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Chandrasekara U, Mancuso M, Seneci L, Bourke L, Trembath DF, Sumner J, Zdenek CN, Fry BG. A Russian Doll of Resistance: Nested Gains and Losses of Venom Immunity in Varanid Lizards. Int J Mol Sci 2024; 25:2628. [PMID: 38473875 DOI: 10.3390/ijms25052628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The interplay between predator and prey has catalyzed the evolution of venom systems, with predators honing their venoms in response to the evolving resistance of prey. A previous study showed that the African varanid species Varanus exanthematicus has heightened resistance to snake venoms compared to the Australian species V. giganteus, V. komodoensis, and V. mertensi, likely due to increased predation by sympatric venomous snakes on V. exanthematicus. To understand venom resistance among varanid lizards, we analyzed the receptor site targeted by venoms in 27 varanid lizards, including 25 Australian varanids. The results indicate an active evolutionary arms race between Australian varanid lizards and sympatric neurotoxic elapid snakes. Large species preying on venomous snakes exhibit inherited neurotoxin resistance, a trait potentially linked to their predatory habits. Consistent with the 'use it or lose it' aspect of venom resistance, this trait was secondarily reduced in two lineages that had convergently evolved gigantism (V. giganteus and the V. komodoensis/V. varius clade), suggestive of increased predatory success accompanying extreme size and also increased mechanical protection against envenomation due to larger scale osteoderms. Resistance was completely lost in the mangrove monitor V. indicus, consistent with venomous snakes not being common in their arboreal and aquatic niche. Conversely, dwarf varanids demonstrate a secondary loss at the base of the clade, with resistance subsequently re-evolving in the burrowing V. acanthurus/V. storri clade, suggesting an ongoing battle with neurotoxic predators. Intriguingly, within the V. acanthurus/V. storri clade, resistance was lost again in V. kingorum, which is morphologically and ecologically distinct from other members of this clade. Resistance was also re-evolved in V. glebopalma which is terrestrial in contrast to the arboreal/cliff dwelling niches occupied by the other members of its clade (V. glebopalma, V. mitchelli, V. scalaris, V. tristis). This 'Russian doll' pattern of venom resistance underscores the dynamic interaction between dwarf varanids and Australian neurotoxic elapid snakes. Our research, which included testing Acanthophis (death adder) venoms against varanid receptors as models for alpha-neurotoxic interactions, uncovered a fascinating instance of the Red Queen Hypothesis: some death adders have developed more potent toxins specifically targeting resistant varanids, a clear sign of the relentless predator-prey arms race. These results offer new insight into the complex dynamics of venom resistance and highlight the intricate ecological interactions that shape the natural world.
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Affiliation(s)
- Uthpala Chandrasekara
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
| | - Marco Mancuso
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
| | - Lorenzo Seneci
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
| | - Lachlan Bourke
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
| | - Dane F Trembath
- Herpetology Department, Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Joanna Sumner
- Museums Victoria Research Institute, Melbourne, VIC 3001, Australia
| | - Christina N Zdenek
- School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
| | - Bryan G Fry
- Adaptive Biotoxicology Lab, School of the Environment, University of Queensland, St Lucia, QLD 4072, Australia
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2
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Nystrom GS, Ellsworth SA, Ward MJ, Rokyta DR. Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus). J Mol Evol 2023; 91:935-962. [PMID: 38091038 DOI: 10.1007/s00239-023-10148-7] [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: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023]
Abstract
Venoms are primarily believed to evolve under strong diversifying selection resulting from persistent coevolution between predator and prey. Recent research has challenged this hypothesis, proposing that venoms from younger venomous lineages (e.g., snakes and cone snails) are governed predominantly by diversifying selection, while venoms from older venomous lineages (e.g., centipedes, scorpions, and spiders) are under stronger purifying selection. However, most research in older lineages has tested selection at more diverse phylogenetic scales. Although these tests are important for evaluating broad macroevolutionary trends underlying venom evolution, they are less equipped to detect species-level evolutionary trends, which likely have large impacts on venom variation seen at more diverse phylogenetic scales. To test for selection among closely related species from an older venomous lineage, we generated high-throughput venom-gland transcriptomes and venom proteomes for four populations of Giant Desert Hairy Scorpions (Hadrurus), including three Hadrurus arizonensis populations and one Hadrurus spadix population. We detected significant episodic and pervasive diversifying selection across a highly abundant toxin family that likely has a major role in venom function ([Formula: see text]KTxs), providing a contrast to the stronger purifying selection identified from other studies on scorpion venoms. Conversely, we detected weak episodic diversifying and/or stronger purifying selection in four toxin families (non-disulfide bridged peptides, phospholipase A2s, scorpine-like antimicrobial peptides, and serine proteases), most of which were less abundant and likely have ancillary functional roles. Finally, although we detected several major toxin families at disproportionate transcriptomic and/or proteomic abundances, we did not identify significant sex-based variation in Hadrurus venoms.
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Affiliation(s)
- Gunnar S Nystrom
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA.
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3
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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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4
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Smith CF, Nikolakis ZL, Perry BW, Schield DR, Meik JM, Saviola AJ, Castoe TA, Parker J, Mackessy SP. The best of both worlds? Rattlesnake hybrid zones generate complex combinations of divergent venom phenotypes that retain high toxicity. Biochimie 2023; 213:176-189. [PMID: 37451532 DOI: 10.1016/j.biochi.2023.07.008] [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: 01/28/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Studying the consequences of hybridization between closely related species with divergent traits can reveal patterns of evolution that shape and maintain extreme trophic adaptations. Snake venoms are an excellent model system for examining the evolutionary and ecological patterns that underlie highly selected polymorphic traits. Here we investigate hybrid venom phenotypes that result from natural introgression between two rattlesnake species that express highly divergent venom phenotypes: Crotalus o. concolor and C. v. viridis. Though not yet documented, interbreeding between these species may lead to novel venom phenotypes with unique activities that break the typical trends of venom composition in rattlesnakes. The characteristics of these unusual phenotypes could unveil the roles of introgression in maintaining patterns of venom composition and variation, including the near ubiquitous dichotomy between neurotoxic or degradative venoms observed across rattlesnakes. We use RADseq data to infer patterns of gene flow and hybrid ancestry between these diverged lineages and link these genetic data with analyses of venom composition, biological activity, and whole animal model toxicity tests to understand the impacts of introgression on venom composition. We find that introgressed populations express admixed venom phenotypes that do not sacrifice biological activity (lethal toxicity) or overall abundance of dominant toxins compared to parental venoms. These hybridized venoms therefore do not represent a trade-off in functionality between the typical phenotypic extremes but instead represent a unique combination of characters whose expression appears limited to the hybrid zone.
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Affiliation(s)
- Cara F Smith
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA
| | - Zachary L Nikolakis
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, 1333 W. Washington Street, Stephenville, TX, 76402, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Joshua Parker
- Fresno City College, 1101 E. University Avenue, Fresno, CA, 93741, USA
| | - Stephen P Mackessy
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA.
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5
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Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, de la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Castañeda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium. J Mol Evol 2023; 91:514-535. [PMID: 37269364 PMCID: PMC10995822 DOI: 10.1007/s00239-023-10115-2] [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: 10/14/2022] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.
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Affiliation(s)
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Science Department, Cape Fear Community College, Wilmington, NC, 28401, USA
| | | | - Hector Franz-Chavez
- Herp.mx A.C., Colima, Mexico
- Biodiversa A. C., Chapala, Jalisco, 45900, Mexico
| | | | | | | | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Gamaliel Castañeda-Gaytan
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mahmood Sasa
- Centro Investigaciones en Biodiversidad y Ecología Tropical and Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA.
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6
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Zhao HY, He N, Sun Y, Wang YC, Zhang HB, Chen HH, Zhang YQ, Gao JF. Phylogeny-Related Variations in Venomics: A Test in a Subset of Habu Snakes ( Protobothrops). Toxins (Basel) 2023; 15:toxins15050350. [PMID: 37235384 DOI: 10.3390/toxins15050350] [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: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
We conducted a comparative analysis to unveil the divergence among venoms from a subset of Old World habu snakes (Protobothrops) in terms of venomic profiles and toxicological and enzymatic activities. A total of 14 protein families were identified in the venoms from these habu snakes, and 11 of them were shared among these venoms. The venoms of five adult habu snakes were overwhelmingly dominated by SVMP (32.56 ± 13.94%), PLA2 (22.93 ± 9.26%), and SVSP (16.27 ± 4.79%), with a total abundance of over 65%, while the subadult P. mangshanensis had an extremely low abundance of PLA2 (1.23%) but a high abundance of CTL (51.47%), followed by SVMP (22.06%) and SVSP (10.90%). Apparent interspecific variations in lethality and enzymatic activities were also explored in habu snake venoms, but no variations in myotoxicity were found. Except for SVSP, the resemblance of the relatives within Protobothrops in other venom traits was estimated to deviate from Brownian motion evolution based on phylogenetic signals. A comparative analysis further validated that the degree of covariation between phylogeny and venom variation is evolutionarily labile and varies among clades of closely related snakes. Our findings indicate a high level of interspecific variation in the venom proteomes of habu snakes, both in the presence or absence and the relative abundance of venom protein families, and that these venoms might have evolved under a combination of adaptive and neutral mechanisms.
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Affiliation(s)
- Hong-Yan Zhao
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Na He
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yan Sun
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yong-Chen Wang
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Hao-Bing Zhang
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Hui-Hui Chen
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ya-Qi Zhang
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jian-Fang Gao
- Herpetological Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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7
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Schaeffer R, Pascolutti VJ, Jackson TNW, Arbuckle K. Diversity Begets Diversity When Diet Drives Snake Venom Evolution, but Evenness Rather Than Richness Is What Counts. Toxins (Basel) 2023; 15:toxins15040251. [PMID: 37104189 PMCID: PMC10142186 DOI: 10.3390/toxins15040251] [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: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
Snake venoms are primarily used to subjugate prey, and consequently, their evolution has been shown to be predominantly driven by diet-related selection pressure. Venoms tend to be more lethal to prey than non-prey species (except in cases of toxin resistance), prey-specific toxins have been identified, and preliminary work has demonstrated an association between the diversity of diet classes and that of toxicological activities of whole venom. However, venoms are complex mixtures of many toxins, and it remains unclear how toxin diversity is driven by diet. Prey-specific toxins do not encompass the molecular diversity of venoms, and whole venom effects could be driven by one, few, or all components, so the link between diet and venom diversity remains minimally understood. Here, we collated a database of venom composition and diet records and used a combination of phylogenetic comparative methods and two quantitative diversity indices to investigate whether and how diet diversity relates to the toxin diversity of snake venoms. We reveal that venom diversity is negatively related to diet diversity using Shannon's index but positively related using Simpson's index. Since Shannon's index predominantly considers the number of prey/toxins, whereas Simpson's index more strongly reflects evenness, we provide insights into how the diet-venom diversity link is driven. Specifically, species with low diet diversity tend to have venoms dominated by a few abundant (possibly specialised) toxin families, whereas species with diverse diets tend to 'hedge their bets' by having venoms with a more even composition of different toxin classes.
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Affiliation(s)
- Romane Schaeffer
- Département Biologie and Geosciences, Faculté Sciences et Ingénierie, Université Toulouse III-Paul Sabatier, 31062 Toulouse, France
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, UK
| | - Victoria J Pascolutti
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, UK
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kevin Arbuckle
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, UK
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Tsai TS, Tsai IH. Full sequencing and comparison of five venom metalloproteases of Trimeresurus gracilis: The PI-enzyme is most similar to okinalysin but the PIII-enzyme is most similar to Crotalus venom enzymes. Toxicon 2023; 225:107053. [PMID: 36758773 DOI: 10.1016/j.toxicon.2023.107053] [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: 12/05/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
The cDNAs encoding the Zn+2-metalloproteases (SVMPs) of Trimeresurus gracilis (abbreviated as Tgc), a pitviper endemic to Taiwan, were cloned from venom glands and sequenced. The amino-acid sequences of five novel SVMPs, including one P-III, three P-II and one P-I class enzymes, were thus deduced and subjected to BLAST-analyses. The P-III enzyme (designated as Tgc-PIII) is structurally most similar to the PIII-SVMPs of New World pitvipers but not similar to the PIII-SVMP of Ovophis okinavensis. Sequence-similarity analysis of 22 homologous PIII-SVMPs reveal three major structural subtypes of the pitviper PIII-SVMPs, which possibly have different substrate specificities. In addition, Tgc-PIII and the PI-class SVMP (named Tgc-MP) were isolated from the venom and verified by mass spectrometry. All the three deduced sequences of PII-SVMPs (Tgc-PIIs) contain an abnormal Zn+2-binding-site in their catalytic-domain, and an identical "long-disintegrin" domain. The predicted 85-residues disintegrin, gracilisin, bears high similarities to some long-disintegrins of the New-World pitvipers and salmosin3. By BLAST search and comparison, Tgc-MP is 96% similar to okinalysin, the hemorrhagic PI-SVMP of O. okinavensis, rather than any other PI-SVMPs in the databanks. Our results confirm the fast evolution of Tgc-SVMPs as well as their structural similarities to different SVMP-classes of the New-World pitvipers and of O. okinavensis, respectively. The implications of our findings are discussed along with our previous sequence comparisons of venom phospholipases A2 and ten venom serine proteases of Tgc.
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Affiliation(s)
- Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Inn-Ho Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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9
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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10
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Biological and Medical Aspects Related to South American Rattlesnake Crotalus durissus (Linnaeus, 1758): A View from Colombia. Toxins (Basel) 2022; 14:toxins14120875. [PMID: 36548772 PMCID: PMC9784998 DOI: 10.3390/toxins14120875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/16/2022] Open
Abstract
In Colombia, South America, there is a subspecies of the South American rattlesnake Crotalus durissus, C. d. cumanensis, a snake of the Viperidae family, whose presence has been reduced due to the destruction of its habitat. It is an enigmatic snake from the group of pit vipers, venomous, with large articulated front fangs, special designs on its body, and a characteristic rattle on its tail. Unlike in Brazil, the occurrence of human envenomation by C. durisus in Colombia is very rare and contributes to less than 1% of envenomation caused by snakes. Its venom is a complex cocktail of proteins with different biological effects, which evolved with the purpose of paralyzing the prey, killing it, and starting its digestive process, as well as having defense functions. When its venom is injected into humans as the result of a bite, the victim presents with both local tissue damage and with systemic involvement, including a diverse degree of neurotoxic, myotoxic, nephrotoxic, and coagulopathic effects, among others. Its biological effects are being studied for use in human health, including the possible development of analgesic, muscle relaxant, anti-inflammatory, immunosuppressive, anti-infection, and antineoplastic drugs. Several groups of researchers in Brazil are very active in their contributions in this regard. In this work, a review is made of the most relevant biological and medical aspects related to the South American rattlesnake and of what may be of importance for a better understanding of the snake C. d. cumanensis, present in Colombia and Venezuela.
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11
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Fitzpatrick LLJ, Nijman V, Ligabue-Braun R, Nekaris KAI. The Fast and the Furriest: Investigating the Rate of Selection on Mammalian Toxins. Toxins (Basel) 2022; 14:toxins14120842. [PMID: 36548740 PMCID: PMC9782207 DOI: 10.3390/toxins14120842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of venom and the selection pressures that act on toxins have been increasingly researched within toxinology in the last two decades, in part due to the exceptionally high rates of diversifying selection observed in animal toxins. In 2015, Sungar and Moran proposed the 'two-speed' model of toxin evolution linking evolutionary age of a group to the rates of selection acting on toxins but due to a lack of data, mammals were not included as less than 30 species of venomous mammal have been recorded, represented by elusive species which produce small amounts of venom. Due to advances in genomics and transcriptomics, the availability of toxin sequences from venomous mammals has been increasing. Using branch- and site-specific selection models, we present the rates of both episodic and pervasive selection acting upon venomous mammal toxins as a group for the first time. We identified seven toxin groups present within venomous mammals, representing Chiroptera, Eulipotyphla and Monotremata: KLK1, Plasminogen Activator, Desmallipins, PACAP, CRiSP, Kunitz Domain One and Kunitz Domain Two. All but one group (KLK1) was identified by our results to be evolving under both episodic and pervasive diversifying selection with four toxin groups having sites that were implicated in the fitness of the animal by TreeSAAP (Selection on Amino Acid Properties). Our results suggest that venomous mammal ecology, behaviour or genomic evolution are the main drivers of selection, although evolutionary age may still be a factor. Our conclusion from these results indicates that mammalian toxins are following the two-speed model of selection, evolving predominately under diversifying selection, fitting in with other younger venomous taxa like snakes and cone snails-with high amounts of accumulating mutations, leading to more novel adaptions in their toxins.
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Affiliation(s)
- Leah Lucy Joscelyne Fitzpatrick
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Correspondence:
| | - Vincent Nijman
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Avenida Sarmento Leite 245, Porto Alegre 90050-130, Brazil
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Department of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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Myers EA, Strickland JL, Rautsaw RM, Mason AJ, Schramer TD, Nystrom GS, Hogan MP, Yooseph S, Rokyta DR, Parkinson CL. De Novo Genome Assembly Highlights the Role of Lineage-Specific Duplications in the Evolution of Venom in Fea’s Viper. Genome Biol Evol 2022; 14:6603630. [PMID: 35670514 PMCID: PMC9256536 DOI: 10.1093/gbe/evac082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
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Affiliation(s)
- Edward A. Myers
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Biology, University of South Alabama , Mobile, AL 36688, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA
| | - Tristan D. Schramer
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, 4000 Central Florida Blvd , Orlando, FL, 32816, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University , Clemson, SC 29634, USA
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Roldán-Padrón O, Cruz-Pérez MS, Castro-Guillén JL, García-Arredondo JA, Mendiola-Olaya E, Saldaña-Gutiérrez C, Herrera-Paniagua P, Blanco-Labra A, García-Gasca T. Hybridization between Crotalus aquilus and Crotalus polystictus Species: A Comparison of Their Venom Toxicity and Enzymatic Activities. BIOLOGY 2022; 11:661. [PMID: 35625389 PMCID: PMC9138290 DOI: 10.3390/biology11050661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 06/15/2023]
Abstract
Hybridization is defined as the interbreeding of individuals from two populations distinguishable by one or more heritable characteristics. Snake hybridization represents an interesting opportunity to analyze variability and how genetics affect the venom components between parents and hybrids. Snake venoms exhibit a high degree of variability related to biological and biogeographical factors. The aim of this work is to analyze the protein patterns and enzymatic activity of some of the main hemotoxic enzymes in snake venoms, such as serine proteases (trypsin-like, chymotrypsin-like, and elastase-like), metalloproteases, hyaluronidases, and phospholipase A2. The lethal dose of 50 (LD50) of venom from the Crotalus aquilus (Cabf) and Crotalus polystictus (Cpbm) parents and their hybrids in captivity was determined, and phenetic analysis is also conducted, which showed a high similarity between the hybrids and C. polystictus. The protein banding patterns and enzymatic activity analyze by zymography resulted in a combination of proteins from the parental venoms in the hybrids, with variability among them. In some cases, the enzymatic activity is higher in the hybrids with a lower LD50 than in the parents, indicating higher toxicity. These data show the variability among snake venoms and suggest that hybridization is an important factor in changes in protein concentration, peptide variability, and enzymatic activity that affect toxicity and lethality.
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Affiliation(s)
- Octavio Roldán-Padrón
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Martha Sandra Cruz-Pérez
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - José Luis Castro-Guillén
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - José Alejandro García-Arredondo
- Laboratorio de Química Medicinal, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Centro Universitario, Queretaro 76010, Qro, Mexico;
| | - Elizabeth Mendiola-Olaya
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - Carlos Saldaña-Gutiérrez
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Patricia Herrera-Paniagua
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
| | - Alejandro Blanco-Labra
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Gto, Mexico; (J.L.C.-G.); (E.M.-O.)
| | - Teresa García-Gasca
- Laboratorio de Biología Celular y Molecuar, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Queretaro 76230, Qro, Mexico; (O.R.-P.); (M.S.C.-P.); (C.S.-G.); (P.H.-P.)
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14
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Isomoto A, Shoguchi E, Hisata K, Inoue J, Sun Y, Inaba K, Satoh N, Ogawa T, Shibata H. Active Expression of Genes for Protein Modification Enzymes in Habu Venom Glands. Toxins (Basel) 2022; 14:toxins14050300. [PMID: 35622547 PMCID: PMC9146206 DOI: 10.3390/toxins14050300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/09/2022] [Accepted: 04/16/2022] [Indexed: 01/27/2023] Open
Abstract
Genes encoding snake venom toxins have been studied extensively. However, genes involved in the modification and functioning of venom proteins are little known. Protobothrops is a genus of pit vipers, which are venomous and inhabit the Nansei (Southwest) islands of Japan, Taiwan China, Vietnam, Thailand, Myanmar, Nepal, Bhutan, and India. Our previous study decoded the genome of Protobothrops flavoviridis, a species endemic to the Nansei Islands, Japan, and revealed unique evolutionary processes of some venom genes. In this study, we analyzed genes that are highly expressed in venom glands to survey genes for candidate enzymes or chaperone proteins involved in toxin folding and modification. We found that, in addition to genes that encode venom proteins and ribosomal proteins, genes that encode protein disulfide isomerase (PDI) family members (orthologs of human P4HB and PDIA3), Selenoprotein M (SELENOM), and Calreticulin (CALR) are highly expressed in venom glands. Since these enzymes or chaperones are involved in protein modification and potentially possess protein folding functions, we propose that P4HB, SELENOM, CALR, and PDIA3 encode candidate enzymes or chaperones to confer toxic functions upon the venom transcriptome.
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Affiliation(s)
- Akiko Isomoto
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
- Department of Biological Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (A.I.); (T.O.); (H.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Yinrui Sun
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Material, Tohoku University, Sendai 980-8577, Japan;
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Tomohisa Ogawa
- Department of Biological Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (A.I.); (T.O.); (H.S.)
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
- Correspondence: (A.I.); (T.O.); (H.S.)
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15
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Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
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Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Nie X, He Q, Zhou B, Huang D, Chen J, Chen Q, Yang S, Yu X. Exploring the five-paced viper ( Deinagkistrodon acutus) venom proteome by integrating a combinatorial peptide ligand library approach with shotgun LC-MS/MS. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200196. [PMID: 34745239 PMCID: PMC8547348 DOI: 10.1590/1678-9199-jvatitd-2020-0196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/18/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Snake venoms are complex mixtures of toxic proteins or peptides encoded by various gene families that function synergistically to incapacitate prey. In the present study, in order to unravel the proteomic repertoire of Deinagkistrodon acutus venom, some trace abundance components were analyzed. METHODS Shotgun proteomic approach combined with shotgun nano-LC-ESI-MS/MS were employed to characterize the medically important D. acutus venom, after collected samples were enriched with the combinatorial peptide ligand library (CPLL). RESULTS This avenue helped us find some trace components, undetected before, in D. acutus venom. The results indicated that D. acutus venom comprised 84 distinct proteins from 10 toxin families and 12 other proteins. These results are more than twice the number of venom components obtained from previous studies, which were only 29 distinct proteins obtained through RP-HPLC for the venom of the same species. The present results indicated that in D. acutus venom, the most abundant components (66.9%) included metalloproteinases, serine proteinases, and C-type lectin proteins; the medium abundant components (13%) comprised phospholipases A2 (PLA2) and 5'-nucleotidases and nucleases; whereas least abundant components (6%) were aminopeptidases, L-amino acid oxidases (LAAO), neurotoxins and disintegrins; and the trace components. The last were undetected before the use of conventional shotgun proteomics combined with shotgun nano-LC-ESI-MS/MS, such as cysteine-rich secretory proteins Da-CRPa, phospholipases B-like 1, phospholipases B (PLB), nerve growth factors (NGF), glutaminyl-peptide cyclortransferases (QC), and vascular non-inflammatory molecules 2 (VNN2). CONCLUSION These findings demonstrated that the CPLL enrichment method worked well in finding the trace toxin proteins in D. acutus venom, in contrast with the previous venomic characterization of D. acutus by conventional LC-MS/MS. In conclusion, this approach combined with the CPLL enrichment was effective for allowing us to explore the hidden D. acutus venomic profile and extended the list of potential venom toxins.
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Affiliation(s)
- Xuekui Nie
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qiyi He
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Bin Zhou
- Library, Chongqing Normal University, Chongqing, China
| | - Dachun Huang
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Junbo Chen
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qianzi Chen
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Shuqing Yang
- Emergency Department, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Xiaodong Yu
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
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Proteo-Transcriptomic Characterization of Sirex nitobei (Hymenoptera: Siricidae) Venom. Toxins (Basel) 2021; 13:toxins13080562. [PMID: 34437434 PMCID: PMC8402507 DOI: 10.3390/toxins13080562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/26/2022] Open
Abstract
The wood-boring woodwasp Sirex nitobei is a native pest in Asia, infecting and weakening the host trees in numerous ecological and commercial coniferous forest plantations. In China, hosts of S. nitobei are diverse, so the pest has spread to several provinces of China, resulting in considerable economic and ecological damage. During female oviposition, S. nitobei venom along with arthrospores of the symbiotic fungus Amylostereum areolatum or A. chaetica is injected into host trees, and the combination of these two biological factors causes the death of xylem host trees. The presence of venom alone causes only the yellowing and wilting of needles. In this study, we constructed the venom gland transcriptome of S. nitobei for the first time and a total of 15,036 unigenes were acquired. From the unigenes, 11,560 ORFs were identified and 537 encoding protein sequences with signal peptides at the N-terminus. Then, we used the venomics approach to characterize the venom composition of female S. nitobei and predicted 1095 proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. We focused on seven proteins that were both highly expressed in the venom gland transcriptome and predicted in the crude venom proteome. These seven proteins are laccase-2, laccase-3, a protein belonging to the Kazal family, chitooligosaccharidolytic β-N-acetylglucosaminidase, beta-galactosidase, icarapin-like protein, and waprin-Thr1-like protein. Using quantitative real-time PCR (qRT-PCR), we also proved that the genes related to these seven proteins are specifically expressed in the venom glands. Finally, we revealed the functional role of S. nitobei venom in the physiological response of host trees. It can not only promote the colonization of symbiotic fungus but contribute to the development of eggs and larvae. This study provides a deeper understanding of the molecular mechanism of the woodwasp–pine interaction.
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18
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Zhao HY, Wen L, Miao YF, Du Y, Sun Y, Yin Y, Lin CX, Lin LH, Ji X, Gao JF. Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea. BMC Genomics 2021; 22:520. [PMID: 34238212 PMCID: PMC8268360 DOI: 10.1186/s12864-021-07824-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/21/2021] [Indexed: 12/23/2022] Open
Abstract
Background A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes. Results A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A2 (PLA2), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA2 (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLA2s. Conclusions Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07824-7.
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Affiliation(s)
- Hong-Yan Zhao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Lin Wen
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yu-Feng Miao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, 572022, Hainan, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan Sun
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yin Yin
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, 572022, Hainan, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xiang Ji
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, 572022, Hainan, China. .,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China. .,College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
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19
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Abstract
Although oral venom systems are ecologically important characters, how they originated is still unclear. In this study, we show that oral venom systems likely originated from a gene regulatory network conserved across amniotes. This network, which we term the “metavenom network,” comprises over 3,000 housekeeping genes coexpressed with venom and play a role in protein folding and modification. Comparative transcriptomics revealed that the network is conserved between venom glands of snakes and salivary glands of mammals. This suggests that while these tissues have evolved different functions, they share a common regulatory core, that persisted since their common ancestor. We propose several evolutionary mechanisms that can utilize this common regulatory core to give rise to venomous animals from their nonvenomous ancestors. Oral venom systems evolved multiple times in numerous vertebrates enabling the exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focused strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system is difficult, since they tend to evolve rapidly, show complex patterns of expression, and were incorporated into the venom arsenal relatively recently. Here we focus on gene regulatory networks associated with the production of toxins in snakes, rather than the toxins themselves. We found that overall venom gland gene expression was surprisingly well conserved when compared to salivary glands of other amniotes. We characterized the “metavenom network,” a network of ∼3,000 nonsecreted housekeeping genes that are strongly coexpressed with the toxins, and are primarily involved in protein folding and modification. Conserved across amniotes, this network was coopted for venom evolution by exaptation of existing members and the recruitment of new toxin genes. For instance, starting from this common molecular foundation, Heloderma lizards, shrews, and solenodon, evolved venoms in parallel by overexpression of kallikreins, which were common in ancestral saliva and induce vasodilation when injected, causing circulatory shock. Derived venoms, such as those of snakes, incorporated novel toxins, though still rely on hypotension for prey immobilization. These similarities suggest repeated cooption of shared molecular machinery for the evolution of oral venom in mammals and reptiles, blurring the line between truly venomous animals and their ancestors.
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20
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Andrade-Silva D, Zelanis A, Travaglia-Cardoso SR, Nishiyama MY, Serrano SMT. Venom Profiling of the Insular Species Bothrops alcatraz: Characterization of Proteome, Glycoproteome, and N-Terminome Using Terminal Amine Isotopic Labeling of Substrates. J Proteome Res 2021; 20:1341-1358. [PMID: 33404253 DOI: 10.1021/acs.jproteome.0c00737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bothrops alcatraz, a species endemic to Alcatrazes Islands, is regarded as critically endangered due to its small area of occurrence and the declining quality of its habitat. We recently reported the identification of N-glycans attached to toxins of Bothrops species, showing similar compositions in venoms of the B. jararaca complex (B. jararaca, B. insularis, and B. alcatraz). Here, we characterized B. alcatraz venom using electrophoretic, proteomic, and glycoproteomic approaches. Electrophoresis showed that B. alcatraz venom differs from B. jararaca and B. insularis; however, N-glycan removal revealed similarities between them, indicating that the occupation of N-glycosylation sites contributes to interspecies variability in the B. jararaca complex. Metalloproteinase was the major toxin class identified in the B. alcatraz venom proteome followed by serine proteinase and C-type lectin, and overall, the adult B. alcatraz venom resembles that of B. jararaca juvenile specimens. The comparative glycoproteomic analysis of B. alcatraz venom with B. jararaca and B. insularis indicated that there may be differences in the utilization of N-glycosylation motifs among their different toxin classes. Furthermore, we prospected for the first time the N-terminome of a snake venom using the terminal amine isotopic labeling of substrates (TAILS) approach and report the presence of ∼30% of N-termini corresponding to truncated toxin forms and ∼37% N-terminal sequences blocked by pyroglutamic acid in B. alcatraz venom. These findings underscore a low correlation between venom gland transcriptomes and proteomes and support the view that post-translational processes play a major role in shaping venom phenotypes.
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Affiliation(s)
- Débora Andrade-Silva
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, (ICT-UNIFESP), São José dos Campos 12231-280, SP, Brazil
| | | | - Milton Y Nishiyama
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
| | - Solange M T Serrano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
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21
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Smith CF, Mackessy SP. Asymmetrical expression of toxins between the left and right venom glands of an individual prairie rattlesnake (Crotalus viridis viridis). Toxicon 2020; 186:105-108. [PMID: 32777251 DOI: 10.1016/j.toxicon.2020.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
It is assumed that toxin expression is equivalent between left and right glands of a single snake. In the current study, we report venoms that differ in enzyme functionality and overall composition between the left and right gland of a single snake. The right gland produced venom of comparable composition to venom previously extracted from the same individual; however, the left gland produced venom with overall lower protein content and considerably less enzyme activity.
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Affiliation(s)
- Cara Francesca Smith
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639-0017, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639-0017, USA.
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22
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Hamanaka K, Mori A. Toxicity of venom from the mamushi, Gloydius blomhoffii, (Squamata, Crotalinae) to centipedes. Toxicon 2020; 188:11-15. [PMID: 33039367 DOI: 10.1016/j.toxicon.2020.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
Vipers include approximately 300 species and usually feed on vertebrates, but over 30 species of them occasionally eat centipedes. Centipedes have been also known to occur in stomach contents of a Japanese pit viper, mamushi, Gloydius blomhoffii. Toxicity of the venom of mamushi to small mammals has been well studied, but there is no information concerning its toxicity to arthropods. Here, we studied the toxicity of the raw venom to the red-headed centipede, Scolopendra subspinipes mutilans, by comparing with the toxicity to two other common prey animals, a house mouse, Mus musclus, and a pond frog, Pelophylax nigromaculatus. The lethal doses for mice weighing around 21.5 g and frogs weighing around 3.78 g were less than 5 μl (equivalent to ca. 0.23 and 1.32 μl/g, respectively), which presumably corresponds to an approximate dose of mamushi's one envenomation. On the other hand, centipedes weighing around 1.86 g needed 10-36 μl of venom to die (16.0 μl/g on average). This result suggests that the centipedes are much more resistant to the venom than other prey animals, and it is difficult for mamushi to kill or incapacitate centipedes by the venom of a single envenomation.
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Affiliation(s)
- Kyosuke Hamanaka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
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23
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Ochoa A, Broe M, Moriarty Lemmon E, Lemmon AR, Rokyta DR, Gibbs HL. Drift, selection and adaptive variation in small populations of a threatened rattlesnake. Mol Ecol 2020; 29:2612-2625. [PMID: 32557885 DOI: 10.1111/mec.15517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/09/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.
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Affiliation(s)
- Alexander Ochoa
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Michael Broe
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Lisle Gibbs
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
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24
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Modahl CM, Roointan A, Rogers J, Currier K, Mackessy SP. Interspecific and intraspecific venom enzymatic variation among cobras (Naja sp. and Ophiophagus hannah). Comp Biochem Physiol C Toxicol Pharmacol 2020; 232:108743. [PMID: 32194156 DOI: 10.1016/j.cbpc.2020.108743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023]
Abstract
The genera Ophiophagus and Naja comprise part of a clade of snakes referred to as cobras, dangerously venomous front-fanged snakes in the family Elapidae responsible for significant human mortality and morbidity throughout Asia and Africa. We evaluated venom enzyme variation for eleven cobra species and three N. kaouthia populations using SDS-PAGE venom fingerprinting and numerous enzyme assays. Acetylcholinesterase and PLA2 activities were the most variable between species, and PLA2 activity was significantly different between Malaysian and Thailand N. kaouthia populations. Venom metalloproteinase activity was low and significantly different among most species, but levels were identical for N. kaouthia populations; minor variation in venom L-amino acid oxidase and phosphodiesterase activities were seen between cobra species. Naja siamensis venom lacked the α-fibrinogenolytic activity common to other cobra venoms. In addition, venom from N. siamensis had no detectable metalloproteinase activity and exhibited an SDS-PAGE profile with reduced abundance of higher mass proteins. Venom profiles from spitting cobras (N. siamensis, N. pallida, and N. mossambica) exhibited similar reductions in higher mass proteins, suggesting the evolution of venoms of reduced complexity and decreased enzymatic activity among spitting cobras. Generally, the venom proteomes of cobras show highly abundant three-finger toxin diversity, followed by large quantities of PLA2s. However, PLA2 bands and activity were very reduced for N. haje, N. annulifera and N. nivea. Venom compositionalenzy analysis provides insight into the evolution, diversification and distribution of different venom phenotypes that complements venomic data, and this information is critical for the development of effective antivenoms and snakebite treatment.
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Affiliation(s)
- Cassandra M Modahl
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Amir Roointan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jessica Rogers
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA
| | - Katelyn Currier
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA.
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25
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Venom gland transcriptome from Heloderma horridum horridum by high-throughput sequencing. Toxicon 2020; 180:62-78. [PMID: 32283106 DOI: 10.1016/j.toxicon.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 02/01/2023]
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26
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Barua A, Mikheyev AS. Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates. Proc Biol Sci 2020; 287:20200613. [PMID: 32345154 PMCID: PMC7282918 DOI: 10.1098/rspb.2020.0613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Key innovations provide ecological opportunity by enabling access to new resources, colonization of new environments, and are associated with adaptive radiation. The most well-known pattern associated with adaptive radiation is an early burst of phenotypic diversification. Venoms facilitate prey capture and are widely believed to be key innovations leading to adaptive radiation. However, few studies have estimated their evolutionary rate dynamics. Here, we test for patterns of adaptive evolution in venom gene expression data from 52 venomous snake species. By identifying shifts in tempo and mode of evolution along with models of phenotypic evolution, we show that snake venom exhibits the macroevolutionary dynamics expected of key innovations. Namely, all toxin families undergo shifts in their rates of evolution, likely in response to changes in adaptive optima. Furthermore, we show that rapid-pulsed evolution modelled as a Lévy process better fits snake venom evolution than conventional early burst or Ornstein-Uhlenbeck models. While our results support the idea of snake venom being a key innovation, the innovation of venom chemistry lacks clear mechanisms that would lead to reproductive isolation and thus adaptive radiation. Therefore, the extent to which venom directly influences the diversification process is still a matter of contention.
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Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
- Evolutionary genomics group, Australian National University, Canberra ACT 0200, Australia
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27
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Biological Activities and Proteomic Profile of the Venom of Vipera ursinii ssp., a very Rare Karst Viper from Croatia. Toxins (Basel) 2020; 12:toxins12030187. [PMID: 32188060 PMCID: PMC7150868 DOI: 10.3390/toxins12030187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
The karst viper (Vipera ursinii ssp.) favours high-mountain dry grasslands in southern and south-eastern Croatia. It is medically less important than other Vipera species, because of its remote habitat and the very small amount of venom that it injects by its relatively short fangs. The scientific literature on Vipera ursinii deals mostly with the morphology, ecology and distribution range of this snake, due to the species’ conservation issues, while the toxinological aspects of its venom have not so far been investigated. Here we report on the composition and biological activity of the Vipera ursinii ssp. venom. Using a proteomics approach, we have identified 25 proteins in the venom that belong to seven protein families: snake venom metalloproteinase, serine protease, secreted phospholipase A2, cysteine-rich secretory protein, snake C-type lectin-like protein, serine protease inhibitor and nerve growth factor. The Vipera ursinii ssp. venom was found to be distinctively insecticidal. Its lethal toxicity towards crickets was more than five times greater than that of Vipera ammodytes ammodytes venom, while the opposite held in mice. Interestingly, the mode of dying after injecting a mouse with Vipera ursinii ssp. venom may suggest the presence of a neurotoxic component. Neurotoxic effects of European vipers have so far been ascribed exclusively to ammodytoxins and ammodytoxin-like basic secreted phospholipases A2. Structural and immunological analyses of the Vipera ursinii ssp. venom, however, confirmed that ammodytoxin-like proteins are not present in this venom.
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28
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Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. Trait differentiation and modular toxin expression in palm-pitvipers. BMC Genomics 2020; 21:147. [PMID: 32046632 PMCID: PMC7014597 DOI: 10.1186/s12864-020-6545-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis nigroviridis) and Talamancan Palm-Pitvipers (B. nubestris). Results We assembled 1517 coding sequences, including 43 toxins for B. nigroviridis and 1787 coding sequences including 42 toxins for B. nubestris. The venom gland transcriptomes were extremely divergent between these two species with one B. nigroviridis exhibiting a primarily neurotoxic pattern of expression, both B. nubestris expressing primarily hemorrhagic toxins, and a second B. nigroviridis exhibiting a mixed expression phenotype. Weighted gene coexpression analyses identified six submodules of transcript expression variation, one of which was highly associated with SVMPs and a second which contained both subunits of the neurotoxic PLA2 complex. The sub-module association of these toxins suggest common regulatory pathways underlie the variation in their expression and is consistent with known patterns of inheritance of similar haplotypes in other species. We also find evidence that module associated toxin families show fewer gene duplications and transcript losses between species, but module association did not appear to affect sequence diversification. Conclusion Sub-modular regulation of expression likely contributes to the diversification of venom phenotypes within and among species and underscores the role of modularity in facilitating rapid evolution of complex traits.
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Affiliation(s)
- Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 24105, USA
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA. .,Department of Forestry, and Environmental Conservation, Clemson University, Clemson, SC, USA.
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29
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Becchimanzi A, Avolio M, Bostan H, Colantuono C, Cozzolino F, Mancini D, Chiusano ML, Pucci P, Caccia S, Pennacchio F. Venomics of the ectoparasitoid wasp Bracon nigricans. BMC Genomics 2020; 21:34. [PMID: 31924169 PMCID: PMC6954513 DOI: 10.1186/s12864-019-6396-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Venom is one of the most important sources of regulation factors used by parasitic Hymenoptera to redirect host physiology in favour of the developing offspring. This has stimulated a number of studies, both at functional and "omics" level, which, however, are still quite limited for ectophagous parasitoids that permanently paralyze and suppress their victims (i.e., idiobiont parasitoids). RESULTS Here we present a combined transcriptomic and proteomic study of the venom of the generalist idiobiont wasp Bracon nigricans, an ectophagous larval parasitoid of different lepidopteran species, for which we recently described the host regulation strategy and the functional role of the venom in the induction of physiological changes in parasitized hosts. The experimental approach used led to the identification of the main components of B. nigricans venom involved in host regulation. Enzymes degrading lipids, proteins and carbohydrates are likely involved in the mobilization of storage nutrients from the fat body and may concurrently be responsible for the release of neurotoxic fatty acids inducing paralysis, and for the modulation of host immune responses. CONCLUSION The present work contributes to fill the gap of knowledge on venom composition in ectoparasitoid wasps, and, along with our previous physiological study on this species, provides the foundation on which to develop a functional model of host regulation, based both on physiological and molecular data. This paves the way towards a better understanding of parasitism evolution in the basal lineages of Hymenoptera and to the possible exploitation of venom as source of bioinsecticidal molecules.
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Affiliation(s)
- Andrea Becchimanzi
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Maddalena Avolio
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
- Present address: Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
- Present address: Infrastrutture di Ricerca per le Risorse Biologiche Marine, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences and CEINGE Biotecnologie Avanzate, University of Napoli Federico II, Napoli, Italy
| | - Donato Mancini
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Pietro Pucci
- Department of Chemical Sciences and CEINGE Biotecnologie Avanzate, University of Napoli Federico II, Napoli, Italy
| | - Silvia Caccia
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Francesco Pennacchio
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
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30
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Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schröder MS, Wu M, Kuriakose B, Mathew OK, Perumal RC, Koludarov I, Goldstein LD, Senger K, Dixon MD, Velayutham D, Vargas D, Chaudhuri S, Muraleedharan M, Goel R, Chen YJJ, Ratan A, Liu P, Faherty B, de la Rosa G, Shibata H, Baca M, Sagolla M, Ziai J, Wright GA, Vucic D, Mohan S, Antony A, Stinson J, Kirkpatrick DS, Hannoush RN, Durinck S, Modrusan Z, Stawiski EW, Wiley K, Raudsepp T, Kini RM, Zachariah A, Seshagiri S. The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nat Genet 2020; 52:106-117. [PMID: 31907489 PMCID: PMC8075977 DOI: 10.1038/s41588-019-0559-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/22/2019] [Indexed: 12/30/2022]
Abstract
Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the ‘venom-ome’ and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 ‘venom-ome-specific toxins’ (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery. Analysis of a near-chromosomal genome assembly and transcriptome profiling of the Indian cobra identifies genes expressed in the venom glands. These data should help develop a new antivenom.
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Affiliation(s)
- Kushal Suryamohan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | - Sajesh P Krishnankutty
- AgriGenome Labs Private Ltd, Kochi, India.,SciGenom Research Foundation, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Matthew Jevit
- Molecular Cytogenetics laboratory, Texas A&M University, College Station, TX, USA
| | - Markus S Schröder
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Meng Wu
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | | | | | - Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Leonard D Goldstein
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Kate Senger
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | | | - Derek Vargas
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | - Ridhi Goel
- AgriGenome Labs Private Ltd, Kochi, India
| | - Ying-Jiun J Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Peter Liu
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Brendan Faherty
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Guillermo de la Rosa
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuouka, Japan
| | - Miriam Baca
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Meredith Sagolla
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - James Ziai
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Gus A Wright
- College of Veterinary Medicine, Flow Cytometry Shared Resource Laboratory, Texas A&M University, College Station, TX, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Sangeetha Mohan
- Department of Molecular Biology, SciGenom Labs, Kochi, India
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Kochi, India
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | | | - Terje Raudsepp
- Molecular Cytogenetics laboratory, Texas A&M University, College Station, TX, USA
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Arun Zachariah
- SciGenom Research Foundation, Bangalore, India.,Wayanad Wildlife Sanctuary, Sultan Bathery, India
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA. .,SciGenom Research Foundation, Bangalore, India.
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31
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Paulchamy R, Sreeramulu B, Karuppiah H, Arumugam G, Sundaram J. A serine protease-associated lectin in the cytolytic system of blowfly (Chrysomya megacephala) larvae: Evidence and characterization. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21623. [PMID: 31579962 DOI: 10.1002/arch.21623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Cytolytic activity against invading microorganisms is one of the innate forms of immunity in invertebrates. A serine protease-associated sialic acid-specific cytolytic lectin was purified using glutaraldehyde-fixed ox erythrocytes from the larval extract of blowfly (Chrysomya megacephala). The purified lectin lysed vertebrate erythrocytes with effective haemolysis of ox red blood cells (RBCs) in an isotonic medium. The degree of haemolytic (HL) activity of the purified cytolytic lectin depended on its concentration, pH, temperature, and calcium ions. It was sensitive to ethylenediaminetetraacetic acid. The native molecular mass of the C-type lectin was 260 ± 26 kDa, comprising four different polypeptide subunits of 75 kDa (pI ~8), 69 kDa (pI ~7.0), 61 kDa (pI ~5.3), and 55 kDa (pI ~4.6). The association between the C-type lectin and serine protease was confirmed by MALDI-TOF-MS analysis that revealed its homology in the same spectral peak as well as the proteases and phenylmethylsulphonyl fluoride inhibition of HL activity. Haemolysis inhibition by N-acetylneuraminic acid and other sugars revealed the properties of the lectin. The purified lectin distorted the integrity of ox RBCs and Paenalcaligenes hermetiae. This in vitro study documents the presence of a cytolytic system in blowfly (C. megacephala) larvae for the clearance of invading microbial pathogens in their feeding niche.
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Affiliation(s)
- Ramaraj Paulchamy
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
| | | | - Hilda Karuppiah
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
| | - Ganesh Arumugam
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
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32
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Modahl CM, Brahma RK, Koh CY, Shioi N, Kini RM. Omics Technologies for Profiling Toxin Diversity and Evolution in Snake Venom: Impacts on the Discovery of Therapeutic and Diagnostic Agents. Annu Rev Anim Biosci 2019; 8:91-116. [PMID: 31702940 DOI: 10.1146/annurev-animal-021419-083626] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Snake venoms are primarily composed of proteins and peptides, and these toxins have developed high selectivity to their biological targets. This makes venoms interesting for exploration into protein evolution and structure-function relationships. A single venom protein superfamily can exhibit a variety of pharmacological effects; these variations in activity originate from differences in functional sites, domains, posttranslational modifications, and the formations of toxin complexes. In this review, we discuss examples of how the major venom protein superfamilies have diversified, as well as how newer technologies in the omics fields, such as genomics, transcriptomics, and proteomics, can be used to characterize both known and unknown toxins.Because toxins are bioactive molecules with a rich diversity of activities, they can be useful as therapeutic and diagnostic agents, and successful examples of toxin applications in these areas are also reviewed. With the current rapid pace of technology, snake venom research and its applications will only continue to expand.
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Affiliation(s)
- Cassandra M Modahl
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Rajeev Kungur Brahma
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Cho Yeow Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077;
| | - Narumi Shioi
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , , .,Department of Chemistry, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan;
| | - R Manjunatha Kini
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
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33
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Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis. Toxins (Basel) 2019; 11:toxins11100581. [PMID: 31600994 PMCID: PMC6832531 DOI: 10.3390/toxins11100581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 11/16/2022] Open
Abstract
Snake venoms are complex mixtures of toxic proteins encoded by various gene families that function synergistically to incapacitate prey. A huge repertoire of snake venom genes and proteins have been reported, and alternative splicing is suggested to be involved in the production of divergent gene transcripts. However, a genome-wide survey of the transcript repertoire and the extent of alternative splicing still remains to be determined. In this study, the comprehensive analysis of transcriptomes in the venom gland was achieved by using PacBio sequencing. Extensive alternative splicing was observed in three venom protein gene families, metalloproteinase (MP), serine protease (SP), and vascular endothelial growth factors (VEGF). Eleven MP and SP genes and a VEGF gene are expressed as a total of 81, 61, and 8 transcript variants, respectively. In the MP gene family, individual genes are transcribed into different classes of MPs by alternative splicing. We also observed trans-splicing among the clustered SP genes. No other venom genes as well as non-venom counterpart genes exhibited alternative splicing. Our results thus indicate a potential contribution of mRNA alternative and trans-splicing in the production of highly variable transcripts of venom genes in the habu snake.
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34
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Jones BK, Saviola AJ, Reilly SB, Stubbs AL, Arida E, Iskandar DT, McGuire JA, Yates JR, Mackessy SP. Venom Composition in a Phenotypically Variable Pit Viper ( Trimeresurus insularis) across the Lesser Sunda Archipelago. J Proteome Res 2019; 18:2206-2220. [PMID: 30958009 DOI: 10.1021/acs.jproteome.9b00077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genus Trimeresurus comprises a group of venomous pitvipers endemic to Southeast Asia and the Pacific Islands. Of these, Trimeresurus insularis, the White-lipped Island Pitviper, is a nocturnal, arboreal species that occurs on nearly every major island of the Lesser Sunda archipelago. In the current study, venom phenotypic characteristics of T. insularis sampled from eight Lesser Sunda Islands (Flores, Lembata, Lombok, Pantar, Sumba, Sumbawa, Timor, and Wetar) were evaluated via SDS-PAGE, enzymatic activity assays, fibrinogenolytic assays, gelatin zymography, and RP-HPLC, and the Sumbawa sample was characterized by venomic analysis. For additional comparative analyses, venoms were also examined from several species in the Trimeresurus complex, including T. borneensis, T. gramineus, T. puniceus, T. purpureomaculatus, T. stejnegeri, and Protobothrops flavoviridis. Despite the geographical isolation, T. insularis venoms from all eight islands demonstrated remarkable similarities in gel electrophoretic profiles and RP-HPLC patterns, and all populations had protein bands in the mass ranges of phosphodiesterases (PDE), l-amino acid oxidases (LAAO), P-III snake venom metalloproteinases (SVMP), serine proteases, cysteine-rich secretory proteins (CRISP), phospholipases A2 (PLA2), and C-type lectins. An exception was observed in the Lombok sample, which lacked protein bands in the mass range of serine protease and CRISP. Venomic analysis of the Sumbawa venom also identified these protein families, in addition to several proteins of lesser abundance (<1%), including glutaminyl cyclase, aminopeptidase, PLA2 inhibitor, phospholipase B, cobra venom factor, 5'-nucleotidase, vascular endothelial growth factor, and hyaluronidase. All T. insularis venoms exhibited similarities in thrombin-like and PDE activities, while significant differences were observed for LAAO, SVMP, and kallikrein-like activities, though these differences were only observed for a few islands. Slight but noticeable differences were also observed with fibrinogen and gelatin digestion activities. Trimeresurus insularis venoms exhibited overall similarity to the other Trimeresurus complex species examined, with the exception of P. flavoviridis venom, which showed the greatest overall differentiation. Western blot analysis revealed that all major T. insularis venom proteins were recognized by Green Pitviper ( T. albolabris) antivenom, and reactivity was also seen with most venom proteins of the other Trimeresurus species, but incomplete antivenom-venom recognition was observed against P. flavoviridis venom proteins. These results demonstrate significant conservation in the venom composition of T. insularis across the Lesser Sunda archipelago relative to the other Trimeresurus species examined.
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Affiliation(s)
- Brenda Kathryn Jones
- School of Biological Sciences , University of Northern Colorado , 501 20th Street, CB 92 , Greeley , Colorado 80639-0017 , United States
| | - Anthony J Saviola
- School of Biological Sciences , University of Northern Colorado , 501 20th Street, CB 92 , Greeley , Colorado 80639-0017 , United States.,Department of Molecular Medicine and Neurobiology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology , University of California , 3101 Valley Life Sciences Building , Berkeley , California 94720-3160 , United States
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology , University of California , 3101 Valley Life Sciences Building , Berkeley , California 94720-3160 , United States
| | - Evy Arida
- Museum Zoologicum Bogoriense , Indonesian Institute of Sciences (LIPI) , Jalan Raya Bogor-Jakarta Km. 46 , Cibinong 16911 , Indonesia
| | - Djoko T Iskandar
- School of Life Sciences and Technology , Institut Teknologi Bandung , 10, Jalan Ganesa , Bandung , Java 40132 , Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology , University of California , 3101 Valley Life Sciences Building , Berkeley , California 94720-3160 , United States
| | - John R Yates
- Department of Molecular Medicine and Neurobiology , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Stephen P Mackessy
- School of Biological Sciences , University of Northern Colorado , 501 20th Street, CB 92 , Greeley , Colorado 80639-0017 , United States
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35
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Koludarov I, Aird SD. Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure. PeerJ 2019; 7:e6154. [PMID: 30755823 PMCID: PMC6368836 DOI: 10.7717/peerj.6154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/25/2018] [Indexed: 01/28/2023] Open
Abstract
NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
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Affiliation(s)
- Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, Japan
| | - Steven D Aird
- Ecology and Evolution Unit and Division of Faculty Affairs, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, Japan
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36
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Villar-Briones A, Aird SD. Organic and Peptidyl Constituents of Snake Venoms: The Picture Is Vastly More Complex Than We Imagined. Toxins (Basel) 2018; 10:E392. [PMID: 30261630 PMCID: PMC6215107 DOI: 10.3390/toxins10100392] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Small metabolites and peptides in 17 snake venoms (Elapidae, Viperinae, and Crotalinae), were quantified using liquid chromatography-mass spectrometry. Each venom contains >900 metabolites and peptides. Many small organic compounds are present at levels that are probably significant in prey envenomation, given that their known pharmacologies are consistent with snake envenomation strategies. Metabolites included purine nucleosides and their bases, neurotransmitters, neuromodulators, guanidino compounds, carboxylic acids, amines, mono- and disaccharides, and amino acids. Peptides of 2⁻15 amino acids are also present in significant quantities, particularly in crotaline and viperine venoms. Some constituents are specific to individual taxa, while others are broadly distributed. Some of the latter appear to support high anabolic activity in the gland, rather than having toxic functions. Overall, the most abundant organic metabolite was citric acid, owing to its predominance in viperine and crotaline venoms, where it chelates divalent cations to prevent venom degradation by venom metalloproteases and damage to glandular tissue by phospholipases. However, in terms of their concentrations in individual venoms, adenosine, adenine, were most abundant, owing to their high titers in Dendroaspis polylepis venom, although hypoxanthine, guanosine, inosine, and guanine all numbered among the 50 most abundant organic constituents. A purine not previously reported in venoms, ethyl adenosine carboxylate, was discovered in D. polylepis venom, where it probably contributes to the profound hypotension caused by this venom. Acetylcholine was present in significant quantities only in this highly excitotoxic venom, while 4-guanidinobutyric acid and 5-guanidino-2-oxopentanoic acid were present in all venoms.
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Affiliation(s)
- Alejandro Villar-Briones
- Division of Research Support, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan.
| | - Steven D Aird
- Division of Faculty Affairs and Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan.
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37
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Modahl CM, Mrinalini, Frietze S, Mackessy SP. Adaptive evolution of distinct prey-specific toxin genes in rear-fanged snake venom. Proc Biol Sci 2018; 285:rspb.2018.1003. [PMID: 30068680 DOI: 10.1098/rspb.2018.1003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022] Open
Abstract
Venom proteins evolve rapidly, and as a trophic adaptation are excellent models for predator-prey evolutionary studies. The key to a deeper understanding of venom evolution is an integrated approach, combining prey assays with analysis of venom gene expression and venom phenotype. Here, we use such an approach to study venom evolution in the Amazon puffing snake, Spilotes sulphureus, a generalist feeder. We identify two novel three-finger toxins: sulditoxin and sulmotoxin 1. These new toxins are not only two of the most abundant venom proteins, but are also functionally intriguing, displaying distinct prey-specific toxicities. Sulditoxin is highly toxic towards lizard prey, but is non-toxic towards mammalian prey, even at greater than 22-fold higher dosage. By contrast, sulmotoxin 1 exhibits the reverse trend. Furthermore, evolutionary analysis and structural modelling show highest sequence variability in the central loop of these proteins, probably driving taxon-specific toxicity. This is, to our knowledge, the first case in which a bimodal and contrasting pattern of toxicity has been shown for proteins in the venom of a single snake in relation to diet. Our study is an example of how toxin gene neofunctionalization can result in a venom system dominated by one protein superfamily and still exhibit flexibility in prey capture efficacy.
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Affiliation(s)
- Cassandra M Modahl
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO 80639-0017, USA
| | - Mrinalini
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Seth Frietze
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO 80639-0017, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO 80639-0017, USA
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38
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Damm M, Hempel BF, Nalbantsoy A, Süssmuth RD. Comprehensive Snake Venomics of the Okinawa Habu Pit Viper, Protobothrops flavoviridis, by Complementary Mass Spectrometry-Guided Approaches. Molecules 2018; 23:molecules23081893. [PMID: 30060607 PMCID: PMC6222445 DOI: 10.3390/molecules23081893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 11/16/2022] Open
Abstract
The Asian world is home to a multitude of venomous and dangerous snakes, which are used to induce various medical effects in the preparation of traditional snake tinctures and alcoholics, like the Japanese snake wine, named Habushu. The aim of this work was to perform the first quantitative proteomic analysis of the Protobothrops flavoviridis pit viper venom. Accordingly, the venom was analyzed by complimentary bottom-up and top-down mass spectrometry techniques. The mass spectrometry-based snake venomics approach revealed that more than half of the venom is composed of different phospholipases A2 (PLA₂). The combination of this approach and an intact mass profiling led to the identification of the three main Habu PLA₂s. Furthermore, nearly one-third of the total venom consists of snake venom metalloproteinases and disintegrins, and several minor represented toxin families were detected: C-type lectin-like proteins (CTL), cysteine-rich secretory proteins (CRISP), snake venom serine proteases (svSP), l-amino acid oxidases (LAAO), phosphodiesterase (PDE) and 5'-nucleotidase. Finally, the venom of P. flavoviridis contains certain bradykinin-potentiating peptides and related peptides, like the svMP inhibitors, pEKW, pEQW, pEEW and pENW. In preliminary MTT cytotoxicity assays, the highest cancerous-cytotoxicity of crude venom was measured against human neuroblastoma SH-SY5Y cells and shows disintegrin-like effects in some fractions.
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Affiliation(s)
- Maik Damm
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany.
| | | | - Ayse Nalbantsoy
- Department of Bioengineering, Ege University, 35100 Izmir, Turkey.
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39
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The habu genome reveals accelerated evolution of venom protein genes. Sci Rep 2018; 8:11300. [PMID: 30050104 PMCID: PMC6062510 DOI: 10.1038/s41598-018-28749-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/29/2018] [Indexed: 01/11/2023] Open
Abstract
Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition.
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40
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Schezaro-Ramos R, Da Silva SL, Pereira BB, Santa Fé Miguel AT, Mendes B, Mogollón NGS, Hyslop S, Carregari VC, Almeida JR. In vitro effects of Crotalus atrox snake venom on chick and mouse neuromuscular preparations. Comp Biochem Physiol C Toxicol Pharmacol 2018; 209:37-45. [PMID: 29604435 DOI: 10.1016/j.cbpc.2018.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/06/2018] [Accepted: 03/24/2018] [Indexed: 12/25/2022]
Abstract
The neuromuscular effect of venoms is not a major clinical manifestation shared between rattlesnakes native to the Americas, which showed two different venom phenotypes. Taking into account this dichotomy, nerve muscle preparations from mice and chicks were used to investigate the ability of Crotalus atrox venom to induce in vitro neurotoxicity and myotoxicity. Unlike crotalic venoms of South America, low concentrations of C. atrox venom did not result in significant effects on mouse neuromuscular preparations. The venom was more active on avian nerve-muscle, showing reduction of twitch heights after 120 min of incubation with 10, 30 and 100 μg/mL of venom with diminished responses to agonists and KCl. Histological analysis highlighted that C. atrox was myotoxic in both species of experimental animals; as evidenced by degenerative events, including edematous cells, delta lesions, hypercontracted fibers and muscle necrosis, which can lead to neurotoxic action. These results provide key insights into the myotoxicity and low neurotoxicity of C. atrox in two animal models, corroborating with previous genomic and proteomic findings and would be useful for a deeper understanding of venom evolution in snakes belonging to the genus Crotalus.
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Affiliation(s)
- Raphael Schezaro-Ramos
- Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Saulo L Da Silva
- Ikiam - Universidad Regional Amazónica, Km 7 Via Muyuna, Tena, Napo, Ecuador
| | - Beatriz B Pereira
- Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ananda T Santa Fé Miguel
- Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bruno Mendes
- Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Stephen Hyslop
- Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Victor C Carregari
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
| | - José R Almeida
- Ikiam - Universidad Regional Amazónica, Km 7 Via Muyuna, Tena, Napo, Ecuador.
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41
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Aird SD, Arora J, Barua A, Qiu L, Terada K, Mikheyev AS. Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry. Genome Biol Evol 2018; 9:2640-2649. [PMID: 29048530 PMCID: PMC5737360 DOI: 10.1093/gbe/evx199] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022] Open
Abstract
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested. Using a combination of de novo genome sequencing, population genomics, transcriptomics, and proteomics, we compare the two modes of evolution in the pitviper, Protobothrops mucrosquamatus. By partitioning selective constraints and adaptive evolution in a McDonald–Kreitman-type framework, we find support for both hypotheses: venom proteins indeed experience both stronger positive selection, and lower selective constraint than other genes in the genome. Furthermore, the strength of selection may be modulated by expression level, with more abundant proteins experiencing weaker selective constraint, leading to the accumulation of more deleterious mutations. These findings show that snake venoms evolve by a combination of adaptive and neutral mechanisms, both of which explain their extraordinarily high rates of molecular evolution. In addition to positive selection, which optimizes efficacy of the venom in the short term, relaxed selective constraints for deleterious mutations can lead to more rapid turnover of individual proteins, and potentially to exploration of a larger venom phenotypic space.
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Affiliation(s)
- Steven D Aird
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Jigyasa Arora
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Lijun Qiu
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Kouki Terada
- Okinawa Prefectural Institute of Health and the Environment, Biology and Ecology Group, Nanjo-shi, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
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Andrade-Silva D, Ashline D, Tran T, Lopes AS, Travaglia Cardoso SR, Reis MDS, Zelanis A, Serrano SMT, Reinhold V. Structures of N-Glycans of Bothrops Venoms Revealed as Molecular Signatures that Contribute to Venom Phenotype in Viperid Snakes. Mol Cell Proteomics 2018; 17:1261-1284. [PMID: 29716988 DOI: 10.1074/mcp.ra118.000748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/26/2018] [Indexed: 11/06/2022] Open
Abstract
The complexity of snake venoms has long been investigated to explore a myriad of biologically active proteins and peptides that are used for immobilizing or killing prey, and are responsible for the pathological effects observed on envenomation. Glycosylation is the main post-translational modification (PTM) of viperid venoms but currently there is little understanding of how protein glycosylation impacts the variation of venom proteomes. We have previously reported that Bothrops venom glycoproteomes contain a core of components that markedly define their composition and parallel their phylogenetic classification. Here we extend those observations to eight Bothrops species evaluating the N-glycomes by LC-MS as assigned cartoon structures and detailing those structures separately as methylated analogs using ion-trap mass spectrometry (MSn). Following ion disassembly through multiple steps provided sequence and linkage isomeric details that characterized 52 unique compositions in Bothrops venoms. These occurred as 60 structures, of which 26 were identified in the venoms of the Jararaca Complex (B. alcatraz, B. insularis, and B. jararaca), 20 in B. erythromelas, B. jararacussu, B. moojeni and B. neuwiedi venoms, and 22 in B. cotiara venom. Further, quantitative analysis of these N-glycans showed variable relative abundances in the venoms. For the first time a comprehensive set of N-glycan structures present in snake venoms are defined. Despite the fact that glycosylation is not template-defined, the N-glycomes of these venoms mirror the phylogeny cladograms of South American bothropoid snakes reported in studies on morphological, molecular data and feeding habits, exhibiting distinct molecular signatures for each venom. Considering the complexity of N-glycan moieties generally found in glycoproteins, characterized by different degrees of branching, isomer structures, and variable abundances, our findings point to these factors as another level of complexity in Bothrops venoms, features that could dramatically contribute to their distinct biological activities.
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Affiliation(s)
| | - David Ashline
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Thuy Tran
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Aline Soriano Lopes
- ‖Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, 09913-030 Brazil
| | | | - Marcelo da Silva Reis
- ¶Laboratório Especial de Ciclo Celular, Center of Toxins, Immune-Response, and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | - André Zelanis
- ‡‡Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (ICT-UNIFESP), São José dos Campos, 12231-280, Brazil
| | | | - Vernon Reinhold
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824;
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43
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Xiong S, Huang C. Synergistic strategies of predominant toxins in snake venoms. Toxicol Lett 2018; 287:142-154. [PMID: 29428543 DOI: 10.1016/j.toxlet.2018.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/17/2018] [Accepted: 02/03/2018] [Indexed: 12/22/2022]
Abstract
Synergism is a significant phenomenon present in snake venoms that may be an evolving strategy to potentiate toxicities. Synergism exists between different toxins or toxin complexes in various snake venoms, with phospholipaseA2s (PLA2s) (toxins or subunits) the main enablers. The predominant toxins, snake venom PLA2s, metalloproteases (SVMPs), serine proteases (SVSPs) and three-finger toxins (3FTxs), play essential roles in synergistic processes. The hypothetical mechanisms of synergistic effect can be generalized under the effects of amplification and chaperoning. The Toxicity Score is among the few quantitative methods to assess synergism. Selection of toxins involved in synergistically enhanced toxicity as the targets are important for development of novel antivenoms or inhibitors.
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Affiliation(s)
- Shengwei Xiong
- College of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, China
| | - Chunhong Huang
- College of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, China.
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44
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Pla D, Petras D, Saviola AJ, Modahl CM, Sanz L, Pérez A, Juárez E, Frietze S, Dorrestein PC, Mackessy SP, Calvete JJ. Transcriptomics-guided bottom-up and top-down venomics of neonate and adult specimens of the arboreal rear-fanged Brown Treesnake, Boiga irregularis, from Guam. J Proteomics 2017; 174:71-84. [PMID: 29292096 DOI: 10.1016/j.jprot.2017.12.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
The Brown Treesnake (Boiga irregularis) is an arboreal, nocturnal, rear-fanged venomous snake native to northern and eastern regions of Australia, Papua New Guinea and the Solomon Islands. It was inadvertently introduced onto the island of Guam during the late 1940's to early 1950's, and it has caused massive declines and extirpations of the native bird, lizard, and mammal populations. In the current study, we report the characterization of the venom proteome of an adult and a neonate B. irregularis specimens from Guam by a combination of venom gland transcriptomic and venomic analyses. Venom gland transcriptomic analysis of an adult individual identified toxins belonging to 18 protein families, with three-finger toxin isoforms being the most abundantly expressed transcripts, comprising 94% of all venom protein transcript reads. Transcripts for PIII-metalloproteinases, C-type lectins, cysteine-rich secretory proteins, acetylcholinesterases, natriuretic peptides, ficolins, phospholipase A2 (PLA2) inhibitors, PLA2s, vascular endothelial growth factors, Kunitz-type protease inhibitors, cystatins, phospholipase Bs, cobra venom factors, waprins, SVMP inhibitors, matrix metalloproteinases, and hyaluronidases were also identified, albeit, at very low abundances ranging from 0.05% to 1.7% of the transcriptome. The venom proteomes of neonate and adult B. irregularis were also both overwhelmingly (78 and 84%, respectively) dominated by monomeric and dimeric 3FTxs, followed by moderately abundant (21% (N) and 13% (A)) CRISPs, low abundance (1% (N), 3% (A)) PIII-SVMPs, and very low abundance (<0.01%) PLA2 and SVMP inhibitors. The differences in relative toxin abundances identified between neonate and adult snakes likely correlates to shifts in prey preference between the two age classes, from nearly-exclusively lizards to lizards, birds and small mammals. Immunoaffinity antivenomics with experimentally designed rabbit anti-Brown Treesnake (anti-BTS) venom IgGs against homologous venom from adult snakes demonstrated that CRISPs, PIII-SVMPs, and 60-70% of 3FTxs were effectively immunocaptured. Western blot analysis showed that all venom proteins were recognized by anti-BTS IgGs, and cross-reactivity with other rear-fanged snake venoms was also observed. Incubation of anti-BTS venom IgGs with crude B. irregularis venom resulted in a significant decrease in proteolytic (SVMP) activity against azocasein. These results provide the first comparative venomic and anti-venomic analysis of neonate and adult B. irregularis from Guam, further highlighting evolutionary trends in venom composition among rear-fanged venomous snakes. SIGNIFICANCE PARAGRAPH The Brown Treesnake (Boiga irregularis) has caused extensive ecological and economic damage to the island of Guam where it has become a classic example of the negative impacts of invasive species. In the current study, we report the first combined transcriptomic and proteomic analysis of B. irregularis venom of Guam origin. The transcriptome of an adult snake contained toxin sequences belonging to 18 protein families, with three-finger toxin (3FTx) isoforms being the most abundant and representing 94% of all venom protein transcript reads. Our bottom-up and top-down venomic analyses confirmed that 3FTxs are the major components of B. irregularis venom, and a comparative analysis of neonate and adult venoms demonstrate a clear ontogenetic shift in toxin abundance, likely driven by dietary variation between the two age classes. Second-generation antivenomics and Western blot analysis using purified anti-Brown Treesnake rabbit serum IgGs (anti-BTS IgGs) showed strong immunoreactivity toward B. irregularis venom. Interestingly, our anti-BTS IgGs did not cross-react with 3FTxs found in several other rear-fanged snake venoms, or against 3FTxs in the venom of the elapid Ophiophagus hannah, indicating that epitopes in these 3FTx molecules are quite distinct.
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Affiliation(s)
- Davinia Pla
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Daniel Petras
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Anthony J Saviola
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain; School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Cassandra M Modahl
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Libia Sanz
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Alicia Pérez
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Elena Juárez
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Seth Frietze
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA
| | - Pieter C Dorrestein
- University of California San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, CB 92, Greeley, CO 80639, USA.
| | - Juan J Calvete
- Laboratorio de Venómica Estructural y Funcional, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
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Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W. Computational Studies of Snake Venom Toxins. Toxins (Basel) 2017; 10:E8. [PMID: 29271884 PMCID: PMC5793095 DOI: 10.3390/toxins10010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.
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Affiliation(s)
- Paola G Ojeda
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - David Ramírez
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
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46
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New findings from the first transcriptome of the Bothrops moojeni snake venom gland. Toxicon 2017; 140:105-117. [DOI: 10.1016/j.toxicon.2017.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022]
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Tracing the evolution of venom phospholipases A 2 in Gloydius strauchii and related pitvipers: A tale of two acidic isozymes. Toxicon 2017; 141:65-72. [PMID: 29191388 DOI: 10.1016/j.toxicon.2017.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/29/2023]
Abstract
Two acidic Asp49-PLA2s with Glu6 substitution and a neutral Lys49-PLA (designated Gst-K49) were cloned from G. strauchii venom glands, their full amino acid sequences were deduced. The predominant acidic PLA2 (designated Gst-E6a) contains 124 residues and the M18W30 substitutions, while the minor acidic PLA2 (designated Gst-E6b) contains 122 residues and the V18A30 substitutions. Their sequences are most similar to those of the respective orthologous PLA2s of G. intermedius venom. Gst-E6a and Gst-E6b appear to be paralogs and possibly have different predatory targets or functions. The LC-MS/MS results indicate the presence of only three PLA2 gene products in the crude venom, the relative expression levels were in the order of Gst-E6a ≫ Gst-E6b > Gst-K49, as confirmed by qPCR results. In contrast to other Gloydius, G. strauchii venom does not contain neurotoxic or basic anticoagulant Asp49-PLA2s, but Gst-K49 is the first Lys49-PLA2 identified in Gloydius venoms. However, its venom content is relatively low and its pI value 7.3 is much lower than those of other Lys49-PLA2s and. The Lys49-PLA2 genes appear to regress in the venom of most of Gloydius and related rattlesnake, and this evolutionary regression occurred before the dispersal of Asian pitvipers to the New World.
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48
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A Review and Database of Snake Venom Proteomes. Toxins (Basel) 2017; 9:toxins9090290. [PMID: 28927001 PMCID: PMC5618223 DOI: 10.3390/toxins9090290] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Advances in the last decade combining transcriptomics with established proteomics methods have made possible rapid identification and quantification of protein families in snake venoms. Although over 100 studies have been published, the value of this information is increased when it is collated, allowing rapid assimilation and evaluation of evolutionary trends, geographical variation, and possible medical implications. This review brings together all compositional studies of snake venom proteomes published in the last decade. Compositional studies were identified for 132 snake species: 42 from 360 (12%) Elapidae (elapids), 20 from 101 (20%) Viperinae (true vipers), 65 from 239 (27%) Crotalinae (pit vipers), and five species of non-front-fanged snakes. Approximately 90% of their total venom composition consisted of eight protein families for elapids, 11 protein families for viperines and ten protein families for crotalines. There were four dominant protein families: phospholipase A2s (the most common across all front-fanged snakes), metalloproteases, serine proteases and three-finger toxins. There were six secondary protein families: cysteine-rich secretory proteins, l-amino acid oxidases, kunitz peptides, C-type lectins/snaclecs, disintegrins and natriuretic peptides. Elapid venoms contained mostly three-finger toxins and phospholipase A2s and viper venoms metalloproteases, phospholipase A2s and serine proteases. Although 63 protein families were identified, more than half were present in <5% of snake species studied and always in low abundance. The importance of these minor component proteins remains unknown.
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49
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Yang ZM, Yu H, Liu ZZ, Pei JZ, Yang YE, Yan SX, Zhang C, Zhao WL, Wang ZZ, Wang YM, Tsai IH. Serine protease isoforms in Gloydius intermedius venom: Full sequences, molecular phylogeny and evolutionary implications. J Proteomics 2017; 164:19-32. [DOI: 10.1016/j.jprot.2017.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/18/2017] [Accepted: 05/25/2017] [Indexed: 02/07/2023]
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50
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Aird SD, da Silva NJ, Qiu L, Villar-Briones A, Saddi VA, Pires de Campos Telles M, Grau ML, Mikheyev AS. Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa. Toxins (Basel) 2017; 9:E187. [PMID: 28594382 PMCID: PMC5488037 DOI: 10.3390/toxins9060187] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022] Open
Abstract
Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2-6 toxin classes that account for 91-99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A₂ (PLA₂s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA₂s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1-2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6-9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A₂s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15-35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated.
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Affiliation(s)
- Steven D Aird
- Division of Faculty Affairs, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Nelson Jorge da Silva
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
| | - Lijun Qiu
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alejandro Villar-Briones
- Research Support Division, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Vera Aparecida Saddi
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
- Laboratório de Oncogenética e Radiobiologia da Associação de Combate ao Câncer em Goiás, Universidade Federal de Goiás, Rua 239 no. 52-Setor Universitário, Goiânia, Goiás 74065-070, Brazil.
| | - Mariana Pires de Campos Telles
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás 74605-140, Brazil.
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil.
| | - Miguel L Grau
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan.
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