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Marine Drugs
Special Issues
Bioinformatics of Marine Natural Products 2.0
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Bioinformatics of Marine Natural Products 2.0

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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 14113

Special Issue Editors

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
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

Special Issue Information

Dear Colleagues,

Marine organisms continue to draw great attention as a promising source for the sustainable production of novel bioactive compounds and biocatalysts. Considering the growing investment in blue biotechnology and the rapid and continuous advances in bioinformatics and in omics-based approaches for biodiscovery, we are pleased to announce a second edition of the Special Issue “Bioinformatics of Marine Natural Products”. The present Issue aims to investigate the current scenario and the new approaches available for the exploration of the huge amount of big datasets accessible for the identification of new natural marine compounds.

Dr. Alessandra Rogato
Dr. Giovanna Romano
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
  • bioinformatic approach
  • biosynthetic gene clusters
  • cryptic metabolic pathways
  • uncultivable microorganisms
  • meta-omic approaches

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Published Papers (5 papers)

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Research

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18 pages, 1188 KiB  
Article
Transcriptome Sequencing of the Diatom Asterionellopsis thurstonii and In Silico Identification of Enzymes Potentially Involved in the Synthesis of Bioactive Molecules
by Eleonora Montuori, Kevin A. Martinez, Daniele De Luca, Adrianna Ianora and Chiara Lauritano
Mar. Drugs 2023, 21(2), 126; https://doi.org/10.3390/md21020126 - 15 Feb 2023
Cited by 2 | Viewed by 2152
Abstract
Microalgae produce a plethora of primary and secondary metabolites with possible applications in several market sectors, including cosmetics, human nutrition, aquaculture, biodiesel production and treatment/prevention of human diseases. Diatoms, in particular, are the most diversified microalgal group, many species of which are known [...] Read more.
Microalgae produce a plethora of primary and secondary metabolites with possible applications in several market sectors, including cosmetics, human nutrition, aquaculture, biodiesel production and treatment/prevention of human diseases. Diatoms, in particular, are the most diversified microalgal group, many species of which are known to have anti-cancer, anti-oxidant, anti-diabetes, anti-inflammatory and immunomodulatory properties. Compounds responsible for these activities are often still unknown. The aim of this study was to de novo sequence the full transcriptome of two strains of the diatom Asterionellopsis thurstonii, sampled from two different locations and cultured in both control and phosphate starvation conditions. We used an RNA-sequencing approach to in silico identify transcripts potentially involved in the synthesis/degradation of compounds with anti-cancer and immunomodulatory properties. We identified transcript coding for L-asparaginase I, polyketide cyclase/dehydrase, bifunctional polyketide phosphatase/kinase, 1-deoxy-D-xylulose-5-phosphate synthase (fragment), inositol polyphosphate 5-phosphatase INPP5B/F, catechol O-Methyltransferase, digalactosyldiacylglycerol synthase (DGD1), 1,2-diacylglycerol-3-beta-galactosyltransferase and glycerolphosphodiester phosphodiesterase. Differential expression analysis also allowed to identify in which culturing condition these enzymes are more expressed. Overall, these data give new insights on the annotation of diatom genes, enzymatic pathways involved in the generation of bioactive molecules and possible exploitation of Asterionellopsis thurstonii. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 2.0)
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11 pages, 2871 KiB  
Article
Comprehensive Genomic Analysis of Marine Strain Streptomyces sp. 891, an Excellent Producer of Chrysomycin A with Therapeutic Potential
by Xu Hu, Yuqi Tang, Yuanyuan Liu, Xinwei Pei, Ziwei Huang, Fuhang Song and Huawei Zhang
Mar. Drugs 2022, 20(5), 287; https://doi.org/10.3390/md20050287 - 24 Apr 2022
Cited by 5 | Viewed by 2173
Abstract
Chrysomycin A is one of the most promising therapeutic candidates for treating infections caused by multidrug-resistant Gram-positive bacteria. By hybridizing next-step generation (Illumina) and third-generation (PacBio) sequencing technologies, a high-quality chromosome-level genome together with a plasmid was firstly assembled for chrysomycin A-producing marine [...] Read more.
Chrysomycin A is one of the most promising therapeutic candidates for treating infections caused by multidrug-resistant Gram-positive bacteria. By hybridizing next-step generation (Illumina) and third-generation (PacBio) sequencing technologies, a high-quality chromosome-level genome together with a plasmid was firstly assembled for chrysomycin A-producing marine strain 891. Phylogenetic analysis of the 16S rRNA gene and genome sequences revealed that this strain unambiguously belonged to the genus Streptomyces, and its genomic features and functional genes were comprehensively analyzed and annotated. AntiSMASH analysis of this strain unveiled one key biosynthetic gene cluster, T2PKS, responsible for the biosynthesis of chrysomycin, the biosynthesis pathway of which was putatively proposed. These findings definitely shed light on further investigation for construction of a robust industrial strain with high-yield chrysomycin A production using genetic engineering techniques and combinatorial biology approaches. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 2.0)
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15 pages, 25564 KiB  
Article
Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features
by Yuhao Jv, Chenxiang Xi, Yanqiu Zhao, Wei Wang, Yiling Zhang, Kai Liu, Wenlin Liu, Kai Shan, Chunlei Wang, Ruiwen Cao, Cunxi Dai, Yiting Jv, Wenxing Zhu, Haiyong Wang, Qiuxia He and Lujiang Hao
Mar. Drugs 2022, 20(4), 248; https://doi.org/10.3390/md20040248 - 31 Mar 2022
Viewed by 2029
Abstract
The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 (P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular polysaccharide synthesis were screened. The pan-genome of [...] Read more.
The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 (P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular polysaccharide synthesis were screened. The pan-genome of the P. agarivorans strains consists of a core-genome containing 2331 genes, an accessory-genome containing 956 genes, and a unique-genome containing 1519 genes. Clusters of Orthologous Groups analyses showed that P. agarivorans harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The Kyoto Encyclopedia of Genes and Genomes and reconstructed carbohydrate metabolic pathways displayed that P. agarivorans strains can utilize a variety of carbohydrates, such as d-glucose, d-fructose, and d-lactose. Analyses of differentially expressed genes showed that compared with the stationary phase (24 h), strain P. agarivorans Hao 2018 had upregulated expression of genes related to the synthesis of extracellular polysaccharides in the logarithmic growth phase (2 h), and that the expression of these genes affected extracellular polysaccharide transport, nucleotide sugar synthesis, and glycosyltransferase synthesis. This is the first investigation of the genomic and metabolic features of P. agarivorans through pan-genomic and transcriptomic analyses, and these intriguing discoveries provide the possibility to produce novel marine drug lead compounds with high biological activity. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 2.0)
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19 pages, 3419 KiB  
Article
Floridean Starch and Floridoside Metabolic Pathways of Neoporphyra haitanensis and Their Regulatory Mechanism under Continuous Darkness
by Yahui Yu, Xuli Jia, Wenlei Wang, Yuemei Jin, Weizhi Liu, Dongmei Wang, Yunxiang Mao, Chaotian Xie and Tao Liu
Mar. Drugs 2021, 19(12), 664; https://doi.org/10.3390/md19120664 - 26 Nov 2021
Cited by 6 | Viewed by 2719
Abstract
Floridean starch and floridoside are the main storage carbohydrates of red algae. However, their complete metabolic pathways and the origin, function, and regulatory mechanism of their pathway genes have not been fully elucidated. In this study, we identified their metabolic pathway genes and [...] Read more.
Floridean starch and floridoside are the main storage carbohydrates of red algae. However, their complete metabolic pathways and the origin, function, and regulatory mechanism of their pathway genes have not been fully elucidated. In this study, we identified their metabolic pathway genes and analyzed the changes in related gene expression and metabolite content in Neoporphyra haitanensis under continuous dark conditions. Our results showed that genes from different sources, including eukaryotic hosts, cyanobacteria, and bacteria, were combined to construct floridean starch and floridoside metabolic pathways in N. haitanensis. Moreover, compared with those in the control, under continuous dark conditions, floridean starch biosynthesis genes and some degradation genes were significantly upregulated with no significant change in floridean starch content, whereas floridoside degradation genes were significantly upregulated with a significant decrease in floridoside content. This implies that floridean starch content is maintained but floridoside is consumed in N. haitanensis under dark conditions. This study elucidates the “floridean starch–floridoside” metabolic network and its gene origins in N. haitanensis for the first time. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 2.0)
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Review

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26 pages, 5346 KiB  
Review
Recent Advancement in Anticancer Compounds from Marine Organisms: Approval, Use and Bioinformatic Approaches to Predict New Targets
by Giovanna Santaniello, Angela Nebbioso, Lucia Altucci and Mariarosaria Conte
Mar. Drugs 2023, 21(1), 24; https://doi.org/10.3390/md21010024 - 28 Dec 2022
Cited by 3 | Viewed by 3648
Abstract
In recent years, the study of anticancer bioactive compounds from marine sources has received wide interest. Contextually, world regulatory authorities have approved several marine molecules, and new synthetic derivatives have also been synthesized and structurally improved for the treatment of numerous forms of [...] Read more.
In recent years, the study of anticancer bioactive compounds from marine sources has received wide interest. Contextually, world regulatory authorities have approved several marine molecules, and new synthetic derivatives have also been synthesized and structurally improved for the treatment of numerous forms of cancer. However, the administration of drugs in cancer patients requires careful evaluation since their interaction with individual biological macromolecules, such as proteins or nucleic acids, determines variable downstream effects. This is reflected in a constant search for personalized therapies that lay the foundations of modern medicine. The new knowledge acquired on cancer mechanisms has certainly allowed advancements in tumor prevention, but unfortunately, due to the huge complexity and heterogeneity of cancer, we are still looking for a definitive therapy and clinical approaches. In this review, we discuss the significance of recently approved molecules originating from the marine environment, starting from their organism of origin to their structure and mechanism of action. Subsequently, these bio-compounds are used as models to illustrate possible bioinformatics approaches for the search of new targets that are useful for improving the knowledge on anticancer therapies. Full article
(This article belongs to the Special Issue Bioinformatics of Marine Natural Products 2.0)
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