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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 December 2020) | Viewed by 22266

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Dr. Rebecca Pogni

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Guest Editor

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
Interests: oxidative enzymes; metalloproteins; biocatalysis; protein radicals; lignin; fiber; electron paramagnetic resonance (EPR); enzyme immobilization; chitinolytic materials; biomaterials
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Special Issue Information

Dear Colleagues,

This Special Issue is linked to the 10th edition of the “OxiZymes” conference, which will be held on September 22–25, 2020 in Siena, Italy. The purpose of the meeting is to stimulate scientific research on the discovery and mode of action of oxidoreductases and their industrial applications. Initially specifically devoted to research activities on laccases and peroxidases, this series of conferences is now open to contributions related to the whole class of oxidoreductases. The conference will provide a unique opportunity for industrial researchers to meet with foremost young academics for knowledge transfer and to establish research collaborations. The conference format is designed to be highly interactive, with ample time for stimulating discussions, interdisciplinary interactions, and meetings alongside the scientific sessions.

This Special Issue will cover the following topics:

Newly discovered oxizymes;
Oxizyme mechanism and structure;
Oxizyme engineering and computational approaches;
Artificial oxizymes and biomimetic cofactors;
Preparative and biotechnological applications, including the following:
Oxizymes in fine chemicals;
Oxizymes in active pharmaceutical ingredients (API);
Oxizymes in food;
Oxizymes in biorefinery;
Oxizymes in biosensors;
Oxizymes in biomaterials applications.

Prof. Rebecca Pogni

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 submissions that pass pre-check are 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

oxizymes
oxidoreductases and their industrial applications
oxizyme mechanism and structure
oxizyme engineering and computational approaches
artificial oxizymes and biomimetic cofactors

Published Papers (7 papers)

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Research

13 pages, 2514 KiB

Open AccessArticle

Homogentisic Acid and Gentisic Acid Biosynthesized Pyomelanin Mimics: Structural Characterization and Antioxidant Activity

by Maher Al Khatib, Jessica Costa, Daniele Spinelli, Eliana Capecchi, Raffaele Saladino, Maria Camilla Baratto and Rebecca Pogni

Int. J. Mol. Sci. 2021, 22(4), 1739; https://doi.org/10.3390/ijms22041739 - 09 Feb 2021

Cited by 12 | Viewed by 2962

Abstract

Pyomelanin mimics from homogentisic acid (HGA) and gentisic acid (GA) were biosynthesized by the oxidative enzyme T. versicolor laccase at physiological pH to obtain water soluble melanins. The pigments show brown-black color, broad band visible light absorption, a persistent paramagnetism and high antioxidant activity. The EPR approach shows that at least two different radical species are present in both cases, contributing to the paramagnetism of the samples. This achievement can also shed light on the composition of the ochronotic pigment in the Alkaptonuria disease. On the other hand, these soluble pyomelanin mimics, sharing physico-chemical properties with eumelanin, can represent a suitable alternative to replace the insoluble melanin pigment in biotechnological applications. Full article

(This article belongs to the Special Issue OxiZymes)

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14 pages, 2132 KiB

Open AccessArticle

Laccase-Catalyzed 1,4-Dioxane-Mediated Synthesis of Belladine N-Oxides with Anti-Influenza A Virus Activity

by Claudio Zippilli, Lorenzo Botta, Bruno Mattia Bizzarri, Lucia Nencioni, Marta De Angelis, Virginia Protto, Gianluca Giorgi, Maria Camilla Baratto, Rebecca Pogni and Raffaele Saladino

Int. J. Mol. Sci. 2021, 22(3), 1337; https://doi.org/10.3390/ijms22031337 - 29 Jan 2021

Cited by 6 | Viewed by 2283

Abstract

Belladine N-oxides active against influenza A virus have been synthetized by a novel laccase-catalyzed 1,4-dioxane-mediated oxidation of aromatic and side-chain modified belladine derivatives. Electron paramagnetic resonance (EPR) analysis confirmed the role of 1,4-dioxane as a co-oxidant. The reaction was chemo-selective, showing a high functional-group compatibility. The novel belladine N-oxides were active against influenza A virus, involving the early stage of the virus replication life cycle. Full article

(This article belongs to the Special Issue OxiZymes)

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19 pages, 5840 KiB

Open AccessArticle

Protein Engineering Approaches to Enhance Fungal Laccase Production in S. cerevisiae

by Pablo Aza, Felipe de Salas, Gonzalo Molpeceres, David Rodríguez-Escribano, Iñigo de la Fuente and Susana Camarero

Int. J. Mol. Sci. 2021, 22(3), 1157; https://doi.org/10.3390/ijms22031157 - 25 Jan 2021

Cited by 26 | Viewed by 4817

Abstract

Laccases secreted by saprotrophic basidiomycete fungi are versatile biocatalysts able to oxidize a wide range of aromatic compounds using oxygen as the sole requirement. Saccharomyces cerevisiae is a preferred host for engineering fungal laccases. To assist the difficult secretion of active enzymes by yeast, the native signal peptide is usually replaced by the preproleader of S. cerevisiae alfa mating factor (MFα1). However, in most cases, only basal enzyme levels are obtained. During directed evolution in S. cerevisiae of laccases fused to the α-factor preproleader, we demonstrated that mutations accumulated in the signal peptide notably raised enzyme secretion. Here we describe different protein engineering approaches carried out to enhance the laccase activity detected in the liquid extracts of S. cerevisiae cultures. We demonstrate the improved secretion of native and engineered laccases by using the fittest mutated α-factor preproleader obtained through successive laccase evolution campaigns in our lab. Special attention is also paid to the role of protein N-glycosylation in laccase production and properties, and to the introduction of conserved amino acids through consensus design enabling the expression of certain laccases otherwise not produced by the yeast. Finally, we revise the contribution of mutations accumulated in laccase coding sequence (CDS) during previous directed evolution campaigns that facilitate enzyme production. Full article

(This article belongs to the Special Issue OxiZymes)

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14 pages, 2044 KiB

Open AccessArticle

A Fungal Ascorbate Oxidase with Unexpected Laccase Activity

by Verena Braunschmid, Sarah Fuerst, Veronika Perz, Sabine Zitzenbacher, Javier Hoyo, Cesar Fernandez-Sanchez, Tzanko Tzanov, Georg Steinkellner, Karl Gruber, Gibson S. Nyanhongo, Doris Ribitsch and Georg M. Guebitz

Int. J. Mol. Sci. 2020, 21(16), 5754; https://doi.org/10.3390/ijms21165754 - 11 Aug 2020

Cited by 12 | Viewed by 3578

Abstract

Ascorbate oxidases are an enzyme group that has not been explored to a large extent. So far, mainly ascorbate oxidases from plants and only a few from fungi have been described. Although ascorbate oxidases belong to the well-studied enzyme family of multi-copper oxidases, their function is still unclear. In this study, Af_AO1, an enzyme from the fungus Aspergillus flavus, was characterized. Sequence analyses and copper content determination demonstrated Af_AO1 to belong to the multi-copper oxidase family. Biochemical characterization and 3D-modeling revealed a similarity to ascorbate oxidases, but also to laccases. Af_AO1 had a 10-fold higher affinity to ascorbic acid (K_M = 0.16 ± 0.03 mM) than to ABTS (K_M = 1.89 ± 0.12 mM). Furthermore, the best fitting 3D-model was based on the ascorbate oxidase from Cucurbita pepo var. melopepo. The laccase-like activity of Af_AO1 on ABTS (V_max = 11.56 ± 0.15 µM/min/mg) was, however, not negligible. On the other hand, other typical laccase substrates, such as syringaldezine and guaiacol, were not oxidized by Af_AO1. According to the biochemical and structural characterization, Af_AO1 was classified as ascorbate oxidase with unusual, laccase-like activity. Full article

(This article belongs to the Special Issue OxiZymes)

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15 pages, 3101 KiB

Open AccessArticle

Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I

by Joaquin Ramirez-Ramirez, Javier Martin-Diaz, Nina Pastor, Miguel Alcalde and Marcela Ayala

Int. J. Mol. Sci. 2020, 21(16), 5734; https://doi.org/10.3390/ijms21165734 - 10 Aug 2020

Cited by 8 | Viewed by 3132

Abstract

Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel. Full article

(This article belongs to the Special Issue OxiZymes)

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10 pages, 2199 KiB

Open AccessArticle

From Graphite to Laccase Biofunctionalized Few-Layer Graphene: A “One Pot” Approach Using a Chimeric Enzyme

by Ilaria Sorrentino, Ilaria Stanzione, Yannig Nedellec, Alessandra Piscitelli, Paola Giardina and Alan Le Goff

Int. J. Mol. Sci. 2020, 21(11), 3741; https://doi.org/10.3390/ijms21113741 - 26 May 2020

Cited by 7 | Viewed by 2033

Abstract

A chimeric enzyme based on the genetic fusion of a laccase with a hydrophobin domain was employed to functionalize few-layer graphene, previously exfoliated from graphite in the presence of the hydrophobin. The as-produced, biofunctionalized few-layer graphene was characterized by electrochemistry and Raman spectroscopy, and finally employed in the biosensing of phenols such as catechol and dopamine. This strategy paves the way for the functionalization of nanomaterials by hydrophobin domains of chimeric enzymes and their use in a variety of electrochemical applications. Full article

(This article belongs to the Special Issue OxiZymes)

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17 pages, 3538 KiB

Open AccessArticle

Structure and Bioactive Properties of Novel Textile Dyes Synthesised by Fungal Laccase

by Jolanta Polak, Kamila Wlizło, Rebecca Pogni, Elena Petricci, Marcin Grąz, Katarzyna Szałapata, Monika Osińska-Jaroszuk, Justyna Kapral-Piotrowska, Bożena Pawlikowska-Pawlęga and Anna Jarosz-Wilkołazka

Int. J. Mol. Sci. 2020, 21(6), 2052; https://doi.org/10.3390/ijms21062052 - 17 Mar 2020

Cited by 14 | Viewed by 2588

Abstract

Novel sustainable processes involving oxidative enzymatic catalysts are considered as an alternative for classical organic chemistry. The unique physicochemical and bioactive properties of novel bio-products can be obtained using fungal laccase as catalyst. Among them are textile biodyes synthesised during oxidation of substrates belonging to the amine and methoxy organic derivatives. The process of synthesis occurs in mild conditions of pH, temperature, and pressure, and without using harmful oxidants. The effect of fungal laccase activity on the substrates mixture transformation efficiency was analysed in terms of antimicrobial dye synthesis on a large scale. Three new phenazine dyes, obtained in the presence of laccase from Cerrena unicolor, were studied for their structure and properties. The phenazine core structure of the products was a result of tri-molecular transformation of aminomethoxybenzoic acid and aminonaphthalene sulfonic acid isomers. One of the compounds from the synthesised dye, namely 10-((2-carboxy-6-methoxyphenyl)amino)-11-methoxybenzo[a]phenazine-8-carboxylic acid, was able to inhibit the growth of Staphylococcus aureus. The high concentration of substrates (5 g/L) was efficiently transformed during 72 h in the mild conditions of pH 4 with the use of laccase with an activity of 200 U per g of the substrates mixture. The new bioactive dye exhibited excellent dyeing properties with concomitant antibacterial and antioxidative activity. The proposed enzyme-mediated synthesis represents an alternative eco-friendly route for the synthesis of novel antimicrobial compounds with high importance for the medical textile industry. Full article

(This article belongs to the Special Issue OxiZymes)

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