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Special Issue "Marine Enzymes: Sources, Biochemistry and Bioprocesses for Marine Biotechnology"

A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: 31 December 2017

Special Issue Editor

Guest Editor
Dr. Antonio Trincone

Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Comprensorio Olivetti, Edificio 70, Via Campi Flegrei 34, I-80078 Pozzuoli, Napoli, Italy
Website | E-Mail
Fax: +39 081 8041770
Interests: biocatalysis; marine enzymes; marine glycosidases; marine biotechnology; oligosaccharides

Special Issue Information

Dear Colleagues,

The interdisciplinary study of the complexity of marine habitats has increased knowledge of marine forms of life. Marine-originating biocatalysts are attractive to biocatalysis practitioners for novel biochemical and stereochemical features. An in-depth knowledge of the precise biological functions of genes, proteins and enzymes within the marine ecosystem is still considered one of the least developed fields of research; even though in recent years marine habitat has been recognized as an untapped source of novel enzymes and metabolites. Expanding the range of enzymes from marine organisms is one of the key points in future marine biotechnology roadmaps. In particular, the importance of marine biocatalysts is recognized when addressing the exploration of chemical and biological diversity for novel materials and products, and for biomass production and processing, both used in foresight analyses for future research in this field. Convincing examples, such as the specific diversity of molecular assets of biocatalysis using marine enzymes with respect to terrestrial counterparts, are increasingly reported in the literature regarding all marine sources (not only microorganisms and fungi, plants and animals, but also extremophiles and symbiotic microorganisms). Indeed the plasticity of biological adaptations of marine organisms to the wide range of environmental events in specific environments (temperature, salinity, tides, pressure, radiation, light, etc.) provides an enormous reservoir of interesting subjects for basic and applicative studies.

Processes using marine enzymes and marine biomasses are central in different biotechnological fields of applications: (i) in a biorefinery value-chain with marine enzymes for biochemical processes; (ii) in food industries for enzymatic procedures in seafood processing; (iii) in fields of fine chemicals—in pharmaceutical, cosmetics, agriculture and environmental sectors—enzymatic treatments are a tool to improve efficiency and selectivity for extraction/manipulation of structurally complex marine molecules to gain access to bioactive compounds and to provide complex core blocks for hemisynthesis; (iv) the field of marine biomarkers and applications in pollution monitoring (biosensor) and bioremediation could also be of high significance for the appreciation of marine sources for enzymes.

Preeminent conclusions by many scientists in the field of marine biotechnology emphasize that due to marine biological diversity and the specificity of biological metabolisms, the study of marine biocatalysts on a global scale is just starting and possesses huge potential for development and applications with industrial benefits.

In this Special Issue, along with contributions regarding the potential of marine enzymes as useful tools in biocatalysis, results of enzymatic bioprospecting in gross marine environments will also be acknowledged. In addition, studies about structural characterizations, biological functions and aspects related to the complexity of marine enzyme-based bioprocesses will be hosted.

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. Marine Drugs 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 1800 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.

Published Papers (3 papers)

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Research

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Open AccessArticle Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01
Mar. Drugs 2017, 15(2), 37; doi:10.3390/md15020037
Received: 28 October 2016 / Revised: 26 January 2017 / Accepted: 8 February 2017 / Published: 14 February 2017
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Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d
[...] Read more.
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%–25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%–68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%. Full article
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Open AccessArticle Structure-Based Design and Synthesis of a New Phenylboronic-Modified Affinity Medium for Metalloprotease Purification
Mar. Drugs 2017, 15(1), 5; doi:10.3390/md15010005
Received: 17 November 2016 / Revised: 19 December 2016 / Accepted: 21 December 2016 / Published: 27 December 2016
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Abstract
Metalloproteases are emerging as useful agents in the treatment of many diseases including arthritis, cancer, cardiovascular diseases, and fibrosis. Studies that could shed light on the metalloprotease pharmaceutical applications require the pure enzyme. Here, we reported the structure-based design and synthesis of the
[...] Read more.
Metalloproteases are emerging as useful agents in the treatment of many diseases including arthritis, cancer, cardiovascular diseases, and fibrosis. Studies that could shed light on the metalloprotease pharmaceutical applications require the pure enzyme. Here, we reported the structure-based design and synthesis of the affinity medium for the efficient purification of metalloprotease using the 4-aminophenylboronic acid (4-APBA) as affinity ligand, which was coupled with Sepharose 6B via cyanuric chloride as spacer. The molecular docking analysis showed that the boron atom was interacting with the hydroxyl group of Ser176 residue, whereas the hydroxyl group of the boronic moiety is oriented toward Leu175 and His177 residues. In addition to the covalent bond between the boron atom and hydroxyl group of Ser176, the spacer between boronic acid derivatives and medium beads contributes to the formation of an enzyme-medium complex. With this synthesized medium, we developed and optimized a one-step purification procedure and applied it for the affinity purification of metalloproteases from three commercial enzyme products. The native metalloproteases were purified to high homogeneity with more than 95% purity. The novel purification method developed in this work provides new opportunities for scientific, industrial and pharmaceutical projects. Full article
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Review

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Open AccessFeature PaperReview Enzymatic Processes in Marine Biotechnology
Mar. Drugs 2017, 15(4), 93; doi:10.3390/md15040093
Received: 17 February 2017 / Revised: 16 March 2017 / Accepted: 20 March 2017 / Published: 25 March 2017
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Abstract
In previous review articles the attention of the biocatalytically oriented scientific community towards the marine environment as a source of biocatalysts focused on the habitat-related properties of marine enzymes. Updates have already appeared in the literature, including marine examples of oxidoreductases, hydrolases, transferases,
[...] Read more.
In previous review articles the attention of the biocatalytically oriented scientific community towards the marine environment as a source of biocatalysts focused on the habitat-related properties of marine enzymes. Updates have already appeared in the literature, including marine examples of oxidoreductases, hydrolases, transferases, isomerases, ligases, and lyases ready for food and pharmaceutical applications. Here a new approach for searching the literature and presenting a more refined analysis is adopted with respect to previous surveys, centering the attention on the enzymatic process rather than on a single novel activity. Fields of applications are easily individuated: (i) the biorefinery value-chain, where the provision of biomass is one of the most important aspects, with aquaculture as the prominent sector; (ii) the food industry, where the interest in the marine domain is similarly developed to deal with the enzymatic procedures adopted in food manipulation; (iii) the selective and easy extraction/modification of structurally complex marine molecules, where enzymatic treatments are a recognized tool to improve efficiency and selectivity; and (iv) marine biomarkers and derived applications (bioremediation) in pollution monitoring are also included in that these studies could be of high significance for the appreciation of marine bioprocesses. Full article
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