L of Mg²⁺. The proposed cost-effective PLB production and an environmentally friendly PLB-catalyzed system offer a candidate strategy for the industrial production of L-α-GPC. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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16 pages, 4203 KiB

Open AccessArticle

Metabolomics-Guided Analysis of the Biocatalytic Conversion of Sclareol to Ambradiol by Hyphozyma roseoniger

by Efficient N. Ncube, Paul A. Steenkamp, Chris W. van der Westhuyzen, Lucia H. Steenkamp and Ian A. Dubery

Catalysts 2022, 12(1), 55; https://doi.org/10.3390/catal12010055 - 04 Jan 2022

Cited by 6 | Viewed by 1808

Abstract

The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance industry, using whole-cell biotransformation by the dimorphic yeast Hyphozyma roseoniger, was investigated using metabolomics tools. An integrated approach was used to identify and quantify the participating intermediates in this bioconversion using both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled to mass spectrometry (LC–MS). This study entailed growth stage-dependent analysis of H. roseoniger suspensions grown in batch culture over a 14-day period, beginning with a three-day induction period using 20 mg/200 mL sclareol, followed by a further 1 g/200 mL sclareol dose to enable ambradiol production. The progress of the bioconversion and the resulting dynamic changes to the metabolome were monitored using NMR analysis and semi-targeted LC–MS metabolomics. This outlined the molecular conversions occurring within the matrix and no novel intermediates participating in the sclareol to ambradiol conversion could be identified. This study presents new findings about the transformative capabilities of H. roseoniger as a whole cell biocatalyst, highlighting its potential utility in similar applications. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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12 pages, 20330 KiB

Open AccessArticle

Efficient 2,3-Butanediol/Acetoin Production Using Whole-Cell Biocatalyst with a New Nadh/Nad(+) Regeneration System

by Yaping Wang, Yanhong Peng, Xiaoyan Liu, Ronghua Zhou, Xianqing Liao, Yong Min, Yong Hu, Ying Wang and Ben Rao

Catalysts 2021, 11(12), 1422; https://doi.org/10.3390/catal11121422 - 23 Nov 2021

Viewed by 1566

Abstract

An auto-inducing expression system was developed that could express target genes in S. marcescens MG1. Using this system, MG1 was constructed as a whole-cell biocatalyst to produce 2,3-butanediol/acetoin. Formate dehydrogenase (FDH) and 2,3-butanediol dehydrogenase were expressed together to build an NADH regeneration system to transform diacetyl to 2,3-butanediol. After fermentation, the extract of recombinant S. marcescens MG1ABC (pETDuet-bdhA-fdh) showed 2,3-BDH activity of 57.8 U/mg and FDH activity of 0.5 U/mg. And 27.95 g/L of 2,3-BD was achieved with a productivity of 4.66 g/Lh using engineered S. marcescens MG1(Pswnb+pETDuet-bdhA-fdh) after 6 h incubation. Next, to produce 2,3-butanediol from acetoin, NADH oxidase and 2,3-butanediol dehydrogenase from Bacillus subtilis were co-expressed to obtain a NAD+ regeneration system. After fermentation, the recombinant strain S. marcescens MG1ABC (pSWNB+pETDuet-bdhA-yodC) showed AR activity of 212.4 U/mg and NOX activity of 150.1 U/mg. We obtained 44.9 g/L of acetoin with a productivity of 3.74 g/Lh using S. marcescens MG1ABC (pSWNB+pETDuet-bdhA-yodC). This work confirmed that S. marcescens could be designed as a whole-cell biocatalyst for 2,3-butanediol and acetoin production. Full article

(This article belongs to the Special Issue Biocatalysis and Whole-Cell Biotransformation in Biomanufacturing)

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11 pages, 1567 KiB

Open AccessEditor’s ChoiceArticle

Biocatalytic Transformation of 5-Hydroxymethylfurfural into 2,5-di(hydroxymethyl)furan by a Newly Isolated Fusarium striatum Strain

by Alberto Millán, Núria Sala, Mercè Torres and Ramon Canela-Garayoa

Catalysts 2021, 11(2), 216; https://doi.org/10.3390/catal11020216 - 06 Feb 2021

Cited by 14 | Viewed by 2741

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 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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18 pages, 1565 KiB

Open AccessArticle

Optimizing the Production of Recombinant Hydroperoxide Lyase in Escherichia coli Using Statistical Design

by Sophie Vincenti, Magali Mariani, Jessica Croce, Eva Faillace, Virginie Brunini-Bronzini de Caraffa, Liliane Berti and Jacques Maury

Catalysts 2021, 11(2), 176; https://doi.org/10.3390/catal11020176 - 28 Jan 2021

Cited by 2 | Viewed by 2155

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. 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⁻¹_{of culture} of the soluble enzyme was produced in microliter plates and 21,920 U L⁻¹_{of 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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12 pages, 1509 KiB

Open AccessArticle

Spirogyra Oil-Based Biodiesel: Response Surface Optimization of Chemical and Enzymatic Transesterification and Exhaust Emission Behavior

by Saqib Sohail, Muhammad Waseem Mumtaz, Hamid Mukhtar, Tooba Touqeer, Muhammad Kafeel Anjum, Umer Rashid, Wan Azlina Wan Ab Karim Ghani and Thomas Shean Yaw Choong

Catalysts 2020, 10(10), 1214; https://doi.org/10.3390/catal10101214 - 20 Oct 2020

Cited by 5 | Viewed by 3155

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 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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10 pages, 1504 KiB

Open AccessFeature PaperArticle

Discovery and Engineering of an Aldehyde Tolerant 2-deoxy-D-ribose 5-phosphate Aldolase (DERA) from Pectobacterium atrosepticum

by Meera Haridas, Carolin Bisterfeld, Le Min Chen, Stefan R. Marsden, Fabio Tonin, Rosario Médici, Adolfo Iribarren, Elizabeth Lewkowicz, Peter-Leon Hagedoorn, Ulf Hanefeld and Eman Abdelraheem

Catalysts 2020, 10(8), 883; https://doi.org/10.3390/catal10080883 - 05 Aug 2020

Cited by 4 | Viewed by 3487

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 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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21 pages, 3371 KiB

Open AccessFeature PaperReview

Organizing Multi-Enzyme Systems into Programmable Materials for Biocatalysis

by Min-Ju Seo and Claudia Schmidt-Dannert

Catalysts 2021, 11(4), 409; https://doi.org/10.3390/catal11040409 - 24 Mar 2021

Cited by 18 | Viewed by 6751

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 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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25 pages, 1367 KiB

Open AccessFeature PaperReview

Enzymology of Alternative Carbohydrate Catabolic Pathways

by Dominik Kopp, Peter L. Bergquist and Anwar Sunna

Catalysts 2020, 10(11), 1231; https://doi.org/10.3390/catal10111231 - 23 Oct 2020

Cited by 4 | Viewed by 4120

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 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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