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Kowalski K, Marciniak P, Nekaris KAI, Rychlik L. Proteins from shrews' venom glands play a role in gland functioning and venom production. ZOOLOGICAL LETTERS 2024; 10:12. [PMID: 39010181 PMCID: PMC11251227 DOI: 10.1186/s40851-024-00236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024]
Abstract
Venom production has evolved independently many times in the animal kingdom, although it is rare among mammals. Venomous shrews produce venom in their submandibular salivary glands and use it for food acquisition. Only a few toxins have been identified in shrew venoms thus far, and their modes of action require investigation. The biological and molecular processes relating to venom production and gland functioning also remain unknown. To address this gap, we investigated protein content in extracts from venom glands of two shrew species, Neomys fodiens and Sorex araneus, and interpreted their biological functions. Applying a proteomic approach coupled with Gene Ontology enrichment analysis, we identified 313 and 187 putative proteins in venom glands of N. fodiens and S. araneus, respectively. A search of the UniProt database revealed that most of the proteins found in both shrew species were involved in metabolic processes and stress response, while GO enrichment analysis revealed more stress-related proteins in the glands of S. araneus. Molecules that regulate molecule synthesis, cell cycles, and cell divisions are necessary to enable venom regeneration and ensure its effectiveness in predation and food hoarding. The presence of proteins involved in stress response may be the result of shrews' high metabolic rate and the costs of venom replenishment. Some proteins are likely to promote toxin spreading during envenomation and, due to their proteolytic action, reinforce venom toxicity. Finally, finding numerous proteins involved in immune response suggests a potential role of shrew venom gland secretions in protection against pathogens. These findings open up new perspectives for studying biological functions of molecules from shrew venom glands and extend our knowledge on the functioning of eulipotyphlan venom systems. Because the majority of existing and putative venomous mammals use oral venom systems to inject venom into target species, the methods presented here provide a promising avenue for confirming or discovering new taxa of venomous mammals.
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Affiliation(s)
- Krzysztof Kowalski
- Department of Vertebrate Zoology and Ecology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, Toruń, 87-100, Poland.
| | - Paweł Marciniak
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - K Anne-Isola Nekaris
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Leszek Rychlik
- Department of Systematic Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
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2
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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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3
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Chandrasekara U, Broussard EM, Rokyta DR, Fry BG. High-Voltage Toxin'Roll: Electrostatic Charge Repulsion as a Dynamic Venom Resistance Trait in Pythonid Snakes. Toxins (Basel) 2024; 16:176. [PMID: 38668601 PMCID: PMC11053703 DOI: 10.3390/toxins16040176] [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: 02/11/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/29/2024] Open
Abstract
The evolutionary interplay between predator and prey has significantly shaped the development of snake venom, a critical adaptation for subduing prey. This arms race has spurred the diversification of the components of venom and the corresponding emergence of resistance mechanisms in the prey and predators of venomous snakes. Our study investigates the molecular basis of venom resistance in pythons, focusing on electrostatic charge repulsion as a defense against α-neurotoxins binding to the alpha-1 subunit of the postsynaptic nicotinic acetylcholine receptor. Through phylogenetic and bioactivity analyses of orthosteric site sequences from various python species, we explore the prevalence and evolution of amino acid substitutions that confer resistance by electrostatic repulsion, which initially evolved in response to predatory pressure by Naja (cobra) species (which occurs across Africa and Asia). The small African species Python regius retains the two resistance-conferring lysines (positions 189 and 191) of the ancestral Python genus, conferring resistance to sympatric Naja venoms. This differed from the giant African species Python sebae, which has secondarily lost one of these lysines, potentially due to its rapid growth out of the prey size range of sympatric Naja species. In contrast, the two Asian species Python brongersmai (small) and Python bivittatus (giant) share an identical orthosteric site, which exhibits the highest degree of resistance, attributed to three lysine residues in the orthosteric sites. One of these lysines (at orthosteric position 195) evolved in the last common ancestor of these two species, which may reflect an adaptive response to increased predation pressures from the sympatric α-neurotoxic snake-eating genus Ophiophagus (King Cobras) in Asia. All these terrestrial Python species, however, were less neurotoxin-susceptible than pythons in other genera which have evolved under different predatory pressure as: the Asian species Malayopython reticulatus which is arboreal as neonates and juveniles before rapidly reaching sizes as terrestrial adults too large for sympatric Ophiophagus species to consider as prey; and the terrestrial Australian species Aspidites melanocephalus which occupies a niche, devoid of selection pressure from α-neurotoxic predatory snakes. Our findings underline the importance of positive selection in the evolution of venom resistance and suggest a complex evolutionary history involving both conserved traits and secondary evolution. This study enhances our understanding of the molecular adaptations that enable pythons to survive in environments laden with venomous threats and offers insights into the ongoing co-evolution between venomous snakes and their prey.
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Affiliation(s)
- Uthpala Chandrasekara
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia;
| | - Emilie M. Broussard
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; (E.M.B.); (D.R.R.)
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; (E.M.B.); (D.R.R.)
| | - Bryan G. Fry
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia;
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4
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Yasmin R, Thakur S, Blotra A, Sahu A, Vasudevan K, Reza MA, Doley R. Proteome analysis of Daboia russelii venom, a medically important snake from the Indian sub-continent. Toxicon 2024; 237:107532. [PMID: 38030094 DOI: 10.1016/j.toxicon.2023.107532] [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: 09/20/2023] [Revised: 10/31/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Daboia russelii is a category-I medically important snake throughout the Indian sub-continent contributing to majority of snakebite incidences in this part of the world. As such, extensive studies on its venom composition and search of efficient and appropriate interventions for its treatment become crucial. In this study, the proteome of Daboia russelii venom from Tanore, Rajshahi, Bangladesh was profiled using a combination of chromatographic and mass spectrometric techniques. A total of 37 different proteins belonging to 11 different snake venom protein families were detected. Proteomics analysis revealed the presence of major phospholipase A2 toxins. Daboiatoxin (both A and B subunits), the main lethal PLA2 toxin in the venom of Daboia siamensis (Myanmar viper) which is neurotoxic, myotoxic and cytotoxic was detected. Presence of Daboxin P, which is a major protein in the venom of Indian Daboia russelii with strong anticoagulant activity, was also observed. Inconsistent distribution of such lethal toxins in the venom of same species calls for more investigations of snake venoms from lesser explored regions and formulation of better alternatives to the current antivenom therapy for efficient treatment.
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Affiliation(s)
- Rafika Yasmin
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
| | - Susmita Thakur
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
| | - Avni Blotra
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500048, India
| | - Alka Sahu
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500048, India
| | - Karthikeyan Vasudevan
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500048, India
| | - Md Abu Reza
- Molecular Biology and Protein Science Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Robin Doley
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
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Yano Y, Fukuoka R, Maturana AD, Ohdachi SD, Kita M. Mammalian neurotoxins, Blarina paralytic peptides, cause hyperpolarization of human T-type Ca channel hCa v3.2 activation. J Biol Chem 2023; 299:105066. [PMID: 37468103 PMCID: PMC10493266 DOI: 10.1016/j.jbc.2023.105066] [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: 03/20/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Among the rare venomous mammals, the short-tailed shrew Blarina brevicauda has been suggested to produce potent neurotoxins in its saliva to effectively capture prey. Several kallikrein-like lethal proteases have been identified, but the active substances of B. brevicauda remained unclear. Here, we report Blarina paralytic peptides (BPPs) 1 and 2 isolated from its submaxillary glands. Synthetic BPP2 showed mealworm paralysis and a hyperpolarization shift (-11 mV) of a human T-type Ca2+ channel (hCav3.2) activation. The amino acid sequences of BPPs were similar to those of synenkephalins, which are precursors of brain opioid peptide hormones that are highly conserved among mammals. However, BPPs rather resembled centipede neurotoxic peptides SLPTXs in terms of disulfide bond connectivity and stereostructure. Our results suggested that the neurotoxin BPPs were the result of convergent evolution as homologs of nontoxic endogenous peptides that are widely conserved in mammals. This finding is of great interest from the viewpoint of the chemical evolution of vertebrate venoms.
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Affiliation(s)
- Yusuke Yano
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ryo Fukuoka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Andres D Maturana
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Satoshi D Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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6
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Fitzpatrick LLJ, Ligabue-Braun R, Nekaris KAI. Slowly Making Sense: A Review of the Two-Step Venom System within Slow ( Nycticebus spp.) and Pygmy Lorises ( Xanthonycticebus spp.). Toxins (Basel) 2023; 15:514. [PMID: 37755940 PMCID: PMC10536643 DOI: 10.3390/toxins15090514] [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: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Since the early 2000s, studies of the evolution of venom within animals have rapidly expanded, offering new revelations on the origins and development of venom within various species. The venomous mammals represent excellent opportunities to study venom evolution due to the varying functional usages, the unusual distribution of venom across unrelated mammals and the diverse variety of delivery systems. A group of mammals that excellently represents a combination of these traits are the slow (Nycticebus spp.) and pygmy lorises (Xanthonycticebus spp.) of south-east Asia, which possess the only confirmed two-step venom system. These taxa also present one of the most intriguing mixes of toxic symptoms (cytotoxicity and immunotoxicity) and functional usages (intraspecific competition and ectoparasitic defence) seen in extant animals. We still lack many pieces of the puzzle in understanding how this venom system works, why it evolved what is involved in the venom system and what triggers the toxic components to work. Here, we review available data building upon a decade of research on this topic, focusing especially on why and how this venom system may have evolved. We discuss that research now suggests that venom in slow lorises has a sophisticated set of multiple uses in both intraspecific competition and the potential to disrupt the immune system of targets; we suggest that an exudate diet reveals several toxic plants consumed by slow and pygmy lorises that could be sequestered into their venom and which may help heal venomous bite wounds; we provide the most up-to-date visual model of the brachial gland exudate secretion protein (BGEsp); and we discuss research on a complement component 1r (C1R) protein in saliva that may solve the mystery of what activates the toxicity of slow and pygmy loris venom. We conclude that the slow and pygmy lorises possess amongst the most complex venom system in extant animals, and while we have still a lot more to understand about their venom system, we are close to a breakthrough, particularly with current technological advances.
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Affiliation(s)
- Leah Lucy Joscelyne Fitzpatrick
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Avenida Sarmento Leite 245, Porto Alegre 90050-170, Brazil;
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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7
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Paolino G, Di Nicola MR, Avella I, Mercuri SR. Venomous Bites, Stings and Poisoning by European Vertebrates as an Overlooked and Emerging Medical Problem: Recognition, Clinical Aspects and Therapeutic Management. Life (Basel) 2023; 13:1228. [PMID: 37374011 DOI: 10.3390/life13061228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Europe presents a high number of venomous and poisonous animals able to elicit medically relevant symptoms in humans. However, since most of the accidents involving venomous or poisonous animals in Europe are unreported, their incidence and morbidity are severely overlooked. Here we provide an overview of the European vertebrate species of greatest toxicological interest, the clinical manifestations their toxins can cause, and their treatment. We report the clinical symptoms induced by envenomations and poisoning caused by reptiles, fishes, amphibians and mammals in Europe, ranging from mild, local symptoms (e.g., erythema, edema) to systemic and potentially deadly. The present work constitutes a tool for physicians to recognize envenomation/poisoning symptoms caused by the most medically relevant European vertebrates and to decide which approach is the most appropriate to treat them.
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Affiliation(s)
- Giovanni Paolino
- Unit of Dermatology and Cosmetology, I.R.C.C.S. San Raffaele Hospital, Via Olgettina 60, 20132 Milan, Italy
- Unit of Clinical Dermatology, Università Vita-Salute San Raffaele, Via Olgettina 60, 20132 Milan, Italy
| | - Matteo Riccardo Di Nicola
- Unit of Dermatology and Cosmetology, I.R.C.C.S. San Raffaele Hospital, Via Olgettina 60, 20132 Milan, Italy
- Asociación Herpetológica Española, Apartado de Correos 191, 28911 Leganés, Spain
| | - Ignazio Avella
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Santo Raffaele Mercuri
- Unit of Dermatology and Cosmetology, I.R.C.C.S. San Raffaele Hospital, Via Olgettina 60, 20132 Milan, Italy
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Lüddecke T, Paas A, Harris RJ, Talmann L, Kirchhoff KN, Billion A, Hardes K, Steinbrink A, Gerlach D, Fry BG, Vilcinskas A. Venom biotechnology: casting light on nature's deadliest weapons using synthetic biology. Front Bioeng Biotechnol 2023; 11:1166601. [PMID: 37207126 PMCID: PMC10188951 DOI: 10.3389/fbioe.2023.1166601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
Venoms are complex chemical arsenals that have evolved independently many times in the animal kingdom. Venoms have attracted the interest of researchers because they are an important innovation that has contributed greatly to the evolutionary success of many animals, and their medical relevance offers significant potential for drug discovery. During the last decade, venom research has been revolutionized by the application of systems biology, giving rise to a novel field known as venomics. More recently, biotechnology has also made an increasing impact in this field. Its methods provide the means to disentangle and study venom systems across all levels of biological organization and, given their tremendous impact on the life sciences, these pivotal tools greatly facilitate the coherent understanding of venom system organization, development, biochemistry, and therapeutic activity. Even so, we lack a comprehensive overview of major advances achieved by applying biotechnology to venom systems. This review therefore considers the methods, insights, and potential future developments of biotechnological applications in the field of venom research. We follow the levels of biological organization and structure, starting with the methods used to study the genomic blueprint and genetic machinery of venoms, followed gene products and their functional phenotypes. We argue that biotechnology can answer some of the most urgent questions in venom research, particularly when multiple approaches are combined together, and with other venomics technologies.
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Affiliation(s)
- Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- *Correspondence: Tim Lüddecke,
| | - Anne Paas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Richard J. Harris
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, QLD, Australia
| | - Lea Talmann
- Syngenta Crop Protection, Stein, Switzerland
| | - Kim N. Kirchhoff
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - André Billion
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Kornelia Hardes
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- BMBF Junior Research Group in Infection Research “ASCRIBE”, Giessen, Germany
| | - Antje Steinbrink
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany
| | - Doreen Gerlach
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Bryan G. Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany
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Fitzpatrick LLJ, Nijman V, Ligabue-Braun R, Nekaris KAI. The Fast and the Furriest: Investigating the Rate of Selection on Mammalian Toxins. Toxins (Basel) 2022; 14:toxins14120842. [PMID: 36548740 PMCID: PMC9782207 DOI: 10.3390/toxins14120842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of venom and the selection pressures that act on toxins have been increasingly researched within toxinology in the last two decades, in part due to the exceptionally high rates of diversifying selection observed in animal toxins. In 2015, Sungar and Moran proposed the 'two-speed' model of toxin evolution linking evolutionary age of a group to the rates of selection acting on toxins but due to a lack of data, mammals were not included as less than 30 species of venomous mammal have been recorded, represented by elusive species which produce small amounts of venom. Due to advances in genomics and transcriptomics, the availability of toxin sequences from venomous mammals has been increasing. Using branch- and site-specific selection models, we present the rates of both episodic and pervasive selection acting upon venomous mammal toxins as a group for the first time. We identified seven toxin groups present within venomous mammals, representing Chiroptera, Eulipotyphla and Monotremata: KLK1, Plasminogen Activator, Desmallipins, PACAP, CRiSP, Kunitz Domain One and Kunitz Domain Two. All but one group (KLK1) was identified by our results to be evolving under both episodic and pervasive diversifying selection with four toxin groups having sites that were implicated in the fitness of the animal by TreeSAAP (Selection on Amino Acid Properties). Our results suggest that venomous mammal ecology, behaviour or genomic evolution are the main drivers of selection, although evolutionary age may still be a factor. Our conclusion from these results indicates that mammalian toxins are following the two-speed model of selection, evolving predominately under diversifying selection, fitting in with other younger venomous taxa like snakes and cone snails-with high amounts of accumulating mutations, leading to more novel adaptions in their toxins.
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Affiliation(s)
- Leah Lucy Joscelyne Fitzpatrick
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Correspondence:
| | - Vincent Nijman
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Avenida Sarmento Leite 245, Porto Alegre 90050-130, Brazil
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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10
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Forni G, Mikheyev AS, Luchetti A, Mantovani B. Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis. ZOOLOGICAL LETTERS 2022; 8:14. [PMID: 36435814 PMCID: PMC9701443 DOI: 10.1186/s40851-022-00197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens' gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.
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Affiliation(s)
- Giobbe Forni
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
- Dip. Scienze Agrarie e Ambientali, University of Milano, Milano, Italy
| | - Alexander S Mikheyev
- Australian National University, ACT, Canberra, 2600, Australia
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
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11
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Pajic P, Shen S, Qu J, May AJ, Knox S, Ruhl S, Gokcumen O. A mechanism of gene evolution generating mucin function. SCIENCE ADVANCES 2022; 8:eabm8757. [PMID: 36026444 PMCID: PMC9417175 DOI: 10.1126/sciadv.abm8757] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/12/2022] [Indexed: 05/12/2023]
Abstract
How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions. By integrating bioinformatic, phylogenetic, proteomic, and immunohistochemical approaches, we identified 15 undescribed instances of evolutionary convergence, where novel mucins originated by gaining densely O-glycosylated exonic repeat domains. Our results suggest that secreted proteins rich in proline are natural precursors for acquiring mucin function. Our findings have broad implications for understanding the role of exonic repeats in the parallel evolution of new gene functions, especially those involving protein glycosylation.
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Affiliation(s)
- Petar Pajic
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
- Center of Excellence in Bioinformatics and Life Science, Buffalo, NY 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
- Center of Excellence in Bioinformatics and Life Science, Buffalo, NY 14203, USA
| | - Alison J. May
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah Knox
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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12
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Kowalski K, Marciniak P, Rychlik L. A new, widespread venomous mammal species: hemolytic activity of Sorex araneus venom is similar to that of Neomys fodiens venom. ZOOLOGICAL LETTERS 2022; 8:7. [PMID: 35672837 PMCID: PMC9172195 DOI: 10.1186/s40851-022-00191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Venom production has evolved independently many times in the animal kingdom, although it is rare among mammals. Venomous shrews produce toxins in their salivary glands and use their venoms to hunt and store prey. Thus far, the toxicity and composition of shrew venoms have been studied only in two shrew species: the northern short-tailed shrew, Blarina brevicauda, and the Eurasian water shrew, Neomys fodiens. Venom of N. fodiens has potent paralytic activity which enables hunting and storing prey in a comatose state. Here, we assayed the hemolytic effects of extracts from salivary glands of N. fodiens and the common shrew, Sorex araneus, in erythrocytes of Pelophylax sp. frogs. We identified toxins in shrew venom by high-performance liquid chromatography coupled to tandem mass spectrometry. RESULTS Our results prove, confirming a suggestion made four centuries ago, that S. araneus is venomous. We also provide the first experimental evidence that shrew venoms produce potent hemolysis in frog erythrocytes. We found significant concentration-dependent effects of venoms of N. fodiens and S. araneus on hemolysis of red blood cells evaluated as hemoglobin release. Treatment of erythrocytes with N. fodiens venom at concentrations of 1.0 and 0.5 mg/ml and with S. araneus venom at concentration of 1.0 mg/ml caused an increased release of hemoglobin. Our findings confirm that hemolytic effects of N. fodiens venom are stronger than those produced by S. araneus venom. We identified four toxins in the venom of N. fodiens: proenkephalin, phospholipase A2 (PLA2), a disintegrin and metalloproteinase domain-containing protein (ADAM) and lysozyme C, as well as a non-toxic hyaluronidase. In the venom of S. araneus we found five toxins: proenkephalin, kallikrein 1-related peptidase, beta-defensin, ADAM and lysozyme C. PLA2 and ADAMs are likely to produce hemolysis in frog erythrocytes. CONCLUSIONS Our results clearly show that shrew venoms possess hemolytic action that may allow them to hunt larger prey. Since a member of the numerous genus Sorex is venomous, it is likely that venom production among shrews and other eulipotyphlans may be more widespread than it has previously been assumed.
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Affiliation(s)
- Krzysztof Kowalski
- Department of Vertebrate Zoology and Ecology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Paweł Marciniak
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Leszek Rychlik
- Department of Systematic Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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13
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:giac048. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain
- The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - 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
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
- Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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14
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van Thiel J, Khan MA, Wouters RM, Harris RJ, Casewell NR, Fry BG, Kini RM, Mackessy SP, Vonk FJ, Wüster W, Richardson MK. Convergent evolution of toxin resistance in animals. Biol Rev Camb Philos Soc 2022; 97:1823-1843. [PMID: 35580905 PMCID: PMC9543476 DOI: 10.1111/brv.12865] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 12/17/2022]
Abstract
Convergence is the phenomenon whereby similar phenotypes evolve independently in different lineages. One example is resistance to toxins in animals. Toxins have evolved many times throughout the tree of life. They disrupt molecular and physiological pathways in target species, thereby incapacitating prey or deterring a predator. In response, molecular resistance has evolved in many species exposed to toxins to counteract their harmful effects. Here, we review current knowledge on the convergence of toxin resistance using examples from a wide range of toxin families. We explore the evolutionary processes and molecular adaptations driving toxin resistance. However, resistance adaptations may carry a fitness cost if they disrupt the normal physiology of the resistant animal. Therefore, there is a trade‐off between maintaining a functional molecular target and reducing toxin susceptibility. There are relatively few solutions that satisfy this trade‐off. As a result, we see a small set of molecular adaptations appearing repeatedly in diverse animal lineages, a phenomenon that is consistent with models of deterministic evolution. Convergence may also explain what has been called ‘autoresistance’. This is often thought to have evolved for self‐protection, but we argue instead that it may be a consequence of poisonous animals feeding on toxic prey. Toxin resistance provides a unique and compelling model system for studying the interplay between trophic interactions, selection pressures and the molecular mechanisms underlying evolutionary novelties.
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Affiliation(s)
- Jory van Thiel
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Muzaffar A Khan
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Roel M Wouters
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Richard J Harris
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, 4072, Australia
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, U.K
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, 4072, Australia
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.,Department of Biochemistry, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA, 23298, U.S.A
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639-0017, U.S.A
| | - Freek J Vonk
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands.,Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Wolfgang Wüster
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, U.K
| | - Michael K Richardson
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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15
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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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16
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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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17
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Mychajliw AM, Almonte JN, Martinez PA, Hadly EA. Stable isotopes reveal seasonal dietary responses to agroforestry in a venomous mammal, the Hispaniolan solenodon ( Solenodon paradoxus). Ecol Evol 2022; 12:e8761. [PMID: 35356572 PMCID: PMC8948124 DOI: 10.1002/ece3.8761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 12/18/2022] Open
Abstract
While trends in tropical deforestation are alarming, conservation biologists are increasingly recognizing the potential for species survival in human-modified landscapes. Identifying the factors underlying such persistence, however, requires basic ecological knowledge of a species' resource use. Here, we generate such data to guide conservation of an understudied venomous mammal, the Hispaniolan solenodon (Solenodon paradoxus), that occupies a mosaic landscape of agriculture and forest fragments in the western Dominican Republic. Using feces collected in both wet and dry seasons, we found significant differences in the stable isotope values of carbon (δ13C) between pasture (-24.63 ± 2.31‰, Las Mercedes) and agroforestry (-28.07 ± 2.10‰, Mencia). Solenodon populations in agricultural areas occupied wider isotopic niche spaces, which may be explained by more diverse resource within these patches or individuals combining resources across habitats. We detected elevated δ15N values in the dry season of pasture areas (8.22 ± 2.30‰) as compared to the wet season (5.26 ± 2.44‰) and overall narrower isotopic niche widths in the dry season, suggestive of the impacts of aridity on foraging behavior. Our work highlights the importance of considering a more nuanced view of variations in 'modified' or "agricultural" landscapes as compared with strictly protected national parks. We suggest that seasonal differences in foraging should be considered as they intersect with landscape modification by landowners for maintaining resources for focal consumers. This work adds to a growing body of literature highlighting that fecal stable isotopes are a non-invasive and cost-effective monitoring tool that is particularly well-suited for cryptic small mammal species, ensuring actionable and evidenced-based conservation practices in the tropic's rapidly changing landscapes.
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Affiliation(s)
- Alexis M. Mychajliw
- Departments of Biology and Environmental StudiesMiddlebury CollegeMiddleburyVermontUSA
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
| | - Juan N. Almonte
- Museo Nacional de Historia Natural “Prof. Eugenio de Jesús Marcano”Santo DomingoDominican Republic
| | - Pedro A. Martinez
- Escuela de BiologíaUniversidad Autónoma de Santo DomingoSanto DomingoDominican Republic
| | - Elizabeth A. Hadly
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
- Woods Institute of the EnvironmentStanford UniversityStanfordCaliforniaUSA
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18
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Liao Z, Tang X, Chen W, Jiang X, Chen Z, He K, Li Q, Duan Z, He X, Kamau PM, Lv L, Zhang Z, Rong M, Lv Q, Lai R. Shrew's venom quickly causes circulation disorder, analgesia and hypokinesia. Cell Mol Life Sci 2022; 79:35. [PMID: 34989866 PMCID: PMC11071750 DOI: 10.1007/s00018-021-04116-x] [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: 11/01/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/03/2022]
Abstract
Multiple representatives of eulipotyphlan mammals such as shrews have oral venom systems. Venom facilitates shrews to hunt and/or hoard preys. However, little is known about their venom composition, and especially the mechanism to hoard prey in comatose states for meeting their extremely high metabolic rates. A toxin (BQTX) was identified from venomous submaxillary glands of the shrew Blarinella quadraticauda. BQTX is specifically distributed and highly concentrated (~ 1% total protein) in the organs. BQTX shares structural and functional similarities to toxins from snakes, wasps and snails, suggesting an evolutional relevancy of venoms from mammalians and non-mammalians. By potentiating thrombin and factor-XIIa and inhibiting plasmin, BQTX induces acute hypertension, blood coagulation and hypokinesia. It also shows strong analgesic function by inhibiting elastase. Notably, the toxin keeps high plasma stability with a 16-h half-life in-vivo, which likely extends intoxication to paralyze or immobilize prey hoarded fresh for later consumption and maximize foraging profit.
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Affiliation(s)
- Zhiyi Liao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Xiaopeng Tang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wenlin Chen
- No.1 Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University & Yunnan Tumor Hospital, kunming, 650000, Yunnan, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhongzheng Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Quan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zilei Duan
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Xiaoqin He
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Peter Muiruri Kamau
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Longbao Lv
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhiye Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Mingqiang Rong
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Qiumin Lv
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center, and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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19
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Barua A, Koludarov I, Mikheyev AS. Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins. BMC Biol 2021; 19:268. [PMID: 34949191 PMCID: PMC8705180 DOI: 10.1186/s12915-021-01191-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 12/03/2022] Open
Abstract
Background Evolution can occur with surprising predictability when organisms face similar ecological challenges. For most traits, it is difficult to ascertain whether this occurs due to constraints imposed by the number of possible phenotypic solutions or because of parallel responses by shared genetic and regulatory architecture. Exceptionally, oral venoms are a tractable model of trait evolution, being largely composed of proteinaceous toxins that have evolved in many tetrapods, ranging from reptiles to mammals. Given the diversity of venomous lineages, they are believed to have evolved convergently, even though biochemically similar toxins occur in all taxa. Results Here, we investigate whether ancestral genes harbouring similar biochemical activity may have primed venom evolution, focusing on the origins of kallikrein-like serine proteases that form the core of most vertebrate oral venoms. Using syntenic relationships between genes flanking known toxins, we traced the origin of kallikreins to a single locus containing one or more nearby paralogous kallikrein-like clusters. Additionally, phylogenetic analysis of vertebrate serine proteases revealed that kallikrein-like toxins in mammals and reptiles are genetically distinct from non-toxin ones. Conclusions Given the shared regulatory and genetic machinery, these findings suggest that tetrapod venoms evolved by co-option of proteins that were likely already present in saliva. We term such genes ‘toxipotent’—in the case of salivary kallikreins they already had potent vasodilatory activity that was weaponized by venomous lineages. Furthermore, the ubiquitous distribution of kallikreins across vertebrates suggests that the evolution of envenomation may be more common than previously recognized, blurring the line between venomous and non-venomous animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01191-1.
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Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Ivan Koludarov
- Animal Venomics Group, Justus Leibig University, Giessen, Germany
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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20
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Vonk FJ, Bittenbinder MA, Kerkkamp HMI, Grashof DGB, Archer JP, Afonso S, Richardson MK, Kool J, van der Meijden A. A non-lethal method for studying scorpion venom gland transcriptomes, with a review of potentially suitable taxa to which it can be applied. PLoS One 2021; 16:e0258712. [PMID: 34793470 PMCID: PMC8601437 DOI: 10.1371/journal.pone.0258712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
Scorpion venoms are mixtures of proteins, peptides and small molecular compounds with high specificity for ion channels and are therefore considered to be promising candidates in the venoms-to-drugs pipeline. Transcriptomes are important tools for studying the composition and expression of scorpion venom. Unfortunately, studying the venom gland transcriptome traditionally requires sacrificing the animal and therefore is always a single snapshot in time. This paper describes a new way of generating a scorpion venom gland transcriptome without sacrificing the animal, thereby allowing the study of the transcriptome at various time points within a single individual. By comparing these venom-derived transcriptomes to the traditional whole-telson transcriptomes we show that the relative expression levels of the major toxin classes are similar. We further performed a multi-day extraction using our proposed method to show the possibility of doing a multiple time point transcriptome analysis. This allows for the study of patterns of toxin gene activation over time a single individual, and allows assessment of the effects of diet, season and other factors that are known or likely to influence intraindividual venom composition. We discuss the gland characteristics that may allow this method to be successful in scorpions and provide a review of other venomous taxa to which this method may potentially be successfully applied.
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Affiliation(s)
- Freek J. Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Mátyás A. Bittenbinder
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harald M. I. Kerkkamp
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | | | - John P. Archer
- CIBIO-InBIO, Biopolis, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO-InBIO, Biopolis, Universidade do Porto, Porto, Portugal
| | - Michael K. Richardson
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jeroen Kool
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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21
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Lüddecke T, Herzig V, von Reumont BM, Vilcinskas A. The biology and evolution of spider venoms. Biol Rev Camb Philos Soc 2021; 97:163-178. [PMID: 34453398 DOI: 10.1111/brv.12793] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022]
Abstract
Spiders are diverse, predatory arthropods that have inhabited Earth for around 400 million years. They are well known for their complex venom systems that are used to overpower their prey. Spider venoms contain many proteins and peptides with highly specific and potent activities suitable for biomedical or agrochemical applications, but the key role of venoms as an evolutionary innovation is often overlooked, even though this has enabled spiders to emerge as one of the most successful animal lineages. In this review, we discuss these neglected biological aspects of spider venoms. We focus on the morphology of spider venom systems, their major components, biochemical and chemical plasticity, as well as ecological and evolutionary trends. We argue that the effectiveness of spider venoms is due to their unprecedented complexity, with diverse components working synergistically to increase the overall potency. The analysis of spider venoms is difficult to standardize because they are dynamic systems, fine-tuned and modified by factors such as sex, life-history stage and biological role. Finally, we summarize the mechanisms that drive spider venom evolution and highlight the need for genome-based studies to reconstruct the evolutionary history and physiological networks of spider venom compounds with more certainty.
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Affiliation(s)
- Tim Lüddecke
- Department for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Gießen, 35392, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Volker Herzig
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Björn M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26-32, Gießen, 35392, Germany
| | - Andreas Vilcinskas
- Department for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Gießen, 35392, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26-32, Gießen, 35392, Germany
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22
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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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23
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Trim CM, Byrne LJ, Trim SA. Utilisation of compounds from venoms in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:1-66. [PMID: 34147202 DOI: 10.1016/bs.pmch.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Difficult drug targets are becoming the normal course of business in drug discovery, sometimes due to large interacting surfaces or only small differences in selectivity regions. For these, a different approach is merited: compounds lying somewhere between the small molecule and the large antibody in terms of many properties including stability, biodistribution and pharmacokinetics. Venoms have evolved over millions of years to be complex mixtures of stable molecules derived from other somatic molecules, the stability comes from the pressure to be ready for delivery at a moment's notice. Snakes, spiders, scorpions, jellyfish, wasps, fish and even mammals have evolved independent venom systems with complex mixtures in their chemical arsenal. These venom-derived molecules have been proven to be useful tools, such as for the development of antihypotensive angiotensin converting enzyme (ACE) inhibitors and have also made successful drugs such as Byetta® (Exenatide), Integrilin® (Eptifibatide) and Echistatin. Only a small percentage of the available chemical space from venoms has been investigated so far and this is growing. In a new era of biological therapeutics, venom peptides present opportunities for larger target engagement surface with greater stability than antibodies or human peptides. There are challenges for oral absorption and target engagement, but there are venom structures that overcome these and thus provide substrate for engineering novel molecules that combine all desired properties. Venom researchers are characterising new venoms, species, and functions all the time, these provide great substrate for solving the challenges presented by today's difficult targets.
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Affiliation(s)
- Carol M Trim
- Faculty of Science, Engineering and Social Sciences, Natural and Applied Sciences, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury, Kent, United Kingdom
| | - Lee J Byrne
- Faculty of Science, Engineering and Social Sciences, Natural and Applied Sciences, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury, Kent, United Kingdom
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24
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Pardos-Blas JR, Irisarri I, Abalde S, Afonso CML, Tenorio MJ, Zardoya R. The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity. Gigascience 2021; 10:giab037. [PMID: 34037232 PMCID: PMC8152183 DOI: 10.1093/gigascience/giab037] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms. RESULTS Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons, which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny with the Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located in the genome. CONCLUSIONS The new high-quality L. ventricosus genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.
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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
| | - Iker Irisarri
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, D-37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), Goettingen, Wilhelmsplatz 1, D-37073, Germany
| | - 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, 11418 Stockholm, Sweden
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005–139 Faro, Portugal
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cádiz, 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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25
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He K, Eastman TG, Czolacz H, Li S, Shinohara A, Kawada SI, Springer MS, Berenbrink M, Campbell KL. Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers. eLife 2021; 10:e66797. [PMID: 33949308 PMCID: PMC8205494 DOI: 10.7554/elife.66797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
The speciose mammalian order Eulipotyphla (moles, shrews, hedgehogs, solenodons) combines an unusual diversity of semi-aquatic, semi-fossorial, and fossorial forms that arose from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these lifestyles has been confounded by a fragmentary fossil record, unresolved phylogenetic relationships, and potential morphological convergence, calling for novel approaches. The net surface charge of the oxygen-storing muscle protein myoglobin (ZMb), which can be readily determined from its primary structure, provides an objective target to address this question due to mechanistic linkages with myoglobin concentration. Here, we generate a comprehensive 71 species molecular phylogeny that resolves previously intractable intra-family relationships and then ancestrally reconstruct ZMb evolution to identify ancient lifestyle transitions based on protein sequence alone. Our phylogenetically informed analyses confidently resolve fossorial habits having evolved twice in talpid moles and reveal five independent secondary aquatic transitions in the order housing the world's smallest endothermic divers.
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Affiliation(s)
- Kai He
- Department of Biological Sciences, University of ManitobaWinnipegCanada
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical UniversityGuangzhouChina
| | - Triston G Eastman
- Department of Biological Sciences, University of ManitobaWinnipegCanada
| | - Hannah Czolacz
- Department of Evolution, Ecology and Behaviour, University of LiverpoolLiverpoolUnited Kingdom
| | - Shuhao Li
- Department of Biological Sciences, University of ManitobaWinnipegCanada
| | - Akio Shinohara
- Department of Bio-resources, Division of Biotechnology, Frontier Science Research Center, University of MiyazakiMiyazakiJapan
| | - Shin-ichiro Kawada
- Department of Zoology, Division of Vertebrates, National Museum of Nature and ScienceTokyoJapan
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, RiversideRiversideUnited States
| | - Michael Berenbrink
- Department of Evolution, Ecology and Behaviour, University of LiverpoolLiverpoolUnited Kingdom
| | - Kevin L Campbell
- Department of Biological Sciences, University of ManitobaWinnipegCanada
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26
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Hartigan A, Jaimes-Becerra A, Okamura B, Doonan LB, Ward M, Marques AC, Long PF. Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa. PeerJ 2021; 9:e11208. [PMID: 33981497 PMCID: PMC8083181 DOI: 10.7717/peerj.11208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cnidarians are the oldest lineage of venomous animals and use nematocysts to discharge toxins. Whether venom toxins have been recruited to support parasitic lifestyles in the Endocnidozoa (Myxozoa + Polypodium) is, however, unknown. To examine this issue we variously employed transcriptomic, proteomic, associated molecular phylogenies, and localisation studies on representative primitive and derived myxozoans (Malacosporea and Myxosporea, respectively), Polypodium hydriforme, and the free-living staurozoan Calvadosia cruxmelitensis. Our transcriptomics and proteomics analyses provide evidence for expression and translation of venom toxin homologs in myxozoans. Phylogenetic placement of Kunitz type serine protease inhibitors and phospholipase A2 enzymes reveals modification of toxins inherited from ancestral free-living cnidarian toxins, and that venom diversity is reduced in myxozoans concordant with their reduced genome sizes. Various phylogenetic analyses of the Kunitz-type toxin family in Endocnidozoa suggested lineage-specific gene duplications, which offers a possible mechanism for enhancing toxin diversification. Toxin localisation in the malacosporean Buddenbrockia plumatellae substantiates toxin translation and thus illustrates a repurposing of toxin function for endoparasite development and interactions with hosts, rather than for prey capture or defence. Whether myxozoan venom candidates are expressed in transmission stages (e.g. in nematocysts or secretory vesicles) requires further investigation.
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Affiliation(s)
- Ashlie Hartigan
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Faculty of Life Sciences & Medicine, King's College London, University of London, London, United Kingdom
| | - Adrian Jaimes-Becerra
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Liam B Doonan
- Faculty of Life Sciences & Medicine, King's College London, University of London, London, United Kingdom
| | - Malcolm Ward
- Aulesa Biosciences Ltd, Shefford, Bedfordshire, United Kingdom
| | - Antonio C Marques
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paul F Long
- Faculty of Life Sciences & Medicine, King's College London, University of London, London, United Kingdom.,Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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27
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Abstract
Although oral venom systems are ecologically important characters, how they originated is still unclear. In this study, we show that oral venom systems likely originated from a gene regulatory network conserved across amniotes. This network, which we term the “metavenom network,” comprises over 3,000 housekeeping genes coexpressed with venom and play a role in protein folding and modification. Comparative transcriptomics revealed that the network is conserved between venom glands of snakes and salivary glands of mammals. This suggests that while these tissues have evolved different functions, they share a common regulatory core, that persisted since their common ancestor. We propose several evolutionary mechanisms that can utilize this common regulatory core to give rise to venomous animals from their nonvenomous ancestors. Oral venom systems evolved multiple times in numerous vertebrates enabling the exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focused strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system is difficult, since they tend to evolve rapidly, show complex patterns of expression, and were incorporated into the venom arsenal relatively recently. Here we focus on gene regulatory networks associated with the production of toxins in snakes, rather than the toxins themselves. We found that overall venom gland gene expression was surprisingly well conserved when compared to salivary glands of other amniotes. We characterized the “metavenom network,” a network of ∼3,000 nonsecreted housekeeping genes that are strongly coexpressed with the toxins, and are primarily involved in protein folding and modification. Conserved across amniotes, this network was coopted for venom evolution by exaptation of existing members and the recruitment of new toxin genes. For instance, starting from this common molecular foundation, Heloderma lizards, shrews, and solenodon, evolved venoms in parallel by overexpression of kallikreins, which were common in ancestral saliva and induce vasodilation when injected, causing circulatory shock. Derived venoms, such as those of snakes, incorporated novel toxins, though still rely on hypotension for prey immobilization. These similarities suggest repeated cooption of shared molecular machinery for the evolution of oral venom in mammals and reptiles, blurring the line between truly venomous animals and their ancestors.
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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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Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms. Genetica 2021; 149:1-19. [PMID: 33515402 PMCID: PMC7929951 DOI: 10.1007/s10709-021-00113-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a central role in cholesterol homeostasis in humans as a major regulator of LDLR levels. PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane. This, and the inexistence of any other proteolytic substrate but itself could suggest that PCSK9 is an exquisite example of evolutionary fine-tuning. However, the gene has been lost in several mammalian species, and null alleles are present (albeit at low frequencies) in some human populations without apparently deleterious health effects, raising the possibility that the PCSK9 may have become dispensable in the mammalian lineage. To address this issue, we systematically recovered, assembled, corrected, annotated and analysed publicly available PCSK9 sequences for 420 eutherian species to determine the distribution, frequencies, mechanisms and timing of PCSK9 pseudogenization events, as well as the evolutionary pressures underlying the preservation or loss of the gene. We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events have led to PCSK9 loss in most species. These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use of Laurasiatheria species (e.g. pigs) as animal models of human cholesterol-related diseases.
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Jackson TNW, Koludarov I. How the Toxin got its Toxicity. Front Pharmacol 2020; 11:574925. [PMID: 33381030 PMCID: PMC7767849 DOI: 10.3389/fphar.2020.574925] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Venom systems are functional and ecological traits, typically used by one organism to subdue or deter another. A predominant subset of their constituent molecules—“toxins”—share this ecological function and are therefore molecules that mediate interactions between organisms. Such molecules have been referred to as “exochemicals.” There has been debate within the field of toxinology concerning the evolutionary pathways leading to the “recruitment” of a gene product for a toxic role within venom. We review these discussions and the evidence interpreted in support of alternate pathways, along with many of the most popular models describing the origin of novel molecular functions in general. We note that such functions may arise with or without gene duplication occurring and are often the consequence of a gene product encountering a novel “environment,” i.e., a range of novel partners for molecular interaction. After stressing the distinction between “activity” and “function,” we describe in detail the results of a recent study which reconstructed the evolutionary history of a multigene family that has been recruited as a toxin and argue that these results indicate that a pluralistic approach to understanding the origin of novel functions is advantageous. This leads us to recommend that an expansive approach be taken to the definition of “neofunctionalization”—simply the origins of a novel molecular function by any process—and “recruitment”—the “weaponization” of a molecule via the acquisition of a toxic function in venom, by any process. Recruitment does not occur at the molecular level or even at the level of gene expression, but only when a confluence of factors results in the ecological deployment of a physiologically active molecule as a toxin. Subsequent to recruitment, the evolutionary regime of a gene family may shift into a more dynamic form of “birth-and-death.” Thus, recruitment leads to a form of “downwards causation,” in which a change at the ecological level at which whole organisms interact leads to a change in patterns of evolution at the genomic level.
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Affiliation(s)
- Timothy N W Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
| | - Ivan Koludarov
- Animal Venomics Group, Justus Leibig University, Giessen, Germany
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31
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A comparative genomics multitool for scientific discovery and conservation. Nature 2020; 587:240-245. [PMID: 33177664 PMCID: PMC7759459 DOI: 10.1038/s41586-020-2876-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
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Buckley M, Harvey VL, Orihuela J, Mychajliw AM, Keating JN, Milan JNA, Lawless C, Chamberlain AT, Egerton VM, Manning PL. Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews). Mol Biol Evol 2020; 37:2931-2943. [PMID: 32497204 PMCID: PMC7530613 DOI: 10.1093/molbev/msaa137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.
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Affiliation(s)
- Michael Buckley
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Virginia L Harvey
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Johanset Orihuela
- Department of Earth and Environment, Florida International University, Miami, FL
| | - Alexis M Mychajliw
- La Brea Tar Pits & Museum, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Joseph N Keating
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Juan N Almonte Milan
- Museo Nacional de Historia Natural “Prof. Eugenio de Jesús Marcano”, Santo Domingo, Dominican Republic
| | - Craig Lawless
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Andrew T Chamberlain
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Victoria M Egerton
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- The Children’s Museum of Indianapolis, Natural Sciences, Indianapolis, IN
| | - Phillip L Manning
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- The Children’s Museum of Indianapolis, Natural Sciences, Indianapolis, IN
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33
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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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Casewell NR, Jackson TNW, Laustsen AH, Sunagar K. Causes and Consequences of Snake Venom Variation. Trends Pharmacol Sci 2020; 41:570-581. [PMID: 32564899 PMCID: PMC7116101 DOI: 10.1016/j.tips.2020.05.006] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 11/30/2022]
Abstract
Snake venoms are mixtures of toxins that vary extensively between and within snake species. This variability has serious consequences for the management of the world’s 1.8 million annual snakebite victims. Advances in ‘omic’ technologies have empowered toxinologists to comprehensively characterize snake venom compositions, unravel the molecular mechanisms that underpin venom variation, and elucidate the ensuing functional consequences. In this review, we describe how such mechanistic processes have resulted in suites of toxin isoforms that cause diverse pathologies in human snakebite victims and we detail how variation in venom composition can result in treatment failure. Finally, we outline current therapeutic approaches designed to circumvent venom variation and deliver next-generation treatments for the world’s most lethal neglected tropical disease.
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Affiliation(s)
- Nicholas R Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Victoria, Australia
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kartik Sunagar
- Evolutionary Venomics Laboratory, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India
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Zancolli G, Casewell NR. Venom Systems as Models for Studying the Origin and Regulation of Evolutionary Novelties. Mol Biol Evol 2020; 37:2777-2790. [DOI: 10.1093/molbev/msaa133] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties.
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Affiliation(s)
- Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Scheib H, Nekaris KAI, Rode-Margono J, Ragnarsson L, Baumann K, Dobson JS, Wirdateti W, Nouwens A, Nijman V, Martelli P, Ma R, Lewis RJ, Kwok HF, Fry BG. The Toxicological Intersection between Allergen and Toxin: A Structural Comparison of the Cat Dander Allergenic Protein Fel d1 and the Slow Loris Brachial Gland Secretion Protein. Toxins (Basel) 2020; 12:toxins12020086. [PMID: 32012831 PMCID: PMC7076782 DOI: 10.3390/toxins12020086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
Slow lorises are enigmatic animal that represent the only venomous primate lineage. Their defensive secretions have received little attention. In this study we determined the full length sequence of the protein secreted by their unique brachial glands. The full length sequences displayed homology to the main allergenic protein present in cat dander. We thus compared the molecular features of the slow loris brachial gland protein and the cat dander allergen protein, showing remarkable similarities between them. Thus we postulate that allergenic proteins play a role in the slow loris defensive arsenal. These results shed light on these neglected, novel animals.
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Affiliation(s)
- Holger Scheib
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia; (H.S.); (K.B.); (J.S.D.)
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (K.A.-I.N.); (J.R.-M.); (V.N.)
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Johanna Rode-Margono
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (K.A.-I.N.); (J.R.-M.); (V.N.)
- The North of England Zoological Society / Chester Zoo, Chester CH2 1LH, UK
| | - Lotten Ragnarsson
- Institute for Molecular Biosciences, University of Queensland, St Lucia QLD 4072, Australia; (L.R.)
| | - Kate Baumann
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia; (H.S.); (K.B.); (J.S.D.)
| | - James S. Dobson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia; (H.S.); (K.B.); (J.S.D.)
| | | | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Qld 4072, Australia;
| | - Vincent Nijman
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (K.A.-I.N.); (J.R.-M.); (V.N.)
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | | | - Rui Ma
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR;
| | - Richard J. Lewis
- Institute for Molecular Biosciences, University of Queensland, St Lucia QLD 4072, Australia; (L.R.)
| | - Hang Fai Kwok
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR;
- Correspondence: (H.F.K.); (B.G.F.)
| | - Bryan Grieg Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia; (H.S.); (K.B.); (J.S.D.)
- Correspondence: (H.F.K.); (B.G.F.)
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