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Lecaudey LA, Netzer R, Wibberg D, Busche T, Bloecher N. Metatranscriptome analysis reveals the putative venom toxin repertoire of the biofouling hydroid Ectopleura larynx. Toxicon 2024; 237:107556. [PMID: 38072317 DOI: 10.1016/j.toxicon.2023.107556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Cnidarians thriving in biofouling communities on aquaculture net pens represent a significant health risk for farmed finfish due to their stinging cells. The toxins coming into contact with the fish, during net cleaning, can adversely affect their behavior, welfare, and survival, with a particularly serious health risk for the gills, causing direct tissue damage such as formation of thrombi and increasing risks of secondary infections. The hydroid Ectopleura larynx is one of the most common fouling organisms in Northern Europe. However, despite its significant economic, environmental, and operational impact on finfish aquaculture, biological information on this species is scarce and its venom composition has never been investigated. In this study, we generated a whole transcriptome of E. larynx, and identified its putative expressed venom toxin proteins (predicted toxin proteins, not functionally characterized) based on in silico transcriptome annotation mining and protein sequence analysis. The results uncovered a broad and diverse repertoire of putative toxin proteins for this hydroid species. Its toxic arsenal appears to include a wide and complex selection of toxin proteins, covering a large panel of potential biological functions that play important roles in envenomation. The putative toxins identified in this species, such as neurotoxins, GTPase toxins, metalloprotease toxins, ion channel impairing toxins, hemorrhagic toxins, serine protease toxins, phospholipase toxins, pore-forming toxins, and multifunction toxins may cause various major deleterious effects in prey, predators, and competitors. These results provide valuable new insights into the venom composition of cnidarians, and venomous marine organisms in general, and offer new opportunities for further research into novel and valuable bioactive molecules for medicine, agronomics and biotechnology.
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Affiliation(s)
| | - Roman Netzer
- SINTEF Ocean, Aquaculture Department, Brattørkaia 17c, 7010, Trondheim, Norway
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany; Medical School OWL, Bielefeld University, Morgenbreede 1, 33615, Bielefeld, Germany
| | - Nina Bloecher
- SINTEF Ocean, Aquaculture Department, Brattørkaia 17c, 7010, Trondheim, Norway
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Aravind L, Iyer LM, Burroughs AM. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Annu Rev Biomed Data Sci 2022; 5:367-391. [PMID: 35609893 DOI: 10.1146/annurev-biodatasci-122220-101119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological replicators, from genes within a genome to whole organisms, are locked in conflicts. Comparative genomics has revealed a staggering diversity of molecular armaments and mechanisms regulating their deployment, collectively termed biological conflict systems. These encompass toxins used in inter- and intraspecific interactions, self/nonself discrimination, antiviral immune mechanisms, and counter-host effectors deployed by viruses and intragenomic selfish elements. These systems possess shared syntactical features in their organizational logic and a set of effectors targeting genetic information flow through the Central Dogma, certain membranes, and key molecules like NAD+. These principles can be exploited to discover new conflict systems through sensitive computational analyses. This has led to significant advances in our understanding of the biology of these systems and furnished new biotechnological reagents for genome editing, sequencing, and beyond. We discuss these advances using specific examples of toxins, restriction-modification, apoptosis, CRISPR/second messenger-regulated systems, and other enigmatic nucleic acid-targeting systems. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
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Casewell NR, Petras D, Card DC, Suranse V, Mychajliw AM, Richards D, Koludarov I, Albulescu LO, Slagboom J, Hempel BF, Ngum NM, Kennerley RJ, Brocca JL, Whiteley G, Harrison RA, Bolton FMS, Debono J, Vonk FJ, Alföldi J, Johnson J, Karlsson EK, Lindblad-Toh K, Mellor IR, Süssmuth RD, Fry BG, Kuruppu S, Hodgson WC, Kool J, Castoe TA, Barnes I, Sunagar K, Undheim EAB, Turvey ST. Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals. Proc Natl Acad Sci U S A 2019; 116:25745-25755. [PMID: 31772017 PMCID: PMC6926037 DOI: 10.1073/pnas.1906117116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.
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Affiliation(s)
- Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom;
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Vivek Suranse
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Alexis M Mychajliw
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Rancho La Brea, Natural History Museum of Los Angeles County, Los Angeles, CA 90036
- Institute of Low Temperature Science, Hokkaido University, 060-0819 Sapporo, Japan
| | - David Richards
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
- Biomedical Research Centre, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Laura-Oana Albulescu
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | | | - Neville M Ngum
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | - Rosalind J Kennerley
- Durrell Wildlife Conservation Trust, Les Augrès Manor, Trinity, Jersey JE3 5BP, British Channel Islands, United Kingdom
| | - Jorge L Brocca
- SOH Conservación, Apto. 401 Residencial Las Galerías, Santo Domingo, 10130, Dominican Republic
| | - Gareth Whiteley
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Robert A Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Fiona M S Bolton
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Freek J Vonk
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Jessica Alföldi
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Jeremy Johnson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Elinor K Karlsson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Kerstin Lindblad-Toh
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ian R Mellor
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | | | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Sanjaya Kuruppu
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
- Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, SW7 5BD London, United Kingdom
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London, United Kingdom
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