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Avella I, Schulte L, Hurka S, Damm M, Eichberg J, Schiffmann S, Henke M, Timm T, Lochnit G, Hardes K, Vilcinskas A, Lüddecke T. Proteogenomics-guided functional venomics resolves the toxin arsenal and activity of Deinagkistrodon acutus venom. Int J Biol Macromol 2024; 278:135041. [PMID: 39182889 DOI: 10.1016/j.ijbiomac.2024.135041] [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: 07/21/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Snakebite primarily impacts rural communities of Africa, Asia, and Latin America. The sharp-nosed viper (Deinagkistrodon acutus) is among the snakes of highest medical importance in Asia. Despite various studies on its venom using modern venomics techniques, a comprehensive understanding of composition and function of this species' venom remains lacking. We combined proteogenomics with extensive bioactivity profiling to present the first genome-level catalogue of D. acutus venom proteins and their exochemistry. Our analysis identified an unusually simple venom containing 45 components from 20 distinct protein families. Relative toxin abundances indicate that C-type lectin and C-type lectin-related protein (CTL), snake venom metalloproteinase (svMP), snake venom serine protease (svSP), and phospholipase A2 (PLA2) constitute 90 % of the venom. Bioassays targeting key aspects of viperid envenomation showed considerable concentration-dependent cytotoxicity, particularly in kidney and lung cells, and potent protease and PLA2 activity. Factor Xa and thrombin activities were minor, and no plasmin activity was observed. Effects on haemolysis, intracellular calcium (Ca2+) release, and nitric oxide (NO) synthesis were negligible. Our analysis provides the first holistic genome-based overview of the toxin arsenal of D. acutus, predicting the molecular and functional basis of its life-threatening effects, and opens novel avenues for treating envenomation by this highly dangerous snake.
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Affiliation(s)
- Ignazio Avella
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
| | - Lennart Schulte
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany
| | - Sabine Hurka
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Bioeconomy (BioKreativ) "SymBioÖkonomie", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Maik Damm
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Johanna Eichberg
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Susanne Schiffmann
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 60596 Frankfurt am Main, Germany
| | - Marina Henke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 60596 Frankfurt am Main, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Günther Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Kornelia Hardes
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany
| | - Tim Lüddecke
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany.
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Hirst SR, Rautsaw RM, VanHorn CM, Beer MA, McDonald PJ, Rosales García RA, Rodriguez Lopez B, Rubio Rincón A, Franz Chávez H, Vásquez-Cruz V, Kelly Hernández A, Storfer A, Borja M, Castañeda-Gaytán G, Frandsen PB, Parkinson CL, Strickland JL, Margres MJ. Where the "ruber" Meets the Road: Using the Genome of the Red Diamond Rattlesnake to Unravel the Evolutionary Processes Driving Venom Evolution. Genome Biol Evol 2024; 16:evae198. [PMID: 39255072 DOI: 10.1093/gbe/evae198] [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: 06/07/2024] [Revised: 08/15/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
Understanding the proximate and ultimate causes of phenotypic variation is fundamental in evolutionary research, as such variation provides the substrate for selection to act upon. Although trait variation can arise due to selection, the importance of neutral processes is sometimes understudied. We presented the first reference-quality genome of the Red Diamond Rattlesnake (Crotalus ruber) and used range-wide 'omic data to estimate the degree to which neutral and adaptive evolutionary processes shaped venom evolution. We characterized population structure and found substantial genetic differentiation across two populations, each with distinct demographic histories. We identified significant differentiation in venom expression across age classes with substantially reduced but discernible differentiation across populations. We then used conditional redundancy analysis to test whether venom expression variation was best predicted by neutral divergence patterns or geographically variable (a)biotic factors. Snake size was the most significant predictor of venom variation, with environment, prey availability, and neutral sequence variation also identified as significant factors, though to a lesser degree. By directly including neutrality in the model, our results confidently highlight the predominant, yet not singular, role of life history in shaping venom evolution.
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Affiliation(s)
- Samuel R Hirst
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rhett M Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Cameron M VanHorn
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Preston J McDonald
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | | | - Bruno Rodriguez Lopez
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Alexandra Rubio Rincón
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Víctor Vásquez-Cruz
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Veracruz, Mexico
- PIMVS Herpetario Palancoatl, Veracruz, Mexico
| | | | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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3
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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2024; 43:977-997. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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Kalogeropoulos K, Rosca V, O'Brien C, Christensen CR, Grahadi R, Sørensen CV, Overath MD, Espi DR, Jenkins DE, Keller UAD, Laustsen AH, Fryer TJ, Jenkins TP. V-ToCs (Venom Toxin Clustering): A tool for the investigation of sequence and structure similarities in snake venom toxins. Toxicon 2024; 250:108088. [PMID: 39222754 DOI: 10.1016/j.toxicon.2024.108088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/06/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Recently, there has been a major push toward the development of next-generation treatments against snakebite envenoming. However, unlike current antivenoms that rely on animal-derived polyclonal antibodies, most of these novel approaches are reliant on an in-depth understanding of the over 2000 known snake venom toxins. Indeed, by identifying similarities (i.e., conserved epitopes) across these different toxins, it is possible to design cross-reactive treatments, such as broadly-neutralising antibodies, that target these similarities. Therefore, in this project, we built an automated pipeline that generates sequence and structural distance matrices and homology trees across all available snake venom toxin sequences and structures. To facilitate analysis, we also developed a user-friendly and high-throughput visualisation tool, coined "Venom TOxin CluStering" (V-ToCs). This tool allows researchers to easily investigate sequence and structure patterns in snake venom toxins for a wide array of purposes, such as elucidating toxin evolution, and will also hopefully help guide the discovery and development of increasingly broadly-neutralising antivenoms in the near future.
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Affiliation(s)
| | - Vlad Rosca
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carol O'Brien
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Rahmat Grahadi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
| | | | - Max D Overath
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Diego Ruiz Espi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas J Fryer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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5
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Abiola J, Berg AM, Aiyelaagbe O, Adeyi A, König S. Dabsylated Bradykinin Is Cleaved by Snake Venom Proteases from Echis ocellatus. Biomedicines 2024; 12:1027. [PMID: 38790989 PMCID: PMC11118064 DOI: 10.3390/biomedicines12051027] [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: 03/04/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The vasoactive peptide bradykinin (BK) is an important member of the renin-angiotensin system. Its discovery is tightly interwoven with snake venom research, because it was first detected in plasma following the addition of viper venom. While the fact that venoms liberate BK from a serum globulin fraction is well described, its destruction by the venom has largely gone unnoticed. Here, BK was found to be cleaved by snake venom metalloproteinases in the venom of Echis ocellatus, one of the deadliest snakes, which degraded its dabsylated form (DBK) in a few minutes after Pro7 (RPPGFSP↓FR). This is a common cleavage site for several mammalian proteases such as ACE, but is not typical for matrix metalloproteinases. Residual protease activity < 5% after addition of EDTA indicated that DBK is also cleaved by serine proteases to a minor extent. Mass spectrometry-based protein analysis provided spectral proof for several peptides of zinc metalloproteinase-disintegrin-like Eoc1, disintegrin EO4A, and three serine proteases in the venom.
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Affiliation(s)
- Julius Abiola
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Anna Maria Berg
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
| | - Olapeju Aiyelaagbe
- Organic Unit, Department of Chemistry, University of Ibadan, Ibadan 200005, Nigeria
| | - Akindele Adeyi
- Animal Physiology Unit, Department of Zoology, University of Ibadan, Ibadan 200005, Nigeria
| | - Simone König
- IZKF Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Röntgenstr. 21, 48149 Münster, Germany; (J.A.)
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Mochales-Riaño G, Burriel-Carranza B, Barros MI, Velo-Antón G, Talavera A, Spilani L, Tejero-Cicuéndez H, Crochet PA, Piris A, García-Cardenete L, Busais S, Els J, Shobrak M, Brito JC, Šmíd J, Carranza S, Martínez-Freiría F. Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes. Mol Phylogenet Evol 2024; 191:107979. [PMID: 38040070 DOI: 10.1016/j.ympev.2023.107979] [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: 10/05/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.
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Affiliation(s)
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Museu de Ciències Naturals de Barcelona, P° Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | - Margarida Isabel Barros
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillermo Velo-Antón
- Universidad de Vigo, Facultad de Biología, Edificio de Ciencias Experimentales, Bloque B, Planta 2, Laboratorio 39 (Grupo GEA), E-36310 Vigo, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Loukia Spilani
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Alberto Piris
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Luis García-Cardenete
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg, 1, 41092 Seville, Spain
| | - Salem Busais
- Department of Biology, Faculty of Education, Aden University, Yemen
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al Faisal Wildlife Research Centre, Taif, Saudi Arabia
| | - José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Vinicná 7, Prague, Czech Republic
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
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7
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Niu X, Lv Y, Chen J, Feng Y, Cui Y, Lu H, Liu H. The genome assembly and annotation of the white-lipped tree pit viper Trimeresurus albolabris. GIGABYTE 2024; 2024:gigabyte106. [PMID: 38313188 PMCID: PMC10836062 DOI: 10.46471/gigabyte.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.
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Affiliation(s)
- Xiaotong Niu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- School of Ecology, Sun Yat-sen University, Shenzhen, 510275, China
| | - Yakui Lv
- College of Ecology and Environment, Hainan University, Haikou, 570228, China
| | - Jin Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yueheng Feng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
| | - Yilin Cui
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
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8
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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Niu X, Lu H, Shi M, Wang S, Zhou Y, Liu H. Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus. GIGABYTE 2023; 2023:gigabyte97. [PMID: 38023064 PMCID: PMC10644238 DOI: 10.46471/gigabyte.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
The Brown-Spotted Pit viper (Protobothrops mucrosquamatus), also known as the Chinese habu, is a widespread and highly venomous snake distributed from Northeastern India to Eastern China. Genomics research can contribute to our understanding of venom components and natural selection in vipers. Here, we collected, sequenced and assembled the genome of a male P. mucrosquamatus individual from China. We generated a highly continuous reference genome, with a length of 1.53 Gb and 41.18% of repeat elements content. Using this genome, we identified 24,799 genes, 97.97% of which could be annotated. We verified the validity of our genome assembly and annotation process by generating a phylogenetic tree based on the nuclear genome single-copy genes of six other reptile species. The results of our research will contribute to future studies on Protobothrops biology and the genetic basis of snake venom.
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Affiliation(s)
- Xiaotong Niu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- School of Ecology, Sun Yat-sen University, Shenzhen, 510275, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
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10
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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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11
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Liu B, Cui L, Deng Z, Ma Y, Yang D, Gong Y, Xu Y, Lan T, Yang S, Huang S. The genome assembly and annotation of the many-banded krait, Bungarus multicinctus. GIGABYTE 2023; 2023:gigabyte82. [PMID: 37404266 PMCID: PMC10315667 DOI: 10.46471/gigabyte.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Snakes are a vital component of wildlife resources and are widely distributed across the globe. The many-banded krait Bungarus multicinctus is a highly venomous snake found across Southern Asia and central and southern China. Snakes are an ancient reptile group, and their genomes can provide important clues for understanding the evolutionary history of reptiles. Additionally, genomic resources play a crucial role in comprehending the evolution of all species. However, snake genomic resources are still scarce. Here, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides genomic information on the genes involved in venom gland functions.
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Affiliation(s)
- Boyang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Liangyu Cui
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Zhangwen Deng
- Guangxi Forest Inventory and Planning Institute, Nanning 530011, China
| | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Diancheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
| | - Yanan Gong
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
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12
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Almeida JR, Gomes A, Mendes B, Aguiar L, Ferreira M, Brioschi MBC, Duarte D, Nogueira F, Cortes S, Salazar-Valenzuela D, Miguel DC, Teixeira C, Gameiro P, Gomes P. Unlocking the potential of snake venom-based molecules against the malaria, Chagas disease, and leishmaniasis triad. Int J Biol Macromol 2023; 242:124745. [PMID: 37150376 DOI: 10.1016/j.ijbiomac.2023.124745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
Malaria, leishmaniasis and Chagas disease are vector-borne protozoal infections with a disproportionately high impact on the most fragile societies in the world, and despite malaria-focused research gained momentum in the past two decades, both trypanosomiases and leishmaniases remain neglected tropical diseases. Affordable effective drugs remain the mainstay of tackling this burden, but toxicicty, inneficiency against later stage disease, and drug resistance issues are serious shortcomings. One strategy to overcome these hurdles is to get new therapeutics or inspiration in nature. Indeed, snake venoms have been recognized as valuable sources of biomacromolecules, like peptides and proteins, with antiprotozoal activity. This review highlights major snake venom components active against at least one of the three aforementioned diseases, which include phospholipases A2, metalloproteases, L-amino acid oxidases, lectins, and oligopeptides. The relevance of this repertoire of biomacromolecules and the bottlenecks in their clinical translation are discussed considering approaches that should increase the success rate in this arduous task. Overall, this review underlines how venom-derived biomacromolecules could lead to pioneering antiprotozoal treatments and how the drug landscape for neglected diseases may be revolutionized by a closer look at venoms. Further investigations on poorly studied venoms is needed and could add new therapeutics to the pipeline.
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Affiliation(s)
- José Rafael Almeida
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador.
| | - Ana Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal.
| | - Bruno Mendes
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Tena 150150, Ecuador
| | - Luísa Aguiar
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal
| | - Mariana Ferreira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal.
| | | | - Denise Duarte
- Departamento de Biologia Animal, Instituto de Biologia, UNICAMP, Campinas, São Paulo 13083-862, Brazil.
| | - Fátima Nogueira
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Rua Junqueira 100, P-1349-008 Lisboa, Portugal.
| | - Sofia Cortes
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Rua Junqueira 100, P-1349-008 Lisboa, Portugal.
| | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Indoamérica, Quito 170103, Ecuador.
| | - Danilo C Miguel
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Indoamérica, Quito 170103, Ecuador.
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal
| | - Paula Gameiro
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal.
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal.
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13
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Rimbault C, Knudsen PD, Damsbo A, Boddum K, Ali H, Hackney CM, Ellgaard L, Bohn MF, Laustsen AH. A single-chain variable fragment selected against a conformational epitope of a recombinantly produced snake toxin using phage display. N Biotechnol 2023; 76:23-32. [PMID: 37037303 DOI: 10.1016/j.nbt.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
Phage display technology is a powerful tool for selecting monoclonal antibodies against a diverse set of antigens. Within toxinology, however, it remains challenging to generate monoclonal antibodies against many animal toxins, as they are difficult to obtain from venom. Recombinant toxins have been proposed as a solution to overcome this challenge, but so far, few have been used as antigens to generate neutralizing antibodies. Here, we describe the recombinant expression of α-cobratoxin in E. coli and its successful application as an antigen in a phage display selection campaign. From this campaign, an scFv (single chain variable fragment) was isolated with similar binding affinity to a control scFv generated against the native toxin. The selected scFv recognizes a structural epitope, enabling it to inhibit the interaction between the acetylcholine receptor and the native toxin in vitro. This approach represents the first entirely in vitro antibody selection strategy for generating neutralizing monoclonal antibodies against a snake toxin.
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Affiliation(s)
- Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Pelle D Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Anna Damsbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kim Boddum
- Sophion Bioscience A/S, DK-2750 Ballerup, Denmark
| | - Hanif Ali
- Quadrucept Bio Ltd, Kemp House, 152 City Road, London, EC1V 2NX, United Kingdom
| | - Celeste M Hackney
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Markus-Frederik Bohn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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14
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Nguyen GTT, O'Brien C, Wouters Y, Seneci L, Gallissà-Calzado A, Campos-Pinto I, Ahmadi S, Laustsen AH, Ljungars A. High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa. Gigascience 2022; 11:giac121. [PMID: 36509548 PMCID: PMC9744630 DOI: 10.1093/gigascience/giac121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/06/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022] Open
Abstract
Venomous snakes are important parts of the ecosystem, and their behavior and evolution have been shaped by their surrounding environments over the eons. This is reflected in their venoms, which are typically highly adapted for their biological niche, including their diet and defense mechanisms for deterring predators. Sub-Saharan Africa is rich in venomous snake species, of which many are dangerous to humans due to the high toxicity of their venoms and their ability to effectively deliver large amounts of venom into their victims via their bite. In this study, the venoms of 26 of sub-Saharan Africa's medically most relevant elapid and viper species were subjected to parallelized toxicovenomics analysis. The analysis included venom proteomics and in vitro functional characterization of whole venom toxicities, enabling a robust comparison of venom profiles between species. The data presented here corroborate previous studies and provide biochemical details for the clinical manifestations observed in envenomings by the 26 snake species. Moreover, two new venom proteomes (Naja anchietae and Echis leucogaster) are presented here for the first time. Combined, the presented data can help shine light on snake venom evolutionary trends and possibly be used to further improve or develop novel antivenoms.
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Affiliation(s)
- Giang Thi Tuyet Nguyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Carol O'Brien
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yessica Wouters
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Lorenzo Seneci
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Alex Gallissà-Calzado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Isabel Campos-Pinto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Shirin Ahmadi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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15
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Polymerase chain reaction-based snake origin tracing in commercial venom crystals by targeting the mitochondrial D-loop. Toxicon 2022; 219:106933. [PMID: 36174762 DOI: 10.1016/j.toxicon.2022.106933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 12/10/2022]
Abstract
Snake venom is a valuable raw material for numerous therapeutic formulations because of its life-saving pharmacological potential. However, due to their high price, fake "snake venoms" have captured a significant portion of the global market, and there is currently no reliable reported DNA-based method available for quickly distinguishing between fakes and originals. Therefore, in this study, a set of newly designed snake-specific universal primers targeting mitochondrial D-loop fragments were employed to detect snake origins in commercial venom crystals by only simplex polymerase chain reaction analysis. Under the optimal thermal cycling conditions, only the 145-149 bp snake-specific mitochondrial D-loop fragments from pure and mixed backgrounds were amplified by the newly designed primers. Specificity was achieved by confirming no DNA amplification occurred in the DNA admixture of ten different chordates, and universality by individual DNA amplification of nine different snakes. The primers that efficiently amplified the minimum mitochondrial DNA contained in a total of 10-2 ng in a 10.0 μl reaction were also successfully able to detect the snake origin in commercial cobra venom crystals. These findings suggest that the newly designed primers can be used to differentiate the original and fake commercial snake venom crystals in order to achieve the highest standards of snake venom-based medications through amplifying the snake-specific mitochondrial D-loop fragments.
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