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Marine Drugs
Special Issues
Bioinformatics of Marine Natural Products
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Bioinformatics of Marine Natural Products

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

Deadline for manuscript submissions: closed (6 August 2020) | Viewed by 36907

Special Issue Editors

Dr. Giovanna Romano

E-Mail Website
Guest Editor
Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Naples, Italy
Interests: bioactive metabolites from marine organisms for pharmaceutical, nutraceutical and cosmeceutical applications; novel strategies to identify marine-derived compounds; including-omic approaches
Special Issues, Collections and Topics in MDPI journals
Dr. Alessandra Rogato

E-Mail Website
Guest Editor
Institute of Bioscience and BioResources, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Napoli, Italy
Interests: marine functional genomics; Molecular genetics; nutrients sensing and uptake; marine diatoms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in bioinformatics and the increasing availability of sequenced genomes provide more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts from marine organisms. For example, many microorganisms have the potential to produce a far greater number of natural products than have been isolated to date, since most biosynthetic gene clusters are either silent or expressed at very low levels when they are cultured under standard laboratory conditions. The identification of biosynthetic gene and gene clusters through bioinformatics approach and their eventual heterologous expression, will give a great impulse for natural products identification and drug discovery from marine organisms.

Dr. Giovanna Romano
Dr. Alessandra Rogato
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 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. 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 2900 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
  • biosynthetic genes
  • biosynthetic gene clusters
  • bioinformatics approach
  • cryptic metabolic pathways
  • uncultivable microorganisms
  • polyketide synthase
  • metagenomic approach
  • environmental DNA
  • polyketide synthases (PKS)
  • non-ribosomal peptides (NRP)

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Published Papers (7 papers)

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Research

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17 pages, 2432 KiB  
Article
Identification of Prostaglandin Pathway in Dinoflagellates by Transcriptome Data Mining
by Valeria Di Dato, Adrianna Ianora and Giovanna Romano
Mar. Drugs 2020, 18(2), 109; https://doi.org/10.3390/md18020109 - 13 Feb 2020
Cited by 5 | Viewed by 3086
Abstract
Dinoflagellates, a major class of marine eukaryote microalgae composing the phytoplankton, are widely recognised as producers of a large variety of toxic molecules, particularly neurotoxins, which can also act as potent bioactive pharmacological mediators. In addition, similarly to other microalgae, they are also [...] Read more.
Dinoflagellates, a major class of marine eukaryote microalgae composing the phytoplankton, are widely recognised as producers of a large variety of toxic molecules, particularly neurotoxins, which can also act as potent bioactive pharmacological mediators. In addition, similarly to other microalgae, they are also good producers of polyunsaturated fatty acids (PUFAs), important precursors of key molecules involved in cell physiology. Among PUFA derivatives are the prostaglandins (Pgs), important physiological mediators in several physiological and pathological processes in humans, also used as “biological” drugs. Their synthesis is very expensive because of the elevated number of reaction steps required, thus the search for new Pgs production methods is of great relevance. One possibility is their extraction from microorganisms (e.g., diatoms), which have been proved to produce the same Pgs as humans. In the present study, we took advantage of the available transcriptomes for dinoflagellates in the iMicrobe database to search for the Pgs biosynthetic pathway using a bioinformatic approach. Here we show that dinoflagellates express nine Pg-metabolism related enzymes involved in both Pgs synthesis and reduction. Not all of the enzymes were expressed simultaneously in all the species analysed and their expression was influenced by culturing conditions, especially salinity of the growth medium. These results confirm the existence of a biosynthetic pathway for these important molecules in unicellular microalgae other than diatoms, suggesting a broad diffusion and conservation of the Pgs pathway, which further strengthen their importance in living organisms. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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25 pages, 3756 KiB  
Article
Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival
by Laila Ziko, Mustafa Adel, Mohamed N. Malash and Rania Siam
Mar. Drugs 2019, 17(5), 273; https://doi.org/10.3390/md17050273 - 08 May 2019
Cited by 15 | Viewed by 5774
Abstract
The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea [...] Read more.
The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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11 pages, 732 KiB  
Article
In Silico Analysis of Relationship between Proteins from Plastid Genome of Red Alga Palmaria sp. (Japan) and Angiotensin I Converting Enzyme Inhibitory Peptides
by Yuya Kumagai, Yoshikatsu Miyabe, Tomoyuki Takeda, Kohsuke Adachi, Hajime Yasui and Hideki Kishimura
Mar. Drugs 2019, 17(3), 190; https://doi.org/10.3390/md17030190 - 25 Mar 2019
Cited by 22 | Viewed by 4104
Abstract
Plastid proteins are one of the main components in red algae. In order to clarify the angiotensin I converting enzyme (ACE) inhibitory peptides from red alga Palmaria sp. (Japan), we determined the plastid genome sequence. The genome possesses 205 protein coding genes, which [...] Read more.
Plastid proteins are one of the main components in red algae. In order to clarify the angiotensin I converting enzyme (ACE) inhibitory peptides from red alga Palmaria sp. (Japan), we determined the plastid genome sequence. The genome possesses 205 protein coding genes, which were classified as genetic systems, ribosomal proteins, photosystems, adenosine triphosphate (ATP) synthesis, metabolism, transport, or unknown. After comparing ACE inhibitory peptides between protein sequences and a database, photosystems (177 ACE inhibitory peptides) were found to be the major source of ACE inhibitory peptides (total of 751). Photosystems consist of phycobilisomes, photosystem I, photosystem II, cytochrome complex, and a redox system. Among them, photosystem I (53) and II (51) were the major source of ACE inhibitory peptides. We found that the amino acid sequence of apcE (14) in phycobilisomes, psaA (18) and psaB (13) in photosystem I, and psbB (11) and psbC (10) in photosystem II covered a majority of bioactive peptide sequences. These results are useful for evaluating the bioactive peptides from red algae. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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16 pages, 9807 KiB  
Article
In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA
by Desirée Kaufmann, Alesia A. Tietze and Daniel Tietze
Mar. Drugs 2019, 17(3), 180; https://doi.org/10.3390/md17030180 - 19 Mar 2019
Cited by 8 | Viewed by 3158
Abstract
Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, [...] Read more.
Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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14 pages, 2023 KiB  
Article
Comparative Analyses of Metabolomic Fingerprints and Cytotoxic Activities of Soft Corals from the Colombian Caribbean
by Liliana Santacruz, Olivier P. Thomas, Carmenza Duque, Mónica Puyana and Edisson Tello
Mar. Drugs 2019, 17(1), 37; https://doi.org/10.3390/md17010037 - 09 Jan 2019
Cited by 7 | Viewed by 4549
Abstract
Soft corals (Cnidaria, Anthozoa, Octocorallia) are a diverse group of marine invertebrates that inhabit various marine environments in tropical and subtropical areas. Several species are recognized as prolific sources of compounds with a wide array of biological activities. Recent advances in analytical techniques, [...] Read more.
Soft corals (Cnidaria, Anthozoa, Octocorallia) are a diverse group of marine invertebrates that inhabit various marine environments in tropical and subtropical areas. Several species are recognized as prolific sources of compounds with a wide array of biological activities. Recent advances in analytical techniques, supported by robust statistical analyses, have allowed the analysis and characterization of the metabolome present in a single living organism. In this study, a liquid chromatography-high resolution mass spectrometry metabolomic approach was applied to analyze the metabolite composition of 28 soft corals present in the Caribbean coast of Colombia. Multivariate data analysis was used to correlate the chemical fingerprints of soft corals with their cytotoxic activity against tumor cell lines for anticancer purpose. Some diterpenoids were identified as specific markers to discriminate between cytotoxic and non-cytotoxic crude extracts of soft corals against tumor cell lines. In the models generated from the comparative analysis of PLS-DA for tumor lines, A549 and SiHa, the diterpene 13-keto-1,11-dolabell-3(E),7(E),12(18)-triene yielded a high score in the variable importance in projection. These results highlight the potential of metabolomic approaches towards the identification of cytotoxic agents against cancer of marine origin. This workflow can be useful in several studies, mainly those that are time consuming, such as traditional bioprospecting of marine natural products. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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Review

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30 pages, 548 KiB  
Review
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
by Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone and Maria Luisa Chiusano
Mar. Drugs 2019, 17(10), 576; https://doi.org/10.3390/md17100576 - 11 Oct 2019
Cited by 25 | Viewed by 6047
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential [...] Read more.
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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18 pages, 748 KiB  
Review
Marine Natural Products from Microalgae: An -Omics Overview
by Chiara Lauritano, Maria Immacolata Ferrante and Alessandra Rogato
Mar. Drugs 2019, 17(5), 269; https://doi.org/10.3390/md17050269 - 07 May 2019
Cited by 68 | Viewed by 9311
Abstract
Over the last decade, genome sequences and other -omics datasets have been produced for a wide range of microalgae, and several others are on the way. Marine microalgae possess distinct and unique metabolic pathways, and can potentially produce specific secondary metabolites with biological [...] Read more.
Over the last decade, genome sequences and other -omics datasets have been produced for a wide range of microalgae, and several others are on the way. Marine microalgae possess distinct and unique metabolic pathways, and can potentially produce specific secondary metabolites with biological activity (e.g., antipredator, allelopathic, antiproliferative, cytotoxic, anticancer, photoprotective, as well as anti-infective and antifouling activities). Because microalgae are very diverse, and adapted to a broad variety of environmental conditions, the chances to find novel and unexplored bioactive metabolites with properties of interest for biotechnological and biomedical applications are high. This review presents a comprehensive overview of the current efforts and of the available solutions to produce, explore and exploit -omics datasets, with the aim of identifying species and strains with the highest potential for the identification of novel marine natural products. In addition, funding efforts for the implementation of marine microalgal -omics resources and future perspectives are presented as well. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products)
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