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Ellsworth SA, Rautsaw RM, Ward MJ, Holding ML, Rokyta DR. Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes. J Mol Evol 2024:10.1007/s00239-024-10191-y. [PMID: 39026042 DOI: 10.1007/s00239-024-10191-y] [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: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
Gene duplication followed by nucleotide differentiation is one of the simplest mechanisms to develop new functions for genes. However, the evolutionary processes underlying the divergence of multigene families remain controversial. We used multigene families found within the diversity of toxic proteins in centipede venom to test two hypotheses related to venom evolution: the two-speed mode of venom evolution and the rapid accumulation of variation in exposed residues (RAVER) model. The two-speed mode of venom evolution proposes that different types of selection impact ancient and younger venomous lineages with negative selection being the predominant form in ancient lineages and positive selection being the dominant form in younger lineages. The RAVER hypothesis proposes that, instead of different types of selection acting on different ages of venomous lineages, the different types of selection will selectively contribute to amino acid variation based on whether the residue is exposed to the solvent where it can potentially interact directly with toxin targets. This hypothesis parallels the longstanding understanding of protein evolution that suggests that residues found within the structural or active regions of the protein will be under negative or purifying selection, and residues that do not form part of these areas will be more prone to positive selection. To test these two hypotheses, we compared the venom of 26 centipedes from the order Scolopendromorpha from six currently recognized species from across North America using both transcriptomics and proteomics. We first estimated their phylogenetic relationships and uncovered paraphyly among the genus Scolopendra and evidence for cryptic diversity among currently recognized species. Using our phylogeny, we then characterized the diverse venom components from across the identified clades using a combination of transcriptomics and proteomics. We conducted selection-based analyses in the context of predicted three-dimensional properties of the venom proteins and found support for both hypotheses. Consistent with the two-speed hypothesis, we found a prevalence of negative selection across all proteins. Consistent with the RAVER hypothesis, we found evidence of positive selection on solvent-exposed residues, with structural and less-exposed residues showing stronger signal for negative selection. Through the use of phylogenetics, transcriptomics, proteomics, and selection-based analyses, we were able to describe the evolution of venom from an ancient venomous lineage and support principles of protein evolution that directly relate to multigene family evolution.
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Affiliation(s)
- Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Rhett M Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Matthew L Holding
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
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2
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Phan P, Deshwal A, McMahon TA, Slikas M, Andrews E, Becker B, Kumar TKS. A Review of Rattlesnake Venoms. Toxins (Basel) 2023; 16:2. [PMID: 38276526 PMCID: PMC10818703 DOI: 10.3390/toxins16010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Venom components are invaluable in biomedical research owing to their specificity and potency. Many of these components exist in two genera of rattlesnakes, Crotalus and Sistrurus, with high toxicity and proteolytic activity variation. This review focuses on venom components within rattlesnakes, and offers a comparison and itemized list of factors dictating venom composition, as well as presenting their known characteristics, activities, and significant applications in biosciences. There are 64 families and subfamilies of proteins present in Crotalus and Sistrurus venom. Snake venom serine proteases (SVSP), snake venom metalloproteases (SVMP), and phospholipases A2 (PLA2) are the standard components in Crotalus and Sistrurus venom. Through this review, we highlight gaps in the knowledge of rattlesnake venom; there needs to be more information on the venom composition of three Crotalus species and one Sistrurus subspecies. We discuss the activity and importance of both major and minor components in biomedical research and drug development.
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Affiliation(s)
- Phuc Phan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Anant Deshwal
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Tyler Anthony McMahon
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Matthew Slikas
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Elodie Andrews
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Brian Becker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
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Sonoda GG, Tobaruela EDC, Norenburg J, Fabi JP, Andrade SCS. Venomous Noodles: The Evolution of Toxins in Nemertea through Positive Selection and Gene Duplication. Toxins (Basel) 2023; 15:650. [PMID: 37999513 PMCID: PMC10674772 DOI: 10.3390/toxins15110650] [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: 08/30/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023] Open
Abstract
Some, probably most and perhaps all, members of the phylum Nemertea are poisonous, documented so far from marine and benthic specimens. Although the toxicity of these animals has been long known, systematic studies on the characterization of toxins, mechanisms of toxicity, and toxin evolution for this group are scarce. Here, we present the first investigation of the molecular evolution of toxins in Nemertea. Using a proteo-transcriptomic approach, we described toxins in the body and poisonous mucus of the pilidiophoran Lineus sanguineus and the hoplonemertean Nemertopsis pamelaroeae. Using these new and publicly available transcriptomes, we investigated the molecular evolution of six selected toxin gene families. In addition, we also characterized in silico the toxin genes found in the interstitial hoplonemertean, Ototyphlonemertes erneba, a meiofaunal taxa. We successfully identified over 200 toxin transcripts in each of these species. Evidence of positive selection and gene duplication was observed in all investigated toxin genes. We hypothesized that the increased rates of gene duplications observed for Pilidiophora could be involved with the expansion of toxin genes. Studies concerning the natural history of Nemertea are still needed to understand the evolution of their toxins. Nevertheless, our results show evolutionary mechanisms similar to other venomous groups.
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Affiliation(s)
- Gabriel Gonzalez Sonoda
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
- Instituto Butantan, São Paulo 05503-900, Brazil
| | - Eric de Castro Tobaruela
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | | | - João Paulo Fabi
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
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4
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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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5
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Heptinstall TC, Strickland JL, Rosales-Garcia RA, Rautsaw RM, Simpson CL, Nystrom GS, Ellsworth SA, Hogan MP, Borja M, Fernandes Campos P, Grazziotin FG, Rokyta DR, Junqueira-de-Azevedo ILM, Parkinson CL. Venom phenotype conservation suggests integrated specialization in a lizard-eating snake. Toxicon 2023; 229:107135. [PMID: 37146732 PMCID: PMC11000244 DOI: 10.1016/j.toxicon.2023.107135] [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: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
Biological specialization reduces the size of niche space while increasing efficiency in the use of available resources. Specialization often leads to phenotypic changes via natural selection aligning with niche space constraints. Commonly observed changes are in size, shape, behavior, and traits associated with feeding. One often selected trait for dietary specialization is venom, which, in snakes, often shows variation dependent on diet across and within species. The Neotropical Blunt-headed Treesnake (Imantodes cenchoa) is a highly specialized, rear-fanged, arboreal, lizard hunter that displays a long thin body, enlarged eyes, and a large Duvernoy's gland. However, toxin characterization of I. cenchoa has never been completed. Here, we use RNA-seq and mass spectrometry to assemble, annotate, and analyze the venom gland transcriptomes of four I. cenchoa from across their range. We find a lack of significant venom variation at the sequence and expression levels, suggesting venom conservation across the species. We propose this conservation provides evidence of a specialized venom repertoire, adapted to maximize efficiency of capturing and processing lizards. Importantly, this study provides the most complete venom gland transcriptomes of I. cenchoa and evidence of venom specialization in a rear-fanged snake, giving insight into selective pressures of venom across all snake species.
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Affiliation(s)
| | - 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; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA; Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Cassandra L Simpson
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Schyler A Ellsworth
- 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
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35070, Gómez Palacio, Dgo., Mexico
| | | | - Felipe G Grazziotin
- Laboratório Especial de Colecões Zoológicas, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - 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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6
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Sofyantoro F, Yudha DS, Lischer K, Nuringtyas TR, Putri WA, Kusuma WA, Purwestri YA, Swasono RT. Bibliometric Analysis of Literature in Snake Venom-Related Research Worldwide (1933-2022). Animals (Basel) 2022; 12:2058. [PMID: 36009648 PMCID: PMC9405337 DOI: 10.3390/ani12162058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Snake envenomation is a severe economic and health concern affecting countries worldwide. Snake venom carries a wide variety of small peptides and proteins with various immunological and pharmacological properties. A few key research areas related to snake venom, including its applications in treating cancer and eradicating antibiotic-resistant bacteria, have been gaining significant attention in recent years. The goal of the current study was to analyze the global profile of literature in snake venom research. This study presents a bibliometric review of snake venom-related research documents indexed in the Scopus database between 1933 and 2022. The overall number of documents published on a global scale was 2999, with an average annual production of 34 documents. Brazil produced the highest number of documents (n = 729), followed by the United States (n = 548), Australia (n = 240), and Costa Rica (n = 235). Since 1963, the number of publications has been steadily increasing globally. At a worldwide level, antivenom, proteomics, and transcriptomics are growing hot issues for research in this field. The current research provides a unique overview of snake venom research at global level from 1933 through 2022, and it may be beneficial in guiding future research.
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Affiliation(s)
- Fajar Sofyantoro
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Donan Satria Yudha
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Kenny Lischer
- Faculty of Engineering, University of Indonesia, Jakarta 16424, Indonesia
| | - Tri Rini Nuringtyas
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | | | - Wisnu Ananta Kusuma
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Yekti Asih Purwestri
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Respati Tri Swasono
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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7
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Chandrasekara U, Harris RJ, Fry BG. The Target Selects the Toxin: Specific Amino Acids in Snake-Prey Nicotinic Acetylcholine Receptors That Are Selectively Bound by King Cobra Venoms. Toxins (Basel) 2022; 14:toxins14080528. [PMID: 36006190 PMCID: PMC9416539 DOI: 10.3390/toxins14080528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Snake venom is an adaptive ecological trait that has evolved primarily as a form of prey subjugation. Thus, the selection pressure for toxin diversification is exerted by the prey’s physiological targets, with this pressure being particularly acute for specialist feeders, such as the King Cobra species, all of which are snake-prey specialists. However, while extensive research has been undertaken to elucidate key amino acids that guide toxin structure–activity relationships, reciprocal investigations into the specific sites guiding prey-lineage selective effects have been lacking. This has largely been due to the lack of assay systems amenable to systematic amino acid replacements of targeted proteins in the prey’s physiological pathways. To fill this knowledge gap, we used a recently described approach based upon mimotope peptides corresponding to the orthosteric site of nicotinic acetylcholine receptor alpha-1 subunits, a major binding site for snake venom neurotoxins that cause flaccid paralysis. We investigated the venoms of four different types of King Cobra (Cambodian, Javan, Malaysian, and Thai). This approach allowed for the determination of the key amino acid positions in King Cobra snake prey that are selectively bound by the toxins, whereby replacing these amino acids in the snake-prey orthosteric site with those from lizards or rats resulted in a significantly lower level of binding by the venoms, while conversely replacing the lizard or rat amino acids with those from the snake at that position increased the binding. By doing such, we identified three negatively charged amino acids in the snake orthosteric site that are strongly bound by the positively charged neurotoxic three-finger toxins found in King Cobra venom. This study, thus, sheds light on the selection pressures exerted by a specialist prey item for the evolution of lineage-selective toxins.
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8
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Gopalan SS, Perry BW, Schield DR, Smith CF, Mackessy SP, Castoe TA. Origins, genomic structure and copy number variation of snake venom myotoxins. Toxicon 2022; 216:92-106. [PMID: 35820472 DOI: 10.1016/j.toxicon.2022.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
Crotamine, myotoxin a and homologs are short peptides that often comprise major fractions of rattlesnake venoms and have been extensively studied for their bioactive properties. These toxins are thought to be important for rapidly immobilizing mammalian prey and are implicated in serious, and sometimes fatal, responses to envenomation in humans. While high quality reference genomes for multiple venomous snakes are available, the loci that encode myotoxins have not been successfully assembled in any existing genome assembly. Here, we integrate new and existing genomic and transcriptomic data from the Prairie Rattlesnake (Crotalus viridis viridis) to reconstruct, characterize, and infer the chromosomal locations of myotoxin-encoding loci. We integrate long-read transcriptomics (Pacific Bioscience's Iso-Seq) and short-read RNA-seq to infer gene sequence diversity and characterize patterns of myotoxin and paralogous β-defensin expression across multiple tissues. We also identify two long non-coding RNA sequences which both encode functional myotoxins, demonstrating a newly discovered source of venom coding sequence diversity. We also integrate long-range mate-pair chromatin contact data and linked-read sequencing to infer the structure and chromosomal locations of the three myotoxin-like loci. Further, we conclude that the venom-associated myotoxin is located on chromosome 1 and is adjacent to non-venom paralogs. Consistent with this locus contributing to venom composition, we find evidence that the promoter of this gene is selectively open in venom gland tissue and contains transcription factor binding sites implicated in broad trans-regulatory pathways that regulate snake venoms. This study provides the best genomic reconstruction of myotoxin loci to date and raises questions about the physiological roles and interplay between myotoxin and related genes, as well as the genomic origins of snake venom variation.
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Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Cara F Smith
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA; Department of Biochemistry and Molecular Biology, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Stephen P Mackessy
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA.
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9
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Zhao HY, Sun Y, Du Y, Li JQ, Lv JG, Qu YF, Lin LH, Lin CX, Ji X, Gao JF. Venom of the Annulated Sea Snake Hydrophis cyanocinctus: A Biochemically Simple but Genetically Complex Weapon. Toxins (Basel) 2021; 13:548. [PMID: 34437419 PMCID: PMC8402435 DOI: 10.3390/toxins13080548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Given that the venom system in sea snakes has a role in enhancing their secondary adaption to the marine environment, it follows that elucidating the diversity and function of venom toxins will help to understand the adaptive radiation of sea snakes. We performed proteomic and de novo NGS analyses to explore the diversity of venom toxins in the annulated sea snake (Hydrophis cyanocinctus) and estimated the adaptive molecular evolution of the toxin-coding unigenes and the toxicity of the major components. We found three-finger toxins (3-FTxs), phospholipase A2 (PLA2) and cysteine-rich secretory protein (CRISP) in the venom proteome and 59 toxin-coding unigenes belonging to 24 protein families in the venom-gland transcriptome; 3-FTx and PLA2 were the most abundant families. Nearly half of the toxin-coding unigenes had undergone positive selection. The short- (i.p. 0.09 μg/g) and long-chain neurotoxin (i.p. 0.14 μg/g) presented fairly high toxicity, whereas both basic and acidic PLA2s expressed low toxicity. The toxicity of H. cyanocinctus venom was largely determined by the 3-FTxs. Our data show the venom is used by H. cyanocinctus as a biochemically simple but genetically complex weapon and venom evolution in H. cyanocinctus is presumably driven by natural selection to deal with fast-moving prey and enemies in the marine environment.
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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, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Yan Sun
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Jia-Qi Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Jin-Geng Lv
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
| | - Xiang Ji
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
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10
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Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions. Curr Res Toxicol 2021; 2:93-98. [PMID: 34345854 PMCID: PMC8320608 DOI: 10.1016/j.crtox.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
The venom protein-protein interactions in snake venom remain largely unknown. Y2H coupled with MD simulations was used to detect venom protein interactions. Venom PLA2s interact with themselves and Lys49 PLA2 interacts with venom CRISP.
Proteins and peptides are major components of snake venom. Venom protein transcriptomes and proteomes of many snake species have been reported; however, snake venom complexity (i.e., the venom protein-protein interactions, PPIs) remains largely unknown. To detect the venom protein interactions, we used the most common snake venom component, phospholipase A2s (PLA2s) as a “bait” to identify the interactions between PLA2s and 14 of the most common proteins in Western diamondback rattlesnake (Crotalus atrox) venom by using yeast two-hybrid (Y2H) analysis, a technique used to detect PPIs. As a result, we identified PLA2s interacting with themselves, and lysing-49 PLA2 (Lys49 PLA2) interacting with venom cysteine-rich secretory protein (CRISP). To reveal the complex structure of Lys49 PLA2-CRISP interaction at the structural level, we first built the three-dimensional (3D) structures of Lys49 PLA2 and CRISP by a widely used computational program-MODELLER. The binding modes of Lys49 PLA2-CRISP interaction were then predicted through three different docking programs including ClusPro, ZDOCK and HADDOCK. Furthermore, the most likely complex structure of Lys49 PLA2-CRISP was inferred by molecular dynamic (MD) simulations with GROMACS software. The techniques used and results obtained from this study strengthen the understanding of snake venom protein interactions and pave the way for the study of animal venom complexity.
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11
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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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12
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Seneci L, Zdenek CN, Bourke LA, Cochran C, Sánchez EE, Neri-Castro E, Bénard-Valle M, Alagón A, Frank N, Fry BG. A symphony of destruction: Dynamic differential fibrinogenolytic toxicity by rattlesnake (Crotalus and Sistrurus) venoms. Comp Biochem Physiol C Toxicol Pharmacol 2021; 245:109034. [PMID: 33766656 PMCID: PMC8162888 DOI: 10.1016/j.cbpc.2021.109034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/02/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022]
Abstract
What factors influence the evolution of a heavily selected functional trait in a diverse clade? This study adopts rattlesnakes as a model group to investigate the evolutionary history of venom coagulotoxicity in the wider context of phylogenetics, natural history, and biology. Venom-induced clotting of human plasma and fibrinogen was determined and mapped onto the rattlesnake phylogenetic tree to reconstruct the evolution of coagulotoxicity across the group. Our results indicate that venom phenotype is often independent of phylogenetic relationships in rattlesnakes, suggesting the importance of diet and/or other environmental variables in driving venom evolution. Moreover, the striking inter- and intraspecific variability in venom activity on human blood highlights the considerable variability faced by physicians treating envenomation. This study is the most comprehensive effort to date to describe and characterize the evolutionary and biological aspects of coagulotoxins in rattlesnake venom. Further research at finer taxonomic levels is recommended to elucidate patterns of variation within species and lineages.
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Affiliation(s)
- Lorenzo Seneci
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia; Institute of Biology Leiden (IBL), Leiden University, 2333 BE Leiden, the Netherlands
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Lachlan A Bourke
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Chip Cochran
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA 92350, USA
| | - Elda E Sánchez
- National Natural Toxins Research Center (NNTRC), Department of Chemistry, Texas A&M University-Kingsville, MSC 224, 975 West Avenue B, Kingsville, TX 78363, USA
| | - Edgar Neri-Castro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologa, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Melisa Bénard-Valle
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologa, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologa, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | | | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
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13
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Calvete JJ, Lomonte B, Saviola AJ, Bonilla F, Sasa M, Williams DJ, Undheim EA, Sunagar K, Jackson TN. Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance. Toxicon X 2021; 9-10:100070. [PMID: 34195606 PMCID: PMC8234350 DOI: 10.1016/j.toxcx.2021.100070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.
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Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fabián Bonilla
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Mahmood Sasa
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigaciones en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, Costa Rica
| | | | - Eivind A.B. Undheim
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Timothy N.W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
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14
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Deshwal A, Phan P, Datta J, Kannan R, Thallapuranam SK. A Meta-Analysis of the Protein Components in Rattlesnake Venom. Toxins (Basel) 2021; 13:toxins13060372. [PMID: 34071038 DOI: 10.3390/toxins13060372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
The specificity and potency of venom components give them a unique advantage in developing various pharmaceutical drugs. Though venom is a cocktail of proteins, rarely are the synergy and association between various venom components studied. Understanding the relationship between various components of venom is critical in medical research. Using meta-analysis, we observed underlying patterns and associations in the appearance of the toxin families. For Crotalus, Dis has the most associations with the following toxins: PDE; BPP; CRL; CRiSP; LAAO; SVMP P-I and LAAO; SVMP P-III and LAAO. In Sistrurus venom, CTL and NGF have the most associations. These associations can predict the presence of proteins in novel venom and understand synergies between venom components for enhanced bioactivity. Using this approach, the need to revisit the classification of proteins as major components or minor components is highlighted. The revised classification of venom components is based on ubiquity, bioactivity, the number of associations, and synergies. The revised classification can be expected to trigger increased research on venom components, such as NGF, which have high biomedical significance. Using hierarchical clustering, we observed that the genera's venom compositions were similar, based on functional characteristics rather than phylogenetic relationships.
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Affiliation(s)
- Anant Deshwal
- Division of Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jyotishka Datta
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ragupathy Kannan
- Department of Biology, University of Arkansas-Fort Smith, Fort Smith, AR 72913, USA
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15
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Ullah A, Masood R. The Sequence and Three-Dimensional Structure Characterization of Snake Venom Phospholipases B. Front Mol Biosci 2020; 7:175. [PMID: 32850964 PMCID: PMC7419708 DOI: 10.3389/fmolb.2020.00175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/06/2020] [Indexed: 11/23/2022] Open
Abstract
Snake venom phospholipases B (SVPLBs) are the least studied enzymes. They constitute about 1% of Bothrops crude venoms, however, in other snake venoms, it is present in less than 1%. These enzymes are considered the most potent hemolytic agent in the venom. Currently, no structural information is available about these enzymes from snake venom. To better understand its three-dimensional structure and mechanisms of envenomation, the current work describes the first model-based structure report of this enzyme from Bothrops moojeni venom named as B. moojeni phospholipase B (PLB_Bm). The structure model of PLB_Bm was generated using model building software like I-TESSER, MODELLER 9v19, and Swiss-Model. The build PLB_Bm model was validated using validation tools (PROCHECK, ERRAT, and Verif3D). The analysis of the PLB_Bm modeled structure indicates that it contains 491 amino acid residues that form a well-defined four-layer αββα sandwich core and has a typical fold of the N-terminal nucleophile aminohydrolase (Ntn-hydrolase). The overall structure of PLB_Bm contains 18 β-strands and 17 α-helices with many connecting loops. The structure divides into two chains (A and B) after maturation. The A chain is smaller and contains 207 amino acid residues, whereas the B chain is larger and contains 266 amino acid residues. The sequence and structural comparison among homologous snake venom, bacterial, and mammals PLBs indicate that differences in the length and sequence composition may confer variable substrate specificity to these enzymes. Moreover, the surface charge distribution, average volume, and depth of the active site cavity also vary in these enzymes. The present work will provide more information about the structure-function relationship and mechanism of action of these enzymes in snakebite envenomation.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University Peshawar, Peshawar, Pakistan
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16
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Liu ZL, Hu JH, Jiang F, Wu YD. CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning. Bioinformatics 2020; 36:3385-3392. [PMID: 32215567 DOI: 10.1093/bioinformatics/btaa193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/06/2020] [Accepted: 03/22/2020] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION High-throughput sequencing discovers many naturally occurring disulfide-rich peptides or cystine-rich peptides (CRPs) with diversified bioactivities. However, their structure information, which is very important to peptide drug discovery, is still very limited. RESULTS We have developed a CRP-specific structure prediction method called Cystine-Rich peptide Structure Prediction (CRiSP), based on a customized template database with cystine-specific sequence alignment and three machine-learning predictors. The modeling accuracy is significantly better than several popular general-purpose structure modeling methods, and our CRiSP can provide useful model quality estimations. AVAILABILITY AND IMPLEMENTATION The CRiSP server is freely available on the website at http://wulab.com.cn/CRISP. CONTACT wuyd@pkusz.edu.cn or jiangfan@pku.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi-Lin Liu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jing-Hao Hu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,NanoAI Biotech Co., Ltd, Shenzhen 518118, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Shenzhen Bay Laboratory, Shenzhen 518055, China
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17
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Monteiro WM, Contreras-Bernal JC, Bisneto PF, Sachett J, Mendonça da Silva I, Lacerda M, Guimarães da Costa A, Val F, Brasileiro L, Sartim MA, Silva-de-Oliveira S, Bernarde PS, Kaefer IL, Grazziotin FG, Wen FH, Moura-da-Silva AM. Bothrops atrox, the most important snake involved in human envenomings in the amazon: How venomics contributes to the knowledge of snake biology and clinical toxinology. Toxicon X 2020; 6:100037. [PMID: 32550592 PMCID: PMC7285970 DOI: 10.1016/j.toxcx.2020.100037] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
Bothrops atrox snakes are mostly endemic of the Amazon rainforest and is certainly the South American pit viper responsible for most of the snakebites in the region. The composition of B. atrox venom is significantly known and has been used to trace the relevance of the venom phenotype for snake biology and for the impacts in the clinics of human patients involved in accidents by B. atrox. However, in spite of the wide distribution and the great medical relevance of B. atrox snakes, B. atrox taxonomy is not fully resolved and the impacts of the lack of taxonomic resolution on the studies focused on venom or envenoming are currently unknown. B. atrox venom presents different degrees of compositional variability and is generally coagulotoxic, inducing systemic hematological disturbances and local tissue damage in snakebite patients. Antivenoms are the effective therapy for attenuating the clinical signs. This review brings a comprehensive discussion of the literature concerning B. atrox snakes encompassing from snake taxonomy, diet and venom composition, towards clinical aspects of snakebite patients and efficacy of the antivenoms. This discussion is highly supported by the contributions that venomics and antivenomics added for the advancement of knowledge of B. atrox snakes, their venoms and the treatment of accidents they evoke.
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Affiliation(s)
- Wuelton Marcelo Monteiro
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Jorge Carlos Contreras-Bernal
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Pedro Ferreira Bisneto
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Jacqueline Sachett
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Alfredo da Matta, Manaus, Brazil
| | - Iran Mendonça da Silva
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Marcus Lacerda
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas & Maria Deane, Manaus, Brazil
| | - Allyson Guimarães da Costa
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Fernando Val
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Lisele Brasileiro
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Marco Aurélio Sartim
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Sâmella Silva-de-Oliveira
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Paulo Sérgio Bernarde
- Laboratório de Herpetologia, Centro Multidisciplinar, Campus Floresta, Universidade Federal do Acre, Cruzeiro do Sul, AC, Brazil
| | - Igor L. Kaefer
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | | | | | - Ana Maria Moura-da-Silva
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Butantan, São Paulo, Brazil
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18
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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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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: 18] [Impact Index Per Article: 4.5] [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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20
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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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21
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Zdenek CN, den Brouw BO, Dashevsky D, Gloria A, Youngman NJ, Watson E, Green P, Hay C, Dunstan N, Allen L, Fry BG. Clinical implications of convergent procoagulant toxicity and differential antivenom efficacy in Australian elapid snake venoms. Toxicol Lett 2019; 316:171-182. [DOI: 10.1016/j.toxlet.2019.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
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Nielsen VG. Characterization of L-amino Acid Oxidase Derived from Crotalus adamanteus Venom: Procoagulant and Anticoagulant Activities. Int J Mol Sci 2019; 20:ijms20194853. [PMID: 31574907 PMCID: PMC6801523 DOI: 10.3390/ijms20194853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 01/04/2023] Open
Abstract
Snake venom enzymes of the L-amino acid oxidase (LAAO) class are responsible for tissue hemorrhage, edema, and derangement of platelet function. However, what role, if any, these flavoenzymes play in altering plasmatic coagulation have not been well defined. Using coagulation kinetomic analyses (thrombelastograph-based), it was determined that the LAAO derived from Crotalus adamanteus venom displayed a procoagulant activity associated with weak clot strength (no factor XIII activation) similar to thrombin-like enzymes. The procoagulant activity was not modified in the presence of reduced glutathione, demonstrating that the procoagulant activity was likely due to deamination, and not hydrogen peroxide generation by the LAAO. Further, unlike the raw venom of the same species, the purified LAAO was not inhibited by carbon monoxide releasing molecule-2 (CORM-2). Lastly, exposure of the enzyme to phenylmethylsulfonyl fluoride (PMSF) resulted in the LAAO expressing anticoagulant activity, preventing contact activation generated thrombin from forming a clot. In sum, this investigation for the first time characterized the LAAO of a snake venom as both a fibrinogen polymerizing and an anticoagulant enzyme acting via oxidative deamination and not proteolysis as is the case with thrombin-like enzymes (e.g., serine proteases). Using this thrombelastographic approach, future investigation of purified enzymes can define their biochemical nature.
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Affiliation(s)
- Vance G Nielsen
- Department of Anesthesiology, University of Arizona College of Medicine, Tucson, AZ 85719, USA.
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23
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Modahl CM, Mackessy SP. Venoms of Rear-Fanged Snakes: New Proteins and Novel Activities. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00279] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Convergent recruitment of adamalysin-like metalloproteases in the venom of the red bark centipede (Scolopocryptops sexspinosus). Toxicon 2019; 168:1-15. [PMID: 31229627 DOI: 10.1016/j.toxicon.2019.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022]
Abstract
Many venom proteins have presumably been convergently recruited by taxa from diverse venomous lineages. These toxic proteins have characteristics that allow them to remain stable in solution and have a high propensity for toxic effects on prey and/or potential predators. Despite this well-established convergent toxin recruitment, some toxins seem to be lineage specific. To further investigate the toxic proteins found throughout venomous lineages, venom proteomics and venom-gland transcriptomics were performed on two individual red bark centipedes (Scolopocryptops sexspinosus). Combining the protein phenotype with the transcript genotype resulted in the first in-depth venom characterization of S. sexspinosus, including 72 venom components that were identified in both the transcriptome and proteome and 1468 nontoxin transcripts identified in the transcriptome. Ten different toxin families were represented in the venom and venom gland with the majority of the toxins belonging to metalloproteases, CAPS (cysteine-rich secretory protein, antigen 5, and pathogenesis-related 1 proteins), and β-pore-forming toxins. Nine of these toxin families shared a similar proteomic structure to venom proteins previously identified from other centipedes. However, the most highly expressed toxin family, the adamalysin-like metalloproteases, has until now only been observed in the venom of snakes. We confirmed adamalysin-like metalloprotease activity by means of in vivo functional assays. The recruitment of an adamalysin-like metalloprotease into centipede venom represents a striking case of convergent evolution.
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Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Sci Rep 2018; 8:17622. [PMID: 30514908 PMCID: PMC6279745 DOI: 10.1038/s41598-018-35810-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/09/2018] [Indexed: 01/20/2023] Open
Abstract
Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage range-wide sampling of Mojave Rattlesnakes (Crotalus scutulatus) and use a combination of venom, morphological, phylogenetic, population genetic, and environmental data to characterize the striking dichotomy of neurotoxic (Type A) and hemorrhagic (Type B) venoms throughout the range of this species. We find that three of the four previously identified major lineages within C. scutulatus possess a combination of Type A, Type B, and a ‘mixed’ Type A + B venom phenotypes, and that fixation of the two main venom phenotypes occurs on a more fine geographic scale than previously appreciated. We also find that Type A + B individuals occur in regions of inferred introgression, and that this mixed phenotype is comparatively rare. Our results support strong directional local selection leading to fixation of alternative venom phenotypes on a fine geographic scale, and are inconsistent with balancing selection to maintain both phenotypes within a single population. Our comparisons to biotic and abiotic factors further indicate that venom phenotype correlates with fang morphology and climatic variables. We hypothesize that links to fang morphology may be indicative of co-evolution of venom and other trophic adaptations, and that climatic variables may be linked to prey distributions and/or physiology, which in turn impose selection pressures on snake venoms.
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Domínguez-Pérez D, Durban J, Agüero-Chapin G, López JT, Molina-Ruiz R, Almeida D, Calvete JJ, Vasconcelos V, Antunes A. The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba. Genomics 2018; 111:1720-1727. [PMID: 30508561 DOI: 10.1016/j.ygeno.2018.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 01/17/2023]
Abstract
The Harderian gland is a cephalic structure, widely distributed among vertebrates. In snakes, the Harderian gland is anatomically connected to the vomeronasal organ via the nasolacrimal duct, and in some species can be larger than the eyes. The function of the Harderian gland remains elusive, but it has been proposed to play a role in the production of saliva, pheromones, thermoregulatory lipids and growth factors, among others. Here, we have profiled the transcriptomes of the Harderian glands of three non-front-fanged colubroid snakes from Cuba: Caraiba andreae (Cuban Lesser Racer); Cubophis cantherigerus (Cuban Racer); and Tretanorhinus variabilis (Caribbean Water Snake), using Illumina HiSeq2000 100 bp paired-end. In addition to ribosomal and non-characterized proteins, the most abundant transcripts encode putative transport/binding, lipocalin/lipocalin-like, and bactericidal/permeability-increasing-like proteins. Transcripts coding for putative canonical toxins described in venomous snakes were also identified. This transcriptional profile suggests a more complex function than previously recognized for this enigmatic organ.
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Affiliation(s)
- Dany Domínguez-Pérez
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Jordi Durban
- Evolutionary and Translational Venomics Laboratory, CSIC, Jaume Roig, 11, 46010, Valencia, Spain.
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Javier Torres López
- Department of Ecology and Evolutionary Biology, The University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045, USA; Faculty of Biology, University of Havana, 25 St. 455, La Habana 10400, Cuba.
| | - Reinaldo Molina-Ruiz
- Centro de Bioactivos Químicos, Universidad Central "Marta Abreu" de Las Villas, 54830 Santa Clara, Cuba.
| | - Daniela Almeida
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Jaume Roig, 11, 46010, Valencia, Spain.
| | - Vítor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal.
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Shibao PYT, Cologna CT, Morandi-Filho R, Wiezel GA, Fujimura PT, Ueira-Vieira C, Arantes EC. Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion. J Venom Anim Toxins Incl Trop Dis 2018; 24:36. [PMID: 30519258 PMCID: PMC6267030 DOI: 10.1186/s40409-018-0173-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/07/2018] [Indexed: 01/19/2023] Open
Abstract
Background Animal poisons and venoms are sources of biomolecules naturally selected. Rhinella schneideri toads are widespread in the whole Brazilian territory and they have poison glands and mucous gland. Recently, protein from toads’ secretion has gaining attention. Frog skin is widely known to present great number of host defense peptides and we hypothesize toads present them as well. In this study, we used a RNA-seq analysis from R. schneideri skin and biochemical tests with the gland secretion to unravel its protein molecules. Methods Total RNA from the toad skin was extracted using TRizol reagent, sequenced in duplicate using Illumina Hiseq2500 in paired end analysis. The raw reads were trimmed and de novo assembled using Trinity. The resulting sequences were submitted to functional annotation against non-redundant NCBI database and Database of Anuran Defense Peptide. Furthermore, we performed caseinolytic activity test to assess the presence of serine and metalloproteases in skin secretion and it was fractionated by fast liquid protein chromatography using a reverse-phase column. The fractions were partially sequenced by Edman’s degradation. Results We were able to identify several classes of antimicrobial peptides, such as buforins, peroniins and brevinins, as well as PLA2, lectins and galectins, combining protein sequencing and RNA-seq analysis for the first time. In addition, we could isolate a PLA2 from the skin secretion and infer the presence of serine proteases in cutaneous secretion. Conclusions We identified novel toxins and proteins from R. schneideri mucous glands. Besides, this is a pioneer study that presented the in depth characterization of protein molecules richness from this toad secretion. The results obtained herein showed evidence of novel AMP and enzymes that need to be further explored. Electronic supplementary material The online version of this article (10.1186/s40409-018-0173-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Priscila Yumi Tanaka Shibao
- 1Laboratory of Animal Toxins, School of Pharmaceutical Scienes of Ribeirão Preto, University of São Paulo, Avenida do Café s/n, Ribeirão Preto, SP Brazil
| | - Camila Takeno Cologna
- 1Laboratory of Animal Toxins, School of Pharmaceutical Scienes of Ribeirão Preto, University of São Paulo, Avenida do Café s/n, Ribeirão Preto, SP Brazil
| | - Romualdo Morandi-Filho
- 2Laboratory of genetics - LABGEN, Institute of Genetics and Biochemistry, Campus Umuarama, Federal University of Uberlândia, Avenida Pará, Uberlândia, MG 1720 Brazil
| | - Gisele Adriano Wiezel
- 1Laboratory of Animal Toxins, School of Pharmaceutical Scienes of Ribeirão Preto, University of São Paulo, Avenida do Café s/n, Ribeirão Preto, SP Brazil
| | - Patricia Tiemi Fujimura
- 2Laboratory of genetics - LABGEN, Institute of Genetics and Biochemistry, Campus Umuarama, Federal University of Uberlândia, Avenida Pará, Uberlândia, MG 1720 Brazil
| | - Carlos Ueira-Vieira
- 2Laboratory of genetics - LABGEN, Institute of Genetics and Biochemistry, Campus Umuarama, Federal University of Uberlândia, Avenida Pará, Uberlândia, MG 1720 Brazil
| | - Eliane Candiani Arantes
- 2Laboratory of genetics - LABGEN, Institute of Genetics and Biochemistry, Campus Umuarama, Federal University of Uberlândia, Avenida Pará, Uberlândia, MG 1720 Brazil.,3Department of Physics and Chemistry, University of São Paulo, School of Pharmaceutical Sciences of Ribeirão Preto, Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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Wiezel GA, Shibao PYT, Cologna CT, Morandi Filho R, Ueira-Vieira C, De Pauw E, Quinton L, Arantes EC. In-Depth Venome of the Brazilian Rattlesnake Crotalus durissus terrificus: An Integrative Approach Combining Its Venom Gland Transcriptome and Venom Proteome. J Proteome Res 2018; 17:3941-3958. [PMID: 30270628 DOI: 10.1021/acs.jproteome.8b00610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Snake venoms are complex mixtures mainly composed of proteins and small peptides. Crotoxin is one of the most studied components from Crotalus venoms, but many other components are less known due to their low abundance. The venome of Crotalus durissus terrificus, the most lethal Brazilian snake, was investigated by combining its venom gland transcriptome and proteome to create a holistic database of venom compounds unraveling novel toxins. We constructed a cDNA library from C. d. terrificus venom gland using the Illumina platform and investigated its venom proteome through high resolution liquid chromotography-tandem mass spectrometry. After integrating data from both data sets, more than 30 venom components classes were identified by the transcriptomic analysis and 15 of them were detected in the venom proteome. However, few of them (PLA2, SVMP, SVSP, and VEGF) were relatively abundant. Furthermore, only seven expressed transcripts contributed to ∼82% and ∼73% of the abundance in the transcriptome and proteome, respectively. Additionally, novel venom proteins are reported, and we highlight the importance of using different databases to perform the data integration and discuss the structure of the venom components-related transcripts identified. Concluding, this research paves the way for novel investigations and discovery of future pharmacological agents or targets in the antivenom therapy.
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Affiliation(s)
- Gisele A Wiezel
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Priscila Y T Shibao
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Camila T Cologna
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Romualdo Morandi Filho
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Carlos Ueira-Vieira
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Eliane C Arantes
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
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Defining the pathogenic threat of envenoming by South African shield-nosed and coral snakes (genus Aspidelaps), and revealing the likely efficacy of available antivenom. J Proteomics 2018; 198:186-198. [PMID: 30290233 DOI: 10.1016/j.jprot.2018.09.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/15/2018] [Accepted: 09/30/2018] [Indexed: 12/15/2022]
Abstract
While envenoming by the southern African shield-nosed or coral snakes (genus Aspidelaps) has caused fatalities, bites are uncommon. Consequently, this venom is not used in the mixture of snake venoms used to immunise horses for the manufacture of regional SAIMR (South African Institute for Medical Research) polyvalent antivenom. Aspidelaps species are even excluded from the manufacturer's list of venomous snakes that can be treated by this highly effective product. This leaves clinicians, albeit rarely, in a therapeutic vacuum when treating envenoming by these snakes. This is a significantly understudied small group of nocturnal snakes and little is known about their venom compositions and toxicities. Using a murine preclinical model, this study determined that the paralysing toxicity of venoms from Aspidelaps scutatus intermedius, A. lubricus cowlesi and A. l. lubricus approached that of venoms from highly neurotoxic African cobras and mambas. This finding was consistent with the cross-genus dominance of venom three-finger toxins, including numerous isoforms which showed extensive interspecific variation. Our comprehensive analysis of venom proteomes showed that the three Aspidelaps species possess highly similar venom proteomic compositions. We also revealed that the SAIMR polyvalent antivenom cross-reacted extensively in vitro with venom proteins of the three Aspidelaps. Importantly, this cross-genus venom-IgG binding translated to preclinical (in a murine model) neutralisation of A. s. intermedius venom-induced lethality by the SAIMR polyvalent antivenom, at doses comparable with those that neutralise venom from the cape cobra (Naja nivea), which the antivenom is directed against. Our results suggest a wider than anticipated clinical utility of the SAIMR polyvalent antivenom, and here we seek to inform southern African clinicians that this readily available antivenom is likely to prove effective for victims of Aspidelaps envenoming. BIOLOGICAL SIGNIFICANCE: Coral and shield-nosed snakes (genus Aspidelaps) comprise two species and several subspecies of potentially medically important venomous snakes distributed in Namibia, Botswana, Zimbabwe, Mozambique and South Africa. Documented human fatalities, although rare, have occurred from both A. lubricus and A. scutatus. However, their venom proteomes and the pathological effects of envenomings by this understudied group of nocturnal snakes remain uncharacterised. Furthermore, no commercial antivenom is made using venom from species of the genus Aspidelaps. To fill this gap, we have conducted a transcriptomics-guided comparative proteomics analysis of the venoms of the intermediate shield-nose snake (A. s. intermedius), southern coral snake (A. l. lubricus), and Cowle's shield snake (A. l. cowlesi); investigated the mechanism of action underpinning lethality by A. s. intermedius in the murine model; and assessed the in vitro immunoreactivity of the SAIMR polyvalent antivenom towards the venom toxins of A. l. lubricus and A. l. cowlesi, and the in vivo capability of this antivenom at neutralising the lethal effect of A. s. intermedius venom. Our data revealed a high degree of conservation of the global composition of the three Aspidelaps venom proteomes, all characterised by the overwhelming predominance of neurotoxic 3FTxs, which induced classical signs of systemic neurotoxicity in mice. The SAIMR polyvalent antivenom extensively binds to Aspidelaps venom toxins and neutralised, with a potency of 0.235 mg venom/mL antivenom, the lethal effect of A. s. intermedius venom. Our data suggest that the SAIMR antivenom could be a useful therapeutic tool for treating human envenomings by Aspidelaps species.
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Durban J, Sasa M, Calvete JJ. Venom gland transcriptomics and microRNA profiling of juvenile and adult yellow-bellied sea snake, Hydrophis platurus, from Playa del Coco (Guanacaste, Costa Rica). Toxicon 2018; 153:96-105. [DOI: 10.1016/j.toxicon.2018.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023]
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Modeling and molecular dynamics indicate that snake venom phospholipase B-like enzymes are Ntn-hydrolases. Toxicon 2018; 153:106-113. [DOI: 10.1016/j.toxicon.2018.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/14/2018] [Accepted: 08/27/2018] [Indexed: 12/22/2022]
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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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Amazonas DR, Portes-Junior JA, Nishiyama-Jr MY, Nicolau CA, Chalkidis HM, Mourão RH, Grazziotin FG, Rokyta DR, Gibbs HL, Valente RH, Junqueira-de-Azevedo IL, Moura-da-Silva AM. Molecular mechanisms underlying intraspecific variation in snake venom. J Proteomics 2018; 181:60-72. [DOI: 10.1016/j.jprot.2018.03.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/08/2018] [Accepted: 03/31/2018] [Indexed: 10/17/2022]
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Ullah A, Masood R, Ali I, Ullah K, Ali H, Akbar H, Betzel C. Thrombin-like enzymes from snake venom: Structural characterization and mechanism of action. Int J Biol Macromol 2018; 114:788-811. [PMID: 29604354 DOI: 10.1016/j.ijbiomac.2018.03.164] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/08/2018] [Accepted: 03/23/2018] [Indexed: 01/15/2023]
Abstract
Snake venom thrombin-like enzymes (SVTLEs) constitute the major portion (10-24%) of snake venom and these are the second most abundant enzymes present in the crude venom. During envenomation, these enzymes had shown prominently the various pathological effects, such as disturbance in hemostatic system, fibrinogenolysis, fibrinolysis, platelet aggregation, thrombosis, neurologic disorders, activation of coagulation factors, coagulant, procoagulant etc. These enzymes also been used as a therapeutic agent for the treatment of various diseases such as congestive heart failure, ischemic stroke, thrombotic disorders etc. Although the crystal structures of five SVTLEs are available in the Protein Data Bank (PDB), there is no single article present in the literature that has described all of them. The current work describes the structural aspects, structure-based mechanism of action, processing and inhibition of these enzymes. The sequence analysis indicates that these enzymes show a high sequence identity (57-85%) with each other and low sequence identity with trypsin (36-43%), human alpha-thrombin (29-36%) and other snake venom serine proteinases (57-85%). Three-dimensional structural analysis indicates that the loops surrounding the active site are variable both in amino acids composition and length that may convey variable substrate specificity to these enzymes. The surface charge distributions also vary in these enzymes. Docking analysis with suramin shows that this inhibitor preferably binds to the C-terminal region of these enzymes and causes the destabilization of their three-dimensional structure.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan.
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar 25000, Pakistan
| | - Ijaz Ali
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Hamid Ali
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Haji Akbar
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. Phenotypic Variation in Mojave Rattlesnake (Crotalus scutulatus) Venom Is Driven by Four Toxin Families. Toxins (Basel) 2018; 10:toxins10040135. [PMID: 29570631 PMCID: PMC5923301 DOI: 10.3390/toxins10040135] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 02/04/2023] Open
Abstract
Phenotypic diversity generated through altered gene expression is a primary mechanism facilitating evolutionary response in natural systems. By linking the phenotype to genotype through transcriptomics, it is possible to determine what changes are occurring at the molecular level. High phenotypic diversity has been documented in rattlesnake venom, which is under strong selection due to its role in prey acquisition and defense. Rattlesnake venom can be characterized by the presence (Type A) or absence (Type B) of a type of neurotoxic phospholipase A2 (PLA2), such as Mojave toxin, that increases venom toxicity. Mojave rattlesnakes (Crotalus scutulatus), represent this diversity as both venom types are found within this species and within a single panmictic population in the Sonoran Desert. We used comparative venom gland transcriptomics of nine specimens of C. scutulatus from this region to test whether expression differences explain diversity within and between venom types. Type A individuals expressed significantly fewer toxins than Type B individuals owing to the diversity of C-type lectins (CTLs) and snake venom metalloproteinases (SVMPs) found in Type B animals. As expected, both subunits of Mojave toxin were exclusively found in Type A individuals but we found high diversity in four additional PLA2s that was not associated with a venom type. Myotoxin a expression and toxin number variation was not associated with venom type, and myotoxin a had the highest range of expression of any toxin class. Our study represents the most comprehensive transcriptomic profile of the venom type dichotomy in rattlesnakes and C. scutulatus. Even intra-specifically, Mojave rattlesnakes showcase the diversity of snake venoms and illustrate that variation within venom types blurs the distinction of the venom dichotomy.
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Affiliation(s)
- Jason L Strickland
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC 29634, USA.
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.
| | - Christopher L Parkinson
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
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Tessler M, Marancik D, Champagne D, Dove A, Camus A, Siddall ME, Kvist S. Marine Leech Anticoagulant Diversity and Evolution. J Parasitol 2018; 104:210-220. [PMID: 29505345 DOI: 10.1645/17-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Leeches (Annelida: Hirudinea) possess powerful salivary anticoagulants and, accordingly, are frequently employed in modern, authoritative medicine. Members of the almost exclusively marine family Piscicolidae account for 20% of leech species diversity, and they feed on host groups (e.g., sharks) not encountered by their freshwater and terrestrial counterparts. Moreover, some species of Ozobranchidae feed on endangered marine turtles and have been implicated as potential vectors for the tumor-associated turtle herpesvirus. In spite of their ecological importance and unique host associations, there is a distinct paucity of data regarding the salivary transcriptomes of either of these families. Using next-generation sequencing, we profiled transcribed, putative anticoagulants and other salivary bioactive compounds that have previously been linked to blood feeding from 7 piscicolid species (3 elasmobranch feeders; 4 non-cartilaginous fish feeders) and 1 ozobranchid species (2 samples). In total, 149 putative anticoagulants and bioactive loci were discovered in varying constellations throughout the different samples. The putative anticoagulants showed a broad spectrum of described antagonistic pathways, such as inhibition of factor Xa and platelet aggregation, which likely have similar bioactive roles in marine fish and turtles. A transcript with homology to ohanin, originally isolated from king cobras, was found in Cystobranchus vividus but is otherwise unknown from leeches. Estimation of selection pressures for the putative anticoagulants recovered evidence for both positive and purifying selection along several isolated branches in the gene trees, and positive selection was also estimated for a few select codons in a variety of marine species. Similarly, phylogenetic analyses of the amino acid sequences for several anticoagulants indicated divergent evolution.
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Affiliation(s)
- Michael Tessler
- 1 Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024.,2 Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024.,3 Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024
| | - David Marancik
- 4 Department of Pathology, College of Veterinary Medicine, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602
| | - Donald Champagne
- 5 Department of Entomology, University of Georgia, 413 Biological Sciences Building, Athens, Georgia 30602
| | - Alistair Dove
- 6 Georgia Aquarium, 225 Baker Street, Atlanta, Georgia 30313
| | - Alvin Camus
- 4 Department of Pathology, College of Veterinary Medicine, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602
| | - Mark E Siddall
- 2 Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024.,3 Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024
| | - Sebastian Kvist
- 7 Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada.,8 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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38
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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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Krishnan NM, Panda B. Comparative analyses of putative toxin gene homologs from an Old World viper, Daboia russelii. PeerJ 2017; 5:e4104. [PMID: 29230357 PMCID: PMC5721910 DOI: 10.7717/peerj.4104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/07/2017] [Indexed: 11/25/2022] Open
Abstract
Availability of snake genome sequences has opened up exciting areas of research on comparative genomics and gene diversity. One of the challenges in studying snake genomes is the acquisition of biological material from live animals, especially from the venomous ones, making the process cumbersome and time-consuming. Here, we report comparative sequence analyses of putative toxin gene homologs from Russell’s viper (Daboia russelii) using whole-genome sequencing data obtained from shed skin. When compared with the major venom proteins in Russell’s viper studied previously, we found 45–100% sequence similarity between the venom proteins and their putative homologs in the skin. Additionally, comparative analyses of 20 putative toxin gene family homologs provided evidence of unique sequence motifs in nerve growth factor (NGF), platelet derived growth factor (PDGF), Kunitz/Bovine pancreatic trypsin inhibitor (Kunitz BPTI), cysteine-rich secretory proteins, antigen 5, andpathogenesis-related1 proteins (CAP) and cysteine-rich secretory protein (CRISP). In those derived proteins, we identified V11 and T35 in the NGF domain; F23 and A29 in the PDGF domain; N69, K2 and A5 in the CAP domain; and Q17 in the CRISP domain to be responsible for differences in the largest pockets across the protein domain structures in crotalines, viperines and elapids from the in silico structure-based analysis. Similarly, residues F10, Y11 and E20 appear to play an important role in the protein structures across the kunitz protein domain of viperids and elapids. Our study highlights the usefulness of shed skin in obtaining good quality high-molecular weight DNA for comparative genomic studies, and provides evidence towards the unique features and evolution of putative venom gene homologs in vipers.
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Affiliation(s)
- Neeraja M Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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40
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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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Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics 2017; 14:931-939. [DOI: 10.1080/14789450.2017.1377613] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Samuel D. Robinson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
| | | | | | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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Venomics of Remipede Crustaceans Reveals Novel Peptide Diversity and Illuminates the Venom's Biological Role. Toxins (Basel) 2017; 9:toxins9080234. [PMID: 28933727 PMCID: PMC5577568 DOI: 10.3390/toxins9080234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/24/2017] [Indexed: 01/15/2023] Open
Abstract
We report the first integrated proteomic and transcriptomic investigation of a crustacean venom. Remipede crustaceans are the venomous sister group of hexapods, and the venom glands of the remipede Xibalbanus tulumensis express a considerably more complex cocktail of proteins and peptides than previously thought. We identified 32 venom protein families, including 13 novel peptide families that we name xibalbins, four of which lack similarities to any known structural class. Our proteomic data confirm the presence in the venom of 19 of the 32 families. The most highly expressed venom components are serine peptidases, chitinase and six of the xibalbins. The xibalbins represent Inhibitory Cystine Knot peptides (ICK), a double ICK peptide, peptides with a putative Cystine-stabilized α-helix/β-sheet motif, a peptide similar to hairpin-like β-sheet forming antimicrobial peptides, two peptides related to different hormone families, and four peptides with unique structural motifs. Remipede venom components represent the full range of evolutionary recruitment frequencies, from families that have been recruited into many animal venoms (serine peptidases, ICKs), to those having a very narrow taxonomic range (double ICKs), to those unique for remipedes. We discuss the most highly expressed venom components to shed light on their possible functional significance in the predatory and defensive use of remipede venom, and to provide testable ideas for any future bioactivity studies.
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Bao LS, Xia JL. Global analysis of transcriptome sequences highlights accelerated evolution of immune genes in Danio choprae and Danio albolineatus. FISH & SHELLFISH IMMUNOLOGY 2017; 66:390-397. [PMID: 28478255 DOI: 10.1016/j.fsi.2017.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Danio fishes, a small type animal with short sexual cycles, are model vertebrate species. To investigate the genic evolution of this genus, the transcriptomes from Danio choprae and Danio albolineatus were sequenced by Illumina HiSeq 4000 platform. A total of 128,427,304 sequence reads from two Danio fishes were generated by Next Generation Sequencing. The resulting in two assemblies contained 88,682 and 88,029 unigenes in the Danio choprae and Danio albolineatus. Analysis of the orthologs from the Danio choprae and Danio albolineatus provided consistent evidence for the accelerated genic evolution in the Danio fishes. Several genes referring to immune functions under positive selection were identified by branch site model analysis, such as REL, GTF2E1, STAT6, MPG in Danio choprae and CYP17A1, ADORA2A, MYCN in Danio albolineatus. Our data provide novel insights into the adaptation in Danio fishes and is useful for understanding the genetic basis of adaptation in zebrafish.
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Affiliation(s)
- Ling-Sheng Bao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Department of Biological and Environmental Engineering, Changsha University, Changsha, 410003, China
| | - Jin-Lan Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.
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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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Calderón-Celis F, Cid-Barrio L, Encinar JR, Sanz-Medel A, Calvete JJ. Absolute venomics: Absolute quantification of intact venom proteins through elemental mass spectrometry. J Proteomics 2017; 164:33-42. [PMID: 28579478 DOI: 10.1016/j.jprot.2017.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/17/2022]
Abstract
We report the application of a hybrid element and molecular MS configuration for the parallel absolute quantification of μHPLC-separated intact sulfur-containing venom proteins, via ICP triple quadrupole MS and 32S/34S isotope dilution analysis, and identification by ESI-QToF-MS of the toxins of the medically important African black-necked spitting cobra, Naja nigricollis (Tanzania); New Guinea small-eyed snake, Micropechis ikaheka; and Papuan black snake, Pseudechis papuanus. The main advantage of this approach is that only one generic sulfur-containing standard is required to quantify each and all intact Cys- and/or Met-containing toxins of the venom proteome. The results of absolute quantification are in reasonably good agreement with previously reported relative quantification of the most abundant protein families. However, both datasets depart in the quantification of the minor ones, showing a tendency for this set of proteins to be underestimated in standard peptide-centric venomics approaches. The molecular identity, specific toxic activity, and concentration in the venom, are the pillars on which the toxicovenomics-aimed discovery of the most medically-relevant venom toxins, e.g. those that need to be neutralized by an effective therapeutic antivenom, should be based. The pioneering venom proteome-wide absolute quantification shown in this paper represents thus a significant advance towards this goal. The potential of ICP triple quadrupole MS in proteomics in general, and venomics in particular, is critically discussed. BIOLOGICAL SIGNIFICANCE Animal venoms provide excellent model systems for investigating interactions between predators and prey, and the molecular mechanisms that contribute to adaptive protein evolution. On the other hand, numerous cases of snake bites occur yearly by encounters of humans and snakes in their shared natural environment. Snakebite envenoming is a serious global public health issue that affects the most impoverished and geopolitically disadvantaged rural communities in many tropical and subtropical countries. Unveiling the temporal and spatial patterns of venom variability is of fundamental importance to understand the molecular basis of envenoming, a prerequisite for developing therapeutic strategies against snakebite envenoming. Research on venoms has been continuously enhanced by advances in technology. The combined application of next-generation transcriptomic and venomic workflows has demonstrated unparalleled capabilities for venom characterization in unprecedented detail. However, mass spectrometry is not inherently quantitative, and this analytical limitation has sparked the development of methods to determine absolute abundance of proteins in biological samples. Here we show the potential of a hybrid element and molecular MS configuration for the parallel ESI-QToF-MS and ICP-QQQ detection and absolute quantification of intact sulfur-containing venom proteins via 32S/34S isotope dilution analysis. This configuration has been applied to quantify the toxins of the medically important African snake Naja nigricollis (Tanzania), and the Papuan species Micropechis ikaheka and Pseudechis papuanus.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Laura Cid-Barrio
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain.
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain.
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Rokyta DR, Margres MJ, Ward MJ, Sanchez EE. The genetics of venom ontogeny in the eastern diamondback rattlesnake ( Crotalus adamanteus). PeerJ 2017; 5:e3249. [PMID: 28462047 PMCID: PMC5410154 DOI: 10.7717/peerj.3249] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/29/2017] [Indexed: 11/20/2022] Open
Abstract
The same selective forces that give rise to rapid inter- and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. The eastern diamondback rattlesnake was previously shown to undergo an ontogenetic shift in venom composition at sexual maturity, and this shift accounted for more venom variation than geography. To characterize the genetics underlying the ontogenetic venom compositional change in C. adamanteus, we sequenced adult/juvenile pairs of venom-gland transcriptomes from five populations previously shown to have different adult venom compositions. We identified a total of 59 putative toxin transcripts for C. adamanteus, and 12 of these were involved in the ontogenetic change. Three toxins were downregulated, and nine were upregulated in adults relative to juveniles. Adults and juveniles expressed similar total levels of snake-venom metalloproteinases but differed substantially in their featured paralogs, and adults expressed higher levels of Bradykinin-potentiating and C-type natriuretic peptides, nerve growth factor, and specific paralogs of phospholipases A2 and snake venom serine proteinases. Juvenile venom was more toxic to mice, indicating that the expression differences resulted in a phenotypically, and therefore potentially ecologically, significant difference in venom function. We also showed that adult and juvenile venom-gland transcriptomes for a species with known ontogenetic venom variation were equally effective at individually providing a full characterization of the venom genes of a species but that any particular individual was likely to lack several toxins in their transcriptome. A full characterization of a species’ venom-gene complement therefore requires sequencing more than one individual, although the ages of the individuals are unimportant.
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Affiliation(s)
- Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, United States of America
| | - Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL, United States of America.,School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL, United States of America
| | - Elda E Sanchez
- Department of Chemistry, Texas A&M University-Kingsville, Kingsville, TX, United States of America.,National Natural Toxins Research Center, Texas A&M University-Kingsville, Kingsville, TX, United States of America
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Xu N, Zhao HY, Yin Y, Shen SS, Shan LL, Chen CX, Zhang YX, Gao JF, Ji X. Combined venomics, antivenomics and venom gland transcriptome analysis of the monocoled cobra ( Naja kaouthia ) from China. J Proteomics 2017; 159:19-31. [DOI: 10.1016/j.jprot.2017.02.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/23/2017] [Accepted: 02/28/2017] [Indexed: 11/15/2022]
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48
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Rokyta DR, Ward MJ. Venom-gland transcriptomics and venom proteomics of the black-back scorpion (Hadrurus spadix) reveal detectability challenges and an unexplored realm of animal toxin diversity. Toxicon 2017; 128:23-37. [DOI: 10.1016/j.toxicon.2017.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
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49
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Integrating Perspectives on Animal Venom Diversity: An Introduction to the Symposium. Integr Comp Biol 2016; 56:934-937. [DOI: 10.1093/icb/icw112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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50
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Dowell NL, Giorgianni MW, Kassner VA, Selegue JE, Sanchez EE, Carroll SB. The Deep Origin and Recent Loss of Venom Toxin Genes in Rattlesnakes. Curr Biol 2016; 26:2434-2445. [PMID: 27641771 DOI: 10.1016/j.cub.2016.07.038] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/01/2016] [Accepted: 07/15/2016] [Indexed: 11/26/2022]
Abstract
The genetic origin of novel traits is a central but challenging puzzle in evolutionary biology. Among snakes, phospholipase A2 (PLA2)-related toxins have evolved in different lineages to function as potent neurotoxins, myotoxins, or hemotoxins. Here, we traced the genomic origin and evolution of PLA2 toxins by examining PLA2 gene number, organization, and expression in both neurotoxic and non-neurotoxic rattlesnakes. We found that even though most North American rattlesnakes do not produce neurotoxins, the genes of a specialized heterodimeric neurotoxin predate the origin of rattlesnakes and were present in their last common ancestor (∼22 mya). The neurotoxin genes were then deleted independently in the lineages leading to the Western Diamondback (Crotalus atrox) and Eastern Diamondback (C. adamanteus) rattlesnakes (∼6 mya), while a PLA2 myotoxin gene retained in C. atrox was deleted from the neurotoxic Mojave rattlesnake (C. scutulatus; ∼4 mya). The rapid evolution of PLA2 gene number appears to be due to transposon invasion that provided a template for non-allelic homologous recombination.
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Affiliation(s)
- Noah L Dowell
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA.
| | - Matt W Giorgianni
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA
| | - Victoria A Kassner
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA
| | - Jane E Selegue
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry, Texas A&M University-Kingsville, MSC 224, Kingsville, TX 78363, USA
| | - Sean B Carroll
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA.
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