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Chiappa G, Fassio G, Modica MV, Oliverio M. Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae). Toxins (Basel) 2024; 16:348. [PMID: 39195758 PMCID: PMC11359391 DOI: 10.3390/toxins16080348] [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: 07/12/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.
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Affiliation(s)
- Giacomo Chiappa
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
| | - Giulia Fassio
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Via Gregorio Allegri 1, 00198 Rome, Italy;
| | - Marco Oliverio
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Viale dell’Università 32, 00185 Rome, Italy; (G.F.); (M.O.)
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2
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Koch TL, Robinson SD, Salcedo PF, Chase K, Biggs J, Fedosov AE, Yandell M, Olivera BM, Safavi-Hemami H. Prey Shifts Drive Venom Evolution in Cone Snails. Mol Biol Evol 2024; 41:msae120. [PMID: 38935574 PMCID: PMC11296725 DOI: 10.1093/molbev/msae120] [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: 01/03/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
Venom systems are complex traits that have independently emerged multiple times in diverse plant and animal phyla. Within each venomous lineage there typically exists interspecific variation in venom composition where several factors have been proposed as drivers of variation, including phylogeny and diet. Understanding these factors is of broad biological interest and has implications for the development of antivenom therapies and venom-based drug discovery. Because of their high species richness and the presence of several major evolutionary prey shifts, venomous marine cone snails (genus Conus) provide an ideal system to investigate drivers of interspecific venom variation. Here, by analyzing the venom gland expression profiles of ∼3,000 toxin genes from 42 species of cone snail, we elucidate the role of prey-specific selection pressures in shaping venom variation. By analyzing overall venom composition and individual toxin structures, we demonstrate that the shifts from vermivory to piscivory in Conus are complemented by distinct changes in venom composition independent of phylogeny. In vivo injections of venom from piscivorous cone snails in fish further showed a higher potency compared with venom of nonpiscivores demonstrating a selective advantage. Together, our findings provide compelling evidence for the role of prey shifts in directing the venom composition of cone snails and expand our understanding of the mechanisms of venom variation and diversification.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Samuel D Robinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Biggs
- Division of Aquatic and Wildlife Resources, Department of Agriculture, Mangilao, GU 96913, USA
| | - Alexander E Fedosov
- Swedish Museum of Natural History, Department of Zoology, Stockholm 114 18, Sweden
| | - Mark Yandell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Baldomero M Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Helena Safavi-Hemami
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N 2200, Denmark
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3
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Michálek O, King GF, Pekár S. Prey specificity of predatory venoms. Biol Rev Camb Philos Soc 2024. [PMID: 38991997 DOI: 10.1111/brv.13120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
Venom represents a key adaptation of many venomous predators, allowing them to immobilise prey quickly through chemical rather than physical warfare. Evolutionary arms races between prey and a predator are believed to be the main factor influencing the potency and composition of predatory venoms. Predators with narrowly restricted diets are expected to evolve specifically potent venom towards their focal prey, with lower efficacy on alternative prey. Here, we evaluate hypotheses on the evolution of prey-specific venom, focusing on the effect of restricted diet, prey defences, and prey resistance. Prey specificity as a potential evolutionary dead end is also discussed. We then provide an overview of the current knowledge on venom prey specificity, with emphasis on snakes, cone snails, and spiders. As the current evidence for venom prey specificity is still quite limited, we also overview the best approaches and methods for its investigation and provide a brief summary of potential model groups. Finally, possible applications of prey-specific toxins are discussed.
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Affiliation(s)
- Ondřej Michálek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
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4
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Ringeval A, Farhat S, Fedosov A, Gerdol M, Greco S, Mary L, Modica MV, Puillandre N. DeTox: a pipeline for the detection of toxins in venomous organisms. Brief Bioinform 2024; 25:bbae094. [PMID: 38493344 PMCID: PMC10944572 DOI: 10.1093/bib/bbae094] [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: 11/14/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024] Open
Abstract
Venomous organisms have independently evolved the ability to produce toxins 101 times during their evolutionary history, resulting in over 200 000 venomous species. Collectively, these species produce millions of toxins, making them a valuable resource for bioprospecting and understanding the evolutionary mechanisms underlying genetic diversification. RNA-seq is the preferred method for characterizing toxin repertoires, but the analysis of the resulting data remains challenging. While early approaches relied on similarity-based mapping to known toxin databases, recent studies have highlighted the importance of structural features for toxin detection. The few existing pipelines lack an integration between these complementary approaches, and tend to be difficult to run for non-experienced users. To address these issues, we developed DeTox, a comprehensive and user-friendly tool for toxin research. It combines fast execution, parallelization and customization of parameters. DeTox was tested on published transcriptomes from gastropod mollusks, cnidarians and snakes, retrieving most putative toxins from the original articles and identifying additional peptides as potential toxins to be confirmed through manual annotation and eventually proteomic analysis. By integrating a structure-based search with similarity-based approaches, DeTox allows the comprehensive characterization of toxin repertoire in poorly-known taxa. The effect of the taxonomic bias in existing databases is minimized in DeTox, as mirrored in the detection of unique and divergent toxins that would have been overlooked by similarity-based methods. DeTox streamlines toxin annotation, providing a valuable tool for efficient identification of venom components that will enhance venom research in neglected taxa.
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Affiliation(s)
- Allan Ringeval
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, 75005 Paris, France
| | - Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, 75005 Paris, France
| | - Alexander Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, 75005 Paris, France
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Roma, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Lou Mary
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, 75005 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, 57 rue Cuvier, 75005 Paris, France
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Guo Q, Huang M, Li M, Chen J, Cheng S, Ma L, Gao B. Diversity and Evolutionary Analysis of Venom Insulin Derived from Cone Snails. Toxins (Basel) 2024; 16:34. [PMID: 38251250 PMCID: PMC10819828 DOI: 10.3390/toxins16010034] [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: 10/24/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Cone snails possess a diverse array of novel peptide toxins, which selectively target ion channels and receptors in the nervous and cardiovascular systems. These numerous novel peptide toxins are a valuable resource for future marine drug development. In this review, we compared and analyzed the sequence diversity, three-dimensional structural variations, and evolutionary aspects of venom insulin derived from different cone snail species. The comparative analysis reveals that there are significant variations in the sequences and three-dimensional structures of venom insulins from cone snails with different feeding habits. Notably, the venom insulin of some piscivorous cone snails exhibits a greater similarity to humans and zebrafish insulins. It is important to emphasize that these venom insulins play a crucial role in the predatory strategies of these cone snails. Furthermore, a phylogenetic tree was constructed to trace the lineage of venom insulin sequences, shedding light on the evolutionary interconnections among cone snails with diverse diets.
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Affiliation(s)
- Qiqi Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
| | - Meiling Huang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
| | - Ming Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
| | - Jiao Chen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
| | - Shuanghuai Cheng
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
| | - Linlin Ma
- Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (Q.G.); (M.H.); (M.L.); (J.C.); (S.C.)
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6
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Fedosov A, Tucci CF, Kantor Y, Farhat S, Puillandre N. Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production. J Mol Evol 2023; 91:837-853. [PMID: 37962577 PMCID: PMC10730640 DOI: 10.1007/s00239-023-10139-8] [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: 07/14/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Venomous marine gastropods of the family Conidae are among the most diversified predators in marine realm-in large due to their complex venoms. Besides being a valuable source of bioactive neuropeptides conotoxins, cone-snails venoms are an excellent model for molecular evolution studies, addressing origin of key innovations. However, these studies are handicapped by scarce current knowledge on the tissues involved in venom production, as it is generally assumed the sole prerogative of the venom gland (VG). The role of other secretory glands that are present in all Conus species (salivary gland, SG) or only in some species (accessory salivary gland, ASG) remains poorly understood. Here, for the first time, we carry out a detailed analysis of the VG, SG, and ASG transcriptomes in the vermivorous Conus virgo. We detect multiple transcripts clusters in both the SG and ASG, whose annotations imply venom-related functions. Despite the subsets of transcripts highly-expressed in the VG, SG, and ASG being very distinct, SG expresses an L-, and ASG-Cerm08-, and MEFRR- superfamily conotoxins, all previously considered specific for VG. We corroborate our results with the analysis of published SG and VG transcriptomes from unrelated fish-hunting C. geographus, and C. striatus, possibly fish-hunting C. rolani, and worm-hunting Conus quercinus. In spite of low expression levels of conotoxins, some other specific clusters of putative venom-related peptides are present and may be highly expressed in the SG of these species. Further functional studies are necessary to determine the role that these peptides play in envenomation. In the meantime, our results show importance of routine multi-tissue sampling both for accurate interpretation of tissue-specific venom composition in cone-snails, and for better understanding origin and evolution of venom peptides genes.
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Affiliation(s)
- Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Carmen Federica Tucci
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 35020, Legnaro, Italy
| | - Yuri Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninski Prospect, Moscow, 119071, Russian Federation
| | - Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
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7
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Koch TL, Torres JP, Baskin RP, Salcedo PF, Chase K, Olivera BM, Safavi-Hemami H. A toxin-based approach to neuropeptide and peptide hormone discovery. Front Mol Neurosci 2023; 16:1176662. [PMID: 37720554 PMCID: PMC10501145 DOI: 10.3389/fnmol.2023.1176662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Peptide hormones and neuropeptides form a diverse class of bioactive secreted molecules that control essential processes in animals. Despite breakthroughs in peptide discovery, many signaling peptides remain undiscovered. Recently, we demonstrated the use of somatostatin-mimicking toxins from cone snails to identify the invertebrate ortholog of somatostatin. Here, we show that this toxin-based approach can be systematically applied to discover other unknown secretory peptides that are likely to have signaling function. Using large sequencing datasets, we searched for homologies between cone snail toxins and secreted proteins from the snails' prey. We identified and confirmed expression of five toxin families that share strong similarities with unknown secretory peptides from mollusks and annelids and in one case also from ecdysozoans. Based on several lines of evidence we propose that these peptides likely act as signaling peptides that serve important physiological functions. Indeed, we confirmed that one of the identified peptides belongs to the family of crustacean hyperglycemic hormone, a peptide not previously observed in Spiralia. We propose that this discovery pipeline can be broadly applied to other systems in which one organism has evolved molecules to manipulate the physiology of another.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
| | - Joshua P. Torres
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert P. Baskin
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Paula Flórez Salcedo
- Department of Neurobiology, University of Utah, Salt Lake City, UT, United States
| | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
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8
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Drott MT, Park SC, Wang YW, Harrow L, Keller NP, Pringle A. Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range. THE ISME JOURNAL 2023:10.1038/s41396-023-01432-x. [PMID: 37221394 DOI: 10.1038/s41396-023-01432-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023]
Abstract
The poisonous European mushroom Amanita phalloides (the "death cap") is invading California. Whether the death caps' toxic secondary metabolites are evolving as it invades is unknown. We developed a bioinformatic pipeline to identify the MSDIN genes underpinning toxicity and probed 88 death cap genomes from an invasive Californian population and from the European range, discovering a previously unsuspected diversity of MSDINs made up of both core and accessory elements. Each death cap individual possesses a unique suite of MSDINs, and toxin genes are significantly differentiated between Californian and European samples. MSDIN genes are maintained by strong natural selection, and chemical profiling confirms MSDIN genes are expressed and result in distinct phenotypes; our chemical profiling also identified a new MSDIN peptide. Toxin genes are physically clustered within genomes. We contextualize our discoveries by probing for MSDINs in genomes from across the order Agaricales, revealing MSDIN diversity originated in independent gene family expansions among genera. We also report the discovery of an MSDIN in an Amanita outside the "lethal Amanitas" clade. Finally, the identification of an MSDIN gene and its associated processing gene (POPB) in Clavaria fumosa suggest the origin of MSDINs is older than previously suspected. The dynamic evolution of MSDINs underscores their potential to mediate ecological interactions, implicating MSDINs in the ongoing invasion. Our data change the understanding of the evolutionary history of poisonous mushrooms, emphasizing striking parallels to convergently evolved animal toxins. Our pipeline provides a roadmap for exploring secondary metabolites in other basidiomycetes and will enable drug prospecting.
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Affiliation(s)
- Milton T Drott
- Department of Medical Microbiology and Immunology, Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA.
| | - Sung Chul Park
- Department of Medical Microbiology and Immunology, Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Yen-Wen Wang
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lynn Harrow
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, WI, USA.
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9
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Smith EG, Surm JM, Macrander J, Simhi A, Amir G, Sachkova MY, Lewandowska M, Reitzel AM, Moran Y. Micro and macroevolution of sea anemone venom phenotype. Nat Commun 2023; 14:249. [PMID: 36646703 PMCID: PMC9842752 DOI: 10.1038/s41467-023-35794-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Venom is a complex trait with substantial inter- and intraspecific variability resulting from strong selective pressures acting on the expression of many toxic proteins. However, understanding the processes underlying toxin expression dynamics that determine the venom phenotype remains unresolved. By interspecific comparisons we reveal that toxin expression in sea anemones evolves rapidly and that in each species different toxin family dictates the venom phenotype by massive gene duplication events. In-depth analysis of the sea anemone, Nematostella vectensis, revealed striking variation of the dominant toxin (Nv1) diploid copy number across populations (1-24 copies) resulting from independent expansion/contraction events, which generate distinct haplotypes. Nv1 copy number correlates with expression at both the transcript and protein levels with one population having a near-complete loss of Nv1 production. Finally, we establish the dominant toxin hypothesis which incorporates observations in other venomous lineages that animals have convergently evolved a similar strategy in shaping their venom.
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Affiliation(s)
- Edward G Smith
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA. .,School of Life Sciences, University of Warwick, Coventry, United Kingdom.
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Jason Macrander
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA.,Florida Southern College, Biology Department, Lakeland, FL, USA
| | - Adi Simhi
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Hebrew University of Jerusalem, The School of Computer Science & Engineering, Jerusalem, Israel
| | - Guy Amir
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Hebrew University of Jerusalem, The School of Computer Science & Engineering, Jerusalem, Israel
| | - Maria Y Sachkova
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Magda Lewandowska
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adam M Reitzel
- University of North Carolina at Charlotte, Department of Biological Sciences, Charlotte, NC, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Michálek O, Walker AA, Šedo O, Zdráhal Z, King GF, Pekár S. Composition and toxicity of venom produced by araneophagous white-tailed spiders (Lamponidae: Lampona sp.). Sci Rep 2022; 12:21597. [PMID: 36517485 PMCID: PMC9751281 DOI: 10.1038/s41598-022-24694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Prey-specialised spiders are adapted to capture specific prey items, including dangerous prey. The venoms of specialists are often prey-specific and less complex than those of generalists, but their venom composition has not been studied in detail. Here, we investigated the venom of the prey-specialised white-tailed spiders (Lamponidae: Lampona), which utilise specialised morphological and behavioural adaptations to capture spider prey. We analysed the venom composition using proteo-transcriptomics and taxon-specific toxicity using venom bioassays. Our analysis identified 208 putative toxin sequences, comprising 103 peptides < 10 kDa and 105 proteins > 10 kDa. Most peptides belonged to one of two families characterised by scaffolds containing eight or ten cysteine residues. Toxin-like proteins showed similarity to galectins, leucine-rich repeat proteins, trypsins and neprilysins. The venom of Lampona was shown to be more potent against the preferred spider prey than against alternative cricket prey. In contrast, the venom of a related generalist was similarly potent against both prey types. These data provide insights into the molecular adaptations of venoms produced by prey-specialised spiders.
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Affiliation(s)
- Ondřej Michálek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Andrew A Walker
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ondrej Šedo
- Research Group Proteomics, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Research Group Proteomics, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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11
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Gao B, Huang Y, Peng C, Lin B, Liao Y, Bian C, Yang J, Shi Q. High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development. BIODESIGN RESEARCH 2022; 2022:9895270. [PMID: 37850131 PMCID: PMC10521759 DOI: 10.34133/2022/9895270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/23/2022] [Indexed: 10/19/2023] Open
Abstract
Cone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomics, and proteomics) approaches have been recently developed to mine diverse Conus venom samples, with the main aim to predict and identify potentially interesting conopeptides in an efficient way. Some bioinformatics techniques have been applied to predict and design novel conopeptide sequences, related targets, and their binding modes. This review provides an overview of current knowledge on the high diversity of conopeptides and multiomics advances in high-throughput prediction of novel conopeptide sequences, as well as molecular modeling and design of potential drugs based on the predicted or validated interactions between these toxins and their molecular targets.
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Affiliation(s)
- Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yanling Liao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Jiaan Yang
- Research and Development Department, Micro Pharmtech Ltd., Wuhan, Hubei 430075, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
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12
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Kuznetsova KG, Zvonareva SS, Ziganshin R, Mekhova ES, Dgebuadze P, Yen DTH, Nguyen THT, Moshkovskii SA, Fedosov AE. Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus Vexillum. Proc Biol Sci 2022; 289:20221152. [PMID: 35946162 PMCID: PMC9363990 DOI: 10.1098/rspb.2022.1152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Venoms of predatory marine cone snails are intensely studied because of the biomedical applications of the neuropeptides that they contain, termed conotoxins. Meanwhile some gastropod lineages have independently acquired secretory glands strikingly similar to the venom gland of cone snails, suggesting that they possess similar venoms. Here we focus on the most diversified of these clades, the genus Vexillum. Based on the analysis of a multi-species proteo-transcriptomic dataset, we show that Vexillum species indeed produce complex venoms dominated by highly diversified short cysteine-rich peptides, vexitoxins. Vexitoxins possess the same precursor organization, display overlapping cysteine frameworks and share several common post-translational modifications with conotoxins. Some vexitoxins show sequence similarity to conotoxins and adopt similar domain conformations, including a pharmacologically relevant inhibitory cysteine knot motif. The Vexillum envenomation gland (gL) is a notably more recent evolutionary novelty than the conoidean venom gland. Thus, we hypothesize lower divergence between vexitoxin genes, and their ancestral 'somatic' counterparts compared to that in conotoxins, and we find support for this hypothesis in the evolution of the vexitoxin cluster V027. We use this example to discuss how future studies on vexitoxins can inform the origin of conotoxins, and how they may help to address outstanding questions in venom evolution.
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Affiliation(s)
- Ksenia G. Kuznetsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | - Sofia S. Zvonareva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, Moscow 119071, Russia
| | - Rustam Ziganshin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya street, 16/10, Moscow 117997, Russia
| | - Elena S. Mekhova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, Moscow 119071, Russia
| | - Polina Dgebuadze
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, Moscow 119071, Russia
| | - Dinh T. H. Yen
- Russian-Vietnamese Tropical Research and Technology Center, Coastal Branch, 30 Nguyễn Thiện Thuật, Nha Trang, Vietnam
| | - Thanh H. T. Nguyen
- Russian-Vietnamese Tropical Research and Technology Center, Coastal Branch, 30 Nguyễn Thiện Thuật, Nha Trang, Vietnam
| | - Sergei A. Moshkovskii
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
| | - Alexander E. Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, Moscow 119071, Russia
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13
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Divergent Specialization of Simple Venom Gene Profiles among Rear-Fanged Snake Genera ( Helicops and Leptodeira, Dipsadinae, Colubridae). Toxins (Basel) 2022; 14:toxins14070489. [PMID: 35878227 PMCID: PMC9319703 DOI: 10.3390/toxins14070489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera (Leptodeira and Helicops, Colubridae) and two front-fanged genera (Bothrops, Viperidae; Micrurus, Elapidae). We compared patterns of composition, variation, and diversity in venom transcripts within and among all four genera. Venom gland transcriptomes of rear-fanged Helicops and Leptodeira and front-fanged Micrurus are each dominated by expression of single toxin families (C-type lectins, snake venom metalloproteinase, and phospholipase A2, respectively), unlike highly diverse front-fanged Bothrops venoms. In addition, expression patterns of congeners are much more similar to each other than they are to species from other genera. These results illustrate the repeatability of simple venom profiles in rear-fanged snakes and the potential for relatively constrained venom composition within genera.
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14
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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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15
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Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
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Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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16
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Pardos-Blas JR, Tenorio MJ, Galindo JCG, Zardoya R. Comparative Venomics of the Cryptic Cone Snail Species Virroconus ebraeus and Virroconus judaeus. Mar Drugs 2022; 20:149. [PMID: 35200678 PMCID: PMC8875821 DOI: 10.3390/md20020149] [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: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/04/2022] Open
Abstract
The venom duct transcriptomes and proteomes of the cryptic cone snail species Virroconus ebraeus and Virroconus judaeus were obtained and compared. The most abundant and shared conotoxin precursor superfamilies in both species were M, O1, and O2. Additionally, three new putative conotoxin precursor superfamilies (Virro01-03) with cysteine pattern types VI/VII and XVI were identified. The most expressed conotoxin precursor superfamilies were SF-mi2 and M in V. ebraeus, and Cerm03 and M in V. judaeus. Up to 16 conotoxin precursor superfamilies and hormones were differentially expressed between both species, and clustered into two distinct sets, which could represent adaptations of each species to different diets. Finally, we predicted, with machine learning algorithms, the 3D structure model of selected venom proteins including the differentially expressed Cerm03 and SF-mi2, an insulin type 3, a Gastridium geographus GVIA-like conotoxin, and an ortholog to the Pionoconus magus ω-conotoxin MVIIA (Ziconotide).
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Affiliation(s)
- José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
| | - Manuel J. Tenorio
- Departamento de CMIM y Química Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - Juan Carlos G. Galindo
- Departamento de Química Orgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Spain;
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
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17
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Abalde S, Dutertre S, Zardoya R. A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae). Toxins (Basel) 2021; 13:toxins13090642. [PMID: 34564647 PMCID: PMC8472973 DOI: 10.3390/toxins13090642] [Citation(s) in RCA: 8] [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: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/20/2022] Open
Abstract
Venoms are complex mixtures of proteins that have evolved repeatedly in the animal kingdom. Cone snail venoms represent one of the best studied venom systems. In nature, this venom can be dynamically adjusted depending on its final purpose, whether to deter predators or hunt prey. Here, the transcriptome of the venom gland and the proteomes of the predation-evoked and defensive venoms of the molluscivorous cone snail Cylinder ammiralis were catalogued. A total of 242 venom-related transcripts were annotated. The conotoxin superfamilies presenting more different peptides were O1, O2, T, and M, which also showed high expression levels (except T). The three precursors of the J superfamily were also highly expressed. The predation-evoked and defensive venoms showed a markedly distinct profile. A total of 217 different peptides were identified, with half of them being unique to one venom. A total of 59 peptides ascribed to 23 different protein families were found to be exclusive to the predatory venom, including the cono-insulin, which was, for the first time, identified in an injected venom. A total of 43 peptides from 20 protein families were exclusive to the defensive venom. Finally, comparisons of the relative abundance (in terms of number of peptides) of the different conotoxin precursor superfamilies showed that most of them present similar abundance regardless of the diet.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
- Department of Zoology, Swedish Museum of Natural History, Frescativägen 40, 114 18 Stockholm, Sweden
- Correspondence:
| | | | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
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18
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Fedosov A, Zaharias P, Puillandre N. A phylogeny-aware approach reveals unexpected venom components in divergent lineages of cone snails. Proc Biol Sci 2021; 288:20211017. [PMID: 34229491 PMCID: PMC8261202 DOI: 10.1098/rspb.2021.1017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022] Open
Abstract
Marine gastropods of the genus Conus are renowned for their remarkable diversity and deadly venoms. While Conus venoms are increasingly well studied for their biomedical applications, we know surprisingly little about venom composition in other lineages of Conidae. We performed comprehensive venom transcriptomic profiling for Conasprella coriolisi and Pygmaeconus traillii, first time for both respective genera. We complemented reference-based transcriptome annotation by a de novo toxin prediction guided by phylogeny, which involved transcriptomic data on two additional 'divergent' cone snail lineages, Profundiconus, and Californiconus. We identified toxin clusters (SSCs) shared among all or some of the four analysed genera based on the identity of the signal region-a molecular tag present in toxins. In total, 116 and 98 putative toxins represent 29 and 28 toxin gene superfamilies in Conasprella and Pygmaeconus, respectively; about quarter of these only found by semi-manual annotation of the SSCs. Two rare gene superfamilies, originally identified from fish-hunting cone snails, were detected outside Conus rather unexpectedly, so we further investigated their distribution across Conidae radiation. We demonstrate that both these, in fact, are ubiquitous in Conidae, sometimes with extremely high expression. Our findings demonstrate how a phylogeny-aware approach circumvents methodological caveats of similarity-based transcriptome annotation.
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Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russian Federation
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
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19
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Holding ML, Strickland JL, Rautsaw RM, Hofmann EP, Mason AJ, Hogan MP, Nystrom GS, Ellsworth SA, Colston TJ, Borja M, Castañeda-Gaytán G, Grünwald CI, Jones JM, Freitas-de-Sousa LA, Viala VL, Margres MJ, Hingst-Zaher E, Junqueira-de-Azevedo ILM, Moura-da-Silva AM, Grazziotin FG, Gibbs HL, Rokyta DR, Parkinson CL. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proc Natl Acad Sci U S A 2021; 118:e2015579118. [PMID: 33875585 PMCID: PMC8092465 DOI: 10.1073/pnas.2015579118] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.
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Affiliation(s)
- Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | | | - Jason M Jones
- HERP.MX A.C., Villa del Álvarez, Colima 28973, Mexico
| | | | - Vincent Louis Viala
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Ana M Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040, Brazil
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, Brazil
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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20
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Venom Use in Eulipotyphlans: An Evolutionary and Ecological Approach. Toxins (Basel) 2021; 13:toxins13030231. [PMID: 33810196 PMCID: PMC8004749 DOI: 10.3390/toxins13030231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022] Open
Abstract
Venomousness is a complex functional trait that has evolved independently many times in the animal kingdom, although it is rare among mammals. Intriguingly, most venomous mammal species belong to Eulipotyphla (solenodons, shrews). This fact may be linked to their high metabolic rate and a nearly continuous demand of nutritious food, and thus it relates the venom functions to facilitation of their efficient foraging. While mammalian venoms have been investigated using biochemical and molecular assays, studies of their ecological functions have been neglected for a long time. Therefore, we provide here an overview of what is currently known about eulipotyphlan venoms, followed by a discussion of how these venoms might have evolved under ecological pressures related to food acquisition, ecological interactions, and defense and protection. We delineate six mutually nonexclusive functions of venom (prey hunting, food hoarding, food digestion, reducing intra- and interspecific conflicts, avoidance of predation risk, weapons in intraspecific competition) and a number of different subfunctions for eulipotyphlans, among which some are so far only hypothetical while others have some empirical confirmation. The functions resulting from the need for food acquisition seem to be the most important for solenodons and especially for shrews. We also present several hypotheses explaining why, despite so many potentially beneficial functions, venomousness is rare even among eulipotyphlans. The tentativeness of many of the arguments presented in this review highlights our main conclusion, i.e., insights regarding the functions of eulipotyphlan venoms merit additional study.
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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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22
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Abstract
Previous studies have indicated that each conotoxin precursor has a hyperconserved signal region, a rather conserved pro region and a hypervariable mature region, and nucleotide mutations are the main driven factor. However, in this study, we made an in-depth analysis on the M-superfamily conotoxin precursors and found that the diversity of the signal, pro and mature regions are more complicated than previous findings. Different conotoxin precursors can have same signal, pro and/or mature regions, especially different conotoxin precursors with same mature region but different signal and pro regions. In addition, insertions and deletions (indels) were detected in conotoxin precursors. Indels are infrequent in the signal region but frequent in the pro and mature regions. In contrast to deletions that dominate in the pro region, insertions dominate in the mature region. The number of amino acids is crucial for the physiological functions of mature conotoxins, therefore indels, especially insertions in the mature region, play an important role in the sequence and function diversity of conotoxins.
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Affiliation(s)
- Manyi Yang
- Department of Hepatobiliary and Pancreatic Surgery, NHC Key Laboratory of Nanobiological Technology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Maojun Zhou
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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23
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Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations. Mar Drugs 2020; 18:md18100503. [PMID: 33019526 PMCID: PMC7601563 DOI: 10.3390/md18100503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
Marine cone snails belonging to the Conidae family make use of neuroactive peptides in their venom to capture prey. Here we report the proteome profile of the venom duct of Conus eburneus, a cone snail belonging to the Tesseliconus clade. Through tandem mass spectrometry and database searching against the C. eburneus transcriptome and the ConoServer database, we identified 24 unique conopeptide sequences in the venom duct. The majority of these peptides belong to the T and M gene superfamilies and are disulfide-bonded, with cysteine frameworks V, XIV, VI/VII, and III being the most abundant. All seven of the Cys-free peptides are conomarphin variants belonging to the M superfamily that eluted out as dominant peaks in the chromatogram. These conomarphins vary not only in amino acid residues in select positions along the backbone but also have one or more post-translational modifications (PTMs) such as proline hydroxylation, C-term amidation, and γ-carboxylation of glutamic acid. Using molecular dynamics simulations, the conomarphin variants were predicted to predominantly have hairpin-like or elongated structures in acidic pH. These two structures were found to have significant differences in electrostatic properties and the inclusion of PTMs seems to complement this disparity. The presence of polar PTMs (hydroxyproline and γ-carboxyglutamic acid) also appear to stabilize hydrogen bond networks in these conformations. Furthermore, these predicted structures are pH sensitive, becoming more spherical and compact at higher pH. The subtle conformational variations observed here might play an important role in the selection and binding of the peptides to their molecular targets.
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24
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Bjørn-Yoshimoto WE, Ramiro IBL, Yandell M, McIntosh JM, Olivera BM, Ellgaard L, Safavi-Hemami H. Curses or Cures: A Review of the Numerous Benefits Versus the Biosecurity Concerns of Conotoxin Research. Biomedicines 2020; 8:E235. [PMID: 32708023 PMCID: PMC7460000 DOI: 10.3390/biomedicines8080235] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 01/18/2023] Open
Abstract
Conotoxins form a diverse group of peptide toxins found in the venom of predatory marine cone snails. Decades of conotoxin research have provided numerous measurable scientific and societal benefits. These include their use as a drug, diagnostic agent, drug leads, and research tools in neuroscience, pharmacology, biochemistry, structural biology, and molecular evolution. Human envenomations by cone snails are rare but can be fatal. Death by envenomation is likely caused by a small set of toxins that induce muscle paralysis of the diaphragm, resulting in respiratory arrest. The potency of these toxins led to concerns regarding the potential development and use of conotoxins as biological weapons. To address this, various regulatory measures have been introduced that limit the use and access of conotoxins within the research community. Some of these regulations apply to all of the ≈200,000 conotoxins predicted to exist in nature of which less than 0.05% are estimated to have any significant toxicity in humans. In this review we provide an overview of the many benefits of conotoxin research, and contrast these to the perceived biosecurity concerns of conotoxins and research thereof.
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Affiliation(s)
- Walden E. Bjørn-Yoshimoto
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
| | - Iris Bea L. Ramiro
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA;
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - J. Michael McIntosh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
- George E. Whalen Veterans Affairs Medical Center, Salt Lake City, UT 84148, USA
- Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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25
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Hanf ZR, Chavez AS. A Comprehensive Multi-Omic Approach Reveals a Relatively Simple Venom in a Diet Generalist, the Northern Short-Tailed Shrew, Blarina brevicauda. Genome Biol Evol 2020; 12:1148-1166. [PMID: 32520994 PMCID: PMC7486961 DOI: 10.1093/gbe/evaa115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 12/15/2022] Open
Abstract
Animals that use venom to feed on a wide diversity of prey may evolve a complex mixture of toxins to target a variety of physiological processes and prey-defense mechanisms. Blarina brevicauda, the northern short-tailed shrew, is one of few venomous mammals, and is also known to eat evolutionarily divergent prey. Despite their complex diet, earlier proteomic and transcriptomic studies of this shrew's venom have only identified two venom proteins. Here, we investigated with comprehensive molecular approaches whether B. brevicauda venom is more complex than previously understood. We generated de novo assemblies of a B. brevicauda genome and submaxillary-gland transcriptome, as well as sequenced the salivary proteome. Our findings show that B. brevicauda's venom composition is simple relative to their broad diet and is likely limited to seven proteins from six gene families. Additionally, we explored expression levels and rate of evolution of these venom genes and the origins of key duplications that led to toxin neofunctionalization. We also found three proteins that may be involved in endogenous self-defense. The possible synergism of the toxins suggests that vertebrate prey may be the main target of the venom. Further functional assays for all venom proteins on both vertebrate and invertebrate prey would provide further insight into the ecological relevance of venom in this species.
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Affiliation(s)
- Zachery R Hanf
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
| | - Andreas S Chavez
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
- Translational Data Analytics Institute, The Ohio State University
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26
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Lüddecke T, von Reumont BM, Förster F, Billion A, Timm T, Lochnit G, Vilcinskas A, Lemke S. An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders ( Argiope bruennichi). Biomolecules 2020; 10:E978. [PMID: 32630016 PMCID: PMC7407881 DOI: 10.3390/biom10070978] [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: 06/10/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Spiders use venom to subdue their prey, but little is known about the diversity of venoms in different spider families. Given the limited data available for orb-weaver spiders (Araneidae), we selected the wasp spider Argiope bruennichi for detailed analysis. Our strategy combined a transcriptomics pipeline based on multiple assemblies with a dual proteomics workflow involving parallel mass spectrometry techniques and electrophoretic profiling. We found that the remarkably simple venom of A. bruennichi has an atypical composition compared to other spider venoms, prominently featuring members of the cysteine-rich secretory protein, antigen 5 and pathogenesis-related protein 1 (CAP) superfamily and other, mostly high-molecular-weight proteins. We also detected a subset of potentially novel toxins similar to neuropeptides. We discuss the potential function of these proteins in the context of the unique hunting behavior of wasp spiders, which rely mostly on silk to trap their prey. We propose that the simplicity of the venom evolved to solve an economic dilemma between two competing yet metabolically expensive weapon systems. This study emphasizes the importance of cutting-edge methods to encompass the lineages of smaller venomous species that have yet to be characterized in detail, allowing us to understand the biology of their venom systems and to mine this prolific resource for translational research.
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Affiliation(s)
- Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
| | - Björn M. von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Frank Förster
- Institute for Bioinformatics and Systems Biology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany;
| | - André Billion
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
| | - Thomas Timm
- Institute of Biochemistry, Justus-Liebig-University of Gießen, Friedrichstr. 24, 35392 Gießen, Germany; (T.T.); (G.L.)
| | - Günter Lochnit
- Institute of Biochemistry, Justus-Liebig-University of Gießen, Friedrichstr. 24, 35392 Gießen, Germany; (T.T.); (G.L.)
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Sarah Lemke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
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27
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Abalde S, Tenorio MJ, Afonso CML, Zardoya R. Comparative transcriptomics of the venoms of continental and insular radiations of West African cones. Proc Biol Sci 2020; 287:20200794. [PMID: 32546094 DOI: 10.1098/rspb.2020.0794] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework using one Kalloconus species as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus. Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.,Departamento de Biología Animal, Facultad de Biología, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cádiz, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
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28
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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29
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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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30
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Niermann CN, Tate TG, Suto AL, Barajas R, White HA, Guswiler OD, Secor SM, Rowe AH, Rowe MP. Defensive Venoms: Is Pain Sufficient for Predator Deterrence? Toxins (Basel) 2020; 12:toxins12040260. [PMID: 32316477 PMCID: PMC7232307 DOI: 10.3390/toxins12040260] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/26/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022] Open
Abstract
Pain, though unpleasant, is adaptive in calling an animal’s attention to potential tissue damage. A long list of animals representing diverse taxa possess venom-mediated, pain-inducing bites or stings that work by co-opting the pain-sensing pathways of potential enemies. Typically, such venoms include toxins that cause tissue damage or disrupt neuronal activity, rendering painful stings honest indicators of harm. But could pain alone be sufficient for deterring a hungry predator? Some venomologists have argued “no”; predators, in the absence of injury, would “see through” the bluff of a painful but otherwise benign sting or bite. Because most algogenic venoms are also toxic (although not vice versa), it has been difficult to disentangle the relative contributions of each component to predator deterrence. Southern grasshopper mice (Onychomys torridus) are voracious predators of arthropods, feeding on a diversity of scorpion species whose stings vary in painfulness, including painful Arizona bark scorpions (Centruroides sculpturatus) and essentially painless stripe-tailed scorpions (Paravaejovis spinigerus). Moreover, southern grasshopper mice have evolved resistance to the lethal toxins in bark scorpion venom, rendering a sting from these scorpions painful but harmless. Results from a series of laboratory experiments demonstrate that painful stings matter. Grasshopper mice preferred to prey on stripe-tailed scorpions rather than bark scorpions when both species could sting; the preference disappeared when each species had their stingers blocked. A painful sting therefore appears necessary for a scorpion to deter a hungry grasshopper mouse, but it may not always be sufficient: after first attacking and consuming a painless stripe-tailed scorpion, many grasshopper mice went on to attack, kill, and eat a bark scorpion even when the scorpion was capable of stinging. Defensive venoms that result in tissue damage or neurological dysfunction may, thus, be required to condition greater aversion than venoms causing pain alone.
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Affiliation(s)
- Crystal N. Niermann
- Department of Biology, Sam Houston State University, Huntsville, TX 77340, USA; (C.N.N.); (T.G.T.)
| | - Travis G. Tate
- Department of Biology, Sam Houston State University, Huntsville, TX 77340, USA; (C.N.N.); (T.G.T.)
| | - Amber L. Suto
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA; (A.L.S.); (O.D.G.)
| | - Rolando Barajas
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA; (R.B.); (H.A.W.)
| | - Hope A. White
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA; (R.B.); (H.A.W.)
| | - Olivia D. Guswiler
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA; (A.L.S.); (O.D.G.)
| | - Stephen M. Secor
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA;
| | - Ashlee H. Rowe
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA;
| | - Matthew P. Rowe
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA;
- Correspondence: ; Tel.: +1-405-325-6539
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Zancolli G, Calvete JJ, Cardwell MD, Greene HW, Hayes WK, Hegarty MJ, Herrmann HW, Holycross AT, Lannutti DI, Mulley JF, Sanz L, Travis ZD, Whorley JR, Wüster CE, Wüster W. When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species. Proc Biol Sci 2020; 286:20182735. [PMID: 30862287 DOI: 10.1098/rspb.2018.2735] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.
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Affiliation(s)
- Giulia Zancolli
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Juan J Calvete
- 2 Evolutionary and Translational Venomics Laboratory, CSIC , Jaume Roig 11, Valencia 46010 , Spain
| | - Michael D Cardwell
- 3 Department of Biology, San Diego State University , San Diego, CA 92182 , USA
| | - Harry W Greene
- 4 Department of Ecology and Evolutionary Biology, Cornell University , Corson Hall, Ithaca, NY 14853 , USA
| | - William K Hayes
- 5 Department of Earth and Biological Sciences, School of Medicine, Loma Linda University , Loma Linda, CA 92350 , USA
| | - Matthew J Hegarty
- 6 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University , Aberystwyth SY23 3EE , UK
| | - Hans-Werner Herrmann
- 7 Wildlife Conservation and Management, School of Natural Resources and the Environment, University of Arizona , 1064 East Lowell Street (ENR2), Tucson, AZ 85721 , USA
| | - Andrew T Holycross
- 8 Natural History Collections, Arizona State University , 734 W. Alameda Drive, Tempe, AZ 85282 , USA
| | - Dominic I Lannutti
- 9 Department of Biological Sciences, University of Texas at El Paso , 500 W. University, El Paso, TX 79968 , USA
| | - John F Mulley
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Libia Sanz
- 2 Evolutionary and Translational Venomics Laboratory, CSIC , Jaume Roig 11, Valencia 46010 , Spain
| | - Zachary D Travis
- 5 Department of Earth and Biological Sciences, School of Medicine, Loma Linda University , Loma Linda, CA 92350 , USA
| | - Joshua R Whorley
- 10 Seattle Central College, Science, Technology, Engineering & Mathematics Division , 1701 Broadway Ave. E., Seattle, WA 98122 , USA
| | - Catharine E Wüster
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Wolfgang Wüster
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
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Lyons K, Dugon MM, Healy K. Diet Breadth Mediates the Prey Specificity of Venom Potency in Snakes. Toxins (Basel) 2020; 12:toxins12020074. [PMID: 31979380 PMCID: PMC7076792 DOI: 10.3390/toxins12020074] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 12/30/2022] Open
Abstract
Venoms are best known for their ability to incapacitate prey. In predatory groups, venom potency is predicted to reflect ecological and evolutionary drivers relating to diet. While venoms have been found to have preyspecific potencies, the role of diet breadth on venom potencies has yet to be tested at large macroecological scales. Here, using a comparative analysis of 100 snake species, we show that the evolution of prey-specific venom potencies is contingent on the breadth of a species' diet. We find that while snake venom is more potent when tested on species closely related to natural prey items, we only find this prey-specific pattern in species with taxonomically narrow diets. While we find that the taxonomic diversity of a snakes' diet mediates the prey specificity of its venom, the species richness of its diet was not found to affect these prey-specific potency patterns. This indicates that the physiological diversity of a species' diet is an important driver of the evolution of generalist venom potencies. These findings suggest that the venoms of species with taxonomically diverse diets may be better suited to incapacitating novel prey species and hence play an important role for species within changing environments.
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Affiliation(s)
- Keith Lyons
- Correspondence: (K.L.); (K.H.); Tel.: +353-91-493744 (K.H.)
| | | | - Kevin Healy
- Correspondence: (K.L.); (K.H.); Tel.: +353-91-493744 (K.H.)
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33
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Davies EL, Arbuckle K. Coevolution of Snake Venom Toxic Activities and Diet: Evidence that Ecological Generalism Favours Toxicological Diversity. Toxins (Basel) 2019; 11:E711. [PMID: 31817769 PMCID: PMC6950196 DOI: 10.3390/toxins11120711] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/10/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023] Open
Abstract
Snake venom evolution is typically considered to be predominantly driven by diet-related selection pressures. Most evidence for this is based on lethality to prey and non-prey species and on the identification of prey specific toxins. Since the broad toxicological activities (e.g., neurotoxicity, coagulotoxicity, etc.) sit at the interface between molecular toxinology and lethality, these classes of activity may act as a key mediator in coevolutionary interactions between snakes and their prey. Indeed, some recent work has suggested that variation in these functional activities may be related to diet as well, but previous studies have been limited in geographic and/or taxonomic scope. In this paper, we take a phylogenetic comparative approach to investigate relationships between diet and toxicological activity classes on a global scale across caenophidian snakes, using the clinically oriented database at toxinology.com. We generally find little support for specific prey types selecting for particular toxicological effects except that reptile-feeders are more likely to be neurotoxic. We find some support for endothermic prey (with higher metabolic rates) influencing toxic activities, but differently from previous suggestions in the literature. More broadly, we find strong support for a general effect of increased diversity of prey on the diversity of toxicological effects of snake venom. Hence, we provide evidence that selection pressures on the toxicological activities of snake venom has largely been driven by prey diversity rather than specific types of prey. These results complement and extend previous work to suggest that specific matching of venom characteristics to prey may occur at the molecular level and translate into venom lethality, but the functional link between those two is not constrained to a particular toxicological route.
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Affiliation(s)
| | - Kevin Arbuckle
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK;
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34
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Jenner RA, von Reumont BM, Campbell LI, Undheim EAB. Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses. Mol Biol Evol 2019; 36:2748-2763. [PMID: 31396628 PMCID: PMC6878950 DOI: 10.1093/molbev/msz181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Centipedes are among the most ancient groups of venomous predatory arthropods. Extant species belong to five orders, but our understanding of the composition and evolution of centipede venoms is based almost exclusively on one order, Scolopendromorpha. To gain a broader and less biased understanding we performed a comparative proteotranscriptomic analysis of centipede venoms from all five orders, including the first venom profiles for the orders Lithobiomorpha, Craterostigmomorpha, and Geophilomorpha. Our results reveal an astonishing structural diversity of venom components, with 93 phylogenetically distinct protein and peptide families. Proteomically-annotated gene trees of these putative toxin families show that centipede venom composition is highly dynamic across macroevolutionary timescales, with numerous gene duplications as well as functional recruitments and losses of toxin gene families. Strikingly, not a single family is found in the venoms of representatives of all five orders, with 67 families being unique for single orders. Ancestral state reconstructions reveal that centipede venom originated as a simple cocktail comprising just four toxin families, with very little compositional evolution happening during the approximately 50 My before the living orders had diverged. Venom complexity then increased in parallel within the orders, with scolopendromorphs evolving particularly complex venoms. Our results show that even venoms composed of toxins evolving under the strong constraint of negative selection can have striking evolutionary plasticity on the compositional level. We show that the functional recruitments and losses of toxin families that shape centipede venom arsenals are not concentrated early in their evolutionary history, but happen frequently throughout.
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Affiliation(s)
- Ronald A Jenner
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bjoern M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig University Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Animal Venomics, Giessen, Germany
| | - Lahcen I Campbell
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, United Kingdom
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Ecology and Evolutionary Synthesis, Department of Bioscience, University of Oslo, Oslo, Norway
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35
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Michálek O, Kuhn-Nentwig L, Pekár S. High Specific Efficiency of Venom of Two Prey-Specialized Spiders. Toxins (Basel) 2019; 11:E687. [PMID: 31771158 PMCID: PMC6950493 DOI: 10.3390/toxins11120687] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/04/2019] [Accepted: 11/20/2019] [Indexed: 12/15/2022] Open
Abstract
The venom of predators should be under strong selection pressure because it is a costly substance and prey may potentially become resistant. Particularly in prey-specialized predators, venom should be selected for its high efficiency against the focal prey. Very effective venom paralysis has been observed in specialized predators, such as spiders preying on dangerous prey. Here, we compared the toxicity of the venoms of two prey-specialized species, araneophagous Palpimanus sp. and myrmecophagous Zodarion nitidum, and their related generalist species. We injected different venom concentrations into two prey types-the prey preferred by a specialist and an alternative prey-and observed the mortality and the paralysis of the prey within 24 h. We found that the venoms of specialists were far more potent towards the preferred prey than alternative prey. The venoms of generalists were similarly potent towards both prey types. In addition, we tested the efficacy of two venom fractions (smaller and larger than 10 kDa) in araneophagous Palpimanus sp. Compounds larger than 10 kDa paralyzed both prey types, but smaller compounds (<10 kDa) were effective only on preferred prey, suggesting the presence of prey-specific compounds in the latter fraction. Our results confirm that prey-specialized spiders possess highly specific venom that allows them to subdue dangerous prey.
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Affiliation(s)
- Ondřej Michálek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lucia Kuhn-Nentwig
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland;
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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36
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Sudewi AA, Susilawathi NM, Mahardika BK, Mahendra AN, Pharmawati M, Phuong MA, Mahardika GN. Selecting Potential Neuronal Drug Leads from Conotoxins of Various Venomous Marine Cone Snails in Bali, Indonesia. ACS OMEGA 2019; 4:19483-19490. [PMID: 31763573 PMCID: PMC6868881 DOI: 10.1021/acsomega.9b03122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Many conotoxins, natural peptides of marine cone snails, have been identified to target neurons. Here, we provide data on pharmacological families of the conotoxins of 11 species of cone snails collected in Bali. The identified definitive pharmacological families possibly targeting neuronal tissues were α (alpha), ι (iota), κ (kappa), and ρ (rho). These classes shall target nicotinic acetylcholine receptors, voltage-gated Na channels, voltage-gated K channels, and α1-adrenoceptors, respectively. The VI/VII-O3 conotoxins might be prospected as an inhibitor of N-methyl-d-aspartate. Con-ikot-ikot could be applied as an α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor blocker medicine. The definitive pharmacology classes of conotoxins as well as those yet to be elucidated need to be further established and verified.
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Affiliation(s)
- Anak A.
R. Sudewi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Ni M. Susilawathi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Bayu K. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
| | - Agung N. Mahendra
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Made Pharmawati
- Faculty
of Mathematic and Natural Sciences, Udayana
University of Bali, Kampus
Bukit Jimbaran, Badung 80361, Bali, Indonesia
| | - Mark A. Phuong
- Department
of Ecology and Evolutionary Biology, University
of California, Los Angeles, Los
Angeles 90095, California, United States
| | - Gusti N. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
- The Indonesian
Biodiversity Research Center, Jl. Sudirman, Denpasar 80225, Bali, Indonesia
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37
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Schendel V, Rash LD, Jenner RA, Undheim EAB. The Diversity of Venom: The Importance of Behavior and Venom System Morphology in Understanding Its Ecology and Evolution. Toxins (Basel) 2019; 11:E666. [PMID: 31739590 PMCID: PMC6891279 DOI: 10.3390/toxins11110666] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Venoms are one of the most convergent of animal traits known, and encompass a much greater taxonomic and functional diversity than is commonly appreciated. This knowledge gap limits the potential of venom as a model trait in evolutionary biology. Here, we summarize the taxonomic and functional diversity of animal venoms and relate this to what is known about venom system morphology, venom modulation, and venom pharmacology, with the aim of drawing attention to the importance of these largely neglected aspects of venom research. We find that animals have evolved venoms at least 101 independent times and that venoms play at least 11 distinct ecological roles in addition to predation, defense, and feeding. Comparisons of different venom systems suggest that morphology strongly influences how venoms achieve these functions, and hence is an important consideration for understanding the molecular evolution of venoms and their toxins. Our findings also highlight the need for more holistic studies of venom systems and the toxins they contain. Greater knowledge of behavior, morphology, and ecologically relevant toxin pharmacology will improve our understanding of the evolution of venoms and their toxins, and likely facilitate exploration of their potential as sources of molecular tools and therapeutic and agrochemical lead compounds.
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Affiliation(s)
- Vanessa Schendel
- Centre for Advanced Imaging, the University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Lachlan D. Rash
- School of Biomedical Sciences, the University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Ronald A. Jenner
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK;
| | - Eivind A. B. Undheim
- Centre for Advanced Imaging, the University of Queensland, St. Lucia, QLD 4072, Australia;
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
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38
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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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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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40
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Ul-Hasan S, Rodríguez-Román E, Reitzel AM, Adams RM, Herzig V, Nobile CJ, Saviola AJ, Trim SA, Stiers EE, Moschos SA, Keiser CN, Petras D, Moran Y, Colston TJ. The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP). Toxicon X 2019; 4:100016. [PMID: 32550573 PMCID: PMC7286055 DOI: 10.1016/j.toxcx.2019.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium.
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Affiliation(s)
- Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, 95343, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Eduardo Rodríguez-Román
- Center for Microbiology and Cell Biology, Venezuelan Institute for Scientific Research. Caracas, 1020A, Venezuela
| | - Adam M. Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Rachelle M.M. Adams
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43212, USA
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Anthony J. Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Steven A. Trim
- Venomtech Ltd, Discovery Park, Sandwich, Kent, CT13 9ND, UK
| | - Erin E. Stiers
- Department of Biological Science, Clemson University, Clemson, SC, 29634, USA
| | - Sterghios A. Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK
| | - Carl N. Keiser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, USA
- Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Timothy J. Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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41
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Conotoxin Diversity in the Venom Gland Transcriptome of the Magician's Cone, Pionoconus magus. Mar Drugs 2019; 17:md17100553. [PMID: 31569823 PMCID: PMC6835573 DOI: 10.3390/md17100553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Differential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appeared to be more expressed in the former whereas the O2 superfamily was more expressed in the latter.
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Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails. Syst Biol 2019; 68:781-796. [PMID: 30816949 PMCID: PMC6934442 DOI: 10.1093/sysbio/syz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Jl Sesetan-Markisa 6, Denpasar, Bali 80225, Indonesia
| | - Ristiyanti M Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Km.46, Jl. Raya Bogor, Cibinong, Bogor, West Java 16911, Indonesia
| | - Romanus Edy Prabowo
- Aquatic Biology Laboratory, Faculty of Biology, Universitas Jenderal Soedirman, Jalan dr. Suparno 63 Grendeng, Purwokerto, Indonesia, 53122
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Philipp W H Vogt
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 1259 Trumansburg Road, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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Mendoza CB, Masacupan DJM, Batoctoy DCR, Yu ET, Lluisma AO, Salvador‐Reyes LA. Conomarphins cause paralysis in mollusk: Critical and tunable structural elements for bioactivity. J Pept Sci 2019; 25:e3179. [DOI: 10.1002/psc.3179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Charmaine B. Mendoza
- Marine Science InstituteUniversity of the Philippines, Diliman Quezon City Philippines
| | | | | | - Eizadora T. Yu
- Institute of ChemistryUniversity of the Philippines, Diliman Quezon City Philippines
- Philippine Genome CenterUniversity of the Philippines Diliman Quezon City Philippines
| | - Arturo O. Lluisma
- Marine Science InstituteUniversity of the Philippines, Diliman Quezon City Philippines
- Philippine Genome CenterUniversity of the Philippines Diliman Quezon City Philippines
| | - Lilibeth A. Salvador‐Reyes
- Marine Science InstituteUniversity of the Philippines, Diliman Quezon City Philippines
- Philippine Genome CenterUniversity of the Philippines Diliman Quezon City Philippines
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Gerdol M, Cervelli M, Oliverio M, Modica MV. Piercing Fishes: Porin Expansion and Adaptation to Hematophagy in the Vampire Snail Cumia reticulata. Mol Biol Evol 2019; 35:2654-2668. [PMID: 30099551 PMCID: PMC6231492 DOI: 10.1093/molbev/msy156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytolytic pore-forming proteins are widespread in living organisms, being mostly involved in both sides of the host-pathogen interaction, either contributing to the innate defense or promoting infection. In venomous organisms, such as spiders, insects, scorpions, and sea anemones, pore-forming proteins are often secreted as key components of the venom. Coluporins are pore-forming proteins recently discovered in the Mediterranean hematophagous snail Cumia reticulata (Colubrariidae), highly expressed in the salivary glands that discharge their secretion at close contact with the host. To understand their putative functional role, we investigated coluporins' molecular diversity and evolutionary patterns. Coluporins is a well-diversified family including at least 30 proteins, with an overall low sequence similarity but sharing a remarkably conserved actinoporin-like predicted structure. Tracking the evolutionary history of the molluscan porin genes revealed a scattered distribution of this family, which is present in some other lineages of predatory gastropods, including venomous conoidean snails. Comparative transcriptomic analyses highlighted the expansion of porin genes as a lineage-specific feature of colubrariids. Coluporins seem to have evolved from a single ancestral porin gene present in the latest common ancestor of all Caenogastropoda, undergoing massive expansion and diversification in this colubrariid lineage through repeated gene duplication events paired with widespread episodic positive selection. As for other parasites, these findings are congruent with a "one-sided arms race," equipping the parasite with multiple variants in order to broaden its host spectrum. Overall, our results pinpoint a crucial adaptive role for coluporins in the evolution of the peculiar trophic ecology of vampire snails.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, Trieste University, Italy
| | | | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Roma, Italy
| | - Maria Vittoria Modica
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.,UMR5247, University of Montpellier, France
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Effects of Predator-Prey Interactions on Predator Traits: Differentiation of Diets and Venoms of a Marine Snail. Toxins (Basel) 2019; 11:toxins11050299. [PMID: 31130611 PMCID: PMC6563511 DOI: 10.3390/toxins11050299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
Species interactions are fundamental ecological forces that can have significant impacts on the evolutionary trajectories of species. Nonetheless, the contribution of predator-prey interactions to genetic and phenotypic divergence remains largely unknown. Predatory marine snails of the family Conidae exhibit specializations for different prey items and intraspecific variation in prey utilization patterns at geographic scales. Because cone snails utilize venom to capture prey and venom peptides are direct gene products, it is feasible to examine the evolution of genes associated with changes in resource utilization. Here, we compared feeding ecologies and venom duct transcriptomes of individuals from three populations of Conus miliaris, a species that exhibits geographic variation in prey utilization and dietary breadth, in order to determine the extent to which dietary differences are correlated with differences in venom composition, and if expanded niche breadth is associated with increased variation in venom composition. While populations showed little to no overlap in resource utilization, taxonomic richness of prey was greatest at Easter Island. Changes in dietary breadth were associated with differences in expression patterns and increased genetic differentiation of toxin-related genes. The Easter Island population also exhibited greater diversity of toxin-related transcripts, but did not show increased variance in expression of these transcripts. These results imply that differences in dietary breadth contribute more to the structural and regulatory differentiation of venoms than differences in diet.
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Yao G, Peng C, Zhu Y, Fan C, Jiang H, Chen J, Cao Y, Shi Q. High-Throughput Identification and Analysis of Novel Conotoxins from Three Vermivorous Cone Snails by Transcriptome Sequencing. Mar Drugs 2019; 17:md17030193. [PMID: 30917600 PMCID: PMC6471451 DOI: 10.3390/md17030193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
The venom of each Conus species consists of a diverse array of neurophysiologically active peptides, which are mostly unique to the examined species. In this study, we performed high-throughput transcriptome sequencing to extract and analyze putative conotoxin transcripts from the venom ducts of 3 vermivorous cone snails (C. caracteristicus, C. generalis, and C. quercinus), which are resident in offshore waters of the South China Sea. In total, 118, 61, and 48 putative conotoxins (across 22 superfamilies) were identified from the 3 Conus species, respectively; most of them are novel, and some possess new cysteine patterns. Interestingly, a series of 45 unassigned conotoxins presented with a new framework of C-C-C-C-C-C, and their mature regions were sufficiently distinct from any other known conotoxins, most likely representing a new superfamily. O- and M-superfamily conotoxins were the most abundant in transcript number and transcription level, suggesting their critical roles in the venom functions of these vermivorous cone snails. In addition, we identified numerous functional proteins with potential involvement in the biosynthesis, modification, and delivery process of conotoxins, which may shed light on the fundamental mechanisms for the generation of these important conotoxins within the venom duct of cone snails.
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Affiliation(s)
- Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yabing Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Chongxu Fan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Jisheng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Ying Cao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
| | - Manuel J. Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias; Universidad de Cádiz; Puerto Real Spain
| | - Juan E. Uribe
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
- Department of Invertebrate Zoology, Smithsonian Institution; National Museum of Natural History; Washington District of Columbia USA
- Grupo de Evolución, Sistemática y Ecología Molecular; Universidad del Magdalena; Santa Marta Colombia
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
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Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M. Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins (Basel) 2018; 10:toxins10120503. [PMID: 30513724 PMCID: PMC6315676 DOI: 10.3390/toxins10120503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/12/2018] [Accepted: 11/22/2018] [Indexed: 12/24/2022] Open
Abstract
Cone snails (genus Conus) are venomous marine snails that inject prey with a lethal cocktail of conotoxins, small, secreted, and cysteine-rich peptides. Given the diversity and often high affinity for their molecular targets, consisting of ion channels, receptors or transporters, many conotoxins have become invaluable pharmacological probes, drug leads, and therapeutics. Transcriptome sequencing of Conus venom glands followed by de novo assembly and homology-based toxin identification and annotation is currently the state-of-the-art for discovery of new conotoxins. However, homology-based search techniques, by definition, can only detect novel toxins that are homologous to previously reported conotoxins. To overcome these obstacles for discovery, we have created ConusPipe, a machine learning tool that utilizes prominent chemical characters of conotoxins to predict whether a certain transcript in a Conus transcriptome, which has no otherwise detectable homologs in current reference databases, is a putative conotoxin. By using ConusPipe on RNASeq data of 10 species, we report 5148 new putative conotoxin transcripts that have no homologues in current reference databases. 896 of these were identified by at least three out of four models used. These data significantly expand current publicly available conotoxin datasets and our approach provides a new computational avenue for the discovery of novel toxin families.
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Affiliation(s)
- Qing Li
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Maren Watkins
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Samuel D Robinson
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Helena Safavi-Hemami
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
- USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.
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Rončević T, Gerdol M, Spazzali F, Florian F, Mekinić S, Tossi A, Pallavicini A. Parallel identification of novel antimicrobial peptide sequences from multiple anuran species by targeted DNA sequencing. BMC Genomics 2018; 19:827. [PMID: 30458708 PMCID: PMC6245896 DOI: 10.1186/s12864-018-5225-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/06/2018] [Indexed: 12/20/2022] Open
Abstract
Background Antimicrobial peptides (AMPs) are multifunctional effector molecules that often combine direct antimicrobial activities with signaling or immunomodulatory functions. The skin secretions of anurans contain a variety of such bioactive peptides. The identification of AMPs from frog species often requires sacrificing several specimens to obtain small quantities of crude peptides, followed by activity based fractionation to identify the active principles. Results We report an efficient alternative approach to selectively amplify AMP-coding transcripts from very small amounts of tissue samples, based on RNA extraction and cDNA synthesis, followed by PCR amplification and high-throughput sequencing of size-selected amplicons. This protocol exploits the highly conserved signal peptide region of the AMP precursors from Ranidae, Hylidae and Bombinatoridae for the design of family-specific, forward degenerate primers, coupled with a reverse primer targeting the mRNA poly-A tail. Conclusions Analysis of the assembled sequencing output allowed to identify more than a hundred full-length mature peptides, mostly from Ranidae species, including several novel potential AMPs for functional characterization. This (i) confirms the effectiveness of the experimental approach and indicates points for protocol optimization to account for particular cases, and (ii) encourages the application of the same methodology to other multigenic AMP families, also from other genera, sharing common features as in anuran AMPs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5225-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomislav Rončević
- Department of Physics, Faculty of Science, University of Split, 21000, Split, Croatia.
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Fiorella Florian
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Stjepan Mekinić
- Public Institution for the Management of Protected Areas in the County of Split and Dalmatia - "Sea and karst", 21000, Split, Croatia
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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