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Special Issue "Genome Mining and Marine Microbial Natural Products"

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

Deadline for manuscript submissions: 31 December 2017

Special Issue Editors

Guest Editor
Prof. Dr. Kui Hong

Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
E-Mail
Fax: +86-27-68752442
Interests: microbial systematic guided marine microbial drug resources (culture, compounds and genes): ecology, collection, isolation and identification; genomics guided marine microbial natural products discovery and biosynthesis
Guest Editor
Prof. Dr. Changsheng Zhang

Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
Website | E-Mail
Interests: marine actinobacteria; marine natural products; antimicrobial activity; antitumor activity; marine drug development; biosynthesis of marine polycyclic compounds; genome mining of marine actinomycetes
Guest Editor
Prof. Dr. Alan Dobson

School of Microbiology, University College Cork, Cork, Ireland
Website | E-Mail
Interests: marine biotechnology; marine natural products; antibiotics drug discovery; marine enzymes; marine microbial ecology; metagenomics; genomics.

Special Issue Information

Dear Colleagues,

Most of the bioactive secondary metabolites for drug discovery isolated from marine microorganisms have been discovered to date using classical bioassay-guided regimes. This process is currently undergoing significant changes primarily as a result of rapid developments in sequencing technology, synthetic biology and bioinformatics. As increasing numbers of whole-genome sequences become available for marine microorganisms, genome mining has become a very attractive tool for drug discovery. Bioinformatic-based approaches are typically employed to screen, and subsequently identify, novel gene clusters, many of which are responsible for the production of the novel molecules. Many genomes appear however to possess “silent” or cryptic biosynthetic gene clusters, the products of which appear to be regulated by a variety of environmental factors, and therefore remain largely undetected.

In this Special Issue, we focus on the rich genomic resources present within the genomes of marine microorganisms and the use of recently developed tools and technologies to exploit this genetic richness, to facilitate the discovery or find new bioactive molecules with potential biopharmaceutical applications.

For this Special Issue of Marine Drugs, we urge you to consider publishing your review paper or original research in the areas listed below:

  • Bioinformatic tools and their application in genome mining for secondary metabolites
  • Genome mining approaches for the identification of novel secondary metabolites
  • Merging ecology (physical, chemical factors or co-culture) with microbial genome mining for secondary metabolites’ discovery
  • Heterologous systems for the expression of gene clusters to identify novel metabolites
  • Unlocking cryptic pathways, employing genomic based approaches
  • Cutting-edge technology in genome editing and novel metabolites identification

Prof. Dr. Kui Hong
Prof. Dr. Changsheng Zhang
Prof. Dr. Alan Dobson
Guest Editors

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.

Keywords

  • Genome mining
  • Secondary metabolites
  • Natural products
  • Cryptic gene clusters
  • Genome editing
  • Heterologous expression
  • Cryptic gene activation

Published Papers (3 papers)

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Research

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Open AccessArticle Producing Novel Fibrinolytic Isoindolinone Derivatives in Marine Fungus Stachybotrys longispora FG216 by the Rational Supply of Amino Compounds According to Its Biosynthesis Pathway
Mar. Drugs 2017, 15(7), 214; doi:10.3390/md15070214
Received: 22 March 2017 / Revised: 26 June 2017 / Accepted: 3 July 2017 / Published: 5 July 2017
PDF Full-text (1712 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Many fungi in the Stachybotrys genus can produce various isoindolinone derivatives. These compounds are formed by a spontaneous reaction between a phthalic aldehyde precursor and an ammonium ion or amino compounds. In this study, we suggested the isoindolinone biosynthetic gene cluster in Stachybotrys
[...] Read more.
Many fungi in the Stachybotrys genus can produce various isoindolinone derivatives. These compounds are formed by a spontaneous reaction between a phthalic aldehyde precursor and an ammonium ion or amino compounds. In this study, we suggested the isoindolinone biosynthetic gene cluster in Stachybotrys by genome mining based on three reported core genes. Remarkably, there is an additional nitrate reductase (NR) gene copy in the proposed cluster. NR is the rate-limiting enzyme of nitrate reduction. Accordingly, this cluster was speculated to play a role in the balance of ammonium ion concentration in Stachybotrys. Ammonium ions can be replaced by different amino compounds to create structural diversity in the biosynthetic process of isoindolinone. We tested a rational supply of amino compounds ((±)-3-amino-2-piperidinone, glycine, and l-threonine) in the culture of an isoindolinone high-producing marine fungus, Stachybotrys longispora FG216. As a result, we obtained four new kinds of isoindolinone derivatives (FGFC4–GFC7) by this method. Furthermore, high yields of FGFC4–FGFC7 confirmed the outstanding production capacity of FG216. Among the four new isoindolinone derivatives, FGFC6 and FGFC7 showed promising fibrinolytic activities. The knowledge of biosynthesis pathways may be an important attribute for the discovery of novel bioactive marine natural products. Full article
(This article belongs to the Special Issue Genome Mining and Marine Microbial Natural Products)
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Review

Jump to: Research

Open AccessReview Biogenetic Relationships of Bioactive Sponge Merotriterpenoids
Mar. Drugs 2017, 15(9), 285; doi:10.3390/md15090285
Received: 25 July 2017 / Revised: 7 September 2017 / Accepted: 7 September 2017 / Published: 10 September 2017
PDF Full-text (5007 KB) | HTML Full-text | XML Full-text
Abstract
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied.
[...] Read more.
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied. In this review, an in depth structural analysis of sponge merotriterpenoids, including the adociasulfate family of kinesin motor protein inhibitors, provides insight into their biosynthesis. Several key structural features provide clues to the relationships between compounds. All adociasulfates appear to be derived from only four different hydroquinone hexaprenyl diphosphate precursors, each varying in the number and position of epoxidations. Proton-initiated cyclization of these precursors can lead to all carbon skeletons observed amongst sponge merotriterpenoids. Consideration of the enzymes involved in the proposed biosynthetic route suggests a bacterial source, and a hypothetical gene cluster was constructed that may facilitate discovery of the authentic pathway from the sponge metagenome. A similar rationale can be extended to other sponge meroterpenoids, for which no biosynthetic pathways have yet been identified. Full article
(This article belongs to the Special Issue Genome Mining and Marine Microbial Natural Products)
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Figure 1

Open AccessReview Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials
Mar. Drugs 2017, 15(9), 272; doi:10.3390/md15090272
Received: 20 July 2017 / Revised: 12 August 2017 / Accepted: 23 August 2017 / Published: 28 August 2017
PDF Full-text (3888 KB) | HTML Full-text | XML Full-text
Abstract
The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis
[...] Read more.
The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis and chemical structure elucidation, have accelerated the numbers of antimicrobial molecules originating from the ocean moving into clinical trials. The chemical diversity associated with these marine-derived molecules is immense, varying from simple linear peptides and fatty acids to complex alkaloids, terpenes and polyketides, etc. Such an array of structurally distinct molecules performs functionally diverse biological activities against many pathogenic bacteria and fungi, making marine-derived natural products valuable commodities, particularly in the current age of antimicrobial resistance. In this review, we have highlighted several marine-derived natural products (and their synthetic derivatives), which have gained recognition as effective antimicrobial agents over the past five years (2012–2017). These natural products have been categorized based on their chemical structures and the structure-activity mediated relationships of some of these bioactive molecules have been discussed. Finally, we have provided an insight into how genome mining efforts are likely to expedite the discovery of novel antimicrobial compounds. Full article
(This article belongs to the Special Issue Genome Mining and Marine Microbial Natural Products)
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Journal Contact

MDPI AG
Marine Drugs Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
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Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
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