1
|
Yee KT, Macrander J, Vasieva O, Rojnuckarin P. Exploring Toxin Genes of Myanmar Russell's Viper, Daboia siamensis, through De Novo Venom Gland Transcriptomics. Toxins (Basel) 2023; 15:toxins15050309. [PMID: 37235344 DOI: 10.3390/toxins15050309] [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: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The Russell's viper (Daboia siamensis) is a medically important venomous snake in Myanmar. Next-generation sequencing (NGS) shows potential to investigate the venom complexity, giving deeper insights into snakebite pathogenesis and possible drug discoveries. mRNA from venom gland tissue was extracted and sequenced on the Illumina HiSeq platform and de novo assembled by Trinity. The candidate toxin genes were identified via the Venomix pipeline. Protein sequences of identified toxin candidates were compared with the previously described venom proteins using Clustal Omega to assess the positional homology among candidates. Candidate venom transcripts were classified into 23 toxin gene families including 53 unique full-length transcripts. C-type lectins (CTLs) were the most highly expressed, followed by Kunitz-type serine protease inhibitors, disintegrins and Bradykinin potentiating peptide/C-type natriuretic peptide (BPP-CNP) precursors. Phospholipase A2, snake venom serine proteases, metalloproteinases, vascular endothelial growth factors, L-amino acid oxidases and cysteine-rich secretory proteins were under-represented within the transcriptomes. Several isoforms of transcripts which had not been previously reported in this species were discovered and described. Myanmar Russell's viper venom glands displayed unique sex-specific transcriptome profiles which were correlated with clinical manifestation of envenoming. Our results show that NGS is a useful tool to comprehensively examine understudied venomous snakes.
Collapse
Affiliation(s)
- Khin Than Yee
- Department of Medical Research, Ministry of Health, Yangon 11191, Myanmar
| | - Jason Macrander
- Department of Biology, Florida Southern College, Lakeland, FL 33801, USA
| | - Olga Vasieva
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- BioSynthetic Machines, Inc., Chicago, IL 60062, USA
| | - Ponlapat Rojnuckarin
- Excellence Center in Translational Hematology, Division of Hematology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
2
|
Cardoso FC, Servent D, de Lima ME. Editorial: Venom Peptides: A Rich Combinatorial Library for Drug Development. Front Mol Biosci 2022; 9:924023. [PMID: 35647027 PMCID: PMC9136682 DOI: 10.3389/fmolb.2022.924023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Fernanda C. Cardoso
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Fernanda C. Cardoso,
| | - Denis Servent
- CEA, Département Médicaments et Technologies pour La Santé (DMTS), SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Maria Elena de Lima
- Programa de Pós Graduação em Medicina e Biomedicina, Santa Casa de Belo Horizonte, Belo Horizonte, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
3
|
Mendel HC, Kaas Q, Muttenthaler M. Neuropeptide signalling systems - An underexplored target for venom drug discovery. Biochem Pharmacol 2020; 181:114129. [PMID: 32619425 PMCID: PMC7116218 DOI: 10.1016/j.bcp.2020.114129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
Neuropeptides are signalling molecules mainly secreted from neurons that act as neurotransmitters or peptide hormones to affect physiological processes and modulate behaviours. In humans, neuropeptides are implicated in numerous diseases and understanding their role in physiological processes and pathologies is important for therapeutic development. Teasing apart the (patho)physiology of neuropeptides remains difficult due to ligand and receptor promiscuity and the complexity of the signalling pathways. The current approach relies on a pharmacological toolbox of agonists and antagonists displaying high selectivity for independent receptor subtypes, with the caveat that only few selective ligands have been discovered or developed. Animal venoms represent an underexplored source for novel receptor subtype-selective ligands that could aid in dissecting human neuropeptide signalling systems. Multiple endogenous-like neuropeptides as well as peptides acting on neuropeptide receptors are present in venoms. In this review, we summarise current knowledge on neuropeptides and discuss venoms as a source for ligands targeting neuropeptide signalling systems.
Collapse
Affiliation(s)
- Helen C Mendel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Vienna, Austria.
| |
Collapse
|
4
|
Domínguez-Pérez D, Durban J, Agüero-Chapin G, López JT, Molina-Ruiz R, Almeida D, Calvete JJ, Vasconcelos V, Antunes A. The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba. Genomics 2018; 111:1720-1727. [PMID: 30508561 DOI: 10.1016/j.ygeno.2018.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 01/17/2023]
Abstract
The Harderian gland is a cephalic structure, widely distributed among vertebrates. In snakes, the Harderian gland is anatomically connected to the vomeronasal organ via the nasolacrimal duct, and in some species can be larger than the eyes. The function of the Harderian gland remains elusive, but it has been proposed to play a role in the production of saliva, pheromones, thermoregulatory lipids and growth factors, among others. Here, we have profiled the transcriptomes of the Harderian glands of three non-front-fanged colubroid snakes from Cuba: Caraiba andreae (Cuban Lesser Racer); Cubophis cantherigerus (Cuban Racer); and Tretanorhinus variabilis (Caribbean Water Snake), using Illumina HiSeq2000 100 bp paired-end. In addition to ribosomal and non-characterized proteins, the most abundant transcripts encode putative transport/binding, lipocalin/lipocalin-like, and bactericidal/permeability-increasing-like proteins. Transcripts coding for putative canonical toxins described in venomous snakes were also identified. This transcriptional profile suggests a more complex function than previously recognized for this enigmatic organ.
Collapse
Affiliation(s)
- Dany Domínguez-Pérez
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Jordi Durban
- Evolutionary and Translational Venomics Laboratory, CSIC, Jaume Roig, 11, 46010, Valencia, Spain.
| | - Guillermin Agüero-Chapin
- 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, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Javier Torres López
- Department of Ecology and Evolutionary Biology, The University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045, USA; Faculty of Biology, University of Havana, 25 St. 455, La Habana 10400, Cuba.
| | - Reinaldo Molina-Ruiz
- Centro de Bioactivos Químicos, Universidad Central "Marta Abreu" de Las Villas, 54830 Santa Clara, Cuba.
| | - Daniela Almeida
- 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, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Jaume Roig, 11, 46010, Valencia, Spain.
| | - Vítor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| |
Collapse
|
5
|
Chapeaurouge A, Silva A, Carvalho P, McCleary RJR, Modahl CM, Perales J, Kini RM, Mackessy SP. Proteomic Deep Mining the Venom of the Red-Headed Krait, Bungarus flaviceps. Toxins (Basel) 2018; 10:E373. [PMID: 30217057 PMCID: PMC6162843 DOI: 10.3390/toxins10090373] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/28/2018] [Accepted: 09/01/2018] [Indexed: 01/20/2023] Open
Abstract
The use of -omics technologies allows for the characterization of snake venom composition at a fast rate and at high levels of detail. In the present study, we investigated the protein content of Red-headed Krait (Bungarus flaviceps) venom. This analysis revealed a high diversity of snake venom protein families, as evidenced by high-throughput mass spectrometric analysis. We found all six venom protein families previously reported in a transcriptome study of the venom gland of B. flaviceps, including phospholipases A₂ (PLA₂s), Kunitz-type serine proteinase inhibitors (KSPIs), three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), snaclecs, and natriuretic peptides. A combined approach of automated database searches and de novo sequencing of tandem mass spectra, followed by sequence similarity searches, revealed the presence of 12 additional toxin families. De novo sequencing alone was able to identify 58 additional peptides, and this approach contributed significantly to the comprehensive description of the venom. Abundant protein families comprise 3FTxs (22.3%), KSPIs (19%), acetylcholinesterases (12.6%), PLA₂s (11.9%), venom endothelial growth factors (VEGFs, 8.4%), nucleotidases (4.3%), and C-type lectin-like proteins (snaclecs, 3.3%); an additional 11 toxin families are present at significantly lower concentrations, including complement depleting factors, a family not previously detected in Bungarus venoms. The utility of a multifaceted approach toward unraveling the proteome of snake venoms, employed here, allowed detection of even minor venom components. This more in-depth knowledge of the composition of B. flaviceps venom facilitates a better understanding of snake venom molecular evolution, in turn contributing to more effective treatment of krait bites.
Collapse
Affiliation(s)
- Alex Chapeaurouge
- Fundação Oswaldo Cruz-Ceará, Rua São José, 2º Pavimento, Precabura, Eusébio 61760-000, Brazil.
| | - Andreza Silva
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21045-900, Brazil.
| | - Paulo Carvalho
- Computational Mass Spectrometry& Proteomics Group, Carlos Chagas Institute, Fiocruz, Paraná 81350-010, Brazil.
| | - Ryan J R McCleary
- Department of Biology, Stetson University, 421 N. Woodland Blvd, DeLand, FL 32723, USA.
| | - Cassandra Marie Modahl
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Jonas Perales
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21045-900, Brazil.
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th St., CB 92, Greeley, CO 80639-0017, USA.
| |
Collapse
|
6
|
Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W. Computational Studies of Snake Venom Toxins. Toxins (Basel) 2017; 10:E8. [PMID: 29271884 PMCID: PMC5793095 DOI: 10.3390/toxins10010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.
Collapse
Affiliation(s)
- Paola G Ojeda
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - David Ramírez
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
| |
Collapse
|
7
|
New findings from the first transcriptome of the Bothrops moojeni snake venom gland. Toxicon 2017; 140:105-117. [DOI: 10.1016/j.toxicon.2017.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022]
|
8
|
Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics 2017; 14:931-939. [DOI: 10.1080/14789450.2017.1377613] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Samuel D. Robinson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
| | | | | | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| |
Collapse
|
9
|
Affiliation(s)
- Parisa Gazerani
- Department of Health Science & Technology, Aalborg University, Fredrik Bajers Vej 7A2-A2–208, Aalborg East 9220, Denmark
| |
Collapse
|
10
|
Abstract
Animal venoms are complex chemical cocktails, comprising a wide range of biologically active reticulated peptides that target with high selectivity and efficacy a variety of enzymes, membrane receptors, ion channels...Venoms can therefore be seen as large natural libraries of biologically active molecules that are continuously selected and highly refined by the evolution process, up to the point where every molecule is endowed with pharmacological properties that are highly valuable in the context of human use and drug development. Therefore, venom exploration constitutes a prerequisite to drug discovery. However, mass spectrometry and transcriptomics via NGS (Next Generation Sequencing) studies have shown the presence of up to 1000 peptides in the venom of single species of cone snails and spiders. Therefore the global animal venom resource can be seen as a collection of more than 50 to 100 000 000 peptides and proteins of which only ~5000 are known. That extraordinary "Eldorado" of bio-optimized compounds justifies the development of more global and cutting-edge strategies and technologies to explore this resource more efficiently than actually. De novo developed approaches and recently obtained results will be described.
Collapse
|
11
|
Junqueira-de-Azevedo ILM, Campos PF, Ching ATC, Mackessy SP. Colubrid Venom Composition: An -Omics Perspective. Toxins (Basel) 2016; 8:E230. [PMID: 27455326 PMCID: PMC4999846 DOI: 10.3390/toxins8080230] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 01/12/2023] Open
Abstract
Snake venoms have been subjected to increasingly sensitive analyses for well over 100 years, but most research has been restricted to front-fanged snakes, which actually represent a relatively small proportion of extant species of advanced snakes. Because rear-fanged snakes are a diverse and distinct radiation of the advanced snakes, understanding venom composition among "colubrids" is critical to understanding the evolution of venom among snakes. Here we review the state of knowledge concerning rear-fanged snake venom composition, emphasizing those toxins for which protein or transcript sequences are available. We have also added new transcriptome-based data on venoms of three species of rear-fanged snakes. Based on this compilation, it is apparent that several components, including cysteine-rich secretory proteins (CRiSPs), C-type lectins (CTLs), CTLs-like proteins and snake venom metalloproteinases (SVMPs), are broadly distributed among "colubrid" venoms, while others, notably three-finger toxins (3FTxs), appear nearly restricted to the Colubridae (sensu stricto). Some putative new toxins, such as snake venom matrix metalloproteinases, are in fact present in several colubrid venoms, while others are only transcribed, at lower levels. This work provides insights into the evolution of these toxin classes, but because only a small number of species have been explored, generalizations are still rather limited. It is likely that new venom protein families await discovery, particularly among those species with highly specialized diets.
Collapse
Affiliation(s)
- Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Pollyanna F Campos
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Ana T C Ching
- Laboratório de Imunoquímica, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639-0017, USA.
| |
Collapse
|
12
|
|