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Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 36036

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Dr. Antonio Trincone

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Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Comprensorio Olivetti, Edificio 70, Via Campi Flegrei 34, I-80078 Pozzuoli, Napoli, Italy
Interests: biocatalysis; marine enzymes; marine glycosidases; marine biotechnology; oligosaccharides
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Dear Colleagues,

In a historical perspective for food and drink production, biocatalysis has roots that are lost in the mists of time in Western Asiatic regions and probably in other parts of the ancient world; modern usage goes in accord with the knowledge of protein structure, enzymatic kinetics, and reactor design coming throughout chemistry, and biochemistry successes in the last century up to all insights in current molecular research.

In modern literature, the asset of biocatalysis is of great value in a biobased economy for the valorization of easily accessible starting materials from renewables (agricultural residues, food wastes, marine residues, macro and microalgae, etc). The aim is to replace, in the near future, oil-based chemistry to obtain high-value products as well as functional molecules of biotechnological interest, low-cost production of biocatalysts, detoxification and nutritional enrichment in animal feed production or for other chemical conversions for energy and chemical production. As this represents the interface of green chemistry and industrial biotechnology, it embraces a range of industrial fields with many potential contributions from academic and industry scholars in the need of environmental preservation and improvement of occupational health. However, although enzymatic catalysis at a laboratory scale can be efficiently optimized from the perspective of green chemistry, often limitations are present in terms of economic potential. The inherent multidisciplinary perspective of this journal represents the right place for the hosting of this Special Issue, with the multifaceted audience covering all modern aspects of molecular research.

In this Special Issue, articles or reviews will discuss more recent successes in the investigations of biocatalytic processes used in green chemistry covering all fields of applications and fitting into most of the sections of this journal. All novel advances of biocatalytic approach used to reduce the environmental impact are welcome. Sources of enzymes, biochemistry basis, molecular mechanisms, bioreactors, biobased green pretreatments, enzymatic engineering and molecular biology tools, and study of all applicative aspects of biocatalysis will be acknowledged, including quantitative assessment of bioprocesses.

Dr. Antonio Trincone
Guest Editor

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Keywords

biocatalysis
green chemistry
biomasses
biorefinery
enzyme engineering
industrial enzymes

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Related Special Issue

Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses 2.0 in International Journal of Molecular Sciences (3 articles)

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Research

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19 pages, 3850 KiB

Open AccessArticle

Biocatalyzed Synthesis of Flavor Esters and Polyesters: A Design of Experiments (DoE) Approach

by Filippo Fabbri, Federico A. Bertolini, Georg M. Guebitz and Alessandro Pellis

Int. J. Mol. Sci. 2021, 22(16), 8493; https://doi.org/10.3390/ijms22168493 - 6 Aug 2021

Cited by 11 | Viewed by 3184

Abstract

In the present work, different hydrolases were adsorbed onto polypropylene beads to investigate their activity both in short-esters and polyesters synthesis. The software MODDE^® Pro 13 (Sartorius) was used to develop a full-factorial design of experiments (DoE) to analyse the thermostability and selectivity of the immobilized enzyme towards alcohols and acids with different chain lengths in short-esters synthesis reactions. The temperature optima of Candida antarctica lipase B (CaLB), Humicola insolens cutinase (HiC), and Thermobifida cellulosilytica cutinase 1 (Thc_Cut1) were 85 °C, 70 °C, and 50 °C. CaLB and HiC preferred long-chain alcohols and acids as substrate in contrast to Thc_Cut1, which was more active on short-chain monomers. Polymerization of different esters as building blocks was carried out to confirm the applicability of the obtained model on larger macromolecules. The selectivity of both CaLB and HiC was investigated and best results were obtained for dimethyl sebacate (DMSe), leading to polyesters with a M_w of 18 kDa and 6 kDa. For the polymerization of dimethyl adipate (DMA) with BDO and ODO, higher molecular masses were obtained when using CaLB onto polypropylene beads (CaLB_PP) as compared with CaLB immobilized on macroporous acrylic resin beads (i.e., Novozym 435). Namely, for BDO the M_n were 7500 and 4300 Da and for ODO 8100 and 5000 Da for CaLB_PP and for the commercial enzymes, respectively. Thc_Cut1 led to polymers with lower molecular masses, with M_n < 1 kDa. This enzyme showed a temperature optimum of 50 °C with 63% of DMA and BDO when compared to 54% and 27%, at 70 °C and at 85 °C, respectively. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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13 pages, 3344 KiB

Open AccessArticle

Biochemical Characterization of a Novel Exo-Type PL7 Alginate Lyase VsAly7D from Marine Vibrio sp. QY108

by Fengchao Zhang, Zheng Fu, Luyao Tang, Zhelun Zhang, Feng Han and Wengong Yu

Int. J. Mol. Sci. 2021, 22(16), 8402; https://doi.org/10.3390/ijms22168402 - 5 Aug 2021

Cited by 6 | Viewed by 2058

Abstract

Brown algae is a kind of renewable resource for biofuels production. As the major component of carbohydrate in the cell walls of brown algae, alginate can be degraded into unsaturated monosaccharide by exo-type alginate lyases, then converted into 4-deoxy-L-erythro-5-hexoseulose uronate (DEH) by a non-enzyme reaction, which is an important raw material for the preparation of bioethanol. In our research, a novel exo-type alginate lyase, VsAly7D, belonging to the PL7 family was isolated from marine bacterium Vibrio sp. QY108 and recombinantly expressed in Escherichia coli. The purified VsAly7D demonstrated the highest activity at 35 °C, whereas it still maintained 46.5% and 83.1% of its initial activity at 20 °C and 30 °C, respectively. In addition, VsAly7D exhibited the maximum activity under alkaline conditions (pH 8.0), with the simultaneously remaining stability between pH 8.0 and 10.0. Compared with other reported exo-type enzymes, VsAly7D could efficiently degrade alginate, poly-β-D-mannuronate (polyM) and poly-α-L-guluronate (polyG) with highest specific activities (663.0 U/mg, 913.6 U/mg and 894.4 U/mg, respectively). These results showed that recombinant VsAly7D is a suitable tool enzyme for unsaturated alginate monosaccharide preparation and holds great promise for producing bioethanol from brown algae. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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17 pages, 4246 KiB

Open AccessArticle

Product Distributions of Cytochrome P450 OleT_JE with Phenyl-Substituted Fatty Acids: A Computational Study

by Yen-Ting Lin and Sam P. de Visser

Int. J. Mol. Sci. 2021, 22(13), 7172; https://doi.org/10.3390/ijms22137172 - 2 Jul 2021

Cited by 6 | Viewed by 3593

Abstract

There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H₂O₂ in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleT_JE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from C^α and C^β hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the C^α and/or C^β atoms. To understand the bifurcation pathways of substrate activation by P450 OleT_JE leading to decarboxylation, C^α hydroxylation, C^β hydroxylation and C^α−C^β desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleT_JE guides a reaction to a chemoselectivity. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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18 pages, 1629 KiB

Open AccessArticle

Biocatalytic Approach for Direct Esterification of Ibuprofen with Sorbitol in Biphasic Media

by Federico Zappaterra, Maria Elena Maldonado Rodriguez, Daniela Summa, Bruno Semeraro, Stefania Costa and Elena Tamburini

Int. J. Mol. Sci. 2021, 22(6), 3066; https://doi.org/10.3390/ijms22063066 - 17 Mar 2021

Cited by 15 | Viewed by 4465

Abstract

Ibuprofen is a nonsteroidal anti-inflammatory drug (NSAID) introduced in the 1960s and widely used as an analgesic, anti-inflammatory, and antipyretic. In its acid form, the solubility of 21 mg/L greatly limits its bioavailability. Since the bioavailability of a drug product plays a critical role in the design of oral administration dosage, this study investigated the enzymatic esterification of ibuprofen as a strategy for hydrophilization. This work proposes an enzymatic strategy for the covalent attack of highly hydrophilic molecules using acidic functions of commercially available bioactive compounds. The poorly water-soluble drug ibuprofen was esterified in a hexane/water biphasic system by direct esterification with sorbitol using the cheap biocatalyst porcine pancreas lipase (PPL), which demonstrated itself to be a suitable enzyme for the effective production of the IBU-sorbitol ester. This work reports the optimization of the esterification reaction. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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13 pages, 1380 KiB

Open AccessArticle

Nitrofurazone Removal from Water Enhanced by Coupling Photocatalysis and Biodegradation

by Wojciech Smułek, Zuzanna Bielan, Amanda Pacholak, Agata Zdarta, Agnieszka Zgoła-Grześkowiak, Anna Zielińska-Jurek and Ewa Kaczorek

Int. J. Mol. Sci. 2021, 22(4), 2186; https://doi.org/10.3390/ijms22042186 - 22 Feb 2021

Cited by 17 | Viewed by 2781

Abstract

(1) Background: Environmental contamination with antibiotics is particularly serious because the usual methods used in wastewater treatment plants turn out to be insufficient or ineffective. An interesting idea is to support natural biodegradation processes with physicochemical methods as well as with bioaugmentation with efficient microbial degraders. Hence, the aim of our study is evaluation of the effectiveness of different methods of nitrofurazone (NFZ) degradation: photolysis and photodegradation in the presence of two photocatalysts, the commercial TiO₂-P25 and a self-obtained Fe₃O₄@SiO₂/TiO₂ magnetic photocatalyst. (2) Methods: The chemical nature of the photocatalysis products was investigated using a spectrometric method, and then, they were subjected to biodegradation using the strain Achromobacter xylosoxidans NFZ2. Additionally, the effects of the photodegradation products on bacterial cell surface properties and membranes were studied. (3) Results: Photocatalysis with TiO₂-P25 allowed reduction of NFZ by over 90%, demonstrating that this method is twice as effective as photolysis alone. Moreover, the bacterial strain used proved to be effective in the removal of NFZ, as well as its intermediates. (4) Conclusions: The results indicated that photocatalysis alone or coupled with biodegradation with the strain A. xylosoxidans NFZ2 leads to efficient degradation and almost complete mineralization of NFZ. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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11 pages, 2782 KiB

Open AccessArticle

Biosensor-Based Directed Evolution of Methanol Dehydrogenase from Lysinibacillus xylanilyticus

by Thien-Kim Le, Su-Bin Ju, Hyewon Lee, Jin-Young Lee, So-Hyung Oh, Kil-Koang Kwon, Bong-Hyun Sung, Seung-Goo Lee and Soo-Jin Yeom

Int. J. Mol. Sci. 2021, 22(3), 1471; https://doi.org/10.3390/ijms22031471 - 2 Feb 2021

Cited by 16 | Viewed by 4148

Abstract

Methanol dehydrogenase (Mdh), is a crucial enzyme for utilizing methane and methanol as carbon and energy sources in methylotrophy and synthetic methylotrophy. Engineering of Mdh, especially NAD-dependent Mdh, has thus been actively investigated to enhance methanol conversion. However, its poor catalytic activity and low methanol affinity limit its wider application. In this study, we applied a transcriptional factor-based biosensor for the direct evolution of Mdh from Lysinibacillus xylanilyticus (Lxmdh), which has a relatively high turnover rate and low K_M value compared to other wild-type NAD-dependent Mdhs. A random mutant library of Lxmdh was constructed in Escherichia coli and was screened using formaldehyde-detectable biosensors by incubation with low methanol concentrations. Positive clones showing higher fluorescence were selected by fluorescence-activated cell sorting (FACS) system, and their catalytic activities toward methanol were evaluated. The successfully isolated mutants E396V, K318N, and K46E showed high activity, particularly at very low methanol concentrations. In kinetic analysis, mutant E396V, K318N, and K46E had superior methanol conversion efficiency, with 79-, 23-, and 3-fold improvements compared to the wild-type, respectively. These mutant enzymes could thus be useful for engineering synthetic methylotrophy and for enhancing methanol conversion to various useful products. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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22 pages, 3600 KiB

Open AccessArticle

Monokaryotic Pleurotus sapidus Strains with Intraspecific Variability of an Alkene Cleaving DyP-Type Peroxidase Activity as a Result of Gene Mutation and Differential Gene Expression

by Nina-Katharina Krahe, Ralf G. Berger, Martin Witt, Holger Zorn, Alejandra B. Omarini and Franziska Ersoy

Int. J. Mol. Sci. 2021, 22(3), 1363; https://doi.org/10.3390/ijms22031363 - 29 Jan 2021

Cited by 15 | Viewed by 2781

Abstract

The basidiomycete Pleurotus sapidus produced a dye-decolorizing peroxidase (PsaPOX) with alkene cleavage activity, implying potential as a biocatalyst for the fragrance and flavor industry. To increase the activity, a daughter-generation of 101 basidiospore-derived monokaryons (MK) was used. After a pre-selection according to the growth rate, the activity analysis revealed a stable intraspecific variability of the strains regarding peroxidase and alkene cleavage activity of PsaPOX. Ten monokaryons reached activities up to 2.6-fold higher than the dikaryon, with MK16 showing the highest activity. Analysis of the PsaPOX gene identified three different enzyme variants. These were co-responsible for the observed differences in activities between strains as verified by heterologous expression in Komagataella phaffii. The mutation S371H in enzyme variant PsaPOX_high caused an activity increase alongside a higher protein stability, while the eleven mutations in variant PsaPOX_low resulted in an activity decrease, which was partially based on a shift of the pH optimum from 3.5 to 3.0. Transcriptional analysis revealed the increased expression of PsaPOX in MK16 as reason for the higher PsaPOX activity in comparison to other strains producing the same PsaPOX variant. Thus, different expression profiles, as well as enzyme variants, were identified as crucial factors for the intraspecific variability of the PsaPOX activity in the monokaryons. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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16 pages, 14708 KiB

Open AccessArticle

A Novel Digestive α-Amylase from Blue Crab (Portunus segnis) Viscera: Purification, Biochemical Characterization and Application for the Improvement of Antioxidant Potential of Oat Flour

by Hana Maalej, Amina Maalej, Sawsan Affes, Noomen Hmidet and Moncef Nasri

Int. J. Mol. Sci. 2021, 22(3), 1070; https://doi.org/10.3390/ijms22031070 - 22 Jan 2021

Cited by 11 | Viewed by 3347

Abstract

This study reports on the purification and characterization of a digestive α-amylase from blue crab (Portunussegnis) viscera designated Blue Crab Amylase (BCA). The enzyme was purified to homogeneity by ultrafiltration, Sephadex G-100 gel filtration and Sepharose mono Q anion exchange chromatography, with the final purification fold of 424.02, specific activity of 1390.8 U mg⁻¹ and 27.8% recovery. BCA, showing a molecular weight of approximately 45 kDa, possesses desirable biotechnological features, such as optimal temperature of 50 °C, interesting thermal stability which is enhanced in the presence of starch, high stability towards surfactants (Tween 20, Tween 80 and Triton X-100), high specific activity, quite high storage and broad pH range stability. The enzyme displayed Km and Vmax values, of 7.5 ± 0.25 mg mL⁻¹ and 2000 ± 23 μmol min⁻¹ mg⁻¹ for potato starch, respectively. It hydrolyzed various carbohydrates and produced maltose, maltotriose and maltotetraose as the major end products of starch hydrolysis. In addition, the purified enzyme was successfully utilized for the improvement of the antioxidant potential of oat flour, which could be extended to other cereals. Interestingly, besides its suitability for application in different industrial sectors, especially food industries, the biochemical properties of BCA from the blue crab viscera provide novel features with other marine-derived enzymes and better understanding of the biodegradability of carbohydrates in marine environments, particularly in invasive alien crustaceans. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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15 pages, 1714 KiB

Open AccessArticle

Optimization of the Biocatalysis for D-DIBOA Synthesis Using a Quick and Sensitive New Spectrophotometric Quantification Method

by Gema Cabrera, Teresa Linares, Maria Elena de la Calle, Domingo Cantero, Antonio Valle and Jorge Bolivar

Int. J. Mol. Sci. 2020, 21(22), 8523; https://doi.org/10.3390/ijms21228523 - 12 Nov 2020

Cited by 3 | Viewed by 2397

Abstract

D-DIBOA (4-hydroxy-(2H)-1,4-benzoxazin-3-(4H)-one) is an allelopathic-derived compound with interesting herbicidal, fungicidal, and insecticide properties whose production has been successfully achieved by biocatalysis using a genetically engineered Escherichia coli strain. However, improvement and scaling-up of this process are hampered by the current methodology for D-DIBOA quantification, which is based on high-performance liquid chromatographic (HPLC), a time-consuming technique that requires expensive equipment and the use of environmentally unsafe solvents. In this work, we established and validated a rapid, simple, and sensitive spectrophotometric method for the quantification of the D-DIBOA produced by whole-cell biocatalysis, with limits of detection and quantification of 0.0165 and 0.0501 µmol·mL⁻¹ respectively. This analysis takes place in only a few seconds and can be carried out using 100 µL of the sample in a microtiter plate reader. We performed several whole-cell biocatalysis strategies to optimize the process by monitoring D-DIBOA production every hour to keep control of both precursor and D-DIBOA concentrations in the bioreactor. These experiments allowed increasing the D-DIBOA production from the previously reported 5.01 mM up to 7.17 mM (43% increase). This methodology will facilitate processes such as the optimization of the biocatalyst, the scaling up, and the downstream purification. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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Review

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23 pages, 3222 KiB

Open AccessReview

Production of Aldehydes by Biocatalysis

by Veronika Kazimírová and Martin Rebroš

Int. J. Mol. Sci. 2021, 22(9), 4949; https://doi.org/10.3390/ijms22094949 - 6 May 2021

Cited by 19 | Viewed by 5975

Abstract

The production of aldehydes, highly reactive and toxic chemicals, brings specific challenges to biocatalytic processes. Absence of natural accumulation of aldehydes in microorganisms has led to a combination of in vitro and in vivo strategies for both, bulk and fine production. Advances in genetic and metabolic engineering and implementation of computational techniques led to the production of various enzymes with special requirements. Cofactor synthesis, post-translational modifications and structure engineering are applied to prepare active enzymes for one-step or cascade reactions. This review presents the highlights in biocatalytical production of aldehydes with the potential to shape future industrial applications. Full article

(This article belongs to the Special Issue Biocatalysis, a Life Companion for Green Chemistry: Biomolecular Aspects of Bioprocesses)

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