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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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2
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Smith CF, Modahl CM, Ceja Galindo D, Larson KY, Maroney SP, Bahrabadi L, Brandehoff NP, Perry BW, McCabe MC, Petras D, Lomonte B, Calvete JJ, Castoe TA, Mackessy SP, Hansen KC, Saviola AJ. Assessing Target Specificity of the Small Molecule Inhibitor MARIMASTAT to Snake Venom Toxins: A Novel Application of Thermal Proteome Profiling. Mol Cell Proteomics 2024; 23:100779. [PMID: 38679388 PMCID: PMC11154231 DOI: 10.1016/j.mcpro.2024.100779] [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: 11/12/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024] Open
Abstract
New treatments that circumvent the pitfalls of traditional antivenom therapies are critical to address the problem of snakebite globally. Numerous snake venom toxin inhibitors have shown promising cross-species neutralization of medically significant venom toxins in vivo and in vitro. The development of high-throughput approaches for the screening of such inhibitors could accelerate their identification, testing, and implementation and thus holds exciting potential for improving the treatments and outcomes of snakebite envenomation worldwide. Energetics-based proteomic approaches, including thermal proteome profiling and proteome integral solubility alteration (PISA) assays, represent "deep proteomics" methods for high throughput, proteome-wide identification of drug targets and ligands. In the following study, we apply thermal proteome profiling and PISA methods to characterize the interactions between venom toxin proteoforms in Crotalus atrox (Western Diamondback Rattlesnake) and the snake venom metalloprotease (SVMP) inhibitor marimastat. We investigate its venom proteome-wide effects and characterize its interactions with specific SVMP proteoforms, as well as its potential targeting of non-SVMP venom toxin families. We also compare the performance of PISA thermal window and soluble supernatant with insoluble precipitate using two inhibitor concentrations, providing the first demonstration of the utility of a sensitive high-throughput PISA-based approach to assess the direct targets of small molecule inhibitors for snake venom.
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Affiliation(s)
- Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Cassandra M Modahl
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David Ceja Galindo
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Sean P Maroney
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Lilyrose Bahrabadi
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Nicklaus P Brandehoff
- Rocky Mountain Poison and Drug Center, Denver Health and Hospital Authority, Denver, Colorado, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Daniel Petras
- CMFI Cluster of Excellence, University of Tuebingen, Tuebingen, Germany; Department of Biochemistry, University of California Riverside, Riverside, California, USA
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Texas, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA.
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3
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Thakur S, Giri S, Lalremsanga HT, Doley R. Indian green pit vipers: A lesser-known snake group of north-east India. Toxicon 2024; 242:107689. [PMID: 38531479 DOI: 10.1016/j.toxicon.2024.107689] [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: 10/31/2023] [Revised: 03/09/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024]
Abstract
Green pit vipers are one of the most widely distributed group of venomous snakes in south-east Asia. In Indian, green pit vipers are found in the Northern and North-eastern states spreading across eastern and central India and one of the lesser studied venoms. High morphological similarity among them has been a long-established challenge for species identification, however, a total of six species of Indian green pit viper belonging to genus Trimeresurus, Popeia and Viridovipera has been reported from North-east India. Biochemical and biological studies have revealed that venom exhibits substantial variation in protein expression level along with functional variability. The symptoms of envenomation are painful swelling at bite site, bleeding, necrosis along with systemic toxicity such as prolonged coagulopathy. Clinical data of green pit viper envenomated patients from Demow community health centre, Assam advocated against the use of Indian polyvalent antivenom pressing the need for a suitable antivenom for the treatment of green pit viper envenomation. To design effective and specific antivenom for green pit vipers, unveiling the proteome profile of these snakes is needed. In this study, a comparative venomic of green pit vipers of Northern and North-eastern India, their clinical manifestation as well as treatment protocol has been reviewed.
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Affiliation(s)
- Susmita Thakur
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Surajit Giri
- Demow Government Community Health Centre, Raichai, Konwar Dihingia Gaon, Sivasagar, Assam, India
| | - H T Lalremsanga
- Department of Zoology, Mizoram University, Aizawl 796004, Mizoram, India
| | - Robin Doley
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, India.
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4
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Thakur S, Blotra A, Vasudevan K, Malhotra A, Lalremsanga HT, Santra V, Doley R. Proteome Decomplexation of Trimeresurus erythrurus Venom from Mizoram, India. J Proteome Res 2023; 22:215-225. [PMID: 36516484 DOI: 10.1021/acs.jproteome.2c00642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Green pit vipers are the largest group of venomous vipers in tropical and subtropical Asia, which are responsible for most of the bite cases across this region. Among the green pit vipers of the Indian subcontinent, Trimeresurus erythrurus is the most prevalent; however, limited knowledge is available about its venomics. Proteome decomplexation of T. erythrurus venom using mass spectrometry revealed a blend of 53 different proteins/peptides belonging to 10 snake venom protein families. Phospholipase A2 and snake venom serine proteases were found to be the major enzymatic families, and Snaclec was the major nonenzymatic family in this venom. These protein families might be responsible for consumptive coagulopathy in victims. Along with these, snake venom metalloproteases, l-amino acid oxidases, disintegrins, and cysteine-rich secretory proteins were also found, which might be responsible for inducing painful edema, tissue necrosis, blistering, and defibrination in patients. Protein belonging to C-type lectins, C-type natriuretic peptides, and glutaminyl-peptide cyclotransfreases were also observed as trace proteins. The crude venom shows platelet aggregation in the absence of any agonist, suggesting their role in alterations in platelet functions. This study is the first proteomic analysis of T. erythrurus venom, contributing an overview of different snake venom proteins/peptides responsible for various pathophysiological disorders obtained in patients. Data are available via ProteomeXchange with the identifier PXD038311.
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Affiliation(s)
- Susmita Thakur
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Assam, Napaam784028, India
| | - Avni Blotra
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad500048, India
| | - Karthikeyan Vasudevan
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad500048, India
| | - Anita Malhotra
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, BangorLL57 2UW, Gwynedd, U.K
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl796004, Mizoram, India
| | - Vishal Santra
- Society for Nature Conservation, Research and Community Engagement (CONCERN), Nalikul, Hooghly, West Bengal712407, India.,Captive and Field Herpetology, 13 Hirfron, AngleseyLL65 1YU, Wales, U.K.,Gujarat Forest Department, Consultant - Snake Research Institute, Dharampur, Valsad, Gujarat396050, India
| | - Robin Doley
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Assam, Napaam784028, India
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5
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A current perspective on snake venom composition and constituent protein families. Arch Toxicol 2023; 97:133-153. [PMID: 36437303 DOI: 10.1007/s00204-022-03420-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 11/28/2022]
Abstract
Snake venoms are heterogeneous mixtures of proteins and peptides used for prey subjugation. With modern proteomics there has been a rapid expansion in our knowledge of snake venom composition, resulting in the venom proteomes of 30% of vipers and 17% of elapids being characterised. From the reasonably complete proteomic coverage of front-fanged snake venom composition (179 species-68 species of elapids and 111 species of vipers), the venoms of vipers and elapids contained 42 different protein families, although 18 were only reported in < 5% of snake species. Based on the mean abundance and occurrence of the 42 protein families, they can be classified into 4 dominant, 6 secondary, 14 minor, and 18 rare protein families. The dominant, secondary and minor categories account for 96% on average of a snake's venom composition. The four dominant protein families are: phospholipase A2 (PLA2), snake venom metalloprotease (SVMP), three-finger toxins (3FTx), and snake venom serine protease (SVSP). The six secondary protein families are: L-amino acid oxidase (LAAO), cysteine-rich secretory protein (CRiSP), C-type lectins (CTL), disintegrins (DIS), kunitz peptides (KUN), and natriuretic peptides (NP). Venom variation occurs at all taxonomic levels, including within populations. The reasons for venom variation are complex, as variation is not always associated with geographical variation in diet. The four dominant protein families appear to be the most important toxin families in human envenomation, being responsible for coagulopathy, neurotoxicity, myotoxicity and cytotoxicity. Proteomic techniques can be used to investigate the toxicological profile of a snake venom and hence identify key protein families for antivenom immunorecognition.
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Reilly SB, Karin BR, Stubbs AL, Arida E, Arifin U, Kaiser H, Bi K, Hamidy A, Iskandar DT, McGuire JA. Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago. Evolution 2022; 76:2281-2301. [PMID: 35932243 DOI: 10.1111/evo.14592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Zoology Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Hinrich Kaiser
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, California, 92395, USA.,Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djoko T Iskandar
- Basic Sciences Commission, Indonesian Academy of Sciences, 11, Jl. Medan Merdeka, Selatan Jakarta, 10110, Indonesia.,School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung, 40132, Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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Anita S, Sadjuri AR, Rahmah L, Nugroho HA, Mulyadi, Trilaksono W, Ridhani W, Safira N, Bahtiar H, Maharani, Hamidy A, Azhari A. Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia. J Venom Anim Toxins Incl Trop Dis 2022; 28:e20210103. [PMID: 35875602 PMCID: PMC9261747 DOI: 10.1590/1678-9199-jvatitd-2021-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI- LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein familiesin T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusions: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom’s toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.
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Affiliation(s)
- Syahfitri Anita
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia.,Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | | | | | - Herjuno Ari Nugroho
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN) , Cibinong, Indonesia
| | - Mulyadi
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wahyu Trilaksono
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wiwit Ridhani
- PT Dermama Bioteknologi Laboratorium, Betshaida Hospital, Tangerang, Indonesia
| | | | | | - Maharani
- PT Bio Farma (Persero), Bandung, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
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Yong MY, Tan KY, Tan CH. Potential para-specific and geographical utility of Thai Green Pit Viper (Trimeresurus albolabris) Monovalent Antivenom: Neutralization of procoagulant and hemorrhagic activities of diverse Trimeresurus pit viper venoms. Toxicon 2021; 203:85-92. [PMID: 34600909 DOI: 10.1016/j.toxicon.2021.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022]
Abstract
The Trimeresurus complex consists of diverse medically important venomous pit vipers that cause snakebite envenomation. Antivenoms, however, are in limited supply, and are specific to only two out of the many species across Asia. This study thus investigated the immunoreactivities of regional pit viper antivenoms toward selected Trimeresurus pit viper venoms, and examined the neutralization of their hemotoxic activities. Trimeresurus albolabris Monovalent Antivenom (TaMAV, Thailand) exhibited a higher immunoreactivity than Hemato Bivalent Antivenom (HBAV, raised against Trimeresurus stejnegeri and Protobothrops mucrosquamatus, Taiwan) and Gloydius brevicaudus Monovalent Antivenom (GbMAV, China), attributed to its monovalent nature and conserved antigens in the Trimeresurus pit viper venoms. The venoms showed moderate-to-strong in vitro procoagulant and in vivo hemorrhagic effects consistent with hemotoxic envenomation, except for the Sri Lankan Trimeresurus trigonocephalus venom which lacked hemorrhagic activity. TaMAV was able to differentially neutralize both in vitro and in vivo hemotoxic effects of the venoms, with the lowest efficacy shown against the procoagulant effect of T. trigonocephalus venom. The findings suggest that TaMAV is a potentially useful treatment for envenomation caused by hetero-specific Trimeresurus pit vipers, in particular those in Southeast Asia and East Asia. Clinical study is warranted to establish its spectrum of para-specific effectiveness, and dosages need be tailored to the different species in respective regions.
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Affiliation(s)
- Mun Yee Yong
- Venom Research and Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kae Yi Tan
- Protein and Interactomics Laboratory, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choo Hock Tan
- Venom Research and Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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9
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Lee LP, Tan KY, Tan CH. Snake venom proteomics and antivenomics of two Sundaic lance-headed pit vipers: Trimeresurus wiroti (Malaysia) and Trimeresurus puniceus (Indonesia). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100875. [PMID: 34311411 DOI: 10.1016/j.cbd.2021.100875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022]
Abstract
Envenomation by two medically important Sundaic pit vipers, Trimeresurus wiroti (Malaysia) and Trimeresurus puniceus (Indonesia), causes hemotoxic syndrome with a potentially fatal outcome. Research on the compositions and antigenicity of these pit viper venoms is however lacking, limiting our understanding of the pathophysiology and treatment of envenomation. This study investigated the venom proteomes of both species through a protein decomplexation strategy, applying C18 reverse-phase high-performance liquid chromatography followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and protein identification through nano-electrospray ionization liquid chromatography-tandem mass spectrometry (nano-ESI-LCMS/MS) of trypsin-digested peptides. The venom antigenicity was profiled against the Thai Green Pit Viper Antivenom (GPVAV, a hetero-specific antivenom), using indirect enzyme-linked immunosorbent assay (ELISA). The venom proteomes of T. wiroti and T. puniceus consisted of 10 and 12 toxin families, respectively. The major proteins were of diverse snake venom serine proteases (19-30% of total venom proteins), snake venom metalloproteinases (17-26%), disintegrins (9-16%), phospholipases A2 (8-28%) and C-type lectins (~8%). These were putative snake toxins implicated in hemorrhage and coagulopathy, consistent with clinical hemotoxicity. GPVAV showed strong immunorecognition toward high and medium molecular weight proteins (e.g., SVMP and PLA2) in both venoms, while a lower binding activity was observed toward small proteins such as disintegrins. Conserved antigenicity in the major hemotoxins supported toxicity cross-neutralization by GPVAV and indicated that the immunorecognition of low molecular weight toxins may be optimized for improved binding efficacy. Taken together, the study provides insights into the pathophysiology and antivenom treatment of envenomation caused by T. wiroti and T. puniceus in the region.
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Affiliation(s)
- Louisa Pernee Lee
- Venom Research & Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kae Yi Tan
- Protein and Interactomics Laboratory, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Choo Hock Tan
- Venom Research & Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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10
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Reilly SB, Stubbs AL, Arida E, Karin BR, Arifin U, Kaiser H, Bi K, Iskandar DT, McGuire JA. Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco). Syst Biol 2021; 71:221-241. [PMID: 34117769 DOI: 10.1093/sysbio/syab043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9-11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically-distributed non-sister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5-7.5 Ma, with most inter-island colonization events having occurred between 1-3 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five over-water dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Umilaela Arifin
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; and Department of Biology, Victor Valley College, Victorville, California 92395, USA
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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11
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Toxicity and cross-neutralization of snake venoms from two lesser-known arboreal pit vipers in Southeast Asia: Trimeresurus wiroti and Trimeresurus puniceus. Toxicon 2020; 185:91-96. [DOI: 10.1016/j.toxicon.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
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12
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Proteomics and preclinical antivenom neutralization of the mangrove pit viper (Trimeresurus purpureomaculatus, Malaysia) and white-lipped pit viper (Trimeresurus albolabris, Thailand) venoms. Acta Trop 2020; 209:105528. [PMID: 32442435 DOI: 10.1016/j.actatropica.2020.105528] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
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13
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Ullah A, Masood R. The Sequence and Three-Dimensional Structure Characterization of Snake Venom Phospholipases B. Front Mol Biosci 2020; 7:175. [PMID: 32850964 PMCID: PMC7419708 DOI: 10.3389/fmolb.2020.00175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/06/2020] [Indexed: 11/23/2022] Open
Abstract
Snake venom phospholipases B (SVPLBs) are the least studied enzymes. They constitute about 1% of Bothrops crude venoms, however, in other snake venoms, it is present in less than 1%. These enzymes are considered the most potent hemolytic agent in the venom. Currently, no structural information is available about these enzymes from snake venom. To better understand its three-dimensional structure and mechanisms of envenomation, the current work describes the first model-based structure report of this enzyme from Bothrops moojeni venom named as B. moojeni phospholipase B (PLB_Bm). The structure model of PLB_Bm was generated using model building software like I-TESSER, MODELLER 9v19, and Swiss-Model. The build PLB_Bm model was validated using validation tools (PROCHECK, ERRAT, and Verif3D). The analysis of the PLB_Bm modeled structure indicates that it contains 491 amino acid residues that form a well-defined four-layer αββα sandwich core and has a typical fold of the N-terminal nucleophile aminohydrolase (Ntn-hydrolase). The overall structure of PLB_Bm contains 18 β-strands and 17 α-helices with many connecting loops. The structure divides into two chains (A and B) after maturation. The A chain is smaller and contains 207 amino acid residues, whereas the B chain is larger and contains 266 amino acid residues. The sequence and structural comparison among homologous snake venom, bacterial, and mammals PLBs indicate that differences in the length and sequence composition may confer variable substrate specificity to these enzymes. Moreover, the surface charge distribution, average volume, and depth of the active site cavity also vary in these enzymes. The present work will provide more information about the structure-function relationship and mechanism of action of these enzymes in snakebite envenomation.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University Peshawar, Peshawar, Pakistan
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14
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Bocian A, Sławek S, Jaromin M, Hus KK, Buczkowicz J, Łysiak D, Petrílla V, Petrillova M, Legáth J. Comparison of Methods for Measuring Protein Concentration in Venom Samples. Animals (Basel) 2020; 10:E448. [PMID: 32182656 PMCID: PMC7142616 DOI: 10.3390/ani10030448] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 01/15/2023] Open
Abstract
Snake venom is an extremely interesting natural mixture of proteins and peptides, characterized by both high diversity and high pharmacological potential. Much attention has been paid to the study of venom composition of different species and also detailed analysis of the properties of individual components. Since proteins and peptides are the active ingredients in venom, rapidly developing proteomic techniques are used to analyze them. During such analyses, one of the routine operations is to measure the protein concentration in the sample. The aim of this study was to compare five methods used to measure protein content in venoms of two snake species: the Viperids representative, Agkistrodon contortrix, and the Elapids representative, Naja ashei. The study showed that for A. contortrix venom, the concentration of venom protein measured by four methods is very similar and only the NanoDrop method clearly stands out from the rest. However, in the case of N. ashei venom, each technique yields significantly different results. We hope that this report will help to draw attention to the problem of measuring protein concentration, especially in such a complex mixture as animal venoms.
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Affiliation(s)
- Aleksandra Bocian
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Sonja Sławek
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Marcin Jaromin
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Konrad K. Hus
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Justyna Buczkowicz
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Dawid Łysiak
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Vladimir Petrílla
- Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia;
- Zoological Department, Zoological Garden Košice, Široká 31, 040 06 Košice-Kavečany, Slovakia
| | - Monika Petrillova
- Department of General Education Subjects, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia;
| | - Jaroslav Legáth
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia
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15
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Venomics and Cellular Toxicity of Thai Pit Vipers (Trimeresurus macrops and T. hageni). Toxins (Basel) 2020; 12:toxins12010054. [PMID: 31963345 PMCID: PMC7020458 DOI: 10.3390/toxins12010054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
The two venomous pit vipers, Trimeresurus macrops and T. hageni, are distributed throughout Thailand, although their abundance varies among different areas. No species-specific antivenom is available for their bite victims, and the only recorded treatment method is a horse antivenom raised against T. albolabris crude venom. To facilitate assessment of the cross-reactivity of heterologous antivenoms, protein profiles of T. macrops and T. hageni venoms were explored using mass-spectrometry-based proteomics. The results show that 185 and 216 proteins were identified from T. macrops and T. hageni venoms, respectively. Two major protein components in T. macrops and T. hageni venoms were snake venom serine protease and metalloproteinase. The toxicity of the venoms on human monocytes and skin fibroblasts was analyzed, and both showed a greater cytotoxic effect on fibroblasts than monocytic cells, with toxicity occurring in a dose-dependent rather than a time-dependent manner. Exploring the protein composition of snake venom leads to a better understanding of the envenoming of prey. Moreover, knowledge of pit viper venomics facilitates the selection of the optimum heterologous antivenoms for treating bite victims.
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16
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Grabowsky ER, Mackessy SP. Predator-prey interactions and venom composition in a high elevation lizard specialist, Crotalus pricei (Twin-spotted Rattlesnake). Toxicon 2019; 170:29-40. [DOI: 10.1016/j.toxicon.2019.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 01/31/2023]
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17
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Debono J, Bos MHA, Do MS, Fry BG. Clinical implications of coagulotoxic variations in Mamushi (Viperidae: Gloydius) snake venoms. Comp Biochem Physiol C Toxicol Pharmacol 2019; 225:108567. [PMID: 31306806 DOI: 10.1016/j.cbpc.2019.108567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 12/12/2022]
Abstract
Snake bite is currently one of the most neglected tropical diseases affecting much of the developing world. Asian pit vipers are responsible for a considerable amount of envenomations annually and bites can cause a multitude of clinical complications resulting from coagulopathic and neuropathic effects. While intense research has been undertaken for some species of Asian pit viper, functional coagulopathic effects have been neglected for others. We investigated their effects upon the human clotting cascade using venoms of four species of Gloydius and Ovophis okinavensis, a species closely to Gloydius. All species of included within this investigation displayed varying fibrinogenolytic effects, resulting in a net anticoagulant outcome. Gloydius saxatilis and Gloydius ussuriensis displayed the most variable effects from differing localities, sampled from Russia and Korea. As this Gloydius investigation includes some geographical variation, notable results indicate key variations of these species that point to possible limitations in antivenom cross-reactivities, which may have implications for the clinical care of victims envenomed by these snakes.
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Affiliation(s)
- Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Mettine H A Bos
- Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Min Seock Do
- Animal Ecology Lab, Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
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18
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Debono J, Bos MHA, Frank N, Fry B. Clinical implications of differential antivenom efficacy in neutralising coagulotoxicity produced by venoms from species within the arboreal viperid snake genus Trimeresurus. Toxicol Lett 2019; 316:35-48. [PMID: 31509773 DOI: 10.1016/j.toxlet.2019.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022]
Abstract
Snake envenomation globally is attributed to an ever-increasing human population encroaching into snake territories. Responsible for many bites in Asia is the widespread genus Trimeresurus. While bites lead to haemorrhage, only a few species have had their venoms examined in detail. We found that Trimeresurus venom causes haemorrhaging by cleaving fibrinogen in a pseudo-procoagulation manner to produce weak, unstable, short-lived fibrin clots ultimately resulting in an overall anticoagulant effect due to fibrinogen depletion. The monovalent antivenom 'Thai Red Cross Green Pit Viper antivenin', varied in efficacy ranging from excellent neutralisation of T. albolabris venom through to T. gumprechti and T. mcgregori being poorly neutralised and T. hageni being unrecognised by the antivenom. While the results showing excellent neutralisation of some non-T. albolabris venoms (such as T. flavomaculaturs, T. fucatus, and T. macrops) needs to be confirmed with in vivo tests, conversely the antivenom failure T. hageni, and the very poor results against T. gumprechti and T. mcgregori, despite being conducted in the ideal scenario of preincubation of antivenom:venom, indicates that the likelihood of clinically relevant cross-reactivity for these species is low (T. gumprechti and T. mcgregori) to non-existent (T. hageni). These same latter three species were also not inhibited by the serine protease inhibitor AEBSF, suggesting that the toxins leading to a coagulotoxic effect in these species are non-serine proteases while in contrast T. albolabris coagulotoxicity was completely impeded by AEBSF, and thus driven by kallikrein-type serine proteases. There was a conspicuous lack of phylogenetic pattern in venom variation, with the most potent venoms (T. albolabris and T. hageni) being distant to each other on the organismal tree, and with the three most divergent and poorly neutralised venoms (T. gumprechti, T. hageni, and T. mcgregori) were also not each others closest relatives. This reinforces the paradigm that the fundamental dynamic evolution of venom results in organismal phylogeny being a poor predictor of venom potency or antivenom efficacy. This study provides a robust investigation on the differential venom effects from a wide range of Trimeresurus species on coagulation, highlighting differential fibrinogenolytic effects, while also investigating the relative antivenom neutralisation capabilities of the widely available Thai Red Cross Green Pit Viper antivenom. These results therefore have immediate, real-world implications for patients envenomed by Trimeresurus species.
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Affiliation(s)
- Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mettine H A Bos
- Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | | | - Bryan Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia.
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19
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Reilly SB, Stubbs AL, Karin BR, Arida E, Iskandar DT, McGuire JA. Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species. ZOOL SCR 2019. [DOI: 10.1111/zsc.12368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean B. Reilly
- Museum of Vertebrate Zoology, Department of Integrative Biology University of California Berkeley California USA
| | - Alexander L. Stubbs
- Museum of Vertebrate Zoology, Department of Integrative Biology University of California Berkeley California USA
| | - Benjamin R. Karin
- Museum of Vertebrate Zoology, Department of Integrative Biology University of California Berkeley California USA
| | - Evy Arida
- Museum Zoologicum Bogoriense Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Djoko T. Iskandar
- School of Life Sciences and Technology Institut Teknologi Bandung Bandung Indonesia
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, Department of Integrative Biology University of California Berkeley California USA
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