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

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

Deadline for manuscript submissions: 31 July 2021.

Special Issue Editor

Dr. Antonio Trincone
Website
Guest Editor
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
Special Issues and Collections in MDPI journals

Special Issue Information

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • biocatalysis
  • green chemistry
  • biomasses
  • biorefinery
  • enzyme engineering
  • industrial enzymes

Published Papers (5 papers)

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Research

Open AccessArticle
Nitrofurazone Removal from Water Enhanced by Coupling Photocatalysis and Biodegradation
Int. J. Mol. Sci. 2021, 22(4), 2186; https://doi.org/10.3390/ijms22042186 - 22 Feb 2021
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 [...] Read more.
(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
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Open AccessArticle
Biosensor-Based Directed Evolution of Methanol Dehydrogenase from Lysinibacillus xylanilyticus
Int. J. Mol. Sci. 2021, 22(3), 1471; https://doi.org/10.3390/ijms22031471 - 02 Feb 2021
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 [...] Read more.
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 KM 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
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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
Int. J. Mol. Sci. 2021, 22(3), 1363; https://doi.org/10.3390/ijms22031363 - 29 Jan 2021
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 [...] Read more.
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
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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
Int. J. Mol. Sci. 2021, 22(3), 1070; https://doi.org/10.3390/ijms22031070 - 22 Jan 2021
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 [...] Read more.
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
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Open AccessArticle
Optimization of the Biocatalysis for D-DIBOA Synthesis Using a Quick and Sensitive New Spectrophotometric Quantification Method
Int. J. Mol. Sci. 2020, 21(22), 8523; https://doi.org/10.3390/ijms21228523 - 12 Nov 2020
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 [...] Read more.
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
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