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Genetics of Marine Organisms Associated with Human Health

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

Deadline for manuscript submissions: closed (28 February 2020) | Viewed by 48567

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Dr. Helena Ćetković

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Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
Interests: biochemistry; genetic diversity and biodiversity; molecular biology; metagenomi; biosynthetic
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Dr. Maja Herak Bosnar

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Senior Research Associate, Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia

Dr. Matija Harcet

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Special Issue Information

Dear Colleagues,

Marine habitats harbour a large variety of organisms that impact human health. They belong to diverse taxa; from bacteria and unicellular eukaryotes to fungi, animals, plants, and form complex communities. Some of these organisms are a source of natural products with potential or actual medical applications, others are toxic and harmful to humans, and some are used in biomedical research to help understand the molecular basis of human diseases. Molecular genetics and genomic methods offer powerful and ever more indispensable tools for studying marine organisms and all the aspects of their influence on human health.

We would like this Special Issue to focus on all types of genetic research of marine organisms involved in human health, and to provide a link with the more traditional research of marine natural products. Specifically, we are inviting original research and review articles in the following areas:

- genetic biodiversity studies of species or groups of organisms linked with human health, especially in the context of search for novel bioactive compounds

- characterisation of genes involved in biosynthetic pathways of marine natural products

- basic molecular genetic or genomic research of marine organisms involved in human health

- origins, properties, and interactions of genes and proteins from marine organisms whose homologues are associated with human diseases

- genes and genomes of marine organisms used in biomedical research

Dr. Helena Ćetković
Dr. Maja Herak Bosnar
Dr. Matija Harcet
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

genetic diversity and biodiversity
metagenomic approach
biosynthetic pathways
molecular genetics and genomics
disease-related genes
models for biomedical research

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Related Special Issues

Natural Product Genomics and Metabolomics of Marine Bacteria in Marine Drugs (12 articles)
Genetics of Marine Organisms Associated with Human Health 2nd Edition in Marine Drugs

Published Papers (9 papers)

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Editorial

Jump to: Research

3 pages, 162 KiB

Open AccessEditorial

Genetics of Marine Organisms Associated with Human Health

by Maja Herak Bosnar, Helena Ćetković and Matija Harcet

Mar. Drugs 2020, 18(11), 548; https://doi.org/10.3390/md18110548 - 2 Nov 2020

Cited by 1 | Viewed by 2244

Abstract

The aim of this special issue was to provide insight into the field of research on genetics and genomics of marine organisms linked with human health [...] Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

Research

Jump to: Editorial

11 pages, 2019 KiB

Open AccessArticle

Characterization of Regulatory and Transporter Genes in the Biosynthesis of Anti-Tuberculosis Ilamycins and Production in a Heterologous Host

by Jianqiao He, Xin Wei, Zhijie Yang, Yan Li, Jianhua Ju and Junying Ma

Mar. Drugs 2020, 18(4), 216; https://doi.org/10.3390/md18040216 - 17 Apr 2020

Cited by 7 | Viewed by 3527

Abstract

Ilamycins are cyclopeptides with novel structures that have been isolated from different Actinomycetes. They showed strong anti-tuberculosis activity and could serve as important anti-tuberculosis drug leads. The functions of the pre-tailoring and the post-tailoring genes in the biosynthesis of ilamycins have been elucidated, but the functions of the regulatory and transporter genes remain elusive. We reported herein the functions of four genes in ilamycin biosynthetic gene cluster (ila BGC) including two regulatory genes (ilaA and ilaB) and two transporter genes (ilaJ and ilaK) and the heterologous expression of ila BGC. The IlaA and IlaB were unambiguously shown to be negative and positive regulator of ilamycins biosynthesis, respectively. Consistent with these roles, inactivation of ilaA and ilaB (independent of each other) was shown to enhance and abolish the production of ilamycins, respectively. Total yields of ilamycins were enhanced 3.0-fold and 1.9-fold by inactivation of ilaA and overexpression of ilaB compared to those of in the Streptomyces atratus SCSIO ZH16, respectively. In addition, the ila BGC was successfully expressed in Streptomyces coelicolor M1152, which indicated that all biosynthetic elements for the construction of ilamycins were included in the PAC7A6. These results not only lay a foundation for further exploration of ilamycins, but also provide the genetic elements for synthetic biology. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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19 pages, 27785 KiB

Open AccessArticle

High-Throughput Identification of Putative Antimicrobial Peptides from Multi-Omics Data of the Lined Seahorse (Hippocampus erectus)

by Xiyang Chen, Yunhai Yi, Xinxin You, Jie Liu and Qiong Shi

Mar. Drugs 2020, 18(1), 30; https://doi.org/10.3390/md18010030 - 29 Dec 2019

Cited by 18 | Viewed by 4140

Abstract

Lined seahorse (Hippocampus erectus), the most widely cultivated seahorse in China, has been in short supply because of its important medicinal value; meanwhile, unnatural deaths caused by various diseases (especially enteritis) have limited their practical large-scale aquaculture. Antimicrobial peptides (AMPs), as the best alternative to antibiotics, have been extensively applied in agricultural practices. In this study, we identified 290 putative AMP sequences from our previously published genome and transcriptome data of the lined seahorse. Among them, 267 are novel, and 118 were validated by our proteome data generated in the present study. It seems that there is a tissue preference in the distribution of AMP/AMP precursor transcripts, such as lectins in the male pouch. In addition, their transcription levels usually varied during development. Interestingly, the representative lectins kept extremely high levels at the pre-pregnancy stage while at relatively lower levels at other stages. Especially Lectin25, with the highest transcription levels and significant developmental changes, has been reported to be involved in seahorse and human pregnancy. The comparison of transcriptome data between one-day and three-month juveniles indicated that Hemoglobin2 (Hemo2) was significantly upregulated in the body, haslet, and brain. Our proteome data of female and male individuals revealed three putative AMP precursors with sexual specificity, including two male-biased cyclin-dependent kinases (CDK-like16 and CDK-like23) and one female-biased bovine pancreatic trypsin inhibitor 2 (BPTI2). In conclusion, our present high-throughput identification of putative AMP sequences from multi-omics (including genomics, transcriptomics, and proteomics) data provides an overview of AMPs in the popular lined seahorse, which lays a solid foundation for further development of AMP-based fish food additives and human drugs. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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20 pages, 55937 KiB

Open AccessArticle

Characterization of Nme5-Like Gene/Protein from the Red Alga Chondrus Crispus

by Dragutin Perina, Marina Korolija, Andreja Mikoč, Mirna Halasz, Maja Herak Bosnar and Helena Ćetković

Mar. Drugs 2020, 18(1), 13; https://doi.org/10.3390/md18010013 - 21 Dec 2019

Cited by 6 | Viewed by 3884

Abstract

The Nme gene/protein family of nucleoside diphosphate kinases (NDPK) was originally named after its member Nm23-H1/Nme1, the first identified metastasis suppressor. Human Nme proteins are divided in two groups. They all possess nucleoside diphosphate kinase domain (NDK). Group I (Nme1-Nme4) display a single type NDK domain, whereas Group II (Nme5-Nme9) display a single or several different NDK domains, associated or not associated with extra-domains. Data strongly suggest that, unlike Group I, none of the members of Group II display measurable NDPK activity, although some of them autophosphorylate. The multimeric form is required for the NDPK activity. Group I proteins are known to multimerize, while there are no data on the multimerization of Group II proteins. The Group II ancestral type protein was shown to be conserved in several species from three eukaryotic supergroups. Here, we analysed the Nme protein from an early branching eukaryotic lineage, the red alga Chondrus crispus. We show that the ancestral type protein, unlike its human homologue, was fully functional multimeric NDPK with high affinity to various types of DNA and dispersed localization throughout the eukaryotic cell. Its overexpression inhibits both cell proliferation and the anchorage-independent growth of cells in soft agar but fails to deregulate cell apoptosis. We conclude that the ancestral gene has changed during eukaryotic evolution, possibly in correlation with the protein function. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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25 pages, 20446 KiB

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Detecting Neurodevelopmental Toxicity of Domoic Acid and Ochratoxin A Using Rat Fetal Neural Stem Cells

by Santokh Gill and V. M. Ruvin Kumara

Mar. Drugs 2019, 17(10), 566; https://doi.org/10.3390/md17100566 - 4 Oct 2019

Cited by 10 | Viewed by 4087

Abstract

Currently, animal experiments in rodents are the gold standard for developmental neurotoxicity (DNT) investigations; however, testing guidelines for these experiments are insufficient in terms of animal use, time, and costs. Thus, alternative reliable approaches are needed for predicting DNT. We chose rat neural stem cells (rNSC) as a model system, and used a well-known neurotoxin, domoic acid (DA), as a model test chemical to validate the assay. This assay was used to investigate the potential neurotoxic effects of Ochratoxin A (OTA), of which the main target organ is the kidney. However, limited information is available regarding its neurotoxic effects. The effects of DA and OTA on the cytotoxicity and on the degree of differentiation of rat rNSC into astrocytes, neurons, and oligodendrocytes were monitored using cell-specific immunofluorescence staining for undifferentiated rNSC (nestin), neurospheres (nestin and A2B5), neurons (MAP2 clone M13, MAP2 clone AP18, and Doublecortin), astrocytes (GFAP), and oligodendrocytes (A2B5 and mGalc). In the absence of any chemical exposure, approximately 46% of rNSC differentiated into astrocytes and neurons, while 40% of the rNSC differentiated into oligodendrocytes. Both non-cytotoxic and cytotoxic concentrations of DA and OTA reduced the differentiation of rNSC into astrocytes, neurons, and oligodendrocytes. Furthermore, a non-cytotoxic nanomolar (0.05 µM) concentration of DA and 0.2 µM of OTA reduced the percentage differentiation of rNSC into astrocytes and neurons. Morphometric analysis showed that the highest concentration (10 μM) of DA reduced axonal length. These indicate that low, non-cytotoxic concentrations of DA and OTA can interfere with the differentiation of rNSC. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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16 pages, 3184 KiB

Open AccessArticle

Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides

by Kuntong Jia, Chao Bian, Yunhai Yi, Yanping Li, Peng Jia, Duan Gui, Xiyang Zhang, Wenzhi Lin, Xian Sun, Yunyun Lv, Jia Li, Xinxin You, Qiong Shi, Meisheng Yi and Yuping Wu

Mar. Drugs 2019, 17(9), 504; https://doi.org/10.3390/md17090504 - 28 Aug 2019

Cited by 12 | Viewed by 4710

Abstract

Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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16 pages, 3226 KiB

Open AccessArticle

Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes

by Dengdong Wang, Xiyang Chen, Xinhui Zhang, Jia Li, Yunhai Yi, Chao Bian, Qiong Shi, Haoran Lin, Shuisheng Li, Yong Zhang and Xinxin You

Mar. Drugs 2019, 17(9), 503; https://doi.org/10.3390/md17090503 - 28 Aug 2019

Cited by 28 | Viewed by 5250

Abstract

Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by an Illumina HiSeq X-Ten and PacBio Bioscience Sequel platform. A total of 254 putative antimicrobial peptide (AMP) genes were identified, which can be divided into 34 classes according to the annotation of the Antimicrobial Peptides Database (APD3). Their locations in pseudochromosomes were also determined. Thrombin-, lectin-, and scolopendin-derived putative AMPs were the three largest parts. In addition, expressions of putative AMPs were measured by our transcriptome data. Two putative AMP genes (gapdh1 and gapdh2) were involved in glycolysis, which had extremely high expression levels in giant grouper muscle. As it has been reported that AMPs inhibit the growth of a broad spectrum of microbes and participate in regulating innate and adaptive immune responses, genome sequencing of this study provides a comprehensive cataloging of putative AMPs of groupers, supporting antimicrobial research and aquaculture therapy. These genomic resources will be beneficial to further molecular breeding of this economically important fish. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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17 pages, 5182 KiB

Open AccessArticle

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

by Weiwei Chen, Chao Bian, Xinxin You, Jia Li, Lizhen Ye, Zhengyong Wen, Yunyun Lv, Xinhui Zhang, Junmin Xu, Shaosen Yang, Ruobo Gu, Xueqiang Lin and Qiong Shi

Mar. Drugs 2019, 17(7), 426; https://doi.org/10.3390/md17070426 - 20 Jul 2019

Cited by 10 | Viewed by 14655

Abstract

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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14 pages, 5099 KiB

Open AccessArticle

Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias

by Chao Bian, Jia Li, Xueqiang Lin, Xiyang Chen, Yunhai Yi, Xinxin You, Yiping Zhang, Yunyun Lv and Qiong Shi

Mar. Drugs 2019, 17(7), 386; https://doi.org/10.3390/md17070386 - 28 Jun 2019

Cited by 22 | Viewed by 5118

Abstract

Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias. Full article

(This article belongs to the Special Issue Genetics of Marine Organisms Associated with Human Health)

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