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Menezes C, Thakur NL. Sea anemone venom: Ecological interactions and bioactive potential. Toxicon 2022; 208:31-46. [DOI: 10.1016/j.toxicon.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
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2
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R L Morlighem JÉ, Huang C, Liao Q, Braga Gomes P, Daniel Pérez C, de Brandão Prieto-da-Silva ÁR, Ming-Yuen Lee S, Rádis-Baptista G. The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology. Mar Drugs 2018; 16:E207. [PMID: 29899267 PMCID: PMC6025448 DOI: 10.3390/md16060207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 02/08/2023] Open
Abstract
Marine invertebrates, such as sponges, tunicates and cnidarians (zoantharians and scleractinian corals), form functional assemblages, known as holobionts, with numerous microbes. This type of species-specific symbiotic association can be a repository of myriad valuable low molecular weight organic compounds, bioactive peptides and enzymes. The zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa) is one such example of a marine holobiont that inhabits the coastal reefs of the tropical Atlantic coast and is an interesting source of secondary metabolites and biologically active polypeptides. In the present study, we analyzed the entire holo-transcriptome of P. variabilis, looking for enzyme precursors expressed in the zoantharian-microbiota assemblage that are potentially useful as industrial biocatalysts and biopharmaceuticals. In addition to hundreds of predicted enzymes that fit into the classes of hydrolases, oxidoreductases and transferases that were found, novel enzyme precursors with multiple activities in single structures and enzymes with incomplete Enzyme Commission numbers were revealed. Our results indicated the predictive expression of thirteen multifunctional enzymes and 694 enzyme sequences with partially characterized activities, distributed in 23 sub-subclasses. These predicted enzyme structures and activities can prospectively be harnessed for applications in diverse areas of industrial and pharmaceutical biotechnology.
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Affiliation(s)
- Jean-Étienne R L Morlighem
- Northeast Biotechnology Network (RENORBIO), Post-Graduation Program in Biotechnology, Federal University of Ceará, Fortaleza 60440-900, Brazil.
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza 60165-081, Brazil.
| | - Chen Huang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Qiwen Liao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Paula Braga Gomes
- Department of Biology, Federal Rural University of Pernambuco, Recife 52171-900, Brazil.
| | - Carlos Daniel Pérez
- Academic Center in Vitória, Federal University of Pernambuco, Vitória de Santo Antão 50670-901, Pernambuco, Brazil.
| | | | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau 519020, China.
| | - Gandhi Rádis-Baptista
- Northeast Biotechnology Network (RENORBIO), Post-Graduation Program in Biotechnology, Federal University of Ceará, Fortaleza 60440-900, Brazil.
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza 60165-081, Brazil.
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3
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Domínguez-Pérez D, Campos A, Alexei Rodríguez A, Turkina MV, Ribeiro T, Osorio H, Vasconcelos V, Antunes A. Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa. Mar Drugs 2018; 16:E42. [PMID: 29364843 PMCID: PMC5852470 DOI: 10.3390/md16020042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/14/2017] [Accepted: 01/15/2018] [Indexed: 12/11/2022] Open
Abstract
Cnidarian toxic products, particularly peptide toxins, constitute a promising target for biomedicine research. Indeed, cnidarians are considered as the largest phylum of generally toxic animals. However, research on peptides and toxins of sea anemones is still limited. Moreover, most of the toxins from sea anemones have been discovered by classical purification approaches. Recently, high-throughput methodologies have been used for this purpose but in other Phyla. Hence, the present work was focused on the proteomic analyses of whole-body extract from the unexplored sea anemone Bunodactis verrucosa. The proteomic analyses applied were based on two methods: two-dimensional gel electrophoresis combined with MALDI-TOF/TOF and shotgun proteomic approach. In total, 413 proteins were identified, but only eight proteins were identified from gel-based analyses. Such proteins are mainly involved in basal metabolism and biosynthesis of antibiotics as the most relevant pathways. In addition, some putative toxins including metalloproteinases and neurotoxins were also identified. These findings reinforce the significance of the production of antimicrobial compounds and toxins by sea anemones, which play a significant role in defense and feeding. In general, the present study provides the first proteome map of the sea anemone B. verrucosa stablishing a reference for future studies in the discovery of new compounds.
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Affiliation(s)
- Dany Domínguez-Pérez
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Alexandre Campos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Armando Alexei Rodríguez
- Department of Experimental and Clinical Peptide Chemistry, Hanover Medical School (MHH), Feodor-Lynen-Straße 31, D-30625 Hannover, Germany.
| | - Maria V Turkina
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, SE-581 85 Linköping, Sweden.
| | - Tiago Ribeiro
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
| | - Hugo Osorio
- Instituto de Investigação e Inovação em Saúde- i3S, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.
- Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal.
- Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.
| | - Vítor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
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4
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Krishnarjuna B, MacRaild CA, Sunanda P, Morales RAV, Peigneur S, Macrander J, Yu HH, Daly M, Raghothama S, Dhawan V, Chauhan S, Tytgat J, Pennington MW, Norton RS. Structure, folding and stability of a minimal homologue from Anemonia sulcata of the sea anemone potassium channel blocker ShK. Peptides 2018; 99:169-178. [PMID: 28993277 DOI: 10.1016/j.peptides.2017.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 01/01/2023]
Abstract
Peptide toxins elaborated by sea anemones target various ion-channel sub-types. Recent transcriptomic studies of sea anemones have identified several novel candidate peptides, some of which have cysteine frameworks identical to those of previously reported sequences. One such peptide is AsK132958, which was identified in a transcriptomic study of Anemonia sulcata and has a cysteine framework similar to that of ShK from Stichodactyla helianthus, but is six amino acid residues shorter. We have determined the solution structure of this novel peptide using NMR spectroscopy. The disulfide connectivities and structural scaffold of AsK132958 are very similar to those of ShK but the structure is more constrained. Toxicity assays were performed using grass shrimp (Palaemonetes sp) and Artemia nauplii, and patch-clamp electrophysiology assays were performed to assess the activity of AsK132958 against a range of voltage-gated potassium (KV) channels. AsK132958 showed no activity against grass shrimp, Artemia nauplii, or any of the KV channels tested, owing partly to the absence of a functional Lys-Tyr dyad. Three AsK132958 analogues, each containing a Tyr in the vicinity of Lys19, were therefore generated in an effort to restore binding, but none showed activity against any of KV channels tested. However, AsK132958 and its analogues are less susceptible to proteolysis than that of ShK. Our structure suggests that Lys19, which might be expected to occupy the pore of the channel, is not sufficiently accessible for binding, and therefore that AsK132958 must have a distinct functional role that does not involve KV channels.
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Affiliation(s)
- Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Punnepalli Sunanda
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000, Leuven, Belgium
| | - Jason Macrander
- Department of Evolution, Ecology, Organismal Biology, Ohio State University, 1315 Kinnear Rd, Columbus, OH 43212, USA; Department of Biology, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Heidi H Yu
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Marymegan Daly
- Department of Evolution, Ecology, Organismal Biology, Ohio State University, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | | | - Vikas Dhawan
- Peptides International, Louisville, KY 40299, USA
| | | | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000, Leuven, Belgium
| | | | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
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Abstract
Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids. Here, we provide detailed information on the Dynamic Management for Codon Compression (DYNAMCC) approaches that allow us to precisely define the desired amino acid composition to be introduced to a specific target site. DYNAMCC allows us to set usage thresholds and to eliminate undesirable stop and wild-type codons, thus allowing us to control library size and subsequently downstream screening efforts. The DYNAMCC algorithms are free of charge and are implemented in a website for easy access and usage: www.dynamcc.com .
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Affiliation(s)
- Gur Pines
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA. .,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA.,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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6
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Mayer AMS, Rodríguez AD, Taglialatela-Scafati O, Fusetani N. Marine Pharmacology in 2012-2013: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis, and Antiviral Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action. Mar Drugs 2017; 15:md15090273. [PMID: 28850074 PMCID: PMC5618412 DOI: 10.3390/md15090273] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 12/23/2022] Open
Abstract
The peer-reviewed marine pharmacology literature from 2012 to 2013 was systematically reviewed, consistent with the 1998–2011 reviews of this series. Marine pharmacology research from 2012 to 2013, conducted by scientists from 42 countries in addition to the United States, reported findings on the preclinical pharmacology of 257 marine compounds. The preclinical pharmacology of compounds isolated from marine organisms revealed antibacterial, antifungal, antiprotozoal, antituberculosis, antiviral and anthelmitic pharmacological activities for 113 marine natural products. In addition, 75 marine compounds were reported to have antidiabetic and anti-inflammatory activities and affect the immune and nervous system. Finally, 69 marine compounds were shown to display miscellaneous mechanisms of action which could contribute to novel pharmacological classes. Thus, in 2012–2013, the preclinical marine natural product pharmacology pipeline provided novel pharmacology and lead compounds to the clinical marine pharmaceutical pipeline, and contributed significantly to potentially novel therapeutic approaches to several global disease categories.
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Affiliation(s)
- Alejandro M S Mayer
- Department of Pharmacology, Chicago College of Osteopathic Medicine, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Abimael D Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, PR 00926, USA.
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Ledoux JB, Antunes A. Beyond the beaten path: improving natural products bioprospecting using an eco-evolutionary framework - the case of the octocorals. Crit Rev Biotechnol 2017. [PMID: 28651436 DOI: 10.1080/07388551.2017.1331335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Marine natural products (NPs) represent an impressive source of novel bioactive molecules with major biotechnological applications. Nevertheless, the usual chemical and applied perspective leading most of bioprospecting projects come along with various limitations blurring our understanding of the extensive marine chemical diversity. Here, we propose several guidelines: (i) to optimize bioprospecting and (ii) to refine our knowledge on marine chemical ecology focusing on octocorals, one of the most promising sources of marine NPs. We identified a significant phylogenetic bias in the octocoral bioprospecting, which calls for the development of a concerted discovery strategy. Given the gap existing between the number of isolated NPs and the knowledge regarding their functions, we provide an ecologically centered workflow prioritizing biological function ahead of chemical identification. Furthermore, we illustrate how -omic technologies should rapidly increase our knowledge on solving different aspects of the ecology and evolution of marine NPs.
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Affiliation(s)
- Jean-Baptiste Ledoux
- a CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research , University of Porto , Porto , Portugal.,b Institut de Ciències del Mar (ICM-CSIC) , Barcelona , Spain
| | - Agostinho Antunes
- a CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research , University of Porto , Porto , Portugal.,c Department of Biology, Faculty of Sciences , University of Porto , Porto , Portugal
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8
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Marine genomics: News and views. Mar Genomics 2017; 31:1-8. [DOI: 10.1016/j.margen.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/23/2022]
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9
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Macrander J, Broe M, Daly M. Tissue-Specific Venom Composition and Differential Gene Expression in Sea Anemones. Genome Biol Evol 2016; 8:2358-75. [PMID: 27389690 PMCID: PMC5010892 DOI: 10.1093/gbe/evw155] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 12/19/2022] Open
Abstract
Cnidarians represent one of the few groups of venomous animals that lack a centralized venom transmission system. Instead, they are equipped with stinging capsules collectively known as nematocysts. Nematocysts vary in abundance and type across different tissues; however, the venom composition in most species remains unknown. Depending on the tissue type, the venom composition in sea anemones may be vital for predation, defense, or digestion. Using a tissue-specific RNA-seq approach, we characterize the venom assemblage in the tentacles, mesenterial filaments, and column for three species of sea anemone (Anemonia sulcata, Heteractis crispa, and Megalactis griffithsi). These taxa vary with regard to inferred venom potency, symbiont abundance, and nematocyst diversity. We show that there is significant variation in abundance of toxin-like genes across tissues and species. Although the cumulative toxin abundance for the column was consistently the lowest, contributions to the overall toxin assemblage varied considerably among tissues for different toxin types. Our gene ontology (GO) analyses also show sharp contrasts between conserved GO groups emerging from whole transcriptome analysis and tissue-specific expression among GO groups in our differential expression analysis. This study provides a framework for future characterization of tissue-specific venom and other functionally important genes in this lineage of simple bodied animals.
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Affiliation(s)
- Jason Macrander
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
| | - Michael Broe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
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Baten A, Ngangbam AK, Waters DLE, Benkendorff K. Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters. Mar Drugs 2016; 14:md14070135. [PMID: 27447649 PMCID: PMC4962025 DOI: 10.3390/md14070135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/25/2022] Open
Abstract
Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known. Illumina HiSeq 2000 transcriptome sequencing of hypobranchial glands, prostate glands, albumen glands, capsule glands, and mantle and foot tissues of D. orbita generated over 201 million high quality reads that were de novo assembled into 219,437 contigs. Annotation with reference to the Nr, Swiss-Prot and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases identified candidate-coding regions in 76,152 of these contigs, with transcripts for many enzymes in various metabolic pathways associated with secondary metabolite biosynthesis represented. This study revealed that D. orbita expresses a number of genes associated with indole, sulfur and histidine metabolism pathways that are relevant to Tyrian purple precursor biosynthesis, and many of which were not found in the fully annotated genomes of three other molluscs in the KEGG database. However, there were no matches to known bromoperoxidase enzymes within the D. orbita transcripts. These transcriptome data provide a significant molecular resource for gastropod research in general and Tyrian purple producing Muricidae in particular.
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Affiliation(s)
- Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia.
| | - Ajit Kumar Ngangbam
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore NSW 2480, Australia.
| | - Daniel L E Waters
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia.
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore NSW 2480, Australia.
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11
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Jellyfish Bioactive Compounds: Methods for Wet-Lab Work. Mar Drugs 2016; 14:md14040075. [PMID: 27077869 PMCID: PMC4849079 DOI: 10.3390/md14040075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 02/03/2016] [Accepted: 02/18/2016] [Indexed: 11/17/2022] Open
Abstract
The study of bioactive compounds from marine animals has provided, over time, an endless source of interesting molecules. Jellyfish are commonly targets of study due to their toxic proteins. However, there is a gap in reviewing successful wet-lab methods employed in these animals, which compromises the fast progress in the detection of related biomolecules. Here, we provide a compilation of the most effective wet-lab methodologies for jellyfish venom extraction prior to proteomic analysis-separation, identification and toxicity assays. This includes SDS-PAGE, 2DE, gel chromatography, HPLC, DEAE, LC-MS, MALDI, Western blot, hemolytic assay, antimicrobial assay and protease activity assay. For a more comprehensive approach, jellyfish toxicity studies should further consider transcriptome sequencing. We reviewed such methodologies and other genomic techniques used prior to the deep sequencing of transcripts, including RNA extraction, construction of cDNA libraries and RACE. Overall, we provide an overview of the most promising methods and their successful implementation for optimizing time and effort when studying jellyfish.
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12
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Macrander J, Broe M, Daly M. Multi-copy venom genes hidden in de novo transcriptome assemblies, a cautionary tale with the snakelocks sea anemone Anemonia sulcata (Pennant, 1977). Toxicon 2015; 108:184-8. [PMID: 26464059 DOI: 10.1016/j.toxicon.2015.09.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/29/2015] [Indexed: 12/20/2022]
Abstract
Using a partial transcriptome of the snakelocks anemone (Anemonia sulcata) we identify toxin gene candidates that were incorrectly assembled into several Trinity components. Our approach recovers hidden diversity found within some toxin gene families that would otherwise go undetected when using Trinity, a widely used program for venom-focused transcriptome reconstructions. Unidentified hidden transcripts may significantly impact conclusions made regarding venom composition (or other multi-copy conserved genes) when using Trinity or other de novo assembly programs.
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Affiliation(s)
- Jason Macrander
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA.
| | - Michael Broe
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
| | - Marymegan Daly
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
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Salamone M, Nicosia A, Bennici C, Quatrini P, Catania V, Mazzola S, Ghersi G, Cuttitta A. Comprehensive Analysis of a Vibrio parahaemolyticus Strain Extracellular Serine Protease VpSP37. PLoS One 2015; 10:e0126349. [PMID: 26162075 PMCID: PMC4498684 DOI: 10.1371/journal.pone.0126349] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/01/2015] [Indexed: 02/04/2023] Open
Abstract
Proteases play an important role in the field of tissue dissociation combined with regenerative medicine. During the years new sources of proteolytic enzymes have been studied including proteases from different marine organisms both eukaryotic and prokaryotic. Herein we have purified a secreted component of an isolate of Vibrio parahaemolyticus, with electrophoretic mobilities corresponding to 36 kDa, belonging to the serine proteases family. Sequencing of the N-terminus enabled the in silico identification of the whole primary structure consisting of 345 amino acid residues with a calculated molecular mass of 37.4 KDa. The purified enzyme, named VpSP37, contains a Serine protease domain between residues 35 and 276 and a canonical Trypsin/Chimotrypsin 3D structure. Functional assays were performed to evaluate protease activity of purified enzyme. Additionally the performance of VpSP37 was evaluated in tissue dissociations experiments and the use of such enzyme as a component of enzyme blend for tissue dissociation procedures is strongly recommended.
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Affiliation(s)
- Monica Salamone
- Laboratory of Molecular Ecology and Biotechnology, National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Detached Unit of Capo Granitola, Torretta Granitola 91021, Trapani, Sicily, Italy
| | - Aldo Nicosia
- Laboratory of Molecular Ecology and Biotechnology, National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Detached Unit of Capo Granitola, Torretta Granitola 91021, Trapani, Sicily, Italy
| | - Carmelo Bennici
- Laboratory of Molecular Ecology and Biotechnology, National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Detached Unit of Capo Granitola, Torretta Granitola 91021, Trapani, Sicily, Italy
| | - Paola Quatrini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF),Università di Palermo, Viale delle Scienze, edificio 16, Palermo, Sicily, Italy
| | - Valentina Catania
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF),Università di Palermo, Viale delle Scienze, edificio 16, Palermo, Sicily, Italy
| | - Salvatore Mazzola
- National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Calata porta di Massa, 80133, Napoli, Italy
| | - Giulio Ghersi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF),Università di Palermo, Viale delle Scienze, edificio 16, Palermo, Sicily, Italy
- National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Calata porta di Massa, 80133, Napoli, Italy
- ABIEL S.r.l., Via del Mare 3, Torretta Granitola 91021, Trapani, Sicily, Italy
| | - Angela Cuttitta
- Laboratory of Molecular Ecology and Biotechnology, National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Detached Unit of Capo Granitola, Torretta Granitola 91021, Trapani, Sicily, Italy
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF),Università di Palermo, Viale delle Scienze, edificio 16, Palermo, Sicily, Italy
- National Research Council, Institute for Marine and Coastal Environment (IAMC-CNR), Calata porta di Massa, 80133, Napoli, Italy
- ABIEL S.r.l., Via del Mare 3, Torretta Granitola 91021, Trapani, Sicily, Italy
- * E-mail:
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Zhang YY, Huang Y, He QZ, Luo J, Zhu L, Lu SS, Liu JY, Huang PF, Zeng XZ, Liang SP. Structural and Functional Diversity of Peptide Toxins from Tarantula Haplopelma hainanum (Ornithoctonus hainana) Venom Revealed by Transcriptomic, Peptidomic, and Patch Clamp Approaches. J Biol Chem 2015; 290:14192-207. [PMID: 25770214 DOI: 10.1074/jbc.m114.635458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 11/06/2022] Open
Abstract
Spider venom is a complex mixture of bioactive peptides to subdue their prey. Early estimates suggested that over 400 venom peptides are produced per species. In order to investigate the mechanisms responsible for this impressive diversity, transcriptomics based on second generation high throughput sequencing was combined with peptidomic assays to characterize the venom of the tarantula Haplopelma hainanum. The genes expressed in the venom glands were identified, and the bioactivity of their protein products was analyzed using the patch clamp technique. A total of 1,136 potential toxin precursors were identified that clustered into 90 toxin groups, of which 72 were novel. The toxin peptides clustered into 20 cysteine scaffolds that included between 4 and 12 cysteines, and 14 of these groups were newly identified in this spider. Highly abundant toxin peptide transcripts were present and resulted from hypermutation and/or fragment insertion/deletion. In combination with variable post-translational modifications, this genetic variability explained how a limited set of genes can generate hundreds of toxin peptides in venom glands. Furthermore, the intraspecies venom variability illustrated the dynamic nature of spider venom and revealed how complex components work together to generate diverse bioactivities that facilitate adaptation to changing environments, types of prey, and milking regimes in captivity.
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Affiliation(s)
- Yi-Ya Zhang
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Yong Huang
- the State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Quan-Ze He
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Ji Luo
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Li Zhu
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Shan-Shan Lu
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Jin-Yan Liu
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Peng-Fei Huang
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Xiong-Zhi Zeng
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
| | - Song-Ping Liang
- From the Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, China and
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15
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Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. Sea anemones possess dynamic mitogenome structures. Mol Phylogenet Evol 2014; 75:184-93. [DOI: 10.1016/j.ympev.2014.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/31/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022]
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16
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Abstract
This review covers the literature published in 2012 for marine natural products, with 1035 citations (673 for the period January to December 2012) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1241 for 2012), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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17
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Peters H, O'Leary BC, Hawkins JP, Carpenter KE, Roberts CM. Conus: first comprehensive conservation red list assessment of a marine gastropod mollusc genus. PLoS One 2013; 8:e83353. [PMID: 24376693 PMCID: PMC3871662 DOI: 10.1371/journal.pone.0083353] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/01/2013] [Indexed: 11/18/2022] Open
Abstract
Marine molluscs represent an estimated 23% of all extant marine taxa, but research into their conservation status has so far failed to reflect this importance, with minimal inclusion on the authoritative Red List of the International Union for the Conservation of Nature (IUCN). We assessed the status of all 632 valid species of the tropical marine gastropod mollusc, Conus (cone snails), using Red List standards and procedures to lay the groundwork for future decadal monitoring, one of the first fully comprehensive global assessments of a marine taxon. Three-quarters (75.6%) of species were not currently considered at risk of extinction owing to their wide distribution and perceived abundance. However, 6.5% were considered threatened with extinction with a further 4.1% near threatened. Data deficiency prevented 13.8% of species from being categorised although they also possess characteristics that signal concern. Where hotspots of endemism occur, most notably in the Eastern Atlantic, 42.9% of the 98 species from that biogeographical region were classified as threatened or near threatened with extinction. All 14 species included in the highest categories of Critically Endangered and Endangered are endemic to either Cape Verde or Senegal, with each of the three Critically Endangered species restricted to single islands in Cape Verde. Threats to all these species are driven by habitat loss and anthropogenic disturbance, in particular from urban pollution, tourism and coastal development. Our findings show that levels of extinction risk to which cone snails are exposed are of a similar magnitude to those seen in many fully assessed terrestrial taxa. The widely held view that marine species are less at risk is not upheld.
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Affiliation(s)
- Howard Peters
- Environment Department, University of York, York, United Kingdom
| | - Bethan C O'Leary
- Environment Department, University of York, York, United Kingdom
| | - Julie P Hawkins
- Environment Department, University of York, York, United Kingdom
| | - Kent E Carpenter
- International Union for Conservation of Nature, Global Marine Species Assessment, Biological Sciences, Old Dominion University, Norfolk, Virginia, United States Of America
| | - Callum M Roberts
- Environment Department, University of York, York, United Kingdom
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18
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Evidence of accelerated evolution and ectodermal-specific expression of presumptive BDS toxin cDNAs from Anemonia viridis. Mar Drugs 2013; 11:4213-31. [PMID: 24177670 PMCID: PMC3853724 DOI: 10.3390/md11114213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/10/2013] [Accepted: 09/13/2013] [Indexed: 12/14/2022] Open
Abstract
Anemonia viridis is a widespread and extensively studied Mediterranean species of sea anemone from which a large number of polypeptide toxins, such as blood depressing substances (BDS) peptides, have been isolated. The first members of this class, BDS-1 and BDS-2, are polypeptides belonging to the β-defensin fold family and were initially described for their antihypertensive and antiviral activities. BDS-1 and BDS-2 are 43 amino acid peptides characterised by three disulfide bonds that act as neurotoxins affecting Kv3.1, Kv3.2 and Kv3.4 channel gating kinetics. In addition, BDS-1 inactivates the Nav1.7 and Nav1.3 channels. The development of a large dataset of A. viridis expressed sequence tags (ESTs) and the identification of 13 putative BDS-like cDNA sequences has attracted interest, especially as scientific and diagnostic tools. A comparison of BDS cDNA sequences showed that the untranslated regions are more conserved than the protein-coding regions. Moreover, the KA/KS ratios calculated for all pairwise comparisons showed values greater than 1, suggesting mechanisms of accelerated evolution. The structures of the BDS homologs were predicted by molecular modelling. All toxins possess similar 3D structures that consist of a triple-stranded antiparallel β-sheet and an additional small antiparallel β-sheet located downstream of the cleavage/maturation site; however, the orientation of the triple-stranded β-sheet appears to differ among the toxins. To characterise the spatial expression profile of the putative BDS cDNA sequences, tissue-specific cDNA libraries, enriched for BDS transcripts, were constructed. In addition, the proper amplification of ectodermal or endodermal markers ensured the tissue specificity of each library. Sequencing randomly selected clones from each library revealed ectodermal-specific expression of ten BDS transcripts, while transcripts of BDS-8, BDS-13, BDS-14 and BDS-15 failed to be retrieved, likely due to under-representation in our cDNA libraries. The calculation of the relative abundance of BDS transcripts in the cDNA libraries revealed that BDS-1, BDS-3, BDS-4, BDS-5 and BDS-6 are the most represented transcripts.
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