Special Issue "Novel Enzyme and Whole-Cell Biocatalysts"

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

Deadline for manuscript submissions: 31 January 2020.

Special Issue Editors

Guest Editor
Prof. Anwar Sunna Website 1 Website 2 E-Mail
Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Phone: +61-2-9850-4220
Interests: biocatalysis; synthetic biology; bioengineering: proteins; nanoparticles
Guest Editor
Prof. Richard Daniellou Website E-Mail
Institut de Chimie Organique et Analytique (ICOA), Université d’Orléans UMR-CNRS 7311, BP 6759, rue de Chartres, 45067 Orléans CEDEX 2, France
Phone: +33-2-3849-4978
Interests: biocatalysts; enzymology; glycobiochemistry; glycosyltransferases; glycosidases

Special Issue Information

Dear Colleagues,

Global trends towards sustainability, the reduction of organic waste, and landfill avoidance are driving the demand for greener products with improved properties. Recent advances in synthetic biology, molecular biology, computational tools, and metabolic engineering have promoted the discovery of new enzymes and the rational design of whole-cell biocatalysts. Accordingly, with increased demand for sustainable and environmentally friendly biomanufacturing, 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, we would like to highlight these current advances in the field of biocatalysis, with special emphasis on novel enzymes and whole-cell biocatalysts for applications in industry, health, or cosmetics.

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

Manuscript Submission Information

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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. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 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
  • Glycosyl transferases
  • Protein engineering
  • Carbohydrates
  • Biocatalysis
  • Synthetic biology
  • Industrial enzymes
  • Thermostable enzymes
  • Glycoside hydrolases
  • Cell-free biocatalysis
  • Natural and non-natural multi-enzyme pathways
  • Bio-based chemicals

Published Papers (7 papers)

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Research

Open AccessArticle
Deciphering the Role of V88L Substitution in NDM-24 Metallo-β-Lactamase
Catalysts 2019, 9(9), 744; https://doi.org/10.3390/catal9090744 - 02 Sep 2019
Abstract
The New Delhi metallo-β-lactamase-1 (NDM-1) is a typical carbapenemase and plays a crucial role in antibiotic-resistance bacterial infection. Phylogenetic analysis, performed on known NDM-variants, classified NDM enzymes in seven clusters. Three of them include a major number of NDM-variants. In this study, we [...] Read more.
The New Delhi metallo-β-lactamase-1 (NDM-1) is a typical carbapenemase and plays a crucial role in antibiotic-resistance bacterial infection. Phylogenetic analysis, performed on known NDM-variants, classified NDM enzymes in seven clusters. Three of them include a major number of NDM-variants. In this study, we evaluated the role of the V88L substitution in NDM-24 by kinetical and structural analysis. Functional results showed that V88L did not significantly increase the resistance level in the NDM-24 transformant toward penicillins, cephalosporins, meropenem, and imipenem. Concerning ertapenem, E. coli DH5α/NDM-24 showed a MIC value 4-fold higher than that of E. coli DH5α/NDM-1. The determination of the kcat, Km, and kcat/Km values for NDM-24, compared with NDM-1 and NDM-5, demonstrated an increase of the substrate hydrolysis compared to all the β-lactams tested, except penicillins. The thermostability testing revealed that V88L generated a destabilized effect on NDM-24. The V88L substitution occurred in the β-strand and low β-sheet content in the secondary structure, as evidenced by the CD analysis data. In conclusion, the V88L substitution increases the enzyme activity and decreases the protein stability. This study characterizes the role of the V88L substitution in NDM-24 and provides insight about the NDM variants evolution. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
Highly Selective Oxidation of 5-Hydroxymethylfurfural to 5-Hydroxymethyl-2-Furancarboxylic Acid by a Robust Whole-Cell Biocatalyst
Catalysts 2019, 9(6), 526; https://doi.org/10.3390/catal9060526 - 12 Jun 2019
Abstract
Value-added utilization of biomass-derived 5-hydroxymethylfurfural (HMF) to produce useful derivatives is of great interest. In this work, extremely radiation resistant Deinococcus wulumuqiensis R12 was explored for the first time as a new robust biocatalyst for selective oxidation of HMF to 5-hydroxymethylfuroic acid (HMFCA). [...] Read more.
Value-added utilization of biomass-derived 5-hydroxymethylfurfural (HMF) to produce useful derivatives is of great interest. In this work, extremely radiation resistant Deinococcus wulumuqiensis R12 was explored for the first time as a new robust biocatalyst for selective oxidation of HMF to 5-hydroxymethylfuroic acid (HMFCA). Its resting cells exhibited excellent catalytic performance in a broad range of pH and temperature values, and extremely high tolerance to HMF and the HMFCA product. An excellent yield of HMFCA (up to 90%) was achieved when the substrate concentration was set to 300 mM under the optimized reaction conditions. In addition, 511 mM of product was obtained within 20 h by employing a fed-batch strategy, affording a productivity of 44 g/L per day. Of significant synthetic interest was the finding that the D. wulumuqiensis R12 cells were able to catalyze the selective oxidation of other structurally diverse aldehydes to their corresponding acids with good yield and high selectivity, indicating broad substrate scope and potential widespread applications in biotechnology and organic chemistry. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
Immobilization of β-Galactosidases on the Lactobacillus Cell Surface Using the Peptidoglycan-Binding Motif LysM
Catalysts 2019, 9(5), 443; https://doi.org/10.3390/catal9050443 - 12 May 2019
Abstract
Lysin motif (LysM) domains are found in many bacterial peptidoglycan hydrolases. They can bind non-covalently to peptidoglycan and have been employed to display heterologous proteins on the bacterial cell surface. In this study, we aimed to use a single LysM domain derived from [...] Read more.
Lysin motif (LysM) domains are found in many bacterial peptidoglycan hydrolases. They can bind non-covalently to peptidoglycan and have been employed to display heterologous proteins on the bacterial cell surface. In this study, we aimed to use a single LysM domain derived from a putative extracellular transglycosylase Lp_3014 of Lactobacillus plantarum WCFS1 to display two different lactobacillal β-galactosidases, the heterodimeric LacLM-type from Lactobacillus reuteri and the homodimeric LacZ-type from Lactobacillus delbrueckii subsp. bulgaricus, on the cell surface of different Lactobacillus spp. The β-galactosidases were fused with the LysM domain and the fusion proteins, LysM-LacLMLreu and LysM-LacZLbul, were successfully expressed in Escherichia coli and subsequently displayed on the cell surface of L. plantarum WCFS1. β-Galactosidase activities obtained for L. plantarum displaying cells were 179 and 1153 U per g dry cell weight, or the amounts of active surface-anchored β-galactosidase were 0.99 and 4.61 mg per g dry cell weight for LysM-LacLMLreu and LysM-LacZLbul, respectively. LysM-LacZLbul was also displayed on the cell surface of other Lactobacillus spp. including L. delbrueckii subsp. bulgaricus, L. casei and L. helveticus, however L. plantarum is shown to be the best among Lactobacillus spp. tested for surface display of fusion LysM-LacZLbul, both with respect to the immobilization yield as well as the amount of active surface-anchored enzyme. The immobilized fusion LysM-β-galactosidases are catalytically efficient and can be reused for several repeated rounds of lactose conversion. This approach, with the β-galactosidases being displayed on the cell surface of non-genetically modified food-grade organisms, shows potential for applications of these immobilized enzymes in the synthesis of prebiotic galacto-oligosaccharides. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
Effects of Random Mutagenesis and In Vivo Selection on the Specificity and Stability of a Thermozyme
Catalysts 2019, 9(5), 440; https://doi.org/10.3390/catal9050440 - 11 May 2019
Abstract
Factors that give enzymes stability, activity, and substrate recognition result from the combination of few weak molecular interactions, which can be difficult to study through rational protein engineering approaches. We used irrational random mutagenesis and in vivo selection to test if a β-glycosidase [...] Read more.
Factors that give enzymes stability, activity, and substrate recognition result from the combination of few weak molecular interactions, which can be difficult to study through rational protein engineering approaches. We used irrational random mutagenesis and in vivo selection to test if a β-glycosidase from the thermoacidophile Saccharolobus solfataricus (Ssβ-gly) could complement an Escherichia coli strain unable to grow on lactose. The triple mutant of Ssβ-gly (S26L, P171L, and A235V) was more active than the wild type at 85 °C, inactivated at this temperature almost 300-fold quicker, and showed a 2-fold higher kcat on galactosides. The three mutations, which were far from the active site, were analyzed to test their effect at the structural level. Improved activity on galactosides was induced by the mutations. The S26L and P171L mutations destabilized the enzyme through the removal of a hydrogen bond and increased flexibility of the peptide backbone, respectively. However, the flexibility added by S26L mutation improved the activity at T > 60 °C. This study shows that random mutagenesis and biological selection allowed the identification of residues that are critical in determining thermal activity, stability, and substrate recognition. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
Change of the Product Specificity of a Cyclodextrin Glucanotransferase by Semi-Rational Mutagenesis to Synthesize Large-Ring Cyclodextrins
Catalysts 2019, 9(3), 242; https://doi.org/10.3390/catal9030242 - 06 Mar 2019
Abstract
Cyclodextrin glucanotransferases (CGTases) convert starch to cyclodextrins (CD) of various sizes. To engineer a CGTase for the synthesis of large-ring CD composed of 9 to 12 glucose units, a loop structure of the protein involved in substrate binding was targeted for semi-rational mutagenesis. [...] Read more.
Cyclodextrin glucanotransferases (CGTases) convert starch to cyclodextrins (CD) of various sizes. To engineer a CGTase for the synthesis of large-ring CD composed of 9 to 12 glucose units, a loop structure of the protein involved in substrate binding was targeted for semi-rational mutagenesis. Based on multiple protein alignments and protein structure information, a mutagenic megaprimer was designed to encode a partial randomization of eight amino acid residues within the loop region. The library obtained encoding amino acid sequences occurring in wild type CGTases in combination with a screening procedure yielded sequences displaying a changed CD product specificity. As a result, variants of the CGTase from the alkaliphilic Bacillus sp. G825-6 synthesizing mainly CD9 to CD12 could be obtained. When the mutagenesis experiment was performed with the CGTase G825-6 variant Y183R, the same loop alterations that increased the total CD synthesis activity resulted in lower activities of the variant enzymes created. In the presence of the amino acid residue R183, the synthesis of CD8 was suppressed and larger CD were obtained as the main products. The alterations not only affected the product specificity, but also influenced the thermal stability of some of the CGTase variants indicating the importance of the loop structure for the stability of the CGTase. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
Characterisation of the First Archaeal Mannonate Dehydratase from Thermoplasma acidophilum and Its Potential Role in the Catabolism of D-Mannose
Catalysts 2019, 9(3), 234; https://doi.org/10.3390/catal9030234 - 03 Mar 2019
Abstract
Mannonate dehydratases catalyse the dehydration reaction from mannonate to 2-keto-3-deoxygluconate as part of the hexuronic acid metabolism in bacteria. Bacterial mannonate dehydratases present in this gene cluster usually belong to the xylose isomerase-like superfamily, which have been the focus of structural, biochemical and [...] Read more.
Mannonate dehydratases catalyse the dehydration reaction from mannonate to 2-keto-3-deoxygluconate as part of the hexuronic acid metabolism in bacteria. Bacterial mannonate dehydratases present in this gene cluster usually belong to the xylose isomerase-like superfamily, which have been the focus of structural, biochemical and physiological studies. Mannonate dehydratases from archaea have not been studied in detail. Here, we identified and characterised the first archaeal mannonate dehydratase (TaManD) from the thermoacidophilic archaeon Thermoplasma acidophilum. The recombinant TaManD enzyme was optimally active at 65 °C and showed high specificity towards D-mannonate and its lactone, D-mannono-1,4-lactone. The gene encoding for TaManD is located adjacent to a previously studied mannose-specific aldohexose dehydrogenase (AldT) in the genome of T. acidophilum. Using nuclear magnetic resonance (NMR) spectroscopy, we showed that the mannose-specific AldT produces the substrates for TaManD, demonstrating the possibility for an oxidative metabolism of mannose in T. acidophilum. Among previously studied mannonate dehydratases, TaManD showed closest homology to enzymes belonging to the xylose isomerase-like superfamily. Genetic analysis revealed that closely related mannonate dehydratases among archaea are not located in a hexuronate gene cluster like in bacteria, but next to putative aldohexose dehydrogenases, implying a different physiological role of mannonate dehydratases in those archaeal species. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Open AccessArticle
An Innovative Biocatalyst for Continuous 2G Ethanol Production from Xylo-Oligomers by Saccharomyces cerevisiae through Simultaneous Hydrolysis, Isomerization, and Fermentation (SHIF)
Catalysts 2019, 9(3), 225; https://doi.org/10.3390/catal9030225 - 01 Mar 2019
Abstract
Many approaches have been considered aimed at ethanol production from the hemicellulosic fraction of biomass. However, the industrial implementation of this process has been hindered by some bottlenecks, one of the most important being the ease of contamination of the bioreactor by bacteria [...] Read more.
Many approaches have been considered aimed at ethanol production from the hemicellulosic fraction of biomass. However, the industrial implementation of this process has been hindered by some bottlenecks, one of the most important being the ease of contamination of the bioreactor by bacteria that metabolize xylose. This work focuses on overcoming this problem through the fermentation of xylulose (the xylose isomer) by native Saccharomyces cerevisiae using xylo-oligomers as substrate. A new concept of biocatalyst is proposed, containing xylanases and xylose isomerase (XI) covalently immobilized on chitosan, and co-encapsulated with industrial baker’s yeast in Ca-alginate gel spherical particles. Xylo-oligomers are hydrolyzed, xylose is isomerized, and finally xylulose is fermented to ethanol, all taking place simultaneously, in a process called simultaneous hydrolysis, isomerization, and fermentation (SHIF). Among several tested xylanases, Multifect CX XL A03139 was selected to compose the biocatalyst bead. Influences of pH, Ca2+, and Mg2+ concentrations on the isomerization step were assessed. Experiments of SHIF using birchwood xylan resulted in an ethanol yield of 0.39 g/g, (76% of the theoretical), selectivity of 3.12 gethanol/gxylitol, and ethanol productivity of 0.26 g/L/h. Full article
(This article belongs to the Special Issue Novel Enzyme and Whole-Cell Biocatalysts)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: A facile, covalent enzyme immobilisation technology that retains enzyme activity through orthogonal conjugation

Author: Colin Scott

Title: Exploring microbial diversity for the discovery of robust biocatalysts active at elevated temperatures

Author: Garabed Antranikian

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