1
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Gorbushin A, Ruparčič M, Anderluh G. Littoporins: Novel actinoporin-like proteins in caenogastropod genus Littorina. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109698. [PMID: 38871141 DOI: 10.1016/j.fsi.2024.109698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
In the course of searching for genes controlling the immune system in caenogastropod mollusks, we characterized and phylogenetically placed five new actinoporin-like cytolysins expressed in periwinkles of the genus Littorina. These newly discovered proteins, named littoporins (LitP), contain a central cytolysin/lectin domain and exhibit a predicted protein fold that is almost identical to the three-dimensional structures of actinoporins. Two of these proteins, LitP-1 and LitP-2, were found to be upregulated in L. littorea kidney tissues and immune cells in response to natural and experimental infection with the trematode Himasthla elongata, suggesting their potential role as perforins in the systemic anti-trematode immune response. The primary sequence divergence of littoporins is hypothesized to be attributed to the taxonomic range of cell membranes they can recognize and permeabilize.
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Affiliation(s)
- Alexander Gorbushin
- Sechenov Institute of Evolutionary Physiology and Biochemistry (IEPhB RAS), St Petersburg, Russia.
| | - Matija Ruparčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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2
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Fischer N, Tóth A, Jancsó A, Thulstrup P, Diness F. Inducing α-Helicity in Peptides by Silver Coordination to Cysteine. Chemistry 2024; 30:e202304064. [PMID: 38456607 DOI: 10.1002/chem.202304064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α-helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed-phase HPLC separation as well as towards a physiological level of chloride ions, based on far-UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N-terminal nucleation site for inducing α-helicity into longer peptides. This type of silver-mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions.
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Affiliation(s)
- Niklas Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Annamária Tóth
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Attila Jancsó
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Peter Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
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3
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Achimba F, Faezov B, Cohen B, Dunbrack R, Holford M. Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides. Mol Cancer Ther 2024; 23:139-147. [PMID: 38015557 PMCID: PMC10831335 DOI: 10.1158/1535-7163.mct-23-0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/04/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
The regulation of cellular processes by ion channels has become central to the study of cancer mechanisms. Designing molecules that can modify ion channels specific to tumor cells is a promising area of targeted drug delivery and therapy. Despite their potential in drug discovery, venom peptides-a group of natural products-have largely remained understudied and under-characterized. In general, venom peptides display high specificity and selectivity for their target ion channels. Therefore, they may represent an effective strategy for selectively targeting the dysregulation of ion channels in tumor cells. This review examines existing venom peptide therapies for different cancer types and focuses on the application of snail venom peptides in hepatocellular carcinoma (HCC), the most common form of primary liver cancer worldwide. We provide insights into the mode of action of venom peptides that have been shown to target tumors. We also explore the benefit of using new computational methods like de novo protein structure prediction to screen venom peptides and identify potential druggable candidates. Finally, we summarize the role of cell culture, animal, and organoid models in developing effective therapies against HCC and highlight the need for creating models that represent the most disproportionately affected ethnicities in HCC.
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Affiliation(s)
- Favour Achimba
- The PhD Program in Biochemistry, Graduate Center, City University of New York, New York, New York
- Hunter College, City University of New York, New York, New York
| | - Bulat Faezov
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Brandon Cohen
- Hunter College, City University of New York, New York, New York
| | - Roland Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mandë Holford
- The PhD Program in Biochemistry, Graduate Center, City University of New York, New York, New York
- Hunter College, City University of New York, New York, New York
- The PhD Program in Chemistry, Graduate Center of the City University of New York, New York, New York
- The PhD Program in Biology, Graduate Center of the City University of New York, New York, New York
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, New York
- Department of Biochemistry, Weill Cornell Medicine, New York, New York
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4
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Aristide L, Fernández R. Genomic Insights into Mollusk Terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in Out-of-the-Sea Transitions. Genome Biol Evol 2023; 15:evad176. [PMID: 37793176 PMCID: PMC10581543 DOI: 10.1093/gbe/evad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process.
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Affiliation(s)
- Leandro Aristide
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
| | - Rosa Fernández
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
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5
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Farhat S, Modica MV, Puillandre N. Whole Genome Duplication and Gene Evolution in the Hyperdiverse Venomous Gastropods. Mol Biol Evol 2023; 40:msad171. [PMID: 37494290 PMCID: PMC10401626 DOI: 10.1093/molbev/msad171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied. Among the available gastropods genomes, only eight, with uneven quality assemblies, belong to neogastropods. Here, we generated chromosome-level assemblies of two species belonging to the Tonnoidea and Muricoidea superfamilies (Monoplex corrugatus and Stramonita haemastoma). The two obtained high-quality genomes had 3 and 2.2 Gb, respectively, and 92-89% of the total assembly conformed 35 pseudochromosomes in each species. Through the analysis of syntenic blocks, Hox gene cluster duplication, and synonymous substitutions distribution pattern, we inferred the occurrence of a whole genome duplication event in both genomes. As these species are known to release venom, toxins were annotated in both genomes, but few of them were found in homologous chromosomes. A comparison of the expression of ohnolog genes (using transcriptomes from osphradium and salivary glands in S. haemastoma), where both copies were differentially expressed, showed that most of them had similar expression profiles. The high quality of these genomes makes them valuable reference in their respective taxa, facilitating the identification of genome-level processes at the origin of their evolutionary success.
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Affiliation(s)
- Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Roma, Italy
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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6
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Venom system variation and the division of labor in the colonial hydrozoan Hydractinia symbiolongicarpus. Toxicon X 2022; 14:100113. [PMID: 35287376 PMCID: PMC8917316 DOI: 10.1016/j.toxcx.2022.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Cnidarians (jellyfish, hydroids, sea anemones, and corals) possess a unique method for venom production, maintenance, and deployment through a decentralized system composed of different types of venom-filled stinging structures called nematocysts. In many species, nematocyst types are distributed heterogeneously across functionally distinct tissues. This has led to a prediction that different nematocyst types contain specific venom components. The colonial hydrozoan, Hydractinia symbiolongicarpus, is an ideal system to study the functional distribution of nematocyst types and their venoms, given that they display a division of labor through functionally distinct polyps within the colony. Here, we characterized the composition and distribution of nematocysts (cnidome) in the different polyp types and show that the feeding polyp (gastrozooid) has a distinct cnidome compared to the reproductive (gonozooid) and predatory polyp (dactylozooid). We generated a nematocyst-specific reporter line to track nematocyst development (nematogenesis) in H. symbiolongicarpus, and were able to confirm that nematogenesis primarily occurs in the mid-region of the gastrozooid and throughout stolons (tubes of epithelia that connect the polyps in the colony). This reporter line enabled us to isolate a nematocyst-specific lineage of cells for de novo transcriptome assembly, annotate venom-like genes (VLGs) and determine differential expression (DE) across polyp types. We show that a majority of VLGs are upregulated in gastrozooids, consistent with it being the primary site of active nematogenesis. However, despite gastrozooids producing more nematocysts, we found a number of VLGs significantly upregulated in dactylozooids, suggesting that these VLGs may be important for prey-capture. Our transgenic Hydractinia reporter line provides an opportunity to explore the complex interplay between venom composition, nematocyst diversity, and ecological partitioning in a colonial hydrozoan that displays a division of labor. Functionally specific polyp types in Hydractinia symbiolongicarpus have distinct cnidomes. We present a nematocyst-targeted transgenic line for H. symbiolongicarpus, showcasing active areas of nematogenesis. 105 venom-like genes (VLGs) were annotated from an assembled nematocyst-enriched transcriptome. Several VLGs were significantly upregulated in feeding polyps, consistent with being a site of active nematogenesis. Differential expression analysis suggests that different polyp types express distinct combinations of VLGs.
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7
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Verdes A, Taboada S, Hamilton BR, Undheim EAB, Sonoda GG, Andrade SCS, Morato E, Isabel Marina A, Cárdenas CA, Riesgo A. Evolution, expression patterns and distribution of novel ribbon worm predatory and defensive toxins. Mol Biol Evol 2022; 39:6580756. [PMID: 35512366 PMCID: PMC9132205 DOI: 10.1093/molbev/msac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribbon worms are active predators that use an eversible proboscis to inject venom into their prey and defend themselves with toxic epidermal secretions. Previous work on nemertean venom has largely focused on just a few species and has not investigated the different predatory and defensive secretions in detail. Consequently, our understanding of the composition and evolution of ribbon worm venoms is still very limited. Here, we present a comparative study of nemertean venom combining RNA-seq differential gene expression analyses of venom-producing tissues, tandem mass spectrometry-based proteomics of toxic secretions, and mass spectrometry imaging of proboscis sections, to shed light onto the composition and evolution of predatory and defensive toxic secretions in Antarctonemertes valida. Our analyses reveal a wide diversity of putative defensive and predatory toxins with tissue-specific gene expression patterns and restricted distributions to the mucus and proboscis proteomes respectively, suggesting that ribbon worms produce distinct toxin cocktails for predation and defense. Our results also highlight the presence of numerous lineage-specific toxins, indicating that venom evolution is highly divergent across nemerteans, producing toxin cocktails that might be finely tuned to subdue different prey. Our data also suggest that the hoplonemertean proboscis is a highly specialized predatory organ that seems to be involved in a variety of biological functions besides predation, including secretion and sensory perception. Overall, our results advance our knowledge into the diversity and evolution of nemertean venoms and highlight the importance of combining different types of data to characterize toxin composition in understudied venomous organisms.
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Affiliation(s)
- Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
| | - Sergi Taboada
- Department of Life Sciences, Natural History Museum, London, UK.,Departament of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Brett R Hamilton
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gabriel G Sonoda
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Sonia C S Andrade
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Esperanza Morato
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Isabel Marina
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
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8
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Achrak E, Ferd J, Schulman J, Dang T, Krampis K, Holford M. VenomFlow: An Automated Bioinformatic Pipeline for Identification of Disulfide-Rich Peptides from Venom Arsenals. Methods Mol Biol 2022; 2498:89-97. [PMID: 35727542 DOI: 10.1007/978-1-0716-2313-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Animal venoms are among the most complex natural secretions known, comprising a mixture of bioactive compounds often referred to as toxins. Venom arsenals are predominately made up of cysteine-rich peptide toxins that manipulate molecular targets, such as ion channels and receptors, making these venom peptides attractive candidates for the development of therapeutics to benefit human health. With the rise of omic strategies that utilize transcriptomic, proteomic, and bioinformatic methods, we are able to identify more venom proteins and peptides than ever before. However, identification and characterization of bioactive venom peptides remains a significant challenge due to the unique chemical structure and enormous number of peptides found in each venom arsenal (upward of 200 per organism). Here, we introduce a rapid and user-friendly in silico bioinformatic pipeline for the de novo identification and characterization of raw RNAseq reads from venom glands to elucidate cysteine-rich peptides from the arsenal of venomous organisms.Implementation: This project develops a user-friendly automated bioinformatics pipeline via a Galaxy workflow to identify novel venom peptides from raw RNAseq reads of terebrid snails. While designed for venomous terebrid snails, with minor adjustments, this pipeline can be made universal to identify secreted disulfide-rich peptide toxins from any venomous organism.
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Affiliation(s)
- Eleonora Achrak
- Department of Biology, Hunter College of the City University of New York, New York, NY, USA
| | - Jennifer Ferd
- Department of Chemistry, Hunter College of the City University of New York, New York, NY, USA
| | - Jessica Schulman
- Department of Bioinformatics, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Trami Dang
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY, USA
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY, USA
| | - Mande Holford
- Department of Chemistry & Biochemistry, Hunter College of the City University of New York, New York, NY, USA.
- The American Museum of Natural History, New York, NY, USA.
- PhD Programs in Biology, Biochemistry, and Chemistry at the CUNY Graduate Center, New York, NY, USA.
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9
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McDermott M, Cerullo AR, Parziale J, Achrak E, Sultana S, Ferd J, Samad S, Deng W, Braunschweig AB, Holford M. Advancing Discovery of Snail Mucins Function and Application. Front Bioeng Biotechnol 2021; 9:734023. [PMID: 34708024 PMCID: PMC8542881 DOI: 10.3389/fbioe.2021.734023] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mucins are a highly glycosylated protein family that are secreted by animals for adhesion, hydration, lubrication, and other functions. Despite their ubiquity, animal mucins are largely uncharacterized. Snails produce mucin proteins in their mucous for a wide array of biological functions, including microbial protection, adhesion and lubrication. Recently, snail mucins have also become a lucrative source of innovation with wide ranging applications across chemistry, biology, biotechnology, and biomedicine. Specifically, snail mucuses have been applied as skin care products, wound healing agents, surgical glues, and to combat gastric ulcers. Recent advances in integrated omics (genomic, transcriptomic, proteomic, glycomic) technologies have improved the characterization of gastropod mucins, increasing the generation of novel biomaterials. This perspective describes the current research on secreted snail mucus, highlighting the potential of this biopolymer, and also outlines a research strategy to fulfill the unmet need of examining the hierarchical structures that lead to the enormous biological and chemical diversity of snail mucus genes.
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Affiliation(s)
- Maxwell McDermott
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Antonio R Cerullo
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - James Parziale
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Eleonora Achrak
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Sharmin Sultana
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Jennifer Ferd
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Safiyah Samad
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - William Deng
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States
| | - Adam B Braunschweig
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States.,Advanced Science Research Center, Graduate Center of New York, Graduate Department of Biochemistry, New York, NY, United States.,PhD Programs in Biochemistry and Chemistry Graduate Center of the City University of New York, New York, NY, United States
| | - Mandë Holford
- Department of Chemistry and Biochemistry, Hunter College, New York, NY, United States.,PhD Programs in Biochemistry and Chemistry Graduate Center of the City University of New York, New York, NY, United States.,PhD Program in Biology Graduate Center of the City University of New York, New York, NY, United States.,Department of Invertebrate Zoology, The American Museum of Natural History, New York, NY, United States
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10
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Gorson J, Fassio G, Lau ES, Holford M. Diet Diversity in Carnivorous Terebrid Snails Is Tied to the Presence and Absence of a Venom Gland. Toxins (Basel) 2021; 13:toxins13020108. [PMID: 33540609 PMCID: PMC7912948 DOI: 10.3390/toxins13020108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 11/30/2022] Open
Abstract
Predator-prey interactions are thought to play a driving role in animal evolution, especially for groups that have developed venom as their predatory strategy. However, how the diet of venomous animals influences the composition of venom arsenals remains uncertain. Two prevailing hypotheses to explain the relationship between diet and venom composition focus on prey preference and the types of compounds in venom, and a positive correlation between dietary breadth and the number of compounds in venom. Here, we examined venom complexity, phylogenetic relationship, collection depth, and biogeography of the Terebridae (auger snails) to determine if repeated innovations in terebrid foregut anatomy and venom composition correspond to diet variation. We performed the first molecular study of the diet of terebrid marine snails by metabarcoding the gut content of 71 terebrid specimens from 17 species. Our results suggest that the presence or absence of a venom gland is strongly correlated with dietary breadth. Specifically, terebrid species without a venom gland displayed greater diversity in their diet. Additionally, we propose a revision of the definition of venom complexity in conoidean snails to more accurately capture the breadth of ecological influences. These findings suggest that prey diet is an important factor in terebrid venom evolution and diversification and further investigations of other understudied organisms, like terebrids, are needed to develop robust hypotheses in this area.
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Affiliation(s)
- Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY 10021, USA; (J.G.); (G.F.); (E.S.L.)
- Graduate Programs in Biology, Biochemistry, Chemistry, Graduate Center, City University of New York, New York, NY 10016, USA
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA
| | - Giulia Fassio
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY 10021, USA; (J.G.); (G.F.); (E.S.L.)
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, I-00185 Rome, Italy
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, I-00198 Rome, Italy
| | - Emily S. Lau
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY 10021, USA; (J.G.); (G.F.); (E.S.L.)
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY 10021, USA; (J.G.); (G.F.); (E.S.L.)
- Graduate Programs in Biology, Biochemistry, Chemistry, Graduate Center, City University of New York, New York, NY 10016, USA
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
- Correspondence:
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11
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Hallan A, Criscione F, Fedosov A, Puillandre N. Few and far apart: integrative taxonomy of Australian species of Gladiobela and Pagodibela (Conoidea : Raphitomidae) reveals patterns of wide distributions and low abundance. INVERTEBR SYST 2021. [DOI: 10.1071/is20017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The deep-sea malacofauna of temperate Australia remains comparatively poorly known. However, a recent influx of DNA-suitable material obtained from a series of deep-sea cruises has facilitated integrative taxonomic study on the Conoidea (Caenogastropoda:Neogastropoda). Building on a recent molecular phylogeny of the conoidean family Raphitomidae, this study focussed on the genera Gladiobela and Pagodibela (both Criscione, Hallan, Puillandre & Fedosov, 2020). We subjected a representative mtDNA cox1 dataset of deep-sea raphitomids to ABGD, which recognised 14 primary species hypotheses (PSHs), 9 of which were converted to secondary species hypotheses (SSHs). Following the additional examination of the shell and hypodermic radula features, as well as consideration of bathymetric and geographic data, seven of these SSHs were recognised as new to science and given full species rank. Subsequently, systematic descriptions are provided herein. Of these, five are attributed to Gladiobela (three of which are endemic to Australia and two more widely distributed) and two are placed in Pagodibela (one endemic to southern Australia and one widespread in the Pacific). The rarity of many ‘turrids’ reported in previous studies is confirmed herein, as particularly indicated by highly disjunct geographic records for two taxa. Additionally, several of the studied taxa exhibit wide Indo-Pacific distributions, suggesting that wide geographic ranges in deep-sea ‘turrids’ may be more common than previously assumed. Finally, impediments to deep-sea ‘turrid’ taxonomy in light of such comparative rarity and unexpectedly wide distributions are discussed.
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12
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Cerullo AR, Lai TY, Allam B, Baer A, Barnes WJP, Barrientos Z, Deheyn DD, Fudge DS, Gould J, Harrington MJ, Holford M, Hung CS, Jain G, Mayer G, Medina M, Monge-Nájera J, Napolitano T, Espinosa EP, Schmidt S, Thompson EM, Braunschweig AB. Comparative Animal Mucomics: Inspiration for Functional Materials from Ubiquitous and Understudied Biopolymers. ACS Biomater Sci Eng 2020; 6:5377-5398. [DOI: 10.1021/acsbiomaterials.0c00713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Antonio R. Cerullo
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Tsoi Ying Lai
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Alexander Baer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - W. Jon P. Barnes
- Centre for Cell Engineering, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Zaidett Barrientos
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Dimitri D. Deheyn
- Marine Biology Research Division-0202, Scripps Institute of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Douglas S. Fudge
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - John Gould
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, New South Wales 2308, Australia
| | - Matthew J. Harrington
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Mandë Holford
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, New York 10024, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The PhD Program in Biology, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Chia-Suei Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Gaurav Jain
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, Pennsylvania 16802, United States
| | - Julian Monge-Nájera
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Tanya Napolitano
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Emmanuelle Pales Espinosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Stephan Schmidt
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Eric M. Thompson
- Sars Centre for Marine Molecular Biology, Thormøhlensgt. 55, 5020 Bergen, Norway
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | - Adam B. Braunschweig
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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13
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Modica MV, Gorson J, Fedosov AE, Malcolm G, Terryn Y, Puillandre N, Holford M. Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification. Syst Biol 2020; 69:413-430. [PMID: 31504987 PMCID: PMC7164365 DOI: 10.1093/sysbio/syz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- UMR5247, Université de Montpellier CC 1703, Place Eugène Bataillon 34095 Montpellier, France
| | - Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Alexander E Fedosov
- Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, 33, Moscow 119071, Russia
| | - Gavin Malcolm
- Bird Hill, Barnes Lane, Milford on Sea, Hampshire, UK
| | - Yves Terryn
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
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14
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Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE. Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus. Genome Biol Evol 2020; 12:684-700. [PMID: 32333764 PMCID: PMC7259678 DOI: 10.1093/gbe/evaa083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense, and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study, we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis and two specimens of Clavus davidgilmouri were analyzed, leading to the identification of a total of 1,176 putative venom peptide toxins (drillipeptides). Based on the combined evidence of secretion signal sequence identity, entire precursor similarity search (BLAST), and the orthology inference, putative Clavus toxins were assigned to 158 different gene families. The majority of identified transcripts comprise signal, pro-, mature peptide, and post-regions, with a typically short (<50 amino acids) and cysteine-rich mature peptide region. Thus, drillipeptides are structurally similar to conotoxins. However, convincing homology with known groups of Conus toxins was only detected for very few toxin families. Among these are Clavus counterparts of Conus venom insulins (drillinsulins), porins (drilliporins), and highly diversified lectins (drillilectins). The short size of most drillipeptides and structural similarity to conotoxins were unexpected, given that most related conoidean gastropod families (Terebridae and Turridae) possess longer mature peptide regions. Our findings indicate that, similar to conotoxins, drillipeptides may represent a valuable resource for future pharmacological exploration.
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Affiliation(s)
- Aiping Lu
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Qing Li
- Eccles Institute of Human Genetics, University of Utah
- High-Throughput Genomics and Bioinformatic Analysis Shared Resource, Huntsman Cancer Institute, University of Utah
| | | | - Gisela P Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah
- Utah Center for Genetic Discovery, University of Utah
| | - Zhiping Weng
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School
| | | | - Helena Safavi-Hemami
- Department of Biochemistry, University of Utah
- Department of Biology, University of Copenhagen, Denmark
| | - Alexander E Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
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15
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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16
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Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. Toxins (Basel) 2019; 11:toxins11110623. [PMID: 31661832 PMCID: PMC6891753 DOI: 10.3390/toxins11110623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components such as chymotrypsin and L-rhamnose-binding lectin. The large majority of conotoxins appeared to be from new gene superfamilies, three of which are highly different from previously reported venom peptide toxins. Their low conotoxin diversity and the type of insulin found suggested that these species, for which no ecological information are available, have a worm or molluscan diet associated with a narrow dietary breadth. Our results indicate that Profundiconus venom is highly distinct from that of other cone snails, and therefore important for examining venom evolution in the Conidae family.
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17
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
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 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.
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18
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Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. Mar Drugs 2019; 17:md17080466. [PMID: 31405144 PMCID: PMC6722550 DOI: 10.3390/md17080466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/26/2022] Open
Abstract
The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.
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19
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Using Drosophila behavioral assays to characterize terebrid venom-peptide bioactivity. Sci Rep 2018; 8:15276. [PMID: 30323294 PMCID: PMC6189199 DOI: 10.1038/s41598-018-33215-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022] Open
Abstract
The number of newly discovered peptides from the transcriptomes and proteomes of animal venom arsenals is rapidly increasing, resulting in an abundance of uncharacterized peptides. There is a pressing need for a systematic, cost effective, and scalable approach to identify physiological effects of venom peptides. To address this discovery-to-function gap, we developed a sequence driven:activity-based hybrid approach for screening venom peptides that is amenable to large-venom peptide libraries with minimal amounts of peptide. Using this approach, we characterized the physiological and behavioral phenotypes of two peptides from the venom of predatory terebrid marine snails, teretoxins Tv1 from Terebra variegata and Tsu1.1 from Terebra subulata. Our results indicate that Tv1 and Tsu1.1 have distinct bioactivity. Tv1 (100 µM) had an antinociceptive effect in adult Drosophila using a thermal nociception assay to measure heat avoidance. Alternatively, Tsu1.1 (100 µM) increased food intake. These findings describe the first functional bioactivity of terebrid venom peptides in relation to pain and diet and indicate that Tv1 and Tsu1.1 may, respectively, act as antinociceptive and orexigenic agents. Tv1 and Tsu1.1 are distinct from previously identified venom peptides, expanding the toolkit of peptides that can potentially be used to investigate the physiological mechanisms of pain and diet.
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20
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Pekár S, Líznarová E, Bočánek O, Zdráhal Z. Venom of prey-specialized spiders is more toxic to their preferred prey: A result of prey-specific toxins. J Anim Ecol 2018; 87:1639-1652. [PMID: 30125357 DOI: 10.1111/1365-2656.12900] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/14/2018] [Indexed: 12/19/2022]
Abstract
In specialized predators, a variety of adaptations have evolved to such a level of specificity that they allow very effective exploitation of focal prey. Venom is an essential adaptive trait of predatory venomous species, such as spiders, yet our knowledge of spider venom is incomplete. In agreement with the prey preference hypothesis, we expected that the venom of spider specialists should be more toxic to focal than to alternative prey, because it is composed of prey-specific toxins. Here we used spiders with three types of trophic specializations: specialists that were ant-eating, termite-eating and spider-eating. We compared the efficacy of prey capture of preferred and alternative prey (measured as paralysis latency) with that of related generalists and profiled the venom of the studied species using proteomic methods. We used 22 spider species: six myrmecophagous, two termitophagous, three araneophagous and 11 euryphagous generalist species belonging to different families. We found that ten of the eleven specialist species induced significantly shorter paralysis latency in preferred prey than in alternative prey. Generalists exhibited either similar efficiency on both prey types or slightly higher efficiency on preferred prey. Multivariate analysis of proteomic profiles (peptides and proteins) revealed significant differences between trophic specializations, particularly in peptides. Specialists appear to have venom composed of unique specific compounds as revealed by the multivariate ordination and indicator analysis. These components are likely prey-specific toxins.
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Affiliation(s)
- Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Líznarová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondřej Bočánek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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21
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Möller C, Dovell S, Melaun C, Marí F. Definition of the R-superfamily of conotoxins: Structural convergence of helix-loop-helix peptidic scaffolds. Peptides 2018; 107:75-82. [PMID: 30040981 DOI: 10.1016/j.peptides.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/13/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
The F14 conotoxins define a four-cysteine, three-loop conotoxin scaffold that produce tightly folded structures held together by two disulfide bonds with a CCCC arrangement (conotoxin framework 14). Here we describe the precursors of the F14 conotoxins from the venom of Conus anabathrum and Conus villepinii. Using transcriptomic and cDNA cloning analysis, the full-length of the precursors of flf14a and flf14b from the transcriptome of C. anabathrum revealed a unique signal sequence that defines the new conotoxin R-superfamily. Using the signal sequence as a primer, we cloned seven additional previously undescribed toxins of the R-superfamily from C. villepinii. The propeptide regions of the R-conotoxins are unusually long and with prevalent proline residues in repeating pentads which qualifies them as Pro-rich motifs (PRMs), which can be critical for protein-protein interactions or they can be cleaved to release short linear peptides that may be part of the envenomation mélange. Additionally, we determined the three-dimensional structure of vil14a by solution 1H-NMR and found that the structure of this conotoxin displays a cysteine-stabilized α-helix-loop-helix (Cs α/α) fold. The structure is well-defined over the helical regions (backbone RMSD for residues 2-13 and 17-26 is 0.63 ± 0.14 Å), with conformational flexibility in the triple Gly region of the second loop as well as the N- and C- termini. Structurally, the F14 conotoxins overlap with the Cs α/α scorpion toxins and other peptidic natural products, and in spite of their different exogenomic origins, there is convergence into this scaffold from several classes of living organisms that express these peptides.
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Affiliation(s)
- Carolina Möller
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA
| | - Sanaz Dovell
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA
| | - Christian Melaun
- Justus Liebig Universität Giessen, Institut für Allg. Zoologie und Entwicklungsbiologie, Giessen, Germany
| | - Frank Marí
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA; Marine Biochemical Sciences, Chemical Sciences Division, National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, USA.
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22
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Bioactive Compounds Isolated from Neglected Predatory Marine Gastropods. Mar Drugs 2018; 16:md16040118. [PMID: 29621159 PMCID: PMC5923405 DOI: 10.3390/md16040118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/21/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022] Open
Abstract
A diverse range of predatory marine gastropods produce toxins, yet most of these molecules remain uncharacterized. Conus species have received the most attention from researchers, leading to several conopeptides reaching clinical trials. This review aims to summarize what is known about bioactive compounds isolated from species of neglected marine gastropods, especially in the Turridae, Terebridae, Babyloniidae, Muricidae, Buccinidae, Colubrariidae, Nassariidae, Cassidae, and Ranellidae families. Multiple species have been reported to contain bioactive compounds with potential toxic activity, but most of these compounds have not been characterized or even clearly identified. The bioactive properties and potential applications of echotoxins and related porins from the Ranellidae family are discussed in more detail. Finally, the review concludes with a call for research on understudied species.
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23
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Verdes A, Simpson D, Holford M. Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae). Genome Biol Evol 2018; 10:249-268. [PMID: 29293976 PMCID: PMC5778601 DOI: 10.1093/gbe/evx279] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 12/14/2022] Open
Abstract
Amphinomids, more commonly known as fireworms, are a basal lineage of marine annelids characterized by the presence of defensive dorsal calcareous chaetae, which break off upon contact. It has long been hypothesized that amphinomids are venomous and use the chaetae to inject a toxic substance. However, studies investigating fireworm venom from a morphological or molecular perspective are scarce and no venom gland has been identified to date, nor any toxin characterized at the molecular level. To investigate this question, we analyzed the transcriptomes of three species of fireworms-Eurythoe complanata, Hermodice carunculata, and Paramphinome jeffreysii-following a venomics approach to identify putative venom compounds. Our venomics pipeline involved de novo transcriptome assembly, open reading frame, and signal sequence prediction, followed by three different homology search strategies: BLAST, HMMER sequence, and HMMER domain. Following this pipeline, we identified 34 clusters of orthologous genes, representing 13 known toxin classes that have been repeatedly recruited into animal venoms. Specifically, the three species share a similar toxin profile with C-type lectins, peptidases, metalloproteinases, spider toxins, and CAP proteins found among the most highly expressed toxin homologs. Despite their great diversity, the putative toxins identified are predominantly involved in three major biological processes: hemostasis, inflammatory response, and allergic reactions, all of which are commonly disrupted after fireworm stings. Although the putative fireworm toxins identified here need to be further validated, our results strongly suggest that fireworms are venomous animals that use a complex mixture of toxins for defense against predators.
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Affiliation(s)
- Aida Verdes
- Department of Chemistry, Hunter College Belfer Research Center, and The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York
- Department of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain
| | - Danny Simpson
- Department of Population Health, New York University School of Medicine
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, and The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York
- Department of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
- Department of Biochemistry, Weill Cornell Medical College, Cornell University
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24
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Verdes A, Holford M. Beach to Bench to Bedside: Marine Invertebrate Biochemical Adaptations and Their Applications in Biotechnology and Biomedicine. Results Probl Cell Differ 2018; 65:359-376. [PMID: 30083928 DOI: 10.1007/978-3-319-92486-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ocean covers more than 70% of the surface of the planet and harbors very diverse ecosystems ranging from tropical coral reefs to the deepest ocean trenches, with some of the most extreme conditions of pressure, temperature, and light. Organisms living in these environments have been subjected to strong selective pressures through millions of years of evolution, resulting in a plethora of remarkable adaptations that serve a variety of vital functions. Some of these adaptations, including venomous secretions and light-emitting compounds or ink, represent biochemical innovations in which marine invertebrates have developed novel and unique bioactive compounds with enormous potential for basic and applied research. Marine biotechnology, defined as the application of science and technology to marine organisms for the production of knowledge, goods, and services, can harness the enormous possibilities of these unique bioactive compounds acting as a bridge between biological knowledge and applications. This chapter highlights some of the most exceptional biochemical adaptions found specifically in marine invertebrates and describes the biotechnological and biomedical applications derived from them to improve the quality of human life.
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Affiliation(s)
- Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain.
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
- The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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Gorson J, Holford M. Small Packages, Big Returns: Uncovering the Venom Diversity of Small Invertebrate Conoidean Snails. Integr Comp Biol 2016; 56:962-972. [PMID: 27371389 PMCID: PMC6058754 DOI: 10.1093/icb/icw063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Venomous organisms used in research were historically chosen based on size and availability. This opportunity-driven strategy created a species bias in which snakes, scorpions, and spiders became the primary subjects of venom research. Increasing technological advancements have enabled interdisciplinary studies using genomics, transcriptomics, and proteomics to expand venom investigation to animals that produce small amounts of venom or lack traditional venom producing organs. One group of non-traditional venomous organisms that have benefitted from the rise of -omic technologies is the Conoideans. The Conoidean superfamily of venomous marine snails includes, the Terebridae, Turridae (s.l), and Conidae. Conoidea venom is used for both predation and defense, and therefore under strong selection pressures. The need for conoidean venom peptides to be potent and specific to their molecular targets has made them important tools for investigating cellular physiology and bioactive compounds that are beneficial to improving human health. A convincing case for the potential of Conoidean venom is made with the first commercially available conoidean venom peptide drug Ziconotide (Prialt®), an analgesic derived from Conus magus venom that is used to treat chronic pain in HIV and cancer patients. Investigation of conoidean venom using -omics technology provides significant insights into predator-driven diversification in biodiversity and identifies novel compounds for manipulating cellular communication, especially as it pertains to disease and disorders.
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Affiliation(s)
- J Gorson
- *Department of Chemistry, Hunter College, The City University of New York, Belfer Research Building, NY, 10021 USA
- Departments of Biology, Chemistry, and Biochemistry, The Graduate City, The City University of New York, NY, 10016 USA
- Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, 10024 USA
| | - M Holford
- *Department of Chemistry, Hunter College, The City University of New York, Belfer Research Building, NY, 10021 USA
- Departments of Biology, Chemistry, and Biochemistry, The Graduate City, The City University of New York, NY, 10016 USA
- Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, 10024 USA
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Integrating Perspectives on Animal Venom Diversity: An Introduction to the Symposium. Integr Comp Biol 2016; 56:934-937. [DOI: 10.1093/icb/icw112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Verdes A, Anand P, Gorson J, Jannetti S, Kelly P, Leffler A, Simpson D, Ramrattan G, Holford M. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins. Toxins (Basel) 2016; 8:117. [PMID: 27104567 PMCID: PMC4848642 DOI: 10.3390/toxins8040117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022] Open
Abstract
Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa.
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Affiliation(s)
- Aida Verdes
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Prachi Anand
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Juliette Gorson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Stephen Jannetti
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Patrick Kelly
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Abba Leffler
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine 550 1st Avenue, New York, NY 10016, USA.
| | - Danny Simpson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Tandon School of Engineering, New York University 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Girish Ramrattan
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Mandë Holford
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
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Moon J, Gorson J, Wright ME, Yee L, Khawaja S, Shin HY, Karma Y, Musunri RL, Yun M, Holford M. Characterization and Recombinant Expression of Terebrid Venom Peptide from Terebra guttata. Toxins (Basel) 2016; 8:toxins8030063. [PMID: 26950153 PMCID: PMC4810208 DOI: 10.3390/toxins8030063] [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: 01/01/2016] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 01/26/2023] Open
Abstract
Venom peptides found in terebrid snails expand the toolbox of active compounds that can be applied to investigate cellular physiology and can be further developed as future therapeutics. However, unlike other predatory organisms, such as snakes, terebrids produce very small quantities of venom, making it difficult to obtain sufficient amounts for biochemical characterization. Here, we describe the first recombinant expression and characterization of terebrid peptide, teretoxin Tgu6.1, from Terebra guttata. Tgu6.1 is a novel forty-four amino acid teretoxin peptide with a VI/VII cysteine framework (C-C-CC-C-C) similar to O, M and I conotoxin superfamilies. A ligation-independent cloning strategy with an ompT protease deficient strain of E. coli was employed to recombinantly produce Tgu6.1. Thioredoxin was introduced in the plasmid to combat disulfide folding and solubility issues. Specifically Histidine-6 tag and Ni-NTA affinity chromatography were applied as a purification method, and enterokinase was used as a specific cleavage protease to effectively produce high yields of folded Tgu6.1 without extra residues to the primary sequence. The recombinantly-expressed Tgu6.1 peptide was bioactive, displaying a paralytic effect when injected into a Nereis virens polychaete bioassay. The recombinant strategy described to express Tgu6.1 can be applied to produce high yields of other disulfide-rich peptides.
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Affiliation(s)
- John Moon
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | - Juliette Gorson
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
| | - Mary Elizabeth Wright
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
| | - Laurel Yee
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | - Samer Khawaja
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | - Hye Young Shin
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | - Yasmine Karma
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | | | - Michelle Yun
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
| | - Mande Holford
- Hunter College, City University of New York, Belfer Research Center 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
- The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10026, USA.
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Bioinformatics-Aided Venomics. Toxins (Basel) 2015; 7:2159-87. [PMID: 26110505 PMCID: PMC4488696 DOI: 10.3390/toxins7062159] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/12/2022] Open
Abstract
Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.
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